{"entity": "label", "iuid": "61f96da801e04285b15d39e8302337fa", "timestamp": "2026-04-12T02:48:14.844Z", "links": {"self": {"href": "https://publications.scilifelab.se/label/NGI%20Uppsala%20%28SNP%26SEQ%20Technology%20Platform%29.json"}, "display": {"href": "https://publications.scilifelab.se/label/NGI%20Uppsala%20%28SNP%26SEQ%20Technology%20Platform%29"}}, "value": "NGI Uppsala (SNP&SEQ Technology Platform)", "started": "2013", "ended": "2019", "created": "2017-05-02T12:10:02.751Z", "modified": "2021-03-15T14:24:35.415Z", "accounts": [{"entity": "account", "iuid": "32a436398938412b93e7ddcef018c708", "timestamp": "2026-04-12T02:48:14.844Z", "links": {"self": {"href": "https://publications.scilifelab.se/account/christopher.erdmann%40scilifelab.uu.se.json"}, "display": {"href": "https://publications.scilifelab.se/account/christopher.erdmann%40scilifelab.uu.se"}}, "email": "christopher.erdmann@scilifelab.uu.se", "name": "Christopher Erdmann", "orcid": "", "role": "curator", "status": "enabled", "login": "2024-08-16T11:56:57.787Z", "created": "2024-08-16T10:01:32.844Z", "modified": "2025-10-17T13:05:06.782Z"}, {"entity": "account", "iuid": "63525022c5204321b7c5dacabd6a5367", "timestamp": "2026-04-12T02:48:14.844Z", "links": {"self": {"href": "https://publications.scilifelab.se/account/ulrika.liljedahl%40medsci.uu.se.json"}, "display": {"href": "https://publications.scilifelab.se/account/ulrika.liljedahl%40medsci.uu.se"}}, "email": "ulrika.liljedahl@medsci.uu.se", "name": "Ulrika Liljedahl", "orcid": null, "role": "curator", "status": "enabled", "login": "2026-03-16T07:34:57.517Z", "created": "2017-09-18T13:38:27.959Z", "modified": "2026-03-16T07:34:57.517Z"}, {"entity": "account", "iuid": "66178c433a274c59915e7e0a4a79b0dc", "timestamp": "2026-04-12T02:48:14.844Z", "links": {"self": {"href": "https://publications.scilifelab.se/account/johanna.lagensjo%40medsci.uu.se.json"}, "display": {"href": 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"links": {"self": {"href": "https://publications.scilifelab.se/account/jessica.nordlund%40medsci.uu.se.json"}, "display": {"href": "https://publications.scilifelab.se/account/jessica.nordlund%40medsci.uu.se"}}, "email": "jessica.nordlund@medsci.uu.se", "name": "Jessica Nordlind", "orcid": "0000-0001-8699-9959", "role": "curator", "status": "enabled", "login": "2024-11-05T17:29:55.257Z", "created": "2019-11-22T13:05:04.763Z", "modified": "2024-11-05T17:29:55.257Z"}, {"entity": "account", "iuid": "eaba3ceb6c484b64be969a9c1f11fb21", "timestamp": "2026-04-12T02:48:14.844Z", "links": {"self": {"href": "https://publications.scilifelab.se/account/tomas.axelsson%40medsci.uu.se.json"}, "display": {"href": "https://publications.scilifelab.se/account/tomas.axelsson%40medsci.uu.se"}}, "email": "tomas.axelsson@medsci.uu.se", "name": "Tomas Axelsson", "orcid": null, "role": "curator", "status": "enabled", "login": "2023-05-30T11:54:02.369Z", "created": "2017-09-18T13:32:15.853Z", "modified": "2023-05-30T11:54:02.369Z"}], "publications_count": 1731, "publications": [{"entity": "publication", "iuid": "b31162b460c7480c87a7be42d41b600a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b31162b460c7480c87a7be42d41b600a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b31162b460c7480c87a7be42d41b600a"}}, "title": "The HUNT study identifies host genetic factors reproducibly associated with human gut microbiota composition", "authors": [{"family": "Moksnes", "given": "Marta Riise", "initials": "MR", "orcid": "0000-0002-2690-5153", "researcher": {"href": "https://publications.scilifelab.se/researcher/15fd5ce3d43a4b76a7a7e710e8724a6f.json"}}, {"family": "Coward", "given": "Eivind", "initials": "E", "orcid": "0009-0008-1323-3555", "researcher": {"href": "https://publications.scilifelab.se/researcher/6a4792db14b645b9b5134243f9ca7b60.json"}}, {"family": "Nethander", "given": "Maria", "initials": "M", "orcid": "0000-0003-3688-906X", "researcher": {"href": "https://publications.scilifelab.se/researcher/53d61951f51c4d40bef24672866382cb.json"}}, {"family": "Dekkers", "given": "Koen", "initials": "K", "orcid": "0000-0002-4074-7235", "researcher": {"href": "https://publications.scilifelab.se/researcher/ee8d56ef781e42d5b6f21b551054a3e7.json"}}, {"family": "Grahnemo", "given": "Louise", "initials": "L", "orcid": "0000-0001-5276-6612", "researcher": {"href": "https://publications.scilifelab.se/researcher/bb1ac8fe74954a5db43e8e6538cf8235.json"}}, {"family": "T\u00f6rnqvist", "given": "Anna E", "initials": "AE"}, {"family": "Li", "given": "Lei", "initials": "L"}, {"family": "Lundmark", "given": "Per", "initials": "P", "orcid": "0009-0006-2334-8802", "researcher": {"href": "https://publications.scilifelab.se/researcher/f30b1a2e60d646c4a0cc0be06ffe77dd.json"}}, {"family": "Pertiwi", "given": "Kamalita", "initials": "K", "orcid": "0000-0003-2861-9051", "researcher": {"href": "https://publications.scilifelab.se/researcher/f9cb279b53204e51b202134c82cf680f.json"}}, {"family": "Baldanzi", "given": "Gabriel", "initials": "G", "orcid": "0000-0003-3962-3953", "researcher": {"href": "https://publications.scilifelab.se/researcher/577652ffb15442e1a47a9aaffc3b52e7.json"}}, {"family": "Mjelle", "given": "Robin", "initials": "R"}, {"family": "Moll", "given": "Janne Marie", "initials": "JM", "orcid": "0000-0002-3514-4528", "researcher": {"href": "https://publications.scilifelab.se/researcher/52e482fb976e4bb3a212d98b981c9f2f.json"}}, {"family": "Eklund", "given": "Aron Charles", "initials": "AC", "orcid": "0000-0003-0861-1001", "researcher": {"href": "https://publications.scilifelab.se/researcher/9f1b0f6b48de45f7916e14d6a4defb09.json"}}, {"family": "Nielsen", "given": "Henrik Bj\u00f8rn", "initials": "HB", "orcid": "0000-0003-2281-5713", "researcher": {"href": "https://publications.scilifelab.se/researcher/c1d5f2e0565a46bcbccfc973eec9e838.json"}}, {"family": "Svensson", "given": "Johan", "initials": "J", "orcid": "0000-0002-4487-6405", "researcher": {"href": "https://publications.scilifelab.se/researcher/fdbca5fe77124646b51e9c55dae4d361.json"}}, {"family": "Langhammer", "given": "Arnulf", "initials": "A", "orcid": "0000-0001-5296-6673", "researcher": {"href": "https://publications.scilifelab.se/researcher/755b4b39d8054f2ea3e28476a7b0ae39.json"}}, {"family": "Giske\u00f8deg\u00e5rd", "given": "Guro F", "initials": "GF", "orcid": "0000-0003-2157-8824", "researcher": {"href": "https://publications.scilifelab.se/researcher/57d6962d8112403fb823764ce0a0d6c6.json"}}, {"family": "Brumpton", "given": "Ben", "initials": "B", "orcid": "0000-0002-3058-1059", "researcher": {"href": "https://publications.scilifelab.se/researcher/da9d23aaf1dc4d18a0a13e4847ea9955.json"}}, {"family": "Hjort", "given": "Rebecka", "initials": "R"}, {"family": "Ness-Jensen", "given": "Eivind", "initials": "E", "orcid": "0000-0001-6005-0729", "researcher": {"href": "https://publications.scilifelab.se/researcher/d619713fc5764a5e9b88c7c012cf0cf1.json"}}, {"family": "Engstr\u00f6m", "given": "Gunnar", "initials": "G", "orcid": "0000-0002-8618-9152", "researcher": {"href": "https://publications.scilifelab.se/researcher/b40c03613a3a46368ed855fc95b79e31.json"}}, {"family": "Pelaseyed", "given": "Thaher", "initials": "T", "orcid": "0000-0002-6434-3913", "researcher": {"href": "https://publications.scilifelab.se/researcher/9dc0aa3d9762420caa7efaaa19c1174b.json"}}, {"family": "Micha\u00eblsson", "given": "Karl", "initials": "K", "orcid": "0000-0003-2815-1217", "researcher": {"href": "https://publications.scilifelab.se/researcher/eff63868e95240f695d47e871e31947f.json"}}, {"family": "Orho-Melander", "given": "Marju", "initials": "M", "orcid": "0000-0002-3578-2503", "researcher": {"href": "https://publications.scilifelab.se/researcher/7e54fbe6f0fc4eed93108b382e1b2952.json"}}, {"family": "Fall", "given": "Tove", "initials": "T", "orcid": "0000-0003-2071-5866", "researcher": {"href": "https://publications.scilifelab.se/researcher/4ed3f066719f43b291743a8bdaf3d2a0.json"}}, {"family": "Hveem", "given": "Kristian", "initials": "K"}, {"family": "Ohlsson", "given": "Claes", "initials": "C", "orcid": "0000-0002-9633-2805", "researcher": {"href": "https://publications.scilifelab.se/researcher/995dac358caa4a169fc889b7a3eef44a.json"}}], "type": "journal-article", "published": "2026-03-00", "journal": {"title": "Nat Genet", "issn": "1061-4036", "volume": "58", "issue": "3", "pages": "530-539", "issn-l": "1061-4036"}, "abstract": "The gut microbiota is associated with human health and disease. Here we conducted a genome-wide association study of host genetic factors influencing gut microbiota composition in 12,652 individuals from the Tr\u00f8ndelag Health Study (HUNT), with replication in Nordic cohorts (n = 16,017-21,976). We identified 12 reproducible SNP-species associations across six genomic loci, including known (LCT, ABO) and novel (HLA-DQB1, MUC12, SLC37A2, FUT2) regions. Additionally, we detected genetic signals associated with gut microbiota functional modules at three loci (LCT, ABO, FUT2). Follow-up analyses suggest that these host-microbiota associations are linked to the pathogenesis of celiac disease and hemorrhoidal disease. Mendelian randomization analyses provided evidence supporting a causal effect of body mass index on gut microbiota composition. These findings highlight the interplay between host genetics and gut microbiota for human health and disease.", "doi": "10.1038/s41588-026-02502-4", "pmid": "41688637", "labels": {"National Genomics Infrastructure": "Service", "NGI SNP genotyping": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12987729"}, {"db": "pii", "key": "10.1038/s41588-026-02502-4"}], "notes": [], "created": "2026-03-19T16:36:31.375Z", "modified": "2026-03-24T09:08:07.330Z"}, {"entity": "publication", "iuid": "1021326661cc476399928b055a37a4e8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1021326661cc476399928b055a37a4e8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1021326661cc476399928b055a37a4e8"}}, "title": "Genome-wide association analyses highlight the role of the intestinal molecular environment in human gut microbiota variation.", "authors": [{"family": "Dekkers", "given": "Koen F", "initials": "KF", "orcid": "0000-0002-4074-7235", "researcher": {"href": "https://publications.scilifelab.se/researcher/ee8d56ef781e42d5b6f21b551054a3e7.json"}}, {"family": "Pertiwi", "given": "Kamalita", "initials": "K", "orcid": "0000-0003-2861-9051", "researcher": {"href": "https://publications.scilifelab.se/researcher/f9cb279b53204e51b202134c82cf680f.json"}}, {"family": "Baldanzi", "given": "Gabriel", "initials": "G", "orcid": "0000-0003-3962-3953", "researcher": {"href": "https://publications.scilifelab.se/researcher/577652ffb15442e1a47a9aaffc3b52e7.json"}}, {"family": "Lundmark", "given": "Per", "initials": "P", "orcid": "0009-0006-2334-8802", "researcher": {"href": "https://publications.scilifelab.se/researcher/f30b1a2e60d646c4a0cc0be06ffe77dd.json"}}, {"family": "Hammar", "given": "Ulf", "initials": "U"}, {"family": "Moksnes", "given": "Marta Riise", "initials": "MR", "orcid": "0000-0002-2690-5153", "researcher": {"href": "https://publications.scilifelab.se/researcher/15fd5ce3d43a4b76a7a7e710e8724a6f.json"}}, {"family": "Coward", "given": "Eivind", "initials": "E", "orcid": "0009-0008-1323-3555", "researcher": {"href": "https://publications.scilifelab.se/researcher/6a4792db14b645b9b5134243f9ca7b60.json"}}, {"family": "Nethander", "given": "Maria", "initials": "M", "orcid": "0000-0003-3688-906X", "researcher": {"href": "https://publications.scilifelab.se/researcher/53d61951f51c4d40bef24672866382cb.json"}}, {"family": "Salih", "given": "Ghassan Ali", "initials": "GA", "orcid": "0009-0003-5938-8222", "researcher": {"href": "https://publications.scilifelab.se/researcher/d6d97b18c7cc44dcbc9aed652c6f7c46.json"}}, {"family": "Miari", "given": "Mariam", "initials": "M"}, {"family": "Nguyen", "given": "Diem", "initials": "D", "orcid": "0000-0002-9680-5772", "researcher": {"href": "https://publications.scilifelab.se/researcher/d78958133e474831ac76dacc36f68cbb.json"}}, {"family": "Sayols-Baixeras", "given": "Sergi", "initials": "S"}, {"family": "Eklund", "given": "Aron C", "initials": "AC", "orcid": "0000-0003-0861-1001", "researcher": {"href": "https://publications.scilifelab.se/researcher/9f1b0f6b48de45f7916e14d6a4defb09.json"}}, {"family": "Holm", "given": "Jacob Bak", "initials": "JB", "orcid": "0000-0003-1756-0875", "researcher": {"href": "https://publications.scilifelab.se/researcher/359fa6a18dc549a8852dd3990ccde1f1.json"}}, {"family": "Nielsen", "given": "H Bj\u00f8rn", "initials": "HB", "orcid": "0000-0003-2281-5713", "researcher": {"href": "https://publications.scilifelab.se/researcher/c1d5f2e0565a46bcbccfc973eec9e838.json"}}, {"family": "Volpiano", "given": "Camila Gazolla", "initials": "CG"}, {"family": "M\u00e9ric", "given": "Guillaume", "initials": "G", "orcid": "0000-0001-6288-9958", "researcher": {"href": "https://publications.scilifelab.se/researcher/229f8c463d1a4eef945c2b62b77977ab.json"}}, {"family": "Thangam", "given": "Manonanthini", "initials": "M", "orcid": "0000-0002-7164-6525", "researcher": {"href": "https://publications.scilifelab.se/researcher/d09c26b1d20c4539b46824ee62c69ded.json"}}, {"family": "Hakaste", "given": "Liisa", "initials": "L"}, {"family": "Tuomi", "given": "Tiinamaija", "initials": "T"}, {"family": "Ahlqvist", "given": "Emma", "initials": "E", "orcid": "0000-0002-6513-2384", "researcher": {"href": "https://publications.scilifelab.se/researcher/415b737a7da04f13ab0fd104c375b097.json"}}, {"family": "Smith", "given": "Christopher A", "initials": "CA"}, {"family": "Allen", "given": "Marie", "initials": "M"}, {"family": "Reimann", "given": "Frank", "initials": "F", "orcid": "0000-0001-9399-6377", "researcher": {"href": "https://publications.scilifelab.se/researcher/8d899786a20c44dcbb8aec2e895c6ba9.json"}}, {"family": "Gribble", "given": "Fiona M", "initials": "FM", "orcid": "0000-0002-4232-2898", "researcher": {"href": "https://publications.scilifelab.se/researcher/3381ad13c9464a80bbf910009844722e.json"}}, {"family": "Ohlsson", "given": "Claes", "initials": "C", "orcid": "0000-0002-9633-2805", "researcher": {"href": "https://publications.scilifelab.se/researcher/995dac358caa4a169fc889b7a3eef44a.json"}}, {"family": "Hveem", "given": "Kristian", "initials": "K"}, {"family": "Melander", "given": "Olle", "initials": "O"}, {"family": "Nilsson", "given": "Peter M", "initials": "PM", "orcid": "0000-0002-5652-8459", "researcher": {"href": "https://publications.scilifelab.se/researcher/f23c2a10ac2a4d73a8f62b94855635f1.json"}}, {"family": "Engstr\u00f6m", "given": "Gunnar", "initials": "G"}, {"family": "Smith", "given": "J Gustav", "initials": "JG"}, {"family": "Micha\u00eblsson", "given": "Karl", "initials": "K"}, {"family": "\u00c4rnl\u00f6v", "given": "Johan", "initials": "J"}, {"family": "Orho-Melander", "given": "Marju", "initials": "M", "orcid": "0000-0002-3578-2503", "researcher": {"href": "https://publications.scilifelab.se/researcher/7e54fbe6f0fc4eed93108b382e1b2952.json"}}, {"family": "Fall", "given": "Tove", "initials": "T", "orcid": "0000-0003-2071-5866", "researcher": {"href": "https://publications.scilifelab.se/researcher/4ed3f066719f43b291743a8bdaf3d2a0.json"}}], "type": "journal article", "published": "2026-03-00", "journal": {"title": "Nat. Genet.", "issn": "1546-1718", "volume": "58", "issue": "3", "pages": "540-549", "issn-l": "1061-4036"}, "abstract": "Despite the importance of the gut microbiome to health, the role of human genetic variation in shaping its composition remains poorly understood. Here we report genome-wide association analyses of harmonized metagenomic data from 16,017 adults in four Swedish population-based studies, with replication in 12,652 people from the Norwegian HUNT study. We identified variants in the OR51E1-OR51E2 locus, encoding sensors for microbiome-derived fatty acids, associated with microbial richness. We further identified 15 study-wide significant genetic associations (P < 5.4 \u00d7 10-11) involving eight loci and 14 common bacterial species, of which 11 associations at six loci were replicated. The results confirm previously reported associations at LCT, ABO and FUT2, and provide evidence for new loci MUC12, CORO7-HMOX2, SLC5A11, FOXP1 and FUT3-FUT6, with supporting data from metabolomics and gene expression analyses. Our findings link gut microbial variation genetically to gastrointestinal functions, including enteroendocrine fatty acid sensing, bile composition and mucosal layer composition.", "doi": "10.1038/s41588-026-02512-2", "pmid": "41688638", "labels": {"National Genomics Infrastructure": "Service", "NGI SNP genotyping": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12987725"}, {"db": "pii", "key": "10.1038/s41588-026-02512-2"}], "notes": [], "created": "2026-03-19T16:36:11.040Z", "modified": "2026-03-19T16:36:12.549Z"}, {"entity": "publication", "iuid": "833c3f2b059a4f12856d43fb4a7e02e3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/833c3f2b059a4f12856d43fb4a7e02e3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/833c3f2b059a4f12856d43fb4a7e02e3"}}, "title": "Rare germline variants contribute to glioma predisposition: Whole-genome analysis of a regional cohort of glioma patients.", "authors": [{"family": "Rosenbaum", "given": "Adam", "initials": "A", "orcid": "0009-0003-4573-5174", "researcher": {"href": "https://publications.scilifelab.se/researcher/9e6fcd448d744a99945a361353add88f.json"}}, {"family": "Wibom", "given": "Carl", "initials": "C"}, {"family": "Hammermeister Suger", "given": "Austin", "initials": "A", "orcid": "0000-0002-6599-2202", "researcher": {"href": "https://publications.scilifelab.se/researcher/2d5c4526d1504762a430373285155fab.json"}}, {"family": "Pensch", "given": "Raphaela", "initials": "R", "orcid": "0000-0002-0313-8369", "researcher": {"href": "https://publications.scilifelab.se/researcher/7bfb52298bf146c9a327c2fbe2e5e7cb.json"}}, {"family": "Roy", "given": "Ananya", "initials": "A"}, {"family": "Br\u00e4nnstr\u00f6m", "given": "Thomas", "initials": "T", "orcid": "0000-0002-4201-8204", "researcher": {"href": "https://publications.scilifelab.se/researcher/086ede39254945288fb9c708f98eb0cd.json"}}, {"family": "Rentoft", "given": "Matilda", "initials": "M"}, {"family": "Forsberg-Nilsson", "given": "Karin", "initials": "K", "orcid": "0000-0003-0692-6245", "researcher": {"href": "https://publications.scilifelab.se/researcher/5da04859250141a0a7271a69c7da9176.json"}}, {"family": "Lindblad-Toh", "given": "Kerstin", "initials": "K"}, {"family": "Lindstr\u00f6m", "given": "Sara", "initials": "S"}, {"family": "Dahlin", "given": "Anna Margareta", "initials": "AM"}, {"family": "Melin", "given": "Beatrice", "initials": "B", "orcid": "0000-0002-9982-3757", "researcher": {"href": "https://publications.scilifelab.se/researcher/4ee34db763294de2b7dec15a9ffe8aee.json"}}], "type": "journal article", "published": "2026-02-12", "journal": {"title": "Neurooncol Adv", "issn": "2632-2498", "volume": "8", "issue": "1", "pages": "vdag038", "issn-l": null}, "abstract": "Gliomas are the most common malignant primary tumor of the central nervous system and show a high mortality, particularly at higher grades. Cancer predisposition syndromes and common low-penetrance single nucleotide polymorphisms have been shown to contribute to glioma risk, but the contribution of rare germline variants remains incompletely understood. Here, we investigated rare germline variants in glioma patients.\n\nWe performed whole-genome sequencing on 113 glioma patients from Northern Sweden, analyzing rare germline variants across 651 genes. Variants were compared to population controls (ACpop, gnomAD) and validated in TCGA glioma data, a UK Biobank glioma nested case-control study, and a separate cohort of 105 Swedish glioblastomas.\n\n17.6% of glioma cases carried a Pathogenic or Likely Pathogenic (P/LP) variant within 1 of the 651 genes, and the number of alleles carrying a P/LP was significantly more than in the reference data (P = ). Many of the observed candidate genes also harbored P/LP variants in our Swedish validation cohort. Overall, gene-based comparison of rare coding variants indicated an enrichment in several genes, including 3.2 \u00d7 10 - 3TP53, CREBBP, and DNMT3A.\n\nRare P/LP germline variants were more frequent among glioma patients than in the reference population within our predefined gene set. These results suggest a contribution of rare germline variants to glioma risk, particularly in genes involved in DNA repair. While several genes are indicated as enriched with rare variants, only TP53 validates across all 3 patient sets.", "doi": "10.1093/noajnl/vdag038", "pmid": "41878702", "labels": {"National Genomics Infrastructure": "Service", "NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC13007284"}, {"db": "pii", "key": "vdag038"}], "notes": [], "created": "2026-03-26T20:20:23.541Z", "modified": "2026-03-26T20:20:24.274Z"}, {"entity": "publication", "iuid": "2eb354120b4e4f18a6b6912af75d7656", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2eb354120b4e4f18a6b6912af75d7656.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2eb354120b4e4f18a6b6912af75d7656"}}, "title": "Comprehensive profiling of CRISPR/dCas9 epigenome editors indicates a complex link between on and off target effects", "authors": [{"family": "Pahlevan Kakhki", "given": "Majid", "initials": "M", "orcid": "0000-0002-5407-3147", "researcher": {"href": "https://publications.scilifelab.se/researcher/5f376c85cfbe4711ae41d9ee5ade8f09.json"}}, {"family": "Rangani", "given": "Fatemeh", "initials": "F"}, {"family": "Ewing", "given": "Ewoud", "initials": "E", "orcid": "0000-0001-8644-366X", "researcher": {"href": "https://publications.scilifelab.se/researcher/aea9350a4f864d8e8781ab111b4f9273.json"}}, {"family": "Starvaggi Cucuzza", "given": "Chiara", "initials": "C", "orcid": "0000-0002-9088-7658", "researcher": {"href": "https://publications.scilifelab.se/researcher/0ead2e8f98754d1586891eda5adb9e1a.json"}}, {"family": "Zheleznyakova", "given": "Galina", "initials": "G"}, {"family": "Kalomoiri", "given": "Maria", "initials": "M"}, {"family": "Kenny", "given": "Lea", "initials": "L"}, {"family": "Raghavan", "given": "Anika", "initials": "A"}, {"family": "Rao Prakash", "given": "Chandana", "initials": "C"}, {"family": "van den Hoeven", "given": "Gabe", "initials": "G"}, {"family": "Venkata S. Badam", "given": "Tejaswi", "initials": "T"}, {"family": "Covacu", "given": "Ruxandra", "initials": "R"}, {"family": "Andreou", "given": "Ioanna", "initials": "I"}, {"family": "Needhamsen", "given": "Maria", "initials": "M"}, {"family": "Kular", "given": "Lara", "initials": "L", "orcid": "0000-0002-2907-6071", "researcher": {"href": "https://publications.scilifelab.se/researcher/09563004a20543dc934dd4d3b1ceebd7.json"}}, {"family": "Jagodic", "given": "Maja", "initials": "M", "orcid": "0000-0003-0756-889X", "researcher": {"href": "https://publications.scilifelab.se/researcher/b651ef39c6b0436992e2305f425eba72.json"}}], "type": "journal-article", "published": "2026-01-31", "journal": {"title": "Genome Biol.", "issn": "1474-760X", "issn-l": "1474-7596", "volume": "27", "issue": "1", "pages": null}, "abstract": "CRISPR/dCas9-based epigenome editing systems, including DNA methylation epimodifiers, have greatly advanced molecular functional studies, revolutionizing their precision and applicability. Despite their promise, challenges such as the magnitude and stability of the on-target editing and unwanted off-target effects underscore the need for improved tool characterization and design.\n\nWe systematically compare specific targeting and genome-wide off-target effects of available and novel dCas9-based DNA methylation editing tools over time. We demonstrate that multimerization of the catalytic domain of DNA methyltransferase 3A enhances editing potency but also induces widespread, early methylation deposition at low-to-medium methylated promoter-related regions with specific gRNAs and also with non-targeting gRNAs. A small fraction of the methylation changes associated with transcriptional dysregulation and mapped predominantly to bivalent chromatin associating both with transcriptional repression and activation. Additionally, specific non-targeting control gRNAs cause pervasive and long-lasting methylation-independent transcriptional alterations particularly in genes linked to RNA and energy metabolism. CRISPRoff emerges as the most efficient tool for stable promoter targeting, with fewer and less stable off-target effects compared to other epimodifiers but with persistent transcriptome alterations.\n\nOur findings highlight the delicate balance between potency and specificity of epigenome editing and provide critical insights into the design and application of future tools to improve their precision and minimize unintended consequences.", "doi": "10.1186/s13059-026-03967-6", "pmid": "41620608", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "NGI SNP genotyping": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12924462"}, {"db": "pii", "key": "10.1186/s13059-026-03967-6"}], "notes": [], "created": "2026-02-06T08:02:40.826Z", "modified": "2026-03-24T09:10:47.840Z"}, {"entity": "publication", "iuid": "cc266f15720044ff97f0c84859c74dbf", "links": {"self": {"href": "https://publications.scilifelab.se/publication/cc266f15720044ff97f0c84859c74dbf.json"}, "display": {"href": "https://publications.scilifelab.se/publication/cc266f15720044ff97f0c84859c74dbf"}}, "title": "Airborne eDNA captures three decades of ecosystem biodiversity.", "authors": [{"family": "Sullivan", "given": "Alexis R", "initials": "AR"}, {"family": "Karlsson", "given": "Edvin", "initials": "E"}, {"family": "Svensson", "given": "Daniel", "initials": "D", "orcid": "0000-0002-4476-9255", "researcher": {"href": "https://publications.scilifelab.se/researcher/75bc51f60237478abec1fb2969abc873.json"}}, {"family": "Brindefalk", "given": "Bj\u00f6rn", "initials": "B", "orcid": "0000-0001-8524-778X", "researcher": {"href": "https://publications.scilifelab.se/researcher/75f852c1e5144ff3acda53bcec520001.json"}}, {"family": "Villegas", "given": "Jose Antonio", "initials": "JA"}, {"family": "Mikko", "given": "Amanda", "initials": "A", "orcid": "0009-0002-7701-8180", "researcher": {"href": "https://publications.scilifelab.se/researcher/3bca394a219142d68195e45f756dd686.json"}}, {"family": "Bellieny", "given": "Daniel", "initials": "D"}, {"family": "Siddique", "given": "Abu Bakar", "initials": "AB", "orcid": "0000-0002-3178-523X", "researcher": {"href": "https://publications.scilifelab.se/researcher/a19c155f873b4ec194a0ba07d9bbff92.json"}}, {"family": "Johansson", "given": "Anna-Mia", "initials": "AM"}, {"family": "Grahn", "given": "H\u00e5kan", "initials": "H", "orcid": "0000-0002-8936-3101", "researcher": {"href": "https://publications.scilifelab.se/researcher/c5806ae054ec4cf1b67ee151bfd95b2f.json"}}, {"family": "Sundell", "given": "David", "initials": "D"}, {"family": "Norman", "given": "Anita", "initials": "A", "orcid": "0000-0002-9499-758X", "researcher": {"href": "https://publications.scilifelab.se/researcher/a1966d9c4e0f4c2c89702c8ef319264c.json"}}, {"family": "Esseen", "given": "Per-Anders", "initials": "PA"}, {"family": "Sj\u00f6din", "given": "Andreas", "initials": "A", "orcid": "0000-0001-5350-4219", "researcher": {"href": "https://publications.scilifelab.se/researcher/6398d7c06a414ea6bcaf2579a8587452.json"}}, {"family": "Singh", "given": "Navinder J", "initials": "NJ", "orcid": "0000-0002-5131-0004", "researcher": {"href": "https://publications.scilifelab.se/researcher/0bae3b76bb4a4f95a77e41cd929637ff.json"}}, {"family": "Brodin", "given": "Tomas", "initials": "T", "orcid": "0000-0003-1086-7567", "researcher": {"href": "https://publications.scilifelab.se/researcher/8140649bc5e140369d031c78fc416ae2.json"}}, {"family": "Forsman", "given": "Mats", "initials": "M", "orcid": "0000-0002-4466-5325", "researcher": {"href": "https://publications.scilifelab.se/researcher/b52b5a759a3e452b80728241c50c76dd.json"}}, {"family": "Stenberg", "given": "Per", "initials": "P", "orcid": "0000-0003-4738-4788", "researcher": {"href": "https://publications.scilifelab.se/researcher/3e9b9949cf994f6c93d60261eb530d1b.json"}}], "type": "journal article", "published": "2025-12-18", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "16", "issue": "1", "pages": "11281", "issn-l": "2041-1723"}, "abstract": "Biodiversity loss threatens ecosystems and human well-being, making accurate, large-scale monitoring crucial. Environmental DNA (eDNA) has enabled species detection from substrates such as water, without the need for direct observation. Lately, airborne eDNA has been showing promise for tracking organisms from insects to mammals in terrestrial ecosystems. Conventional biodiversity assessments are often labor-intensive and limited in scope, leaving gaps in our understanding of ecosystem response to environmental change. Here, we demonstrate that airborne eDNA can detect organisms across the tree of life, quantify changes in abundance congruent with traditional monitoring, and reveal land-use induced regional decline of diversity in a northern boreal ecosystem over more than three decades. By analyzing 34 years of archived aerosol filters, we reconstruct weekly temporal relative abundance data for more than 2700 genera using non-targeted methods. This study provides unified, ecosystem-scale biodiversity surveillance spanning multiple decades, with data collected at weekly intervals on both the individual species and community level. Previously, large scale analyses of ecosystem changes, targeting all types of organisms, has been prohibitively expensive and difficult to attempt. Here, we present a way of holistically doing this type of analysis in a single framework.", "doi": "10.1038/s41467-025-67676-7", "pmid": "41413054", "labels": {"National Genomics Infrastructure": "Service", "NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12717267"}, {"db": "pii", "key": "10.1038/s41467-025-67676-7"}], "notes": [], "created": "2026-03-25T07:37:10.622Z", "modified": "2026-03-25T07:37:11.494Z"}, {"entity": "publication", "iuid": "fdb2a58a717e4bbca202566f67f5792b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/fdb2a58a717e4bbca202566f67f5792b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/fdb2a58a717e4bbca202566f67f5792b"}}, "title": "A co-speciation dilemma and a lifestyle transition with genomic consequences in Wolbachia of Neotropical Drosophila", "authors": [{"family": "Papachristos", "given": "Konstantinos", "initials": "K", "orcid": "0000-0002-4777-9088", "researcher": {"href": "https://publications.scilifelab.se/researcher/2bf7a545a218455fa134b3dd8bb1b895.json"}}, {"family": "Miller", "given": "Wolfgang J", "initials": "WJ"}, {"family": "Klasson", "given": "Lisa", "initials": "L", "orcid": "0000-0002-5874-7153", "researcher": {"href": "https://publications.scilifelab.se/researcher/409de77af489419db6d2b599b590d02f.json"}}], "type": "journal-article", "published": "2025-12-10", "journal": {"title": "BMC Genomics", "issn": "1471-2164", "volume": "27", "issue": "1", "pages": "41", "issn-l": "1471-2164"}, "abstract": "Long-term persistent symbiotic associations may result in co-speciation and can be inferred if species trees of hosts and symbionts are congruent in topology and divergence times. Co-speciation has been seen to occur relatively frequently in obligate associations, but is less common in parasitic or facultative ones, mainly due to the difference in horizontal transmission rates. The long-term vertical inheritance and close host association of obligate endosymbionts also generally result in smaller genomes than in facultative endosymbionts. Here, we investigate co-speciation and genome reduction using highly similar strains of the endosymbiont Wolbachia infecting Drosophila species from the willistoni and saltans groups, where only one strain, wPau, infecting D. paulistorum, is obligate.\n\nWe sequenced the Wolbachia genomes from five species of the willistoni and saltans groups and constructed phylogenies. Topological congruence was found between these Wolbachia strains and the nuclear DNA of their hosts, except for wPau and D. paulistorum, but full topological congruence was observed between Wolbachia and the host mitochondrial DNA. However, assuming temporal congruence, we estimated extremely low evolutionary rates in Wolbachia of 10- 10-10- 11 changes/site/year. Additionally, the obligate wPau strain was found to have a larger genome than closely related facultative strains, mainly due to an ongoing expansion of an IS4 element. Furthermore, wPau has lost a large proportion of its prophage WO genes, but the cif genes, known to be involved in the CI phenotype, are intact. Finally, nine of the eleven genes from the prophage WO-associated Undecim cluster are uniquely duplicated.\n\nThe congruent topologies between Wolbachia and their willistoni and saltans group hosts indicate co-speciation. However, the high similarity between Wolbachia strains, which results in low mutation rate estimates, challenges this interpretation. Contrary to the expectations of the genome reduction theory, we observed an increase in genome size in the obligate wPau strain, potentially driven by a decreased population size. Finally, the duplication of the Undecim cluster, despite a major loss of other prophage-associated genes, suggests that the genes in the Undecim cluster are under strong selection and potentially play a role in the obligate association between wPau and their D. paulistorum hosts.", "doi": "10.1186/s12864-025-12340-z", "pmid": "41366724", "labels": {"National Genomics Infrastructure": "Service", "NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12801941"}, {"db": "pii", "key": "10.1186/s12864-025-12340-z"}], "notes": [], "created": "2026-01-19T08:58:08.199Z", "modified": "2026-01-20T07:53:24.298Z"}, {"entity": "publication", "iuid": "b8ca2a2dba2049ec8de7192c162898c4", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b8ca2a2dba2049ec8de7192c162898c4.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b8ca2a2dba2049ec8de7192c162898c4"}}, "title": "Homo sapiens-specific evolution unveiled by ancient southern African genomes.", "authors": [{"family": "Jakobsson", "given": "Mattias", "initials": "M", "orcid": "0000-0001-7840-7853", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a4abe0fcb20492d9ec849c9fbf58a71.json"}}, {"family": "Bernhardsson", "given": "Carolina", "initials": "C", "orcid": "0000-0002-3258-275X", "researcher": {"href": "https://publications.scilifelab.se/researcher/b8fce67de4e14fa68c0edadfec0de085.json"}}, {"family": "McKenna", "given": "James", "initials": "J"}, {"family": "Hollfelder", "given": "Nina", "initials": "N", "orcid": "0000-0002-1567-8450", "researcher": {"href": "https://publications.scilifelab.se/researcher/0f81a63833c146999d73fa38f588ea06.json"}}, {"family": "Vicente", "given": "Mario", "initials": "M"}, {"family": "Edlund", "given": "Hanna", "initials": "H"}, {"family": "Coutinho", "given": "Alexandra", "initials": "A"}, {"family": "Sj\u00f6din", "given": "Per", "initials": "P"}, {"family": "Brink", "given": "James", "initials": "J"}, {"family": "Zipfel", "given": "Bernhard", "initials": "B", "orcid": "0000-0002-4251-884X", "researcher": {"href": "https://publications.scilifelab.se/researcher/74d1041d932a49c9bc2baca44273d4a4.json"}}, {"family": "Malmstr\u00f6m", "given": "Helena", "initials": "H", "orcid": "0000-0002-6456-8055", "researcher": {"href": "https://publications.scilifelab.se/researcher/3b3397b2842142bea34c222f6683c0eb.json"}}, {"family": "Lombard", "given": "Marlize", "initials": "M", "orcid": "0000-0002-0675-0414", "researcher": {"href": "https://publications.scilifelab.se/researcher/e04e97bbc9914f358864988174b9b58d.json"}}, {"family": "Schlebusch", "given": "Carina M", "initials": "CM", "orcid": "0000-0002-8160-9621", "researcher": {"href": "https://publications.scilifelab.se/researcher/682f10853c1145649b8c76680605dd9b.json"}}], "type": "journal article", "published": "2025-12-03", "journal": {"title": "Nature", "issn": "1476-4687", "issn-l": "0028-0836", "volume": null, "issue": null, "pages": null}, "abstract": "Homo sapiens evolved hundreds of thousands of years ago in Africa, later spreading across the globe1, but the early evolutionary process is debated2-6. Here we present whole-genome sequencing data for 28 ancient southern African individuals, including six individuals with 25\u00d7 to 7.2\u00d7 genome coverage, dated to between 10,200 and 150 calibrated years before present (cal. BP). All ancient southern Africans dated to more than 1,400 cal. BP show a genetic make-up that is outside the range of genetic variation in modern-day humans (including southern African Khoe-San people, although some retain up to 80% ancient southern African ancestry), manifesting in a large fraction of Homo sapiens-specific variants that are unique to ancient southern Africans. Homo sapiens-specific variants at amino acid-altering sites fixed for all humans-which are likely to have evolved rapidly on the Homo sapiens branch-were enriched for genes associated with kidney function. Some Homo sapiens-specific variants fixed in ancient southern Africans-which are likely to have adapted rapidly on the southern African branch-were enriched for genes associated with protection against ultraviolet light. The ancient southern Africans show little spatiotemporal stratification for 9,000 years, consistent with a large, stable Holocene population transcending archaeological phases. While southern Africa served as a long-standing geographical refugium, there is outward gene flow over 8,000 years ago; however, inward gene flow manifests only after around 1,400 years ago. The ancient genomes reported here are therefore key to the evolution of Homo sapiens, and are important for advancing our understanding of human genomic variation.", "doi": "10.1038/s41586-025-09811-4", "pmid": "41339558", "labels": {"National Genomics Infrastructure": "Service", "NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41586-025-09811-4"}], "notes": [], "created": "2025-12-04T08:12:48.745Z", "modified": "2025-12-05T10:16:26.469Z"}, {"entity": "publication", "iuid": "bed19b398aa143d28064d622d7f4babf", "links": {"self": {"href": "https://publications.scilifelab.se/publication/bed19b398aa143d28064d622d7f4babf.json"}, "display": {"href": "https://publications.scilifelab.se/publication/bed19b398aa143d28064d622d7f4babf"}}, "title": "Holotype genome of the lesula provides insights into demography and evolution of a threatened primate lineage.", "authors": [{"family": "Jensen", "given": "Axel", "initials": "A", "orcid": "0000-0003-1766-560X", "researcher": {"href": "https://publications.scilifelab.se/researcher/7f139b7f3dac49e28ef6430637d88592.json"}}, {"family": "Horton", "given": "Emma R", "initials": "ER"}, {"family": "Koko", "given": "Mardoch\u00e9 B", "initials": "MB"}, {"family": "Detwiler", "given": "Kate M", "initials": "KM"}, {"family": "Guschanski", "given": "Katerina", "initials": "K", "orcid": "0000-0002-8493-5457", "researcher": {"href": "https://publications.scilifelab.se/researcher/84b8b0757f02429b9bd419acb42ab6a3.json"}}], "type": "journal article", "published": "2025-12-01", "journal": {"title": "Genome Biol.", "issn": "1474-760X", "issn-l": "1474-7596", "volume": "26", "issue": "1", "pages": "408"}, "abstract": "The development of genome sequencing techniques has revolutionized evolutionary biology, facilitating the study of adaptation and speciation at the genome level. Genomic data has also become a cornerstone in conservation management, allowing inferences of population demography and genetic diversity.\n\nWe sequence the genome of the holotype specimen of the elusive lesula (Cercopithecus lomamiensis), a recently described member of the guenons (tribe Cercopithecini), endemic to the Democratic Republic of the Congo. Using published and novel genomic data, we explore the evolutionary and demographic history of C. lomamiensis and its sister species C. hamlyni. We estimate that the two species split ca. 3\u20134 million years ago, and find that they both show high genetic diversity despite being listed as Vulnerable on the IUCN Red List. We identify signatures of positive selection in genes involved in pelage coloration and immune functions, as well as skeletal morphology and locomotor behavior, potentially related to the terrestrial lifestyle of C. lomamiensis and C. hamlyni, which stand out among the otherwise arboreal Cercopithecus genus. We specifically explore whether introgression from more distantly related terrestrial guenons was involved in the evolution of terrestriality in the hamlyni group, but found low molecular convergence suggesting that putative terrestrial adaptations occurred largely independently.\n\nThis study provides insights into the demography and evolutionary history in a poorly known, threatened primate lineage. Furthermore, our results suggest that genomic erosion is not an imminent threat to these species, and that conservation management should prioritize actions to prevent further population decline.\n\nThe online version contains supplementary material available at 10.1186/s13059-025-03877-z.", "doi": "10.1186/s13059-025-03877-z", "pmid": "41327385", "labels": {"National Genomics Infrastructure": "Service", "NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12667059"}, {"db": "pii", "key": "10.1186/s13059-025-03877-z"}], "notes": [], "created": "2025-12-04T13:28:29.798Z", "modified": "2025-12-21T19:09:46.579Z"}, {"entity": "publication", "iuid": "823c71158dcd4b9fb085d01e55d13e48", "links": {"self": {"href": "https://publications.scilifelab.se/publication/823c71158dcd4b9fb085d01e55d13e48.json"}, "display": {"href": "https://publications.scilifelab.se/publication/823c71158dcd4b9fb085d01e55d13e48"}}, "title": "scFFPE-ATAC enables high-throughput single cell chromatin accessibility profiling in formalin-fixed paraffin-embedded samples.", "authors": [{"family": "Yadav", "given": "Ram Prakash", "initials": "RP"}, {"family": "Xing", "given": "Pengwei", "initials": "P"}, {"family": "Zhao", "given": "Miao", "initials": "M", "orcid": "0000-0002-4895-1177", "researcher": {"href": "https://publications.scilifelab.se/researcher/b9c4e2515b414dee94aaeca71569699b.json"}}, {"family": "Hollander", "given": "Peter", "initials": "P"}, {"family": "Strell", "given": "Carina", "initials": "C", "orcid": "0000-0002-3783-7256", "researcher": {"href": "https://publications.scilifelab.se/researcher/eb77b417ef2b479fb267969c3a557617.json"}}, {"family": "Xie", "given": "Minglu", "initials": "M"}, {"family": "Salehi", "given": "Maede", "initials": "M"}, {"family": "Torell", "given": "Emma", "initials": "E"}, {"family": "Sj\u00f6blom", "given": "Tobias", "initials": "T", "orcid": "0000-0001-6668-4140", "researcher": {"href": "https://publications.scilifelab.se/researcher/909f00a5bf6e465f9ff560b12bcd863a.json"}}, {"family": "Enblad", "given": "Gunilla", "initials": "G", "orcid": "0000-0002-0594-724X", "researcher": {"href": "https://publications.scilifelab.se/researcher/11313af3f4a241ecb93af23ab2652195.json"}}, {"family": "Amini", "given": "Rose-Marie", "initials": "RM", "orcid": "0000-0003-0901-5252", "researcher": {"href": "https://publications.scilifelab.se/researcher/c157abcd61fa4900b5ad502b408d6d95.json"}}, {"family": "Swartling", "given": "Fredrik Johansson", "initials": "FJ", "orcid": "0000-0002-8460-4367", "researcher": {"href": "https://publications.scilifelab.se/researcher/69679cebbc90496f9c5b32f56d966654.json"}}, {"family": "Glimelius", "given": "Ingrid", "initials": "I"}, {"family": "Micke", "given": "Patrick", "initials": "P", "orcid": "0000-0003-1210-5961", "researcher": {"href": "https://publications.scilifelab.se/researcher/fc0cba74e74a4c39a8f96319cb9a3034.json"}}, {"family": "Hellstr\u00f6m", "given": "Mats", "initials": "M"}, {"family": "Chen", "given": "Xingqi", "initials": "X", "orcid": "0000-0002-5657-2839", "researcher": {"href": "https://publications.scilifelab.se/researcher/ef7ddc09e57745909175e41ac2d1b647.json"}}], "type": "journal article", "published": "2025-11-14", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "16", "issue": "1", "pages": "10022", "issn-l": "2041-1723"}, "abstract": "Formalin-fixed paraffin-embedded (FFPE) samples are the gold standard for tissue preservation in clinical and research settings. Current single-cell chromatin accessibility technologies cannot resolve cell-type-specific epigenetic profiles in FFPE tissues due to extensive DNA damage. We present scFFPE-ATAC, a high-throughput single-cell chromatin accessibility assay for FFPE samples that integrates an FFPE-adapted Tn5 transposase, ultra-high-throughput DNA barcoding (>56 million barcodes per run), T7 promoter-mediated DNA damage repair, and in vitro transcription. We benchmark scFFPE-ATAC on FFPE mouse spleen and validate its performance against fresh tissue. We apply it to human lymph node samples archived for 8-12 years and to lung cancer FFPE tissues, revealing distinct regulatory trajectories between tumor center and invasive edge. Analysis of archived follicular lymphoma and transformed diffuse large B-cell lymphoma samples identifies relapse- and transformation-associated epigenetic dynamics. scFFPE-ATAC enables retrospective, spatial, and mechanistic epigenetic studies in long-term archived specimens.", "doi": "10.1038/s41467-025-66170-4", "pmid": "41238550", "labels": {"National Genomics Infrastructure": "Service", "NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-025-66170-4"}, {"db": "pmc", "key": "PMC12618699"}], "notes": [], "created": "2025-11-17T09:00:46.632Z", "modified": "2025-11-17T09:00:47.092Z"}, {"entity": "publication", "iuid": "5087e22117c64ebbbc4b4299bfc98b9a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5087e22117c64ebbbc4b4299bfc98b9a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5087e22117c64ebbbc4b4299bfc98b9a"}}, "title": "A [11C]PBR28 PET study on the associations between sleep health and microglial density.", "authors": [{"family": "Balter", "given": "Leonie Jt", "initials": "LJ"}, {"family": "Malmros", "given": "Jonatan", "initials": "J"}, {"family": "Stenkrona", "given": "Per", "initials": "P"}, {"family": "Varrone", "given": "Andrea", "initials": "A"}, {"family": "Forsberg", "given": "Anton", "initials": "A"}, {"family": "Gustavsson", "given": "Erik", "initials": "E"}, {"family": "Mouyobo", "given": "Cedrique E", "initials": "CE"}, {"family": "Kalpouzos", "given": "Gr\u00e9goria", "initials": "G"}, {"family": "Papenberg", "given": "Goran", "initials": "G"}], "type": "journal article", "published": "2025-11-14", "journal": {"title": "J Neuroinflammation", "issn": "1742-2094", "volume": "22", "issue": "1", "pages": "270", "issn-l": "1742-2094"}, "abstract": "Sleep disturbances and inflammation are interconnected through shared regulatory mechanisms and are both implicated in age-related diseases. However, their connection at the level of brain-specific inflammation remains underexamined in humans. This study investigated whether specific dimensions of sleep are associated with microglial density, as measured by translocator protein (TSPO) levels, a biomarker of neuroinflammation. TSPO levels were measured using a single [11C]PBR28 positron emission tomography (PET) scan in 39 healthy adults aged 50-81 years (Mage = 66.7, SD = 8.9; 19 females, 20 males). Sleep dimensions were assessed using the Karolinska Sleep Questionnaire on three occasions over five years, twice before and once around the time of PET imaging. Shorter sleep, more frequent napping, daytime fatigue, and sleep insufficiency were associated with higher TSPO levels in the middle frontal cortex (MFC). Conversely, longer sleep was associated with higher TSPO levels in the hippocampus and putamen. Exploratory factor analysis and bootstrapping confirmed a negative association between a factor representing shorter sleep and MFC TSPO levels. Additionally, a greater deviation from optimal sleep duration over the five years, in either direction from eight hours, was associated with higher current TSPO levels in all but one examined brain regions. Peripheral C-reactive protein levels did not significantly correlate with the sleep variables or TSPO levels in any of the brain regions. Analyses were adjusted for age and sex. These findings suggest that insufficient and prolonged sleep durations are associated with elevated microglial density in frontostriatal and limbic systems, respectively, among healthy middle-aged and older adults, without any associations with peripheral inflammation. Further longitudinal studies are needed to clarify directionality and whether changes in sleep duration over time may serve as early indicators of brain health.", "doi": "10.1186/s12974-025-03613-1", "pmid": "41239401", "labels": {"National Genomics Infrastructure": "Service", "NGI SNP genotyping": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12619189"}, {"db": "pii", "key": "10.1186/s12974-025-03613-1"}], "notes": [], "created": "2025-11-18T15:39:15.446Z", "modified": "2025-11-18T15:39:15.465Z"}, {"entity": "publication", "iuid": "f3a1b1396edb4101b0575fbc43ec7415", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f3a1b1396edb4101b0575fbc43ec7415.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f3a1b1396edb4101b0575fbc43ec7415"}}, "title": "Comparative evaluation of Olink Explore 3072 and mass spectrometry with peptide fractionation for plasma proteomics.", "authors": [{"family": "Sissala", "given": "Noora", "initials": "N", "orcid": "0009-0000-0758-8140", "researcher": {"href": "https://publications.scilifelab.se/researcher/3a96666a6a2e478fbdd3cf33d7db1e74.json"}}, {"family": "Baba\u010di\u0107", "given": "Haris", "initials": "H", "orcid": "0000-0003-0813-0005", "researcher": {"href": "https://publications.scilifelab.se/researcher/45a1c5d3d2d34a9e96d112877632784c.json"}}, {"family": "Leo", "given": "Isabelle R", "initials": "IR", "orcid": "0000-0002-7627-6690", "researcher": {"href": "https://publications.scilifelab.se/researcher/21185d9c6a2343f189397cbbb95c6e71.json"}}, {"family": "Cao", "given": "Xiaofang", "initials": "X"}, {"family": "Forshed", "given": "Jenny", "initials": "J"}, {"family": "Eriksson", "given": "Lars E", "initials": "LE", "orcid": "0000-0001-5121-5325", "researcher": {"href": "https://publications.scilifelab.se/researcher/ebb717a9972245a5b2427a4b8421fe6f.json"}}, {"family": "Lehti\u00f6", "given": "Janne", "initials": "J", "orcid": "0000-0002-8100-9562", "researcher": {"href": "https://publications.scilifelab.se/researcher/8406a97bac744a59b1bc951978994581.json"}}, {"family": "Fredolini", "given": "Claudia", "initials": "C", "orcid": "0000-0002-7674-2014", "researcher": {"href": "https://publications.scilifelab.se/researcher/40ac3a5823cb4f998cc8bdb96dcbf195.json"}}, {"family": "\u00c5berg", "given": "Mikael", "initials": "M", "orcid": "0000-0002-7858-8233", "researcher": {"href": "https://publications.scilifelab.se/researcher/90fa86e9aeaa43ea9547e48b4f3f24e3.json"}}, {"family": "Pernemalm", "given": "Maria", "initials": "M", "orcid": "0000-0003-4624-031X", "researcher": {"href": "https://publications.scilifelab.se/researcher/f15f303cb2044cfa81719700137e3603.json"}}], "type": "journal article", "published": "2025-11-04", "journal": {"title": "Commun Chem", "issn": "2399-3669", "issn-l": null, "volume": "8", "issue": "1", "pages": "327"}, "abstract": "Plasma proteomics technologies are advancing rapidly, offering new opportunities for biomarker discovery and precision medicine. Direct comparisons of available technologies are needed to understand how platform selection affects downstream findings. We compared the performance of a peptide fractionation-based mass spectrometry method (HiRIEF LC-MS/MS) and the Olink Explore 3072 proximity extension assays on 88 plasma samples, analyzing 1129 proteins with both methods. The platforms exhibited complementary proteome coverage, high precision, and concordance in estimating sex differences in protein levels. Quantitative agreement between platforms was moderate (median correlation 0.59, interquartile range 0.33-0.75), mainly influenced by technical factors. Finally, we present a publicly available tool for peptide-level analysis of platform agreement and demonstrate its utility in clarifying cross-platform discrepancies in protein and proteoform measurements. Our findings provide insights for platform selection and study design, and highlight the value of combining mass spectrometry and affinity-based approaches for more comprehensive and reliable plasma proteome profiling.", "doi": "10.1038/s42004-025-01753-2", "pmid": "41188494", "labels": {"National Genomics Infrastructure": "Service", "NGI Proteomics": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Affinity Proteomics Stockholm": "Collaborative", "Affinity Proteomics Uppsala": "Collaborative", "Global Proteomics and Proteogenomics": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12586489"}, {"db": "pii", "key": "10.1038/s42004-025-01753-2"}], "notes": [], "created": "2025-11-07T07:35:27.214Z", "modified": "2025-11-27T13:03:30.885Z"}, {"entity": "publication", "iuid": "696f138df66747158e7f0f9a47bbd9ae", "links": {"self": {"href": "https://publications.scilifelab.se/publication/696f138df66747158e7f0f9a47bbd9ae.json"}, "display": {"href": "https://publications.scilifelab.se/publication/696f138df66747158e7f0f9a47bbd9ae"}}, "title": "Paleogenomic evidence on the temporal continuity of indigenous goat exploitation in the Canary Islands", "authors": [{"family": "D\u00edaz-P\u00e9rez", "given": "Clara", "initials": "C"}, {"family": "Santana", "given": "Jonathan", "initials": "J", "orcid": "0000-0002-9615-8560", "researcher": {"href": "https://publications.scilifelab.se/researcher/e5a4f0fc23b847b98e0d57d22a8a756d.json"}}, {"family": "Daly", "given": "Kevin G", "initials": "KG"}, {"family": "Ord\u00f3\u00f1ez", "given": "Alejandra C", "initials": "AC"}, {"family": "Serrano", "given": "Javier G", "initials": "JG"}, {"family": "Armas-Quintana", "given": "Sara B", "initials": "SB"}, {"family": "Vacas-Fumero", "given": "Emilio", "initials": "E"}, {"family": "Brito-Mayor", "given": "Aitor", "initials": "A"}, {"family": "Gilson", "given": "Simon Pierre", "initials": "SP"}, {"family": "Morales", "given": "Jacob", "initials": "J"}, {"family": "Marrero Salas", "given": "Efra\u00edn", "initials": "E"}, {"family": "Hern\u00e1ndez", "given": "Juan Carlos", "initials": "JC"}, {"family": "Alberto", "given": "Ver\u00f3nica", "initials": "V"}, {"family": "Moreno", "given": "Marco", "initials": "M"}, {"family": "G\u00fcnther", "given": "Torsten", "initials": "T", "orcid": "0000-0001-9460-390X", "researcher": {"href": "https://publications.scilifelab.se/researcher/84159bff82a64a938bcff107f550c901.json"}}, {"family": "Morell Miranda", "given": "Pedro", "initials": "P"}, {"family": "Valdiosera", "given": "Cristina", "initials": "C", "orcid": "0000-0003-4948-2226", "researcher": {"href": "https://publications.scilifelab.se/researcher/113ef0dde1dd48e388f75c43bd672005.json"}}, {"family": "Hern\u00e1ndez", "given": "Mariano", "initials": "M"}, {"family": "Arnay", "given": "Matilde", "initials": "M"}, {"family": "Fregel", "given": "Rosa", "initials": "R", "orcid": "0000-0002-2951-6508", "researcher": {"href": "https://publications.scilifelab.se/researcher/abfbfec4ddea49f8b4eedcf1e04e01c2.json"}}], "type": "journal-article", "published": "2025-11-00", "journal": {"title": "iScience", "issn": "2589-0042", "issn-l": "2589-0042", "volume": "28", "issue": "11", "pages": "113771"}, "abstract": null, "doi": "10.1016/j.isci.2025.113771", "pmid": null, "labels": {"Ancient DNA": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Stockholm (Genomics Production)": null}, "xrefs": [], "notes": [], "created": "2025-11-05T07:40:52.150Z", "modified": "2025-11-19T07:57:42.304Z"}, {"entity": "publication", "iuid": "edba25a5b1e54a32865c02915ee9ff5e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/edba25a5b1e54a32865c02915ee9ff5e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/edba25a5b1e54a32865c02915ee9ff5e"}}, "title": "Host Traits Impact the Outcome of Metagenomic Library Preparation From Dental Calculus Samples Across Diverse Mammals.", "authors": [{"family": "Moraitou", "given": "Markella", "initials": "M", "orcid": "0000-0003-0860-5920", "researcher": {"href": "https://publications.scilifelab.se/researcher/5f3b54ad837e4860a81b0bd5a886b416.json"}}, {"family": "Richards", "given": "John L", "initials": "JL", "orcid": "0000-0003-4428-1580", "researcher": {"href": "https://publications.scilifelab.se/researcher/23d3051397fd422b94afdb6eb8be17c4.json"}}, {"family": "Bolyos", "given": "Chanah", "initials": "C"}, {"family": "Saliari", "given": "Konstantina", "initials": "K", "orcid": "0000-0002-1344-0756", "researcher": {"href": "https://publications.scilifelab.se/researcher/b32afde8cb454fa3bb0e880e2cff5d0b.json"}}, {"family": "Gilissen", "given": "Emmanuel", "initials": "E"}, {"family": "Timmons", "given": "Zena", "initials": "Z"}, {"family": "Kitchener", "given": "Andrew C", "initials": "AC"}, {"family": "Pauwels", "given": "Olivier S G", "initials": "OSG"}, {"family": "Sabin", "given": "Richard", "initials": "R", "orcid": "0000-0003-0699-7596", "researcher": {"href": "https://publications.scilifelab.se/researcher/b7d0503256fd45e687c1eebc9ce0c797.json"}}, {"family": "Kokkini", "given": "Phaedra", "initials": "P", "orcid": "0000-0002-7652-0956", "researcher": {"href": "https://publications.scilifelab.se/researcher/223e41a72db2480aa5fbfd015702b525.json"}}, {"family": "Portela Miguez", "given": "Roberto", "initials": "R", "orcid": "0000-0003-3094-9949", "researcher": {"href": "https://publications.scilifelab.se/researcher/103b88f38bcb494e8b42096d632e9f71.json"}}, {"family": "Guschanski", "given": "Katerina", "initials": "K", "orcid": "0000-0002-8493-5457", "researcher": {"href": "https://publications.scilifelab.se/researcher/84b8b0757f02429b9bd419acb42ab6a3.json"}}], "type": "journal article", "published": "2025-11-00", "journal": {"title": "Mol Ecol Resour", "issn": "1755-0998", "issn-l": "1755-098X", "volume": "25", "issue": "8", "pages": "e70039"}, "abstract": "Dental calculus metagenomics has emerged as a valuable tool for studying the oral microbiomes of humans and a few select mammals. With increasing interest in wild animal microbiomes, it is important to understand how widely this material can be used across the mammalian tree of life, refine the related protocols and understand the expected outcomes and potential challenges of dental calculus sample processing. In this study, we significantly expand the breadth of studied host species, analysing laboratory and bioinformatics metadata of dental calculus samples from 32 ecologically and phylogenetically diverse mammals. Although we confirm the presence of an oral microbiome signature in the metagenomes of all studied mammals, the fraction recognised as oral varies between host species, possibly because of both biological differences and methodological biases. The overall success rate of dental calculus processing, from extractions to sequencing, was ~74%. Although input sample weight was positively associated with the number of produced library molecules, we identify a negative impact of enzymatic inhibition on the library preparation protocol. The inhibition was most prevalent in herbivores and frugivores and is likely diet-derived. In contrast, hosts with an animalivore diet posed fewer challenges during laboratory processing and yielded more DNA relative to sample weight. Our results translate into recommendations for future studies of dental calculus metagenomics from a variety of host species, identifying required sample amounts, and emphasising the utility of dental calculus in exploring the oral microbiome in relation to broader ecological and evolutionary questions.", "doi": "10.1111/1755-0998.70039", "pmid": "40889349", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12550474"}], "notes": [], "created": "2025-09-08T07:07:00.224Z", "modified": "2025-11-28T10:50:40.774Z"}, {"entity": "publication", "iuid": "19188c6729144072978d9a3d01d09133", "links": {"self": {"href": "https://publications.scilifelab.se/publication/19188c6729144072978d9a3d01d09133.json"}, "display": {"href": "https://publications.scilifelab.se/publication/19188c6729144072978d9a3d01d09133"}}, "title": "Genetic Analysis of Apple Autumn Canopy Senescence in a Nordic Climate.", "authors": [{"family": "Skytte Af S\u00e4tra", "given": "Jonas", "initials": "J", "orcid": "0000-0002-2827-4842", "researcher": {"href": "https://publications.scilifelab.se/researcher/00b323220517477eb3c4acda1bb64c81.json"}}], "type": "journal article", "published": "2025-10-30", "journal": {"title": "Physiol Plantarum", "issn": "1399-3054", "volume": "177", "issue": "6", "pages": "e70599", "issn-l": "0031-9317"}, "abstract": "Autumn phenology traits are likely to be essential for the adaptation of apple to boreal climate. However, the genetic control of these traits is not well understood, and, for example, growth cessation does not appear to be controlled by day length as in many other boreal tree species. Here, I combine a quantitative genetic and population genomic approach to study autumn senescence in apple. I phenotyped a diverse germplasm collection for the timing of autumn senescence, performed quantitative trait loci (QTL) mapping in a multiparental population (MPP), and investigated genomic signals of selection to identify candidate genes. The timing of 50% autumn senescence was negatively correlated with adaptation to higher (boreal) climate zones. Two QTL were found to control the timing of autumn senescence in the MPP, exhibiting both dominance and epistatic interactions. The QTL on linkage group (LG) 17 was also variable in the diversity germplasm, while the QTL on LG11 was not. Cultivars adapted to boreal climate showed weak signals of selection at two loci within the genomic region of chromosome 17 corresponding to the LG17 QTL interval, consistent with a recent expansion to northern Sweden. These loci coincide with two predicted UGT85 genes and a possible copy number variation in PHYC, respectively. Thus, this study provides valuable information for further research and breeding of apple in light of the ongoing climate change.", "doi": "10.1111/ppl.70599", "pmid": "41164927", "labels": {"National Genomics Infrastructure": "Service", "NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12573221"}], "notes": [], "created": "2025-11-07T07:26:45.450Z", "modified": "2025-11-14T11:08:25.063Z"}, {"entity": "publication", "iuid": "9ffabc46b92c4c76be483815e6bba9dc", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9ffabc46b92c4c76be483815e6bba9dc.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9ffabc46b92c4c76be483815e6bba9dc"}}, "title": "Epigenetic mediation may explain intergenerational associations between maternal obesogenic lifestyle and children's birth weight: findings from the NorthPop prospective birth cohort.", "authors": [{"family": "De Silva", "given": "Kushan", "initials": "K", "orcid": "0000-0003-0301-0805", "researcher": {"href": "https://publications.scilifelab.se/researcher/0fb44e3f1d204c2a996e747704e2e77f.json"}}, {"family": "Lundberg-Ulfsdotter", "given": "Richard", "initials": "R"}, {"family": "Bod\u00e9n", "given": "Stina", "initials": "S", "orcid": "0000-0002-8958-975X", "researcher": {"href": "https://publications.scilifelab.se/researcher/8dcfadb86b8040499a7af3c4a744d3b2.json"}}, {"family": "Vinnars", "given": "Marie-Therese", "initials": "MT"}, {"family": "Ryden", "given": "Patrik", "initials": "P", "orcid": "0000-0002-0577-123X", "researcher": {"href": "https://publications.scilifelab.se/researcher/65e733a3351940749605f054834eebef.json"}}, {"family": "West", "given": "Christina E", "initials": "CE", "orcid": "0000-0001-9599-2580", "researcher": {"href": "https://publications.scilifelab.se/researcher/be2972e4afa744e5aa0525a4c9d89348.json"}}, {"family": "Domell\u00f6f", "given": "Magnus", "initials": "M"}, {"family": "Harlid", "given": "Sophia", "initials": "S", "orcid": "0000-0001-8540-6891", "researcher": {"href": "https://publications.scilifelab.se/researcher/76a824f2687b460890ae6d9ef40d97c9.json"}}], "type": "journal article", "published": "2025-10-29", "journal": {"title": "Clin Epigenetics", "issn": "1868-7083", "volume": "17", "issue": "1", "pages": "180", "issn-l": "1868-7075"}, "abstract": "Epigenetic alterations during fetal development have been proposed as key factors explaining associations between maternal lifestyle during pregnancy and later health outcomes in the offspring, pertaining to the developmental origin of health and disease hypothesis.\n\nTo assess the association of maternal lifestyle with offsprings' birth weight and underlying epigenetic mediatory mechanisms in the NorthPop prospective birth cohort.\n\nA three-step analytic pipeline was applied. In 722 mother-child pairs, overall associations between ten maternal lifestyle factors and the offspring's standardized birth weight were first evaluated by multiple linear regression. Three high-dimensional mediation methods, based on sure independence screening and penalized regression, were then applied on the beta methylation matrix to identify candidate CpG mediators in cord blood driving the significant overall associations. Finally, robust and ordinary least squares (OLS) regression-based classical mediation methods were used with candidate CpG probes to assess single- and multiple (parallel and serial)-mediator models on a low-dimensional space.\n\nGestational weight gain (GWG) (\u03b2-adj = 0.03; p = 2 \u00d7 10-5) and maternal BMI at the beginning of pregnancy (\u03b2-adj = 0.036; p = 1 \u00d7 10-4) were significantly associated with the offspring's standardized birth weight. High-dimensional mediation analyses identified pooled sets of four (cg19242268 [TCEA2]; cg08461903 [N/A]; cg14798382 [CHERP/C19orf44] and cg21516291 [SLC35C2]) and five (cg17040807 [CYGB]; cg19242268 [TCEA2]; cg26552621 [CIRBP]; cg04457572 [CDH23] and cg06457011 [PLCG1]) candidate CpG mediators related to GWG and BMI at the beginning of pregnancy, respectively. For both exposures, classical mediation analyses revealed a range of significant single- and multiple (both serial and parallel)-mediator models via both robust and OLS regression based approaches. These indicated the likely presence of individual, causally linked multiple, and causally independent multiple mediatory pathways underlying the two significant overall associations.\n\nOur findings support the hypothesis that neonatal health effects related to maternal lifestyle may be partly mediated by epigenetic alterations. Findings also suggest the possible involvement of multiple DNA methylation sites via various mediatory pathways.", "doi": "10.1186/s13148-025-02001-z", "pmid": "41163109", "labels": {"National Genomics Infrastructure": "Service", "NGI SNP genotyping": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12570728"}, {"db": "pii", "key": "10.1186/s13148-025-02001-z"}], "notes": [], "created": "2025-11-07T07:25:46.328Z", "modified": "2025-11-11T13:52:44.760Z"}, {"entity": "publication", "iuid": "85c5bdfdbc81457e81767eab223261e3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/85c5bdfdbc81457e81767eab223261e3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/85c5bdfdbc81457e81767eab223261e3"}}, "title": "Diagnostic and prognostic biomarkers associated with histotype in advanced epithelial ovarian cancer.", "authors": [{"family": "Ittner", "given": "Ella", "initials": "E"}, {"family": "Swenson", "given": "Hugo", "initials": "H"}, {"family": "Werner", "given": "Lucas", "initials": "L"}, {"family": "R\u00f6nnerman", "given": "Elisabeth Werner", "initials": "EW"}, {"family": "Mateoiu", "given": "Constantina", "initials": "C"}, {"family": "Kov\u00e1cs", "given": "Anik\u00f3", "initials": "A"}, {"family": "Dahm-K\u00e4hler", "given": "Pernilla", "initials": "P"}, {"family": "Saed", "given": "Ghassan", "initials": "G"}, {"family": "Karlsson", "given": "Per", "initials": "P"}, {"family": "Parris", "given": "Toshima Z", "initials": "TZ", "orcid": "0000-0003-0834-5540", "researcher": {"href": "https://publications.scilifelab.se/researcher/0d528a2bce6c40829c1a6fed69c9f9ef.json"}}, {"family": "Helou", "given": "Khalil", "initials": "K"}], "type": "journal article", "published": "2025-10-23", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "15", "issue": "1", "pages": "37171", "issn-l": "2045-2322"}, "abstract": "Despite advances in cancer treatments, epithelial ovarian cancer (EOC) remains the leading cause of death among gynecologic cancers. EOC is stratified into five main histopathological subtypes: high-grade serous carcinoma (HGSC), low-grade serous carcinoma (LGSC), endometrioid carcinoma (EC), clear cell carcinoma (CCC), and mucinous carcinoma (MC). However, personalized treatment strategies and reliable biomarkers for all histotypes remain elusive. Building on our previous work with early-stage EOC, we aim to explore diagnostic and prognostic biomarkers in advanced-stage EOC, updated to the latest World Health Organization classification guidelines from 2020, using comprehensive transcriptomic profiling from total RNA sequencing of 146 EOCs. Differential expression analysis identified top 9 histotype-specific gene panels for HGSC, CCC, MC, and EC, including S100A1 (HGSC), ARID3A (CCC), LGALS4 (MC), and PAX9 (EC). We also identified gene candidates associated with overall survival and disease-specific survival, reflecting both favorable (e.g., OTOF, EEF1E1-BLOC1S5, and STAC3) and unfavorable (e.g., SMOC1, GDPGP1, EPRS1) clinical outcome. Additionally, enrichment analysis revealed tumor progression-related pathways unique to each histotype, offering insights into the molecular mechanisms underlying disease progression and potential therapeutic targets. These findings provide valuable insights into the molecular landscape of advanced-stage EOC, paving the way for more effective diagnostic and prognostic tools across diverse histotypes.", "doi": "10.1038/s41598-025-24938-0", "pmid": "41131133", "labels": {"National Genomics Infrastructure": "Service", "NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12550092"}, {"db": "pii", "key": "10.1038/s41598-025-24938-0"}], "notes": [], "created": "2025-11-07T07:25:02.175Z", "modified": "2025-11-28T10:47:09.805Z"}, {"entity": "publication", "iuid": "c34e73cd03bb4bea92a8c1741dafab9d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c34e73cd03bb4bea92a8c1741dafab9d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c34e73cd03bb4bea92a8c1741dafab9d"}}, "title": "Transcriptomic responses of beet to infection by beet mild yellowing virus.", "authors": [{"family": "Puthanveed", "given": "Vinitha", "initials": "V"}, {"family": "Sajeevan", "given": "Radha Sivarajan", "initials": "RS", "orcid": "0000-0002-8671-4981", "researcher": {"href": "https://publications.scilifelab.se/researcher/4d0cdc56cd144c628d3c90000b782581.json"}}, {"family": "Siddique", "given": "Abu Bakar", "initials": "AB"}, {"family": "Alexandersson", "given": "Erik", "initials": "E", "orcid": "0000-0001-6320-2492", "researcher": {"href": "https://publications.scilifelab.se/researcher/eae8dc98de79429495f0a1727a342e9f.json"}}, {"family": "Joshi", "given": "Pratikshya", "initials": "P", "orcid": "0000-0002-6361-5059", "researcher": {"href": "https://publications.scilifelab.se/researcher/46050ddec8f64054b3bab46c5016aebf.json"}}, {"family": "Snell", "given": "Per", "initials": "P"}, {"family": "Lennefors", "given": "Britt-Louise", "initials": "BL"}, {"family": "Kvarnheden", "given": "Anders", "initials": "A", "orcid": "0000-0001-9394-7700", "researcher": {"href": "https://publications.scilifelab.se/researcher/bf67998333e74016847b7a6d3f121e7b.json"}}], "type": "journal article", "published": "2025-10-21", "journal": {"title": "BMC Plant Biol.", "issn": "1471-2229", "volume": "25", "issue": "1", "pages": "1406", "issn-l": "1471-2229"}, "abstract": "Virus yellows (VY) disease of sugar beet is caused by a complex of aphid-transmitted viruses, including beet mild yellowing virus (BMYV). Neonicotinoids have been used for preventing VY through aphid management, but with the recent ban on neonicotinoids in Europe, the risks for outbreaks of VY have increased dramatically. To study the host responses to BMYV infection and identify the differentially expressed genes (DEGs), we conducted an RNAseq experiment using a resistant genotype of wild beet and a susceptible breeding line of sugar beet. The experiment contained four plant treatments: exposure to aphids with or without BMYV, only insecticide spray and untreated control. Leaves were collected for analyses at 0, 1, 4, 14, 21 and 28 days post-inoculation (DPI).\n\nFollowing BMYV inoculation, resistant plants did not show any chlorosis even at 28 DPI, whereas susceptible plants displayed typical virus symptoms. Using RT-qPCR, BMYV was detected already at 1 DPI in both genotypes. At 14, 21 and 28 DPI, the virus titre in young and inoculated leaves of the susceptible genotype was higher. RNAseq revealed more DEGs as a response to BMYV infection for the susceptible genotype. In inoculated leaves, the number of DEGs increased faster for the susceptible genotype, while in young leaves, the trend was similar for susceptible and resistant genotypes. This shows that the plant responses in inoculated leaves to virus infection appeared at a larger scale in the susceptible genotype. Seven of the significantly upregulated genes in the resistant genotype encoded proteins involved in protein processing in the ER. This could be one mechanism contributing to the absence of symptoms in this genotype.\n\nThis study offers new insights into the transcriptomic events and genetic pathways regulating the defence response to BMYV in a partially resistant genotype. We present 14 candidate genes for partial resistance to BMYV and one of the possible mechanisms contributing to reduced virus levels and absence of symptoms. The findings will be of importance for future functional studies to understand the mechanisms of resistance and susceptibility as well as for the breeding of BMYV resistance.", "doi": "10.1186/s12870-025-07514-6", "pmid": "41120973", "labels": {"National Genomics Infrastructure": "Service", "NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12538817"}, {"db": "pii", "key": "10.1186/s12870-025-07514-6"}], "notes": [], "created": "2025-11-07T07:24:57.182Z", "modified": "2025-11-14T11:08:40.919Z"}, {"entity": "publication", "iuid": "d9c76d2925724acb9c140d062e9a55ad", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d9c76d2925724acb9c140d062e9a55ad.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d9c76d2925724acb9c140d062e9a55ad"}}, "title": "Symbiont Diversity of Rice-Associated Leafhoppers (Cicadellidae) in the Tropical Floodplains of the Tonle Sap Lake, Cambodia.", "authors": [{"family": "Phauk", "given": "Sophany", "initials": "S", "orcid": "0000-0002-8019-3206", "researcher": {"href": "https://publications.scilifelab.se/researcher/80bf701bd9c14bd08c081d49b0d6ecad.json"}}, {"family": "Assentato", "given": "Lorenzo", "initials": "L", "orcid": "0000-0003-3699-0483", "researcher": {"href": "https://publications.scilifelab.se/researcher/69a8069f62434b128fb5837b139dbb56.json"}}, {"family": "Sin", "given": "Sopha", "initials": "S"}, {"family": "Uk", "given": "Onnorong", "initials": "O"}, {"family": "Hap", "given": "Sophorn", "initials": "S"}, {"family": "Terenius", "given": "Olle", "initials": "O", "orcid": "0000-0002-9909-1859", "researcher": {"href": "https://publications.scilifelab.se/researcher/3042a807e20d444cafee3f760c38d5d1.json"}}], "type": "journal article", "published": "2025-10-17", "journal": {"title": "Microb. Ecol.", "issn": "1432-184X", "volume": "88", "issue": "1", "pages": "109", "issn-l": "0095-3628"}, "abstract": "Rice-associated leafhoppers (Cicadellidae) play a significant role in rice agroecosystems, contributing not only to direct crop damage but also to the transmission of plant pathogens. This study investigates the symbiont diversity of seventeen leafhopper species from the tropical floodplains of Tonle Sap Lake (TSL), Cambodia. The dominant symbiont across most species was Candidatus (Ca.) Karelsulcia muelleri, an obligate primary endosymbiont essential for nutrient synthesis. The co-obligate symbiont Ca. Nasuia deltocephalinicola was also consistently detected, particularly in Deltocephalinae hosts. In addition, several secondary symbionts, including Sodalis, Arsenophonus, Diplorickettsia, Rickettsia, Wolbachia, and Ca. Lariskella, were identified, showing species-specific associations and potential roles in host fitness and pathogen transmission. Variations in symbiont diversity were observed across cicadellid species, geographic origins, and between sex-associated symbionts, with notable differences in the bacterial composition of Nephotettix virescens. While geographical differences (Battambang vs. Kampong Thom) did not strongly affect microbial composition, sex-associated variations were evident in N. virescens. Females exhibited a higher abundance of Karelsulcia and Nasuia, suggesting possible microbial adaptation related to reproduction. This study highlights the complex and dynamic nature of cicadellid hosts-symbiont interactions and suggests that microbial communities are primarily structured by host species. While geographic distance can influence these communities, this effect is not the same for every species. These findings provide critical insights into the microbial diversity of rice-associated leafhoppers and their potential for ecological roles in rice farming systems. Further studies, including functional analysis and host-symbiont interactions, are crucial to understanding the ecological roles and evolutionary dynamics of these microbial communities.", "doi": "10.1007/s00248-025-02619-9", "pmid": "41105260", "labels": {"National Genomics Infrastructure": "Service", "NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12534257"}, {"db": "pii", "key": "10.1007/s00248-025-02619-9"}], "notes": [], "created": "2025-11-07T07:26:53.717Z", "modified": "2025-11-28T10:41:02.912Z"}, {"entity": "publication", "iuid": "3026cc0df25b4c178a58bdb7ba158810", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3026cc0df25b4c178a58bdb7ba158810.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3026cc0df25b4c178a58bdb7ba158810"}}, "title": "Reduced vascular leakage correlates with breast carcinoma T regulatory cell infiltration but not with metastatic propensity.", "authors": [{"family": "He", "given": "Liqun", "initials": "L", "orcid": "0000-0002-4743-5410", "researcher": {"href": "https://publications.scilifelab.se/researcher/e6e2e4c7f88845bb895842e56a7622ae.json"}}, {"family": "Testini", "given": "Chiara", "initials": "C"}, {"family": "Hekmati", "given": "Neda", "initials": "N", "orcid": "0009-0009-4814-869X", "researcher": {"href": "https://publications.scilifelab.se/researcher/59e525846f61401ab94732e578190274.json"}}, {"family": "Bonello", "given": "Altea", "initials": "A"}, {"family": "Schiza", "given": "Aglaia", "initials": "A"}, {"family": "Nwadozi", "given": "Emmanuel", "initials": "E"}, {"family": "Phillipson", "given": "Mia", "initials": "M", "orcid": "0000-0002-2387-0266", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ebf9ffcab3e4a19add4c6dd51b727b1.json"}}, {"family": "Strell", "given": "Carina", "initials": "C", "orcid": "0000-0002-3783-7256", "researcher": {"href": "https://publications.scilifelab.se/researcher/eb77b417ef2b479fb267969c3a557617.json"}}, {"family": "Welsh", "given": "Michael", "initials": "M", "orcid": "0000-0002-5467-9755", "researcher": {"href": "https://publications.scilifelab.se/researcher/c01673aeb9be429c80da30d5407b2725.json"}}], "type": "journal article", "published": "2025-10-16", "journal": {"title": "Mol Oncol", "issn": "1878-0261", "issn-l": "1574-7891"}, "abstract": "The vasculature and the immune system both play roles in breast cancer progression and metastasis. In an experimental mouse model of Shb-gene deficiency in endothelial cells, breast cancer lung metastasis correlated with immune suppression rather than with vascular leakage. The present study aimed to assess underlying gene expression changes in endothelial and immune cells responsible for this phenotype and to explore their relationship to human disease. Mouse endothelial cell Shb-gene deficiency, leading to 'vessel normalization', resulted in altered expression of chemo/cytokine genes and upregulation of immune checkpoint genes in immune cells. Endothelial cells under these conditions exhibited gene expression patterns compatible with reduced angiogenesis and vascular leakage. Additionally, genes whose products relate to immune cell vascular transmigration and function were affected. In a human triple-negative breast cancer cohort, tumors with reduced vascular leakage exhibited a higher relative proportion of regulatory T cells and larger tumor size. However, these changes were not associated with increased metastasis. In conclusion, a low leakage vascular phenotype reduces tumor cell intravasation/metastasis and modifies the immune response, which in the current context becomes pro-tumoral.", "doi": "10.1002/1878-0261.70144", "pmid": "41102920", "labels": {"National Genomics Infrastructure": "Service", "NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [], "notes": [], "created": "2025-11-07T07:23:33.643Z", "modified": "2025-11-13T17:36:03.258Z"}, {"entity": "publication", "iuid": "d621c8dfa56a43f7a5840112b6226276", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d621c8dfa56a43f7a5840112b6226276.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d621c8dfa56a43f7a5840112b6226276"}}, "title": "Association of estrogen receptor single nucleotide polymorphisms and perinatal depression.", "authors": [{"family": "Bj\u00f6rvang", "given": "Richelle Duque", "initials": "RD", "orcid": "0000-0002-3619-2257", "researcher": {"href": "https://publications.scilifelab.se/researcher/ed3a5bfc2fab4fe4a9c83f44007431e1.json"}}, {"family": "Gumbo", "given": "Lulu Francis", "initials": "LF"}, {"family": "\u00c5rdahl", "given": "Anders", "initials": "A"}, {"family": "Lager", "given": "Susanne", "initials": "S"}, {"family": "Comasco", "given": "Erika", "initials": "E", "orcid": "0000-0002-2174-2068", "researcher": {"href": "https://publications.scilifelab.se/researcher/83fe689667824167ac7cf6a058b5e150.json"}}, {"family": "Fransson", "given": "Emma", "initials": "E"}, {"family": "Skalkidou", "given": "Alkistis", "initials": "A", "orcid": "0000-0002-4935-7532", "researcher": {"href": "https://publications.scilifelab.se/researcher/0d12fb448f9241b2841a8dce8cb42560.json"}}], "type": "journal article", "published": "2025-10-16", "journal": {"title": "PLoS ONE", "issn": "1932-6203", "volume": "20", "issue": "10", "pages": "e0334705", "issn-l": "1932-6203"}, "abstract": "Depression during pregnancy and in the postpartum period have been receiving increasing attention considering the possible complications for the mother and baby if left untreated. Genetic variations in the estrogen receptor genes (ESR) have been implicated in susceptibility to depression. However, only few studies investigated them in perinatal depression (PND) and none on its different trajectories (i.e., patterns of time of onset and persistency of depression). Here, we explored the association of single nucleotide polymorphisms (SNPs) of the ESR1 and ESR2 genes with PND among 2,973 women in Sweden. PND was defined using the Edinburgh Postnatal Depression Scale, the Depression Self-Rating Scale, use of selective serotonin reuptake inhibitor, and/or medical records. PND trajectories were identified as follows: controls (no depression at any point in the perinatal period), antepartum (depression during pregnancy and resolved postpartum), postpartum-onset (no depression during pregnancy with onset after delivery), and persistent (depression throughout the perinatal period). Multivariable logistic regression was performed. Out of 56 SNPs analyzed, one SNP in the ESR1 gene (rs2982712) was nominally significantly associated with PND (OR 0.83, 95% CI 0.71-0.98, p = 0.03) as well as with persistent depression (OR 0.77, 95% CI 0.61-0.98, p = 0.03) in the overdominant model (DD/dd vs. Dd). In addition, we also found two SNPs, namely rs1884051 (OR 0.74, 95% CI 0.56-0.98, p = 0.03) and rs2228480 (OR 0.77, 95% CI 0.60-0.99, p = 0.04) in the ESR1 gene, that were nominally significantly associated with persistent depression only. None of the ESR1 SNPs were associated with antepartum or postpartum-onset depression. None of the ESR2 SNPs, nor any haplotypes, were associated with PND or its trajectories. Our findings suggest a role of ESR1 in PND, especially its persistent trajectory.", "doi": "10.1371/journal.pone.0334705", "pmid": "41100533", "labels": {"National Genomics Infrastructure": "Service", "NGI SNP genotyping": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12530586"}, {"db": "pii", "key": "PONE-D-24-49872"}], "notes": [], "created": "2025-11-07T07:23:59.861Z", "modified": "2025-11-07T07:24:00.268Z"}, {"entity": "publication", "iuid": "4b541203774f4f0f904e27c77dfb6ad1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4b541203774f4f0f904e27c77dfb6ad1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4b541203774f4f0f904e27c77dfb6ad1"}}, "title": "Association between pro-inflammatory proteins and neurofilament in plasma from persons with epilepsy.", "authors": [{"family": "Sarangdhar", "given": "Mayuresh", "initials": "M"}, {"family": "Akel", "given": "Sarah", "initials": "S"}, {"family": "Hosseini Ashtiani", "given": "Saman", "initials": "S"}, {"family": "Axelsson", "given": "Markus", "initials": "M"}, {"family": "Zelano", "given": "Johan", "initials": "J"}], "type": "journal article", "published": "2025-10-13", "journal": {"title": "BMC Med", "issn": "1741-7015", "issn-l": "1741-7015", "volume": "23", "issue": "1", "pages": "554"}, "abstract": "Inflammation and neurodegeneration are emerging as pathophysiological processes of interest in epilepsy. Seizures can both arise from and induce inflammation and difficult-to-treat epilepsy is linked to brain atrophy. However, the interplay between inflammation and neurodegeneration remains poorly understood in epilepsy. This study investigates the association between inflammatory proteins and plasma neurofilament light chain (NEFL or NfL), a known marker of neurodegeneration, particularly in relation to active epilepsy.\r\n\r\nWe performed Olink proteomics on plasma from 176 epilepsy patients aged between 18 and 50 years. To assess systemic inflammation, a composite pro-inflammatory score was derived from the expression of 12 pro-inflammatory proteins. Patients were stratified based on pro-inflammatory score and NEFL and correlation between them was analyzed. Seizure frequency and drug resistance were assessed across patient subgroups.\r\n\r\nPro-inflammatory score and NEFL showed weak positive correlation (r = 0.1); not all patients with high levels of inflammation had high levels of NEFL. In the small proportion of patients (11%, n = 19) with high inflammation and elevated NEFL, seizures (Kruskal-Wallis test H = 9.68, p = 0.02) and drug-resistant epilepsy (\u03c72 = 13.47, p = 0.036, df = 6) were more common, whereas patients with low inflammation and normal NEFL (31.8%, n = 56) tended to have well-controlled epilepsy. Moreover, patients with high inflammation and abnormal NEFL showed protein changes suggestive of potential blood-brain barrier disruption and leukocyte migration.\r\n\r\nInflammation and neurodegeneration are not necessarily linked in all epilepsy patients, but both are more likely to exist in the subset of cases with many seizures. Conversely, absence of both processes indicates well-controlled epilepsy. The combination of plasma NEFL with inflammatory markers could improve seizure prediction and provide novel insights for personalized epilepsy management.", "doi": "10.1186/s12916-025-04425-z", "pmid": "41083978", "labels": {"Affinity Proteomics Uppsala": "Service", "National Genomics Infrastructure": "Service", "NGI Proteomics": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12519617"}, {"db": "pii", "key": "10.1186/s12916-025-04425-z"}], "notes": [], "created": "2025-11-25T19:19:03.981Z", "modified": "2025-11-26T11:05:31.642Z"}, {"entity": "publication", "iuid": "20400326c0944ebda6e786a24f339e26", "links": {"self": {"href": "https://publications.scilifelab.se/publication/20400326c0944ebda6e786a24f339e26.json"}, "display": {"href": "https://publications.scilifelab.se/publication/20400326c0944ebda6e786a24f339e26"}}, "title": "A human pan-disease blood atlas of the circulating proteome.", "authors": [{"family": "\u00c1lvez", 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{"family": "Sutantiwanichkul", "given": "Thanadol", "initials": "T", "orcid": "0000-0002-1072-6863", "researcher": {"href": "https://publications.scilifelab.se/researcher/d1f33fff56f34d72bb1bbc88608ed914.json"}}, {"family": "Svedman", "given": "Fernanda Costa", "initials": "FC", "orcid": "0000-0001-8065-3375", "researcher": {"href": "https://publications.scilifelab.se/researcher/468b2e407aeb49a88b1ef0f7b1e02ce7.json"}}, {"family": "Svensson", "given": "Mattias", "initials": "M", "orcid": "0000-0003-1695-7934", "researcher": {"href": "https://publications.scilifelab.se/researcher/2e3185cf86534a96983b39dd93df454a.json"}}, {"family": "Svenungsson", "given": "Elisabet", "initials": "E"}, {"family": "Lakshmikanth", "given": "Tadepally", "initials": "T", "orcid": "0000-0001-7256-5770", "researcher": {"href": "https://publications.scilifelab.se/researcher/92e81aa6b0cf4ff0a18b14098bf0fcc1.json"}}, {"family": "Tran-Minh", "given": "Khue Hua", "initials": "KH", "orcid": "0000-0002-8964-7489", "researcher": {"href": "https://publications.scilifelab.se/researcher/a94e99b0020f4ef28c00bb20e1a1c8ac.json"}}, {"family": "T\u00fcrkez", "given": "Hasan", "initials": "H", "orcid": "0000-0002-7046-8990", "researcher": {"href": "https://publications.scilifelab.se/researcher/dbae52c6a22f4877b747a4de1ec1ca8a.json"}}, {"family": "Unge", "given": "Christian", "initials": "C"}, {"family": "Venge", "given": "Per", "initials": "P", "orcid": "0000-0001-5863-790X", "researcher": {"href": "https://publications.scilifelab.se/researcher/1695020d4d724ba8b378c992e28e21b1.json"}}, {"family": "Wahren-Herlenius", "given": "Marie", "initials": "M", "orcid": "0000-0002-0915-7245", "researcher": {"href": "https://publications.scilifelab.se/researcher/a8451e7f5e6e4e4da0bace3dfafaeb38.json"}}, {"family": "Woessmann", "given": "Jakob", "initials": "J", "orcid": "0000-0002-2283-7237", "researcher": {"href": "https://publications.scilifelab.se/researcher/18460524ba914a91ad61dd2ec231c3a7.json"}}, {"family": "Yang", "given": "Hong", "initials": "H", "orcid": "0009-0002-0414-2471", "researcher": {"href": "https://publications.scilifelab.se/researcher/b52bdf7cbd1745e3a4578f17322c83f1.json"}}, {"family": "Ye\u015filkaya", "given": "Umit Haluk", "initials": "UH"}, {"family": "Yuan", "given": "Meng", "initials": "M", "orcid": "0000-0002-9248-3294", "researcher": {"href": "https://publications.scilifelab.se/researcher/befeb12cfba142eb9dadf81497d6c419.json"}}, {"family": "Zeybel", "given": "Mujdat", "initials": "M", "orcid": "0000-0001-5440-4623", "researcher": {"href": "https://publications.scilifelab.se/researcher/0559b83985134a0a9283ea39601a95a7.json"}}, {"family": "Zhang", "given": "Cheng", "initials": "C", "orcid": "0000-0002-3721-8586", "researcher": {"href": "https://publications.scilifelab.se/researcher/d1b9559ac41749fa91c4025108947e13.json"}}, {"family": "Zhong", "given": "Wen", "initials": "W", "orcid": "0000-0002-7422-6104", "researcher": {"href": "https://publications.scilifelab.se/researcher/a82c3b7da3b8472392d39ca5f6d5bedb.json"}}, {"family": "Zwahlen", "given": "Martin", "initials": "M", "orcid": "0000-0002-0064-4776", "researcher": {"href": "https://publications.scilifelab.se/researcher/04fb4e913dfb47b9bee48531db50d64c.json"}}, {"family": "von Feilitzen", "given": "Kalle", "initials": "K", "orcid": "0000-0002-0257-7554", "researcher": {"href": "https://publications.scilifelab.se/researcher/9f1e309f8d9247458c59e2ecfbd0c079.json"}}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}, {"family": "Edfors", "given": "Fredrik", "initials": "F", "orcid": "0000-0002-0017-7987", "researcher": {"href": "https://publications.scilifelab.se/researcher/3f0e8af0b9144bcd9fd566d316008a62.json"}}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}], "type": "journal article", "published": "2025-10-09", "journal": {"title": "Science", "issn": "1095-9203", "issn-l": "0036-8075", "volume": null, "issue": null, "pages": "eadx2678"}, "abstract": "The human blood proteome provides a holistic readout of health states through the assessment of thousands of circulating proteins. Here, we present a pan-disease resource to enable the study of diverse disease phenotypes within a harmonized proteomics dataset. By profiling protein concentrations across 59 diseases and healthy cohorts, we identified proteins associated with age, sex, and BMI, as well as disease-specific signatures. This study highlights shared and distinct protein patterns across conditions, demonstrating the power of a unified proteomics approach to uncover biological insights. The dataset, covering 8,262 individuals and up to 5,416 proteins, serves as an online resource for exploring disease-specific protein profiles and advancing precision medicine research.", "doi": "10.1126/science.adx2678", "pmid": "41066540", "labels": {"Autoimmunity and Serology Profiling": "Service", "National Genomics Infrastructure": "Collaborative", "NGI Proteomics": "Collaborative", "NGI Uppsala (SNP&SEQ Technology Platform)": "Collaborative", "Affinity Proteomics Uppsala": "Collaborative"}, "xrefs": [], "notes": [], "created": "2025-10-10T10:37:22.942Z", "modified": "2025-11-07T07:45:07.446Z"}, {"entity": "publication", "iuid": "6d6faf7279134df68f3e4160a4981f61", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6d6faf7279134df68f3e4160a4981f61.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6d6faf7279134df68f3e4160a4981f61"}}, "title": "The genomic landscape of relapsed infant and childhood KMT2A-rearranged acute leukemia.", "authors": [{"family": "Ahlgren", "given": "Louise", "initials": "L"}, {"family": "Pilheden", "given": "Mattias", "initials": "M"}, {"family": "Sturesson", "given": "Helena", "initials": "H"}, {"family": "Song", "given": "Guangchun", "initials": "G", "orcid": "0000-0002-0190-8315", "researcher": {"href": "https://publications.scilifelab.se/researcher/f133bb6165494dfaba8173b0e8191765.json"}}, {"family": "Walsh", "given": "Michael P", "initials": "MP"}, {"family": "Yang", "given": "Minjun", "initials": "M", "orcid": "0000-0002-3324-1498", "researcher": {"href": "https://publications.scilifelab.se/researcher/62822d0b9c6c4a01a53829b9b05443ba.json"}}, {"family": "Maillard", "given": "Maud", "initials": "M"}, {"family": "Zhao", "given": "Huanbin", "initials": "H", "orcid": "0009-0001-4418-6770", "researcher": {"href": "https://publications.scilifelab.se/researcher/02a78b74f32d4670b628a8e3fb78ea0a.json"}}, {"family": "Cheng", "given": "Zhongshan", "initials": "Z"}, {"family": "Singh", "given": "Varsha", "initials": "V"}, {"family": "Castor", "given": "Anders", "initials": "A", "orcid": "0009-0007-4634-0704", "researcher": {"href": "https://publications.scilifelab.se/researcher/ed2d2dab933049f5b69cdf0ff1e1d8a1.json"}}, {"family": "Pronk", "given": "Cornelis Jan", "initials": "CJ", "orcid": "0000-0002-0073-9660", "researcher": {"href": "https://publications.scilifelab.se/researcher/76e42ba48d824aa0b42e871e9f11b00a.json"}}, {"family": "Marquart", "given": "Hanne Vibeke", "initials": "HV", "orcid": "0000-0001-9740-6522", "researcher": {"href": "https://publications.scilifelab.se/researcher/c9476b7116154ea9990d7c61c675c794.json"}}, {"family": "Lausen", "given": "Birgitte", "initials": "B", "orcid": "0000-0002-5306-0774", "researcher": {"href": "https://publications.scilifelab.se/researcher/dc5eadc48e354c4cb70d68d420bfa6fe.json"}}, {"family": "Schneider", "given": "Pauline", "initials": "P", "orcid": "0000-0003-0162-9436", "researcher": {"href": "https://publications.scilifelab.se/researcher/39a9fea74e284217b80716966bca995b.json"}}, {"family": "Barbany", "given": "Gisela", "initials": "G", "orcid": "0000-0003-3185-2962", "researcher": {"href": "https://publications.scilifelab.se/researcher/13fda0d702d543f981898ebd53849817.json"}}, {"family": "Pokrovskaja Tamm", "given": "Katja", "initials": "K", "orcid": "0000-0001-6359-1256", "researcher": {"href": "https://publications.scilifelab.se/researcher/09ec3ee706764024bd748c7a77443845.json"}}, {"family": "Abrahamsson", "given": "Jonas", "initials": "J", "orcid": "0000-0002-9240-3522", "researcher": {"href": "https://publications.scilifelab.se/researcher/0f3199957bd147ec91bbdc04413f1dba.json"}}, {"family": "Lohi", "given": "Olli", "initials": "O", "orcid": "0000-0001-9195-0797", "researcher": {"href": "https://publications.scilifelab.se/researcher/e11a59310dfc40e6a111367914fdba9e.json"}}, {"family": "Fogelstrand", "given": "Linda", "initials": "L", "orcid": "0000-0003-3698-8519", "researcher": {"href": "https://publications.scilifelab.se/researcher/f39ff709aa0646b8ad5e520780a0ad49.json"}}, {"family": "Menendez", "given": "Pablo", "initials": "P"}, {"family": "Pieters", "given": "Rob", "initials": "R", "orcid": "0000-0003-2997-3570", "researcher": {"href": "https://publications.scilifelab.se/researcher/bb567d1e17e0428c843c07682decb31c.json"}}, {"family": "Zhang", "given": "Jinghui", "initials": "J", "orcid": "0000-0003-3350-9682", "researcher": {"href": "https://publications.scilifelab.se/researcher/38fe8464634149a39bc8accf6077bac4.json"}}, {"family": "Lindkvist-Petersson", "given": "Karin", "initials": "K", "orcid": "0000-0002-5209-3160", "researcher": {"href": "https://publications.scilifelab.se/researcher/efe1ac8c58f640ba98b97c6a5e52b9d5.json"}}, {"family": "Yang", "given": "Jun J", "initials": "JJ", "orcid": "0000-0002-0770-9659", "researcher": {"href": "https://publications.scilifelab.se/researcher/023457113ddc4e3a8309d0b4936c097e.json"}}, {"family": "Gruber", "given": "Tanja A", "initials": "TA", "orcid": "0000-0003-1072-7257", "researcher": {"href": "https://publications.scilifelab.se/researcher/c16c5b66f56f40fd93a9f398b0487a64.json"}}, {"family": "Stam", "given": "Ronald W", "initials": "RW", "orcid": "0000-0003-4986-1656", "researcher": {"href": "https://publications.scilifelab.se/researcher/f528aaa6b3ba479f85619e1496e3f395.json"}}, {"family": "Ma", "given": "Jing", "initials": "J"}, {"family": "Hagstr\u00f6m-Andersson", "given": "Anna K", "initials": "AK", "orcid": "0000-0002-2904-1311", "researcher": {"href": "https://publications.scilifelab.se/researcher/bc93a87c663d471ba64fc3be63212a89.json"}}], "type": "journal article", "published": "2025-10-08", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "16", "issue": "1", "pages": "8964", "issn-l": "2041-1723"}, "abstract": "To study the mechanisms of relapse in KMT2A-rearranged (KMT2A-r) acute lymphoblastic (ALL) and acute myeloid leukemia (AML), we performed whole-genome and exome sequencing of infants and children with relapsed ALL/AML (n = 36), and longitudinal deep-sequencing of 257 samples in 30 patients. Somatic alterations in drug-response genes, most commonly in TP53 and IKZF1 (64%), were highly enriched in early relapse ALL (79%, 9-36 months after diagnosis), but rare in very early relapse ALL (<9 months, 9%). A marked chemotherapy-exposure signature was detected for mutations in early relapse ALL but not in very early ALL or AML relapse, in line with different mechanisms of relapse. Longitudinal analyses could track residual leukemia cells, clonal drug responses, and the upcoming relapse. These results highlight that KMT2A-r ALL and AML evade therapy differently and provide insights into the mechanisms of relapse in this highly lethal form of pediatric acute leukemia.", "doi": "10.1038/s41467-025-64190-8", "pmid": "41062506", "labels": {"Clinical Genomics Lund": "Service", "Clinical Genomics": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12508131"}, {"db": "pii", "key": "10.1038/s41467-025-64190-8"}], "notes": [], "created": "2025-10-28T09:43:15.594Z", "modified": "2025-11-07T07:22:38.375Z"}, {"entity": "publication", "iuid": "e105bd630ef34bb0a01ca502b207908e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e105bd630ef34bb0a01ca502b207908e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e105bd630ef34bb0a01ca502b207908e"}}, "title": "Climate-driven deoxygenation promoted potential mercury methylators in the past Black Sea water column", "authors": [{"family": "Zhong", "given": "Meifang", "initials": "M", "orcid": "0000-0001-8995-5468", "researcher": {"href": "https://publications.scilifelab.se/researcher/db04492b3b6c4596a4b6eda2007f4dc1.json"}}, {"family": "Barrenechea Angeles", "given": "In\u00e9s", "initials": "I", "orcid": "0000-0002-8051-4110", "researcher": {"href": "https://publications.scilifelab.se/researcher/117e061371ff48088a21ac74e9321dfa.json"}}, {"family": "More", "given": "Kuldeep D", "initials": "KD", "orcid": "0000-0002-8278-8086", "researcher": {"href": "https://publications.scilifelab.se/researcher/3b7cfdaad6614e6986ddd3a9c25434c4.json"}}, {"family": "Picard", "given": "Ma\u00eflys", "initials": "M"}, {"family": "Bertilsson", "given": "Stefan", "initials": "S", "orcid": "0000-0002-4265-1835", "researcher": {"href": "https://publications.scilifelab.se/researcher/2c17765c2a9f4383b5383138d11ae93f.json"}}, {"family": "Bravo", "given": "Andrea G", "initials": "AG", "orcid": "0000-0002-8341-3462", "researcher": {"href": "https://publications.scilifelab.se/researcher/749bb106ca6b452d82603ef8cf3cbdee.json"}}, {"family": "Bj\u00f6rn", "given": "Erik", "initials": "E", "orcid": "0000-0001-9570-8738", "researcher": {"href": "https://publications.scilifelab.se/researcher/d52d4c83dda84cea9e018199a8cfc304.json"}}, {"family": "Coolen", "given": "Marco J L", "initials": "MJL", "orcid": "0000-0002-0417-920X", "researcher": {"href": "https://publications.scilifelab.se/researcher/044cf58a620c40d8843b06e37942bdf4.json"}}, {"family": "Capo", "given": "Eric", "initials": "E", "orcid": "0000-0001-9143-7061", "researcher": {"href": "https://publications.scilifelab.se/researcher/a4017e9c8167487b882ee2d045d96494.json"}}], "type": "journal-article", "published": "2025-10-08", "journal": {"title": "Nat Water", "issn": "2731-6084", "issn-l": null}, "abstract": null, "doi": "10.1038/s44221-025-00526-4", "pmid": null, "labels": {"National Genomics Infrastructure": "Service", "NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2025-11-07T07:26:40.967Z", "modified": "2025-11-14T11:07:32.517Z"}, {"entity": "publication", "iuid": "25dfec9e03fc41aeb351f41e6acf76d8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/25dfec9e03fc41aeb351f41e6acf76d8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/25dfec9e03fc41aeb351f41e6acf76d8"}}, "title": "Whole Genome Sequencing Reveals How Plasticity and Genetic Differentiation Underlie Sympatric Morphs of Arctic Charr.", "authors": [{"family": "Kurta", "given": "Khrystyna", "initials": "K", "orcid": "0000-0002-9852-1896", "researcher": {"href": "https://publications.scilifelab.se/researcher/3ba96d1e78654b6992ef1c25035e93da.json"}}, {"family": "Fedi", "given": "Mariano Olivera", "initials": "MO"}, {"family": "Baker", "given": "Kendall", "initials": "K"}, {"family": "Barker", "given": "Tom", "initials": "T"}, {"family": "Catchpole", "given": "Leah", "initials": "L"}, {"family": "Ciofi", "given": "Claudio", "initials": "C", "orcid": "0000-0001-8537-8659", "researcher": {"href": "https://publications.scilifelab.se/researcher/f15012e62daf4c28b3c101550f460d35.json"}}, {"family": "Cocco", "given": "Arianna", "initials": "A"}, {"family": "Collins", "given": "Joanna", "initials": "J"}, {"family": "Diedericks", "given": "Genevieve", "initials": "G"}, {"family": "Diroma", "given": "Maria Angela", "initials": "MA"}, {"family": "Durrant", "given": "Alex", "initials": "A"}, {"family": "Hindar", "given": "Kjetil", "initials": "K", "orcid": "0000-0002-2769-2284", "researcher": {"href": "https://publications.scilifelab.se/researcher/0093cfa9f60e4e7db25d898de5c194b9.json"}}, {"family": "Iannucci", "given": "Alessio", "initials": "A", "orcid": "0000-0001-7729-4412", "researcher": {"href": "https://publications.scilifelab.se/researcher/da461c1ddb4649928a998aa9802a5ea3.json"}}, {"family": "Irish", "given": "Naomi", "initials": "N"}, {"family": "Knitlhoffer", "given": "Vanda", "initials": "V"}, {"family": "Laikre", "given": "Linda", "initials": "L", "orcid": "0000-0001-9286-3361", "researcher": {"href": "https://publications.scilifelab.se/researcher/b7c7ebbb5d7a4af582746b6ab2c2d132.json"}}, {"family": "Leit\u00e3o", "given": "Henrique G", "initials": "HG"}, {"family": "Lucchini", "given": "Sacha", "initials": "S"}, {"family": "McTaggart", "given": "Seanna", "initials": "S"}, {"family": "P\u00e1lsson", "given": "Arnar", "initials": "A", "orcid": "0000-0002-6525-8112", "researcher": {"href": "https://publications.scilifelab.se/researcher/dbe0e0cea2254ede8a1149cc2b917b6a.json"}}, {"family": "Pettersson", "given": "Mats E", "initials": "ME", "orcid": "0000-0002-7372-9076", "researcher": {"href": "https://publications.scilifelab.se/researcher/27011c7fbb8a44dda536a4fc876675b0.json"}}, {"family": "Ryman", "given": "Nils", "initials": "N", "orcid": "0000-0003-3342-8479", "researcher": {"href": "https://publications.scilifelab.se/researcher/97201873ea354e959e294d8d2d69be13.json"}}, {"family": "Snorrason", "given": "Sigur\u00f0ur S", "initials": "SS"}, {"family": "Svardal", "given": "Hannes", "initials": "H"}, {"family": "Swarbreck", "given": "David", "initials": "D"}, {"family": "Waterhouse", "given": "Robert M", "initials": "RM"}, {"family": "Watkins", "given": "Christopher", "initials": "C"}, {"family": "Wood", "given": "Jonathan M D", "initials": "JMD", "orcid": "0000-0002-7545-2162", "researcher": {"href": "https://publications.scilifelab.se/researcher/c255ed6ec2f246028326f9fece911f74.json"}}, {"family": "Xiao", "given": "Han", "initials": "H", "orcid": "0009-0000-4699-5590", "researcher": {"href": "https://publications.scilifelab.se/researcher/12a89016ae0d41788407e0b5a342d933.json"}}, {"family": "Gharbi", "given": "Karim", "initials": "K"}, {"family": "J\u00f3nsson", "given": "Zophon\u00edas O", "initials": "ZO", "orcid": "0000-0001-5798-9647", "researcher": {"href": "https://publications.scilifelab.se/researcher/9dabaeca1ef54eb289cc48aab86ae2aa.json"}}, {"family": "Andersson", "given": "Leif", "initials": "L", "orcid": "0000-0002-4085-6968", "researcher": {"href": "https://publications.scilifelab.se/researcher/bd3343c12f994b1fabcae23027d3a76d.json"}}], "type": "journal article", "published": "2025-10-00", "journal": {"title": "Mol. Ecol.", "issn": "1365-294X", "pages": "e70085", "volume": "34", "issue": "19", "issn-l": "0962-1083"}, "abstract": "Salmonids have a remarkable ability to form sympatric morphs after postglacial colonisation of freshwater lakes. These morphs often differ in morphology, feeding and spawning behaviour. Here, we explored the genetic basis of morph differentiation in Arctic charr (n = 283) by first establishing a high-quality reference genome and then using this in whole genome sequencing of distinct morphs present in two Norwegian and two Icelandic lakes. The four lakes represent the spectrum of genetic differentiation between morphs from one lake with no genetic differentiation between morphs, implying phenotypic plasticity, to two lakes with locus-specific genetic differentiation, implying incomplete reproductive isolation, and one lake with strong genome-wide divergence consistent with complete reproductive isolation. As many as 12 putative inversions ranging from 0.45 to 3.25 Mbp in size segregated among the four morphs present in one lake, Thingvallavatn, and these contributed significantly to the genetic differentiation among morphs. None of the putative inversions were found in any of the other lakes, but there were cases of partial haplotype sharing in similar morph contrasts in other lakes. Our findings are consistent with a highly polygenic basis of morph differentiation with population-specific selection on alleles linked to the development of similar morph phenotypes. The results support a model where morph differentiation is first established through phenotypic plasticity, leading to niche expansion and separation. This may be followed by gradual development of reproductive isolation, locus-specific differentiation and eventually complete reproductive isolation and genome-wide divergence.", "doi": "10.1111/mec.70085", "pmid": "40856096", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12456120"}], "notes": [], "created": "2025-09-08T06:59:34.138Z", "modified": "2025-11-28T10:51:42.317Z"}, {"entity": "publication", "iuid": "e851d932ff224ce9a80844e9e4e5cd2c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e851d932ff224ce9a80844e9e4e5cd2c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e851d932ff224ce9a80844e9e4e5cd2c"}}, "title": "The transcription factor LHX2 mediates and enhances oncogenic BMP signaling in medulloblastoma.", "authors": [{"family": "Ohata", "given": "Yae", "initials": "Y"}, {"family": "Ali", "given": "Mohamad M", "initials": "MM", "orcid": "0000-0002-4902-0550", "researcher": {"href": "https://publications.scilifelab.se/researcher/780c944670ff4d7489410895569ac257.json"}}, {"family": "Tsubakihara", "given": "Yutaro", "initials": "Y"}, {"family": "Itoh", "given": "Yuka", "initials": "Y"}, {"family": "Ros\u00e9n", "given": "Gabriela", "initials": "G"}, {"family": "Bergstr\u00f6m", "given": "Tobias", "initials": "T"}, {"family": "Mor\u00e9n", "given": "Anita", "initials": "A"}, {"family": "Gol\u00e1n-Cancela", "given": "Irene", "initials": "I"}, {"family": "Nakada", "given": "Ayana", "initials": "A"}, {"family": "Voytyuk", "given": "Oleksandr", "initials": "O"}, {"family": "Tsuchiya", "given": "Maiko", "initials": "M"}, {"family": "Fukui", "given": "Rei", "initials": "R"}, {"family": "Yamamoto", "given": "Kouhei", "initials": "K"}, {"family": "Mart\u00edn-Rubio", "given": "Paula", "initials": "P", "orcid": "0000-0002-2702-9212", "researcher": {"href": "https://publications.scilifelab.se/researcher/b71065b5619e414bb6401638b76b2160.json"}}, {"family": "Sancho", "given": "Patricia", "initials": "P"}, {"family": "Strell", "given": "Carina", "initials": "C"}, {"family": "Micke", "given": "Patrick", "initials": "P"}, {"family": "Wechsler-Reya", "given": "Robert J", "initials": "RJ"}, {"family": "Hashizume", "given": "Yoshinobu", "initials": "Y"}, {"family": "Miyazono", "given": "Kohei", "initials": "K", "orcid": "0000-0001-7341-0172", "researcher": {"href": "https://publications.scilifelab.se/researcher/7a14a58f628d435a94ad9540478117cb.json"}}, {"family": "Caja", "given": "Laia", "initials": "L", "orcid": "0000-0002-8786-8763", "researcher": {"href": "https://publications.scilifelab.se/researcher/62d8ae2bdac54a6584afeac2b766f628.json"}}, {"family": "Heldin", "given": "Carl-Henrik", "initials": "CH", "orcid": "0000-0002-9508-896X", "researcher": {"href": "https://publications.scilifelab.se/researcher/f705f7c509904a1db721ace2267ca48f.json"}}, {"family": "Swartling", "given": "Fredrik J", "initials": "FJ", "orcid": "0000-0002-8460-4367", "researcher": {"href": "https://publications.scilifelab.se/researcher/69679cebbc90496f9c5b32f56d966654.json"}}, {"family": "Moustakas", "given": "Aristidis", "initials": "A", "orcid": "0000-0001-9131-3827", "researcher": {"href": "https://publications.scilifelab.se/researcher/6c1626d991f3485e81232db174537e6d.json"}}], "type": "journal article", "published": "2025-10-00", "journal": {"title": "Cell Death Differ.", "issn": "1476-5403", "volume": "32", "issue": "10", "pages": "1915-1929", "issn-l": "1350-9047"}, "abstract": "Oncogenic events perturb cerebellar development leading to medulloblastoma, a common childhood brain malignancy. Molecular analyses classify medulloblastoma into the WNT, SHH, Group 3 and Group 4 subgroups. Bone morphogenetic protein (BMP) pathways control cerebellar development and have been linked to the progression of medulloblastoma disease, with major remaining gaps in their mechanistic and clinically-relevant roles. We therefore aimed at exploring BMP mechanisms of action in medulloblastoma. Patient-derived tumors from different subgroups were analyzed in mouse xenografts, complemented by independent tumor immunohistochemical analysis. Cell-based assays analyzed signaling mechanisms. Medulloblastoma cell orthotopic xenografts analyzed tumor growth and metastasis in vivo. Active BMP signaling, detected as nuclear and phosphorylated SMAD1/5, characterized several medulloblastoma subgroups, with enrichment in Group 4, SHH and Group 3 tumors. Spatial transcriptomics in tumor areas, complemented by transcriptomic analysis of multiple cell models, identified BMP-dependent transcriptional induction of the LIM-homeobox gene 2 (LHX2). BMP signaling via SMADs induced LHX2 expression and LHX2 transcriptionally induced BMP type I receptor (ACVR1) expression by association with the proximal promoter region of the ACVR1 gene. BMP signaling and LHX2 gain-of-function expression led to enriched stemness and associated chemoresistance in medulloblastoma cultures. In-mouse orthotopic transplantation of paired primary/recurrent Group 4 medulloblastoma cell populations, correspondingly expressing LHX2-low/BMP-low signaling and LHX2-high/BMP-high signaling, ascribed to the latter (high) group more efficient tumor propagation and spinal cord metastatic potential. Depletion of LHX2 in these recurrent tumor cells suppressed both BMP signaling and tumor propagation in vivo. Thus, LHX2 cooperates with, and enhances, oncogenic BMP signaling in medulloblastoma tumors. The molecular pathway that couples LHX2 function to BMP signaling in medulloblastoma deepens our understanding this malignancy.", "doi": "10.1038/s41418-025-01488-6", "pmid": "40148468", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12501261"}, {"db": "pii", "key": "10.1038/s41418-025-01488-6"}], "notes": [], "created": "2025-09-08T06:54:49.956Z", "modified": "2025-11-28T10:45:02.518Z"}, {"entity": "publication", "iuid": "ae53f79971b5422e8d7b0c5ef5626fe0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ae53f79971b5422e8d7b0c5ef5626fe0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ae53f79971b5422e8d7b0c5ef5626fe0"}}, "title": "Primary and Secondary Symbionts of Cambodian Cicadellidae and the Role of Parasitisation.", "authors": [{"family": "Phauk", "given": "Sophany", "initials": "S", "orcid": "0000-0002-8019-3206", "researcher": {"href": "https://publications.scilifelab.se/researcher/80bf701bd9c14bd08c081d49b0d6ecad.json"}}, {"family": "Assentato", "given": "Lorenzo", "initials": "L", "orcid": "0000-0003-3699-0483", "researcher": {"href": "https://publications.scilifelab.se/researcher/69a8069f62434b128fb5837b139dbb56.json"}}, {"family": "Meas", "given": "Seanghun", "initials": "S", "orcid": "0009-0003-8813-8839", "researcher": {"href": "https://publications.scilifelab.se/researcher/829ed324071b46cc8720d6ffcf68b701.json"}}, {"family": "Terenius", "given": "Olle", "initials": "O", "orcid": "0000-0002-9909-1859", "researcher": {"href": "https://publications.scilifelab.se/researcher/3042a807e20d444cafee3f760c38d5d1.json"}}], "type": "journal article", "published": "2025-10-00", "journal": {"title": "Environ Microbiol Rep", "issn": "1758-2229", "volume": "17", "issue": "5", "pages": "e70196", "issn-l": "1758-2229"}, "abstract": "Leafhoppers (Hemiptera: Cicadellidae) are important vectors of plant pathogens in agricultural systems. Biological control via parasitisation is a key management strategy, but little is known about how microbial symbionts mediate host-parasitoid interactions. Here, we characterise the bacterial communities of six Cambodian leafhopper species (Cofana spectra, Exitianus sp., Goniagnathus punctifer, Maiestas dorsalis, Nephotettix virescens, and Stirellus sp.) and their parasitoids from the families Dryinidae (Hymenoptera) and Halictophagidae (Strepsiptera). We found that the bacterial symbiont Sulcia dominates cicadellid microbiotas, often coexisting with secondary symbionts. For example, Nasuia is present alongside Sulcia in Nephotettix, while Wolbachia is prevalent in Exitianus and Goniagnathus. Parasitoids exhibited distinct microbiotas with greater diversity; Rhodobacteraceae and Comamonadaceae were in dryinids, while Wolbachia was common in Halictophagidae. We analysed the microbiota of individual pairs of host-parasitoid and although parasitism did not significantly alter cicadellid overall microbiotas, some secondary symbionts (e.g., Arsenophonus, Wolbachia, Rickettsia, and Sodalis) were detected in both hosts and parasitoids, suggesting possible microbial transmission that warrants further investigation. These findings improve our understanding of host-parasitoid microbial interactions and highlight the relationship between primary and secondary symbiont communities.", "doi": "10.1111/1758-2229.70196", "pmid": "40957832", "labels": {"National Genomics Infrastructure": "Service", "NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12440678"}], "notes": [], "created": "2025-11-07T07:26:49.751Z", "modified": "2025-11-28T10:50:56.250Z"}, {"entity": "publication", "iuid": "45682d38345b42169cbcba464ca3a942", "links": {"self": {"href": "https://publications.scilifelab.se/publication/45682d38345b42169cbcba464ca3a942.json"}, "display": {"href": "https://publications.scilifelab.se/publication/45682d38345b42169cbcba464ca3a942"}}, "title": "Patients with systemic lupus erythematosus (SLE) have an increased bisphenol A methylation score linked to SLE risk genes and selected clinical subphenotypes.", "authors": [{"family": "Vestin", "given": "Holme", "initials": "H", "orcid": "0009-0005-6622-8897", "researcher": {"href": "https://publications.scilifelab.se/researcher/09ab6d55e8ab4f8b92ae43b924f7453f.json"}}, {"family": "Oparina", "given": "Nina", "initials": "N"}, {"family": "Eloranta", "given": "Maija-Leena", "initials": "ML"}, {"family": "Frodlund", "given": "Martina", "initials": "M"}, {"family": "Gunnarsson", "given": "Iva", "initials": "I"}, {"family": "Sj\u00f6wall", "given": "Christopher", "initials": "C", "orcid": "0000-0003-0900-2048", "researcher": {"href": "https://publications.scilifelab.se/researcher/fe4dd47b8ca1436e8a26fdea33f5e7f6.json"}}, {"family": "Svenungsson", "given": "Elisabet", "initials": "E", "orcid": "0000-0003-3396-3244", "researcher": {"href": "https://publications.scilifelab.se/researcher/0ab5989c3c604a96bf42b1b6f90434a0.json"}}, {"family": "R\u00f6nnblom", "given": "Lars", "initials": "L", "orcid": "0000-0001-9403-6503", "researcher": {"href": "https://publications.scilifelab.se/researcher/053ed3b657124a1bab3a78dc685556e6.json"}}, {"family": "Imgenberg-Kreuz", "given": "Juliana", "initials": "J", "orcid": "0000-0002-7230-8990", "researcher": {"href": "https://publications.scilifelab.se/researcher/5d4c2f630d484ee780c2c12aaabdb939.json"}}, {"family": "Leonard", "given": "Dag", "initials": "D", "orcid": "0000-0002-6275-7282", "researcher": {"href": "https://publications.scilifelab.se/researcher/42ed25c2f495484db4757f4fef51abae.json"}}], "type": "journal article", "published": "2025-09-25", "journal": {"title": "RMD Open", "issn": "2056-5933", "volume": "11", "issue": "3", "issn-l": "2056-5933"}, "abstract": "Bisphenol A (BPA), a xenoestrogen that can alter DNA methylation status, has been implicated in the pathogenesis of systemic lupus erythematosus (SLE). This study aimed to investigate whether methylation changes at BPA-sensitive 5'-C-phosphate-G-3' (CpG) sites are associated with SLE and clinical subphenotypes.\n\nA discovery cohort (n=747) and a replication cohort (n=388) including Swedish patients with SLE and healthy controls were investigated using the Illumina HM450k bead chip. BPA-sensitive CpG sites were selected if differentially methylated in \u22652 of 7 BPA exposure studies and supported by cell line data. A BPAAll score including 19 CpGs and a BPASLE score based on three CpG sites co-localised in the genome with SLE risk loci were calculated for each individual, analysed for associations with clinical data and then compared with publicly available transcriptomic data from BPA-treated cells.\n\nPatients with SLE had significantly higher BPASLE score than controls in the discovery (OR 1.34, p=4.6\u00d710-13), replication (OR 1.28, p=1.1\u00d710-5) and meta-analysis (OR 1.32, p=3.3\u00d710-17). Higher BPAAll score was associated with SLE in the discovery cohort (OR 1.05, p=2.3\u00d710-3) but not in the replication cohort (OR 1.04, p=0.12) with a significant difference in the meta-analysis (OR 1.05, p=7.0\u00d710-4). Both scores were associated with prednisolone treatment (p<0.001), and the BPASLE score was associated with serositis and autoantibodies (p<0.05). Transcriptomic analysis of BPA-treated cells revealed enrichment in pathways such as interferon and mitogen-activated protein kinase signalling.\n\nOur findings reveal a novel association between BPA exposure and DNA methylation changes in SLE, with potential implications for the regulation of immune-related gene expression.", "doi": "10.1136/rmdopen-2025-006021", "pmid": "40998523", "labels": {"National Genomics Infrastructure": "Service", "NGI SNP genotyping": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12481292"}, {"db": "pii", "key": "rmdopen-2025-006021"}], "notes": [], "created": "2025-11-07T07:30:46.128Z", "modified": "2025-11-07T07:30:46.264Z"}, {"entity": "publication", "iuid": "e35988a7938b44638700ddc6625bc6aa", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e35988a7938b44638700ddc6625bc6aa.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e35988a7938b44638700ddc6625bc6aa"}}, "title": "Major Histocompatibility Complex modulation of Batrachochytrium dendrobatidis and Ranavirus infections in amphibians.", "authors": [{"family": "Cortazar-Chinarro", "given": "M", "initials": "M", "orcid": "0000-0003-4604-1441", "researcher": {"href": "https://publications.scilifelab.se/researcher/6eeac642337c4ca5aab0275dcae9a8b9.json"}}, {"family": "Richter-Boix", "given": "A", "initials": "A"}, {"family": "Halvarsson", "given": "P", "initials": "P"}, {"family": "Palomar", "given": "G", "initials": "G"}, {"family": "Bosch", "given": "J", "initials": "J"}], "type": "journal article", "published": "2025-09-24", "journal": {"title": "J. Evol. Biol.", "issn": "1420-9101", "issn-l": "1010-061X"}, "abstract": "Genetic variation in immune genes is an important component of genetic diversity. The genes in the Major Histocompatibility Complex (MHC) provide an excellent model system for studying the mechanisms that generate and maintain genetic diversity in natural populations. While both demographic factors and pathogen-mediated selection processes contribute to the extreme diversity observed in the MHC systems, determining the relative importance of these evolutionary mechanisms has remained challenging. We investigated the role of pathogen-mediated selection in driving MHC diversity in three amphibian species: Ichthyosaura alpestris, Pleurodeles waltl and Pelophilax perezi. Our study examined the relationships between individual MHC diversity, infection status, infection intensity, and co-infection with two major amphibian pathogens: Batrachochytrium dendrobatidis (Bd) and Ranavirus sp. (Rv) in natural populations. Our research demonstrated significant differences in Bd and Rv infection intensities among individuals with varying numbers of MHC loci. However, co-infection showed no discernible influence on infection intensities. We observed stronger associations of specific MHC alleles and supertypes with infection intensity and status in I. alpestris. These findings suggest that, in the context of multi-host infections, MHC genes may provide valuable insights into the evolutionary forces shaping MHC diversity, although the specific effects of individual MHC alleles on disease dynamics are yet to be clarified.", "doi": "10.1093/jeb/voaf112", "pmid": "40990944", "labels": {"National Genomics Infrastructure": "Service", "NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "8262903"}], "notes": [], "created": "2025-11-07T07:26:58.477Z", "modified": "2025-11-07T07:26:58.555Z"}, {"entity": "publication", "iuid": "6668bbc3d5d9465089cd9823657f2d8c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6668bbc3d5d9465089cd9823657f2d8c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6668bbc3d5d9465089cd9823657f2d8c"}}, "title": "Variants in the DDX6-CXCR5 autoimmune disease risk locus influence the regulatory network in immune cells and salivary gland.", "authors": [{"family": "Wiley", "given": "Mandi M", "initials": "MM"}, {"family": "Radziszewski", "given": "Marcin", "initials": "M"}, {"family": "Khatri", "given": "Bhuwan", "initials": "B"}, {"family": "Joachims", "given": "Michelle L", "initials": "ML"}, {"family": "Tessneer", "given": "Kandice L", "initials": "KL"}, {"family": "Stolarczyk", "given": "Anna M", "initials": "AM"}, {"family": "Yao", "given": "Songyuan", "initials": "S"}, {"family": "Li", "given": "James", "initials": "J"}, {"family": "Pritchett-Frazee", "given": "Cherilyn", "initials": "C"}, {"family": "Johnston", "given": "Audrey A", "initials": "AA"}, {"family": "Rasmussen", "given": "Astrid", "initials": "A"}, {"family": "Anaya", "given": "Juan-Manuel", "initials": "JM"}, {"family": "Aqrawi", "given": "Lara A", "initials": "LA"}, {"family": "Bae", "given": "Sang-Cheol", "initials": "SC"}, {"family": "Baecklund", "given": "Eva", "initials": "E"}, {"family": "Bj\u00f6rk", "given": "Albin", "initials": "A"}, {"family": "Brun", "given": "Johan G", "initials": "JG"}, {"family": "Bucher", "given": "Sara Magnusson", "initials": "SM"}, {"family": "Dand", "given": "Nick", "initials": "N"}, {"family": "Eloranta", "given": "Maija-Leena", "initials": "ML"}, {"family": "Engelke", "given": "Fiona", "initials": "F"}, {"family": "Forsblad-d'Elia", "given": "Helena", "initials": "H"}, {"family": "Fugmann", "given": "Cecilia", "initials": "C"}, {"family": "Glenn", "given": "Stuart B", "initials": "SB"}, {"family": "Gong", "given": "Chen", "initials": "C"}, {"family": "Gottenberg", "given": "Jacques-Eric", "initials": "JE"}, {"family": "Hammenfors", "given": "Daniel", "initials": "D"}, {"family": "Imgenberg-Kreuz", "given": "Juliana", "initials": "J"}, {"family": "Jensen", "given": "Janicke Liaaen", "initials": "JL"}, {"family": "Johnsen", "given": "Svein Joar Augl\u00e6nd", "initials": "SJA"}, {"family": "Jonsson", "given": "Malin V", "initials": "MV"}, {"family": "Kelly", "given": "Jennifer A", "initials": "JA"}, {"family": "Khanam", "given": "Sharmily", "initials": "S"}, {"family": "Kim", "given": "Kwangwoo", "initials": "K"}, {"family": "Kvarnstr\u00f6m", "given": "Marika", "initials": "M"}, {"family": "Mandl", "given": "Thomas", "initials": "T"}, {"family": "Mart\u00edn", "given": "Javier", "initials": "J"}, {"family": "Morris", "given": "David L", "initials": "DL"}, {"family": "Nocturne", "given": "Gaetane", "initials": "G"}, {"family": "Norheim", "given": "Katrine Br\u00e6kke", "initials": "KB"}, {"family": "Olsson", "given": "Peter", "initials": "P"}, {"family": "Palm", "given": "\u00d8yvind", "initials": "\u00d8"}, {"family": "Pers", "given": "Jacques-Olivier", "initials": "JO"}, {"family": "Rhodus", "given": "Nelson L", "initials": "NL"}, {"family": "Sj\u00f6wall", "given": "Christopher", "initials": "C"}, {"family": "Skarstein", "given": "Kathrine", "initials": "K"}, {"family": "Taylor", "given": "Kimberly E", "initials": "KE"}, {"family": "Tombleson", "given": "Phil", "initials": "P"}, {"family": "Thorlacius", "given": "Gudny Ella", "initials": "GE"}, {"family": "Venuturupalli", "given": "Swamy R", "initials": "SR"}, {"family": "Vital", "given": "Edward M", "initials": "EM"}, {"family": "Wallace", "given": "Daniel J", "initials": "DJ"}, {"family": "Radfar", "given": "Lida", "initials": "L"}, {"family": "Brennan", "given": "Michael T", "initials": "MT"}, {"family": "James", "given": "Judith A", "initials": "JA"}, {"family": "Scofield", "given": "R Hal", "initials": "RH"}, {"family": "Gaffney", "given": "Patrick M", "initials": "PM"}, {"family": "Criswell", "given": "Lindsey A", "initials": "LA"}, {"family": "Jonsson", "given": "Roland", "initials": "R"}, {"family": "Appel", "given": "Silke", "initials": "S"}, {"family": "Eriksson", "given": "Per", "initials": "P"}, {"family": "Bowman", "given": "Simon J", "initials": "SJ"}, {"family": "Omdal", "given": "Roald", "initials": "R"}, {"family": "R\u00f6nnblom", "given": "Lars", "initials": "L"}, {"family": "Warner", "given": "Blake M", "initials": "BM"}, {"family": "Rischmueller", "given": "Maureen", "initials": "M"}, {"family": "Witte", "given": "Torsten", "initials": "T"}, {"family": "Farris", "given": "A Darise", "initials": "AD"}, {"family": "Mariette", "given": "Xavier", "initials": "X"}, {"family": "Shiboski", "given": "Caroline H", "initials": "CH"}, {"family": "Sj\u00f6gren\u2019s International Collaborative Clinical Alliance (SICCA)", "given": "", "initials": ""}, {"family": "Wahren-Herlenius", "given": "Marie", "initials": "M"}, {"family": "Alarc\u00f3n-Riquelme", "given": "Marta E", "initials": "ME"}, {"family": "PRECISESADS Clinical Consortium", "given": "", "initials": ""}, {"family": "Ng", "given": "Wan-Fai", "initials": "WF"}, {"family": "UK Primary Sj\u00f6gren\u2019s Syndrome Registry", "given": "", "initials": ""}, {"family": "Sivils", "given": "Kathy L", "initials": "KL"}, {"family": "Guthridge", "given": "Joel M", "initials": "JM"}, {"family": "Adrianto", "given": "Indra", "initials": "I"}, {"family": "Vyse", "given": "Timothy J", "initials": "TJ"}, {"family": "Tsao", "given": "Betty P", "initials": "BP"}, {"family": "Nordmark", "given": "Gunnel", "initials": "G"}, {"family": "Lessard", "given": "Christopher J", "initials": "CJ"}], "type": "journal article", "published": "2025-09-00", "journal": {"title": "Ann. Rheum. Dis.", "issn": "1468-2060", "volume": "84", "issue": "9", "pages": "1512-1527", "issn-l": "0003-4967"}, "abstract": "Sj\u00f6gren's disease (SjD) and systemic lupus erythematosus (SLE) share genetic risk at the DDX6-CXCR5 locus (11q23.3). Identifying and functionally characterising shared SNPs spanning this locus can provide new insights into common genetic mechanisms of autoimmunity.\n\nTransdisease meta-analyses, fine-mapping, and bioinformatic analyses prioritised shared likely functional single nucleotide polymorphisms (SNPs) for allele-specific and cell type-specific functional interrogation using electromobility shift, luciferase reporter, and quantitative chromatin conformation capture assays and clustered regularly interspaced short palindromic repeat (CRISPR) gene regulation.\n\nFive shared SNPs were identified as likely functional in primary human immune cells, salivary gland and kidney tissues: rs57494551, rs4936443, rs4938572, rs7117261, and rs4938573. All 5 SNPs exhibited cell type-specific and allele-specific effects on nuclear protein binding affinity and enhancer/promoter regulatory activity in immune, salivary gland epithelial, and kidney epithelial cell models. Mapping of chromatin-chromatin interactions revealed a chromatin regulatory network that expanded beyond DDX6 and CXCR5 to include PHLDB1, lnc-PHLDB1-1, BCL9L, TRAPPC4, among others. Coalescence of functional assays and multiomic data analyses indicated that these SNPs likely modulate the activity of 3 regulatory regions: intronic rs57494551 regulatory region, intergenic SNP haplotype (rs4938572, rs4936443, and rs7117261) regulatory region, and rs4938573 regulatory region upstream of the CXCR5 promoter.\n\nShared genetic susceptibly at the DDX6-CXCR5 locus in SjD and SLE likely alters common mechanisms of autoimmunity, including interferon signalling (DDX6), autophagy (TRAPPC4), and lymphocytic infiltration of disease-target tissues (CXCR5). Further, using multiomic data from patients with SjD, combined with bioinformatic and in vitro functional studies, can provide mechanistic insights into how genetic risk influences the biological pathways that drive complex autoimmunity.", "doi": "10.1016/j.ard.2025.04.023", "pmid": "40447495", "labels": {"National Genomics Infrastructure": "Service", "NGI SNP genotyping": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "mid", "key": "NIHMS2086461"}, {"db": "pmc", "key": "PMC12236377"}, {"db": "pii", "key": "S0003-4967(25)00949-5"}], "notes": [], "created": "2025-11-07T07:33:24.582Z", "modified": "2025-11-07T07:33:24.589Z"}, {"entity": "publication", "iuid": "a321ba70d5a8449193a0b042ea632cc6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a321ba70d5a8449193a0b042ea632cc6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a321ba70d5a8449193a0b042ea632cc6"}}, "title": "Sex Dependent and Sj\u00f6gren Disease Like Immune Responses Against Phosphoantigens in Balb/C Mice.", "authors": [{"family": "Czwakiel", "given": "Paulina", "initials": "P"}, {"family": "Brindefalk", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Eghbali", "given": "Atiyeh", "initials": "A"}, {"family": "Dircksen", "given": "Heinrich", "initials": "H"}, {"family": "Kamal", "given": "Kahkashan", "initials": "K", "orcid": "0000-0003-0968-7454", "researcher": {"href": "https://publications.scilifelab.se/researcher/56449fc911fd48b98b207c394d635507.json"}}, {"family": "Payandeh", "given": "Zahra", "initials": "Z"}, {"family": "Ozata", "given": "Deniz", "initials": "D", "orcid": "0000-0001-5215-8684", "researcher": {"href": "https://publications.scilifelab.se/researcher/933850bed34c4517b01e915cf8831686.json"}}, {"family": "Troye-Blomberg", "given": "Marita", "initials": "M"}, {"family": "Faye", "given": "Ingrid", "initials": "I", "orcid": "0000-0003-4382-7238", "researcher": {"href": "https://publications.scilifelab.se/researcher/28e762d6a5a845e79a7a107f700a82b5.json"}}], "type": "journal article", "published": "2025-09-00", "journal": {"title": "Scand. J. Immunol.", "issn": "1365-3083", "volume": "102", "issue": "3", "pages": "e70052", "issn-l": "0300-9475"}, "abstract": "The initial aim of this study on Balb/C mice was to investigate the putative effects on feeding and appetite of isopentenyl pyrophosphate (IPP) and E-4-hydroxy-3-methyl-but-2-enyl pyrophosphate (HMBPP), also known as phosphoantigens (pAgs). HMBPP was recently shown to increase blood meal appetite in malaria mosquitoes. Both IPP and HMBPP are metabolites produced by the normal gut microbiota and apicomplexan parasites such as Plasmodium. To explore potential effects on appetite, male and female mice were treated by gavage with these metabolites, and body mass and gene expression were monitored in brain, stomach and small intestine at 3 h and 7 weeks. Body mass gain did not clearly differ between pAg-treated and water control mice. However, beginning between 4 and 7 weeks, the salivary glands of IPP-treated males began to swell. With the autoimmune Sj\u00f6gren disease (SjD) in mind, we subsequently investigated the salivary glands after 1, 4 and 7 weeks of IPP treatment. Fast gene set enrichment analysis (FGSEA) of marginal zone B-cell (MZB) transcripts from salivary glands, together with B-cell infiltration in both sexes at 4 weeks, suggested similarities to SjD pathology. Using ELISA, we measured serum autoantibodies against Ro52, Ro60 and La. Multivariate analysis at 7 weeks showed treatment-associated trends: levels of anti-Ro52 and anti-La tended to increase in IPP-treated males, but not in females. Notably, IL-6 serum levels displayed a sex-dependent pattern, and PCA analyses of transcriptomic data from brain, stomach and small intestine-though with some exceptions-also indicated differential responses to pAgs between males and females.", "doi": "10.1111/sji.70052", "pmid": "40898584", "labels": {"Autoimmunity and Serology Profiling": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12405675"}], "notes": [], "created": "2025-09-10T08:38:36.714Z", "modified": "2025-11-07T07:24:59.576Z"}, {"entity": "publication", "iuid": "e679aca133c2422599ac1891a96c1a05", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e679aca133c2422599ac1891a96c1a05.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e679aca133c2422599ac1891a96c1a05"}}, "title": "Resistance and resilience of co-occurring nitrifying microbial guilds to drying-rewetting stress in soil", "authors": [{"family": "M\u00fcller", "given": "Laura J", "initials": "LJ", "orcid": "0009-0009-5747-2432", "researcher": {"href": "https://publications.scilifelab.se/researcher/11dad561c7e24e68b9ed71a015aa2263.json"}}, {"family": "Alicke", "given": "Mara", "initials": "M", "orcid": "0009-0000-0244-9440", "researcher": {"href": "https://publications.scilifelab.se/researcher/c5d4c9a20fc04322a8babeaded66302f.json"}}, {"family": "Romdhane", "given": "Sana", "initials": "S", "orcid": "0000-0003-0295-2278", "researcher": {"href": "https://publications.scilifelab.se/researcher/494ad3e37974440988db1f7b377bae76.json"}}, {"family": "Pold", "given": "Grace", "initials": "G", "orcid": "0000-0002-7536-3944", "researcher": {"href": "https://publications.scilifelab.se/researcher/6a78bb0a7f6043119b6be5e226983d04.json"}}, {"family": "Jones", "given": "Christopher M", "initials": "CM", "orcid": "0000-0002-2723-6019", "researcher": {"href": "https://publications.scilifelab.se/researcher/6c04ad1e78da45ee8b383fb09fc5d44a.json"}}, {"family": "Sagha\u00ef", "given": "Aur\u00e9lien", "initials": "A", "orcid": "0000-0002-7069-2159", "researcher": {"href": "https://publications.scilifelab.se/researcher/0341d780c3ad44e3bce819fbc38c0176.json"}}, {"family": "Hallin", "given": "Sara", "initials": "S", "orcid": "0000-0002-9069-9024", "researcher": {"href": "https://publications.scilifelab.se/researcher/6e3491aec8fe4fbf827e2448c898356e.json"}}], "type": "journal-article", "published": "2025-09-00", "journal": {"title": "Soil Biology and Biochemistry", "issn": "0038-0717", "volume": "208", "pages": "109846", "issn-l": null}, "abstract": null, "doi": "10.1016/j.soilbio.2025.109846", "pmid": null, "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [], "notes": [], "created": "2025-09-08T07:13:11.714Z", "modified": "2025-09-08T07:13:12.028Z"}, {"entity": "publication", "iuid": "c57d8ac1a6904e40856c4f78a2d6803b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c57d8ac1a6904e40856c4f78a2d6803b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c57d8ac1a6904e40856c4f78a2d6803b"}}, "title": "Induced somatic mutation accumulation during skeletal muscle regeneration reduces muscle strength.", "authors": [{"family": "Vrta\u010dnik", "given": "Peter", "initials": "P"}, {"family": "Merino", "given": "Lara G", "initials": "LG", "orcid": "0000-0002-7208-953X", "researcher": {"href": "https://publications.scilifelab.se/researcher/afebb85c860744dc8ad5840caa6f06c0.json"}}, {"family": "Subhash", "given": "Santhilal", "initials": "S", "orcid": "0000-0002-0077-4597", "researcher": {"href": "https://publications.scilifelab.se/researcher/4ca22115b7c9444ab2056126a1c9d36d.json"}}, {"family": "Helgad\u00f3ttir", "given": "Hafd\u00eds T", "initials": "HT", "orcid": "0000-0003-4352-152X", "researcher": {"href": "https://publications.scilifelab.se/researcher/ce4dc1001c944a9d9dfe4c092cfda497.json"}}, {"family": "Bardin", "given": "Matthieu", "initials": "M", "orcid": "0000-0001-9755-8841", "researcher": {"href": "https://publications.scilifelab.se/researcher/c4070871377c4fbcabf6e9a299d01277.json"}}, {"family": "Stefani", "given": "Fabiana", "initials": "F", "orcid": "0009-0008-8933-0773", "researcher": {"href": "https://publications.scilifelab.se/researcher/6f3b815508714611a894e9853362b123.json"}}, {"family": "Wang", "given": "Depin", "initials": "D"}, {"family": "Chen", "given": "Ping", "initials": "P"}, {"family": "Franco", "given": "Irene", "initials": "I", "orcid": "0000-0002-4272-239X", "researcher": {"href": "https://publications.scilifelab.se/researcher/8eac8823b89543f09e9d2cb141bdb587.json"}}, {"family": "Rev\u00eachon", "given": "Gwladys", "initials": "G", "orcid": "0000-0002-4824-6793", "researcher": {"href": "https://publications.scilifelab.se/researcher/356dd0dbbdaa4d21957e516ce11bbd74.json"}}, {"family": "Eriksson", "given": "Maria", "initials": "M", "orcid": "0000-0003-3233-2862", "researcher": {"href": "https://publications.scilifelab.se/researcher/ca8641fd4d16471abf18990610fb89a1.json"}}], "type": "journal article", "published": "2025-09-00", "journal": {"title": "Nat Aging", "issn": "2662-8465", "volume": "5", "issue": "9", "pages": "1739-1749", "issn-l": null}, "abstract": "Aging is associated with a progressive decline in tissue function and regenerative capacity, partly due to genomic instability, one of the hallmarks of aging1,2. Genomic instability encompasses DNA damage and the accumulation of somatic mutations in post-zygotic cells, yet the specific impact of these mutations on age-related tissue dysfunction remains poorly understood. To address this, we developed a mouse model in which genomic instability was induced specifically in muscle progenitor cells3 through targeted deletion of the Msh2 (ref. 4) and Blm5 genes. This allowed us to assess how elevated DNA damage and somatic mutations, from single-nucleotide variants (SNVs) to structural variants, affect muscle regeneration following injury. These mice exhibited impaired muscle regeneration, characterized by smaller muscle fibers, reduced muscle mass gain and decreased grip strength. Importantly, similar muscle deficits were observed in a second mouse model where somatic mutations were elevated with less substantial DNA damage. These findings provide evidence that the accumulation of somatic mutations can potentially compromise the function of somatic cells, contributing to the aging phenotype in skeletal muscle.", "doi": "10.1038/s43587-025-00941-y", "pmid": "40836125", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12443595"}, {"db": "pii", "key": "10.1038/s43587-025-00941-y"}], "notes": [], "created": "2025-09-08T07:07:06.110Z", "modified": "2025-11-19T08:29:17.738Z"}, {"entity": "publication", "iuid": "99d94470f07541c2b23fad1eefd0f74b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/99d94470f07541c2b23fad1eefd0f74b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/99d94470f07541c2b23fad1eefd0f74b"}}, "title": "Genomic studies in Linum shed light on the evolution of the distyly supergene and the molecular basis of convergent floral evolution.", "authors": [{"family": "Zervakis", "given": "Panagiotis-Ioannis", "initials": "PI", "orcid": "0000-0002-5197-3502", "researcher": {"href": "https://publications.scilifelab.se/researcher/295e9debf36c4641aa6c346e915b64ef.json"}}, {"family": "Postel", "given": "Zo\u00e9", "initials": "Z", "orcid": "0000-0003-0502-2375", "researcher": {"href": "https://publications.scilifelab.se/researcher/0481ff1051564262af4e5384cbd17ac3.json"}}, {"family": "Losvik", "given": "Aleksandra", "initials": "A", "orcid": "0000-0001-7669-9266", "researcher": {"href": "https://publications.scilifelab.se/researcher/e85c35a0abd54a7087c94942290179be.json"}}, {"family": "Fracassetti", "given": "Marco", "initials": "M", "orcid": "0000-0002-2962-2669", "researcher": {"href": "https://publications.scilifelab.se/researcher/695213cdd1a645cbbf10d44122237b18.json"}}, {"family": "Sol\u00e9r", "given": "Lucile", "initials": "L", "orcid": "0000-0002-0121-2393", "researcher": {"href": "https://publications.scilifelab.se/researcher/f701059f90fe4c7c9b969079e74aac57.json"}}, {"family": "Proux-W\u00e9ra", "given": "Estelle", "initials": "E", "orcid": "0000-0003-3752-1806", "researcher": {"href": "https://publications.scilifelab.se/researcher/9257ccdfc6484cd9a95f9b2f17f9a8d1.json"}}, {"family": "Bunikis", "given": "Ignas", "initials": "I", "orcid": "0009-0008-8375-0451", "researcher": {"href": "https://publications.scilifelab.se/researcher/d2a9c139b7d64681a5712250d3cf63ff.json"}}, {"family": "Churcher", "given": "Allison", "initials": "A", "orcid": "0000-0003-1902-3002", "researcher": {"href": "https://publications.scilifelab.se/researcher/d97e6fb500a043f08d4f882e802cd91b.json"}}, {"family": "Slotte", "given": "Tanja", "initials": "T", "orcid": "0000-0001-6020-5102", "researcher": {"href": "https://publications.scilifelab.se/researcher/67c69ee78bae41478465a7e5fa63b946.json"}}], "type": "journal article", "published": "2025-09-00", "journal": {"title": "New Phytol.", "issn": "1469-8137", "issn-l": "0028-646X", "volume": "247", "issue": "6", "pages": "2964-2981"}, "abstract": "Distyly, an example of convergent evolution, is governed by a supergene, the S-locus, in several species. Recent studies highlight similar genomic architectures of independently evolved S-loci, but its mode of origin and whether similar regulatory pathways underlie the convergent evolution of distyly remains unclear. We examined the evolution of supergenes and mechanisms underlying distyly in Linum species that diverged c. 33 million years ago (Ma). Using haplotype-resolved genomes and population genomics, we identified and characterized the S-loci of Linum perenne (distylous) and Linum grandiflorum (style length dimorphic), and compared them to that of Linum tenue (distylous). We then tested for a conserved hormonal mechanism regulating style length polymorphism in Linum. The S-locus supergene was consistently hemizygous in short-styled individuals across all three species, although it showed variation in size, gene content, repeat elements and extent of recombination suppression. Two S-linked candidate genes, TSS1 (style length) and WDR-44 (anther height/pollen self-incompatibility), were conserved. Consistent with a brassinosteroid-dependent role of TSS1, epibrassinolide treatment revealed a conserved, morph-specific effect on style length. S-locus structural polymorphism, candidate distyly genes and mechanisms regulating style length remain conserved > 30 Ma in Linum. In combination with findings from other systems, our results suggest that the brassinosteroid pathway frequently contributes to style length polymorphism.", "doi": "10.1111/nph.70392", "pmid": "40682296", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (Uppsala Genome Center)": "Collaborative", "NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "NGI Stockholm (Genomics Production)": "Service", "NGI Other": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12371154"}], "notes": [], "created": "2025-08-19T13:25:54.698Z", "modified": "2025-11-19T10:24:41.159Z"}, {"entity": "publication", "iuid": "2cac753de106445cbf229064ef982197", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2cac753de106445cbf229064ef982197.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2cac753de106445cbf229064ef982197"}}, "title": "Genomic determinants of therapy response in ETV6::RUNX1 leukemia.", "authors": [{"family": "Oksa", "given": "Laura", "initials": "L", "orcid": "0000-0003-4468-9877", "researcher": {"href": "https://publications.scilifelab.se/researcher/5526f0f44427441bb2a49f27f00b5683.json"}}, {"family": "Moisio", "given": "Sanni", "initials": "S", "orcid": "0009-0009-4446-015X", "researcher": {"href": "https://publications.scilifelab.se/researcher/de1112350e9042bfa9a8707d2c255bf5.json"}}, {"family": "Maqbool", "given": "Khurram", "initials": "K", "orcid": "0000-0003-2981-2582", "researcher": {"href": "https://publications.scilifelab.se/researcher/7ea06b85057744018f754c373fef3ca5.json"}}, {"family": "Kramer", "given": "Roger", "initials": "R"}, {"family": "Nikkil\u00e4", "given": "Atte", "initials": "A"}, {"family": "Jayasingha", "given": "Buddika", "initials": "B"}, {"family": "M\u00e4kinen", "given": "Artturi", "initials": "A", "orcid": "0000-0002-5521-9216", "researcher": {"href": "https://publications.scilifelab.se/researcher/74542e2da6d542d8a40b93b692c7b760.json"}}, {"family": "Foroughi-Asl", "given": "Hassan", "initials": "H"}, {"family": "Rounioja", "given": "Samuli", "initials": "S"}, {"family": "Suhonen", "given": "Janne", "initials": "J"}, {"family": "Krali", "given": "Olga", "initials": "O", "orcid": "0000-0002-6436-9531", "researcher": {"href": "https://publications.scilifelab.se/researcher/14a6e2f99d3b4758a10af78b93777779.json"}}, {"family": "Voutilainen", "given": "Miikka", "initials": "M", "orcid": "0000-0001-9367-3471", "researcher": {"href": "https://publications.scilifelab.se/researcher/390e63751ebb46e3873d801ce0c620d1.json"}}, {"family": "Lahnalampi", "given": "Mari", "initials": "M", "orcid": "0000-0003-4050-4935", "researcher": {"href": "https://publications.scilifelab.se/researcher/31d154912d9f4b9ca680f9d019035d46.json"}}, {"family": "Veps\u00e4l\u00e4inen", "given": "Kaisa", "initials": "K"}, {"family": "Huang", "given": "Sui", "initials": "S"}, {"family": "Duque-Afonso", "given": "Jesus", "initials": "J", "orcid": "0000-0002-8287-5673", "researcher": {"href": "https://publications.scilifelab.se/researcher/cc78f208850b4a999859f110a3850bfa.json"}}, {"family": "Hauer", "given": "Julia", "initials": "J", "orcid": "0000-0002-4058-3058", "researcher": {"href": "https://publications.scilifelab.se/researcher/9387a9c586f74172a9d251fff4d71637.json"}}, {"family": "Nordlund", "given": "Jessica", "initials": "J", "orcid": "0000-0001-8699-9959", "researcher": {"href": "https://publications.scilifelab.se/researcher/ddf48c9262134821bcc6ce1180049753.json"}}, {"family": "Wirta", "given": "Valtteri", "initials": "V", "orcid": "0000-0003-3811-5439", "researcher": {"href": "https://publications.scilifelab.se/researcher/cba024b2e3c347f6b981922d984ad2d6.json"}}, {"family": "Lohi", "given": "Olli", "initials": "O", "orcid": "0000-0001-9195-0797", "researcher": {"href": "https://publications.scilifelab.se/researcher/e11a59310dfc40e6a111367914fdba9e.json"}}, {"family": "Hein\u00e4niemi", "given": "Merja", "initials": "M", "orcid": "0000-0001-6190-3439", "researcher": {"href": "https://publications.scilifelab.se/researcher/be7efa5a7c9a4da18b397a07ebd8d9ec.json"}}], "type": "journal article", "published": "2025-09-00", "journal": {"title": "Leukemia", "issn": "1476-5551", "issn-l": "0887-6924", "volume": "39", "issue": "9", "pages": "2125-2139"}, "abstract": "ETV6::RUNX1 leukemia is the second most common subtype of childhood B cell acute lymphoblastic leukemia (B-ALL). Although it generally has a low relapse risk, a significant proportion of B-ALL relapses occur within this subtype due to its relatively high incidence. Measurable residual disease at the end of induction therapy is a well-established biomarker predicting treatment outcomes, while no genomic biomarkers are routinely applied in clinics. In this study, we used multiomic data from ETV6::RUNX1 leukemias to identify genomic features predictive of therapy response at disease presentation. In the deeply characterized sub-cohort we discovered that fast-responding cases frequently exhibited the APOBEC mutational signature and the gene expression signature of high cell cycle activity. In contrast, rearrangements of IGK genes were more frequent in slow responders. Additionally, response-related mutations were identified in transcriptional regulators and tumor suppressor genes (INTS1, NF1, TP53). Copy number analysis revealed that fast responders harbored more frequent deletions of chr12 p-arm, leading to transcriptomic changes affecting genes associated with induction therapy response (KRAS, FKBP4), while a shorter gain in chr12 was more common in slow responders. The identified genetic and transcriptomic markers of treatment sensitivity pave the way for improved disease classification at presentation, potentially improving clinical outcomes.", "doi": "10.1038/s41375-025-02683-7", "pmid": "40634509", "labels": {"NGI SNP genotyping": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "Service", "Clinical Genomics Stockholm": "Service", "Clinical Genomics": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12380598"}, {"db": "pii", "key": "10.1038/s41375-025-02683-7"}], "notes": [], "created": "2025-09-08T11:39:55.025Z", "modified": "2025-11-18T20:46:15.313Z"}, {"entity": "publication", "iuid": "b0aa84ad1a984c4d8b3eb1996eddfbe1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b0aa84ad1a984c4d8b3eb1996eddfbe1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b0aa84ad1a984c4d8b3eb1996eddfbe1"}}, "title": "Disease-specific U1 spliceosomal RNA mutations in mature B-cell neoplasms.", "authors": [{"family": "Nadeu", "given": "Ferran", "initials": "F", "orcid": "0000-0003-2910-9440", "researcher": {"href": "https://publications.scilifelab.se/researcher/d4654f6b3cd74ddfb4d859edff5fbc95.json"}}, {"family": "Shuai", "given": "Shimin", "initials": "S", "orcid": "0000-0002-9527-8018", "researcher": {"href": "https://publications.scilifelab.se/researcher/31c2a26041304b0390208fac7884e36c.json"}}, {"family": "Clot", "given": "Guillem", "initials": "G", "orcid": "0000-0003-2588-7413", "researcher": {"href": "https://publications.scilifelab.se/researcher/aa6a4380b01f4aa9a2fab0f19a0d34d9.json"}}, {"family": "Hilton", "given": "Laura K", "initials": "LK", "orcid": "0000-0002-6413-6586", "researcher": {"href": "https://publications.scilifelab.se/researcher/cebd0963fd1b4f7a836b380f3cb8a22d.json"}}, {"family": "Diaz-Navarro", "given": "Ander", "initials": "A"}, {"family": "Mart\u00edn", "given": "Silvia", "initials": "S"}, {"family": "Royo", "given": "Romina", "initials": "R"}, {"family": "Baumann", "given": "Tycho", "initials": "T"}, {"family": "Kulis", "given": "Marta", "initials": "M"}, {"family": "L\u00f3pez-Oreja", "given": "Irene", "initials": "I"}, {"family": "Cossio", "given": "Manuel", "initials": "M"}, {"family": "Lu", "given": "Junyan", "initials": "J", "orcid": "0000-0002-9211-0746", "researcher": {"href": "https://publications.scilifelab.se/researcher/08813991edd84a809d5a3e0e0bfaaa2e.json"}}, {"family": "Ljungstr\u00f6m", "given": "Viktor", "initials": "V"}, {"family": "Young", "given": "Emma", "initials": "E"}, {"family": "Plevova", "given": "Karla", "initials": "K", "orcid": "0000-0002-6148-8877", "researcher": {"href": "https://publications.scilifelab.se/researcher/2a6c579cb91f4096a7f8a9143262ce9b.json"}}, {"family": "Knisbacher", "given": "Binyamin A", "initials": "BA"}, {"family": "Lin", "given": "Ziao", "initials": "Z"}, {"family": "Hahn", "given": "Cynthia K", "initials": "CK"}, {"family": "Bousquets", "given": "Pablo", "initials": "P", "orcid": "0000-0002-2969-008X", "researcher": {"href": "https://publications.scilifelab.se/researcher/5e3865ff15a94e8abfc95c039825adac.json"}}, {"family": "Alcoceba", "given": "Miguel", "initials": "M", "orcid": "0000-0002-3819-4846", "researcher": {"href": "https://publications.scilifelab.se/researcher/fb06b84631cf4a259476737674499d1c.json"}}, {"family": "Gonz\u00e1lez", "given": "Marcos", "initials": "M"}, {"family": "Colado", "given": "Enrique", "initials": "E", "orcid": "0000-0001-8675-8207", "researcher": {"href": "https://publications.scilifelab.se/researcher/7f9a05ff8f434fbe81d1227335f431ae.json"}}, {"family": "Payer", "given": "\u00c1ngel R", "initials": "\u00c1R"}, {"family": "Aymerich", "given": "Marta", "initials": "M"}, {"family": "Terol", "given": "Mar\u00eda J", "initials": "MJ"}, {"family": "Rivas-Delgado", "given": "Alfredo", "initials": "A"}, {"family": "Enjuanes", "given": "Anna", "initials": "A"}, {"family": "Ruiz-Gasp\u00e0", "given": "S\u00edlvia", "initials": "S"}, {"family": "Chatzikonstantinou", "given": "Thomas", "initials": "T", "orcid": "0000-0003-4105-1253", "researcher": {"href": "https://publications.scilifelab.se/researcher/428007841de74249a101c9cc5182cd5e.json"}}, {"family": "H\u00e4gerstrand", "given": "Daniel", "initials": "D", "orcid": "0000-0001-7270-0776", "researcher": {"href": "https://publications.scilifelab.se/researcher/35a683cea1874ac290d91c325a648be8.json"}}, {"family": "Jylh\u00e4", "given": "Cecilia", "initials": "C"}, {"family": "Skaftason", "given": "Aron", "initials": "A"}, {"family": "Mansouri", "given": "Larry", "initials": "L"}, {"family": "Stranska", "given": "Kamila", "initials": "K", "orcid": "0000-0001-7678-1163", "researcher": {"href": "https://publications.scilifelab.se/researcher/130a65c3d64a4c57bbd619d7dc033b45.json"}}, {"family": "Doubek", "given": "Michael", "initials": "M", "orcid": "0000-0002-1269-6282", "researcher": {"href": "https://publications.scilifelab.se/researcher/7b574229235d455890fd703d2c722a17.json"}}, {"family": "van Gastel-Mol", "given": "Ellen J", "initials": "EJ"}, {"family": "Davis", "given": "Zadie", "initials": "Z"}, {"family": "Walewska", "given": "Renata", "initials": "R"}, {"family": "Scarf\u00f2", "given": "Lydia", "initials": "L", "orcid": "0000-0002-0844-0989", "researcher": {"href": "https://publications.scilifelab.se/researcher/47c4c336efb24d86b41c872d03836c78.json"}}, {"family": "Trentin", "given": "Livio", "initials": "L", "orcid": "0000-0003-1222-6149", "researcher": {"href": "https://publications.scilifelab.se/researcher/005d6d4e9e294ab7a1d7448c9aae45da.json"}}, {"family": "Visentin", "given": "Andrea", "initials": "A", "orcid": "0000-0003-0271-7200", "researcher": {"href": "https://publications.scilifelab.se/researcher/5f11f2e170b04d83a4d0f0ee3fbffdec.json"}}, {"family": "Parikh", "given": "Sameer A", "initials": "SA", "orcid": "0000-0002-3221-7314", "researcher": {"href": "https://publications.scilifelab.se/researcher/88e9511c65bb4c069a0fbeb9d1f46872.json"}}, {"family": "Rabe", "given": "Kari G", "initials": "KG", "orcid": "0000-0002-7313-1875", "researcher": {"href": "https://publications.scilifelab.se/researcher/107eb83790e54331b7069c5eda2e2303.json"}}, {"family": "Moia", "given": "Riccardo", "initials": "R", "orcid": "0000-0001-7393-1138", "researcher": {"href": "https://publications.scilifelab.se/researcher/68e9d84703624f578568c1a2775f3442.json"}}, {"family": "Armand", "given": "Marine", "initials": "M", "orcid": "0000-0001-8906-3128", "researcher": {"href": "https://publications.scilifelab.se/researcher/8d2e8c325db8415cb723a9718d49ae78.json"}}, {"family": "Rossi", "given": "Davide", "initials": "D"}, {"family": "Davi", "given": "Frederic", "initials": "F"}, {"family": "Gaidano", "given": "Gianluca", "initials": "G", "orcid": "0000-0002-4681-0151", "researcher": {"href": "https://publications.scilifelab.se/researcher/b9af4cedf69e47a5a4ecf0da0ed88c8e.json"}}, {"family": "Kay", "given": "Neil E", "initials": "NE", "orcid": "0000-0002-5951-5055", "researcher": {"href": "https://publications.scilifelab.se/researcher/ef074d0fdb0b4070b5216be063317bf8.json"}}, {"family": "Shanafelt", "given": "Tait D", "initials": "TD"}, {"family": "Ghia", "given": "Paolo", "initials": "P", "orcid": "0000-0003-3750-7342", "researcher": {"href": "https://publications.scilifelab.se/researcher/46f24783739d44c7b73a1be28c344a35.json"}}, {"family": "Oscier", "given": "David", "initials": "D"}, {"family": "Langerak", "given": "Anton W", "initials": "AW", "orcid": "0000-0002-2078-3220", "researcher": {"href": "https://publications.scilifelab.se/researcher/769a5b06013b43d6af8d3e13804cd50c.json"}}, {"family": "Be\u00e0", "given": "S\u00edlvia", "initials": "S", "orcid": "0000-0001-7192-2385", "researcher": {"href": "https://publications.scilifelab.se/researcher/49c087ad28194469892e86a69bdd4bab.json"}}, {"family": "L\u00f3pez-Guillermo", "given": "Armando", "initials": "A"}, {"family": "Neuberg", "given": "Donna", "initials": "D", "orcid": "0000-0003-2566-3145", "researcher": {"href": "https://publications.scilifelab.se/researcher/e2f9cbb622f040bebdfcb68657035be1.json"}}, {"family": "Wu", "given": "Catherine J", "initials": "CJ", "orcid": "0000-0002-3348-5054", "researcher": {"href": "https://publications.scilifelab.se/researcher/049091c641354ab2855757db72404195.json"}}, {"family": "Getz", "given": "Gad", "initials": "G", "orcid": "0000-0002-0936-0753", "researcher": {"href": "https://publications.scilifelab.se/researcher/974b292190aa40c4a3b0c1d7ab735376.json"}}, {"family": "Pospisilova", "given": "Sarka", "initials": "S", "orcid": "0000-0001-7136-2680", "researcher": {"href": "https://publications.scilifelab.se/researcher/241cf7f1344c4016b40dfcf439c0b43d.json"}}, {"family": "Stamatopoulos", "given": "Kostas", "initials": "K", "orcid": "0000-0001-8529-640X", "researcher": {"href": "https://publications.scilifelab.se/researcher/772756566c154559b2c70c8f0f44d1ad.json"}}, {"family": "Rosenquist", "given": "Richard", "initials": "R", "orcid": "0000-0002-0211-8788", "researcher": {"href": "https://publications.scilifelab.se/researcher/b570128e641140fb964ae3241414f510.json"}}, {"family": "Huber", "given": "Wolfgang", "initials": "W"}, {"family": "Zenz", "given": "Thorsten", "initials": "T", "orcid": "0000-0001-7890-9845", "researcher": {"href": "https://publications.scilifelab.se/researcher/8f6b107b1ec94de7bbc260f92f2dcc9f.json"}}, {"family": "Colomer", "given": "Dolors", "initials": "D", "orcid": "0000-0001-7486-8484", "researcher": {"href": "https://publications.scilifelab.se/researcher/0747c24c7c744799b7f0e73147dbbd05.json"}}, {"family": "Mart\u00edn-Subero", "given": "Jos\u00e9 I", "initials": "JI", "orcid": "0000-0001-8809-5195", "researcher": {"href": "https://publications.scilifelab.se/researcher/06ccbd6b7051490fb2764ce9da7a418e.json"}}, {"family": "Delgado", "given": "Julio", "initials": "J", "orcid": "0000-0002-5157-4376", "researcher": {"href": "https://publications.scilifelab.se/researcher/def9787862d247299e08c4cdbfb6a993.json"}}, {"family": "Morin", "given": "Ryan D", "initials": "RD", "orcid": "0000-0003-2932-7800", "researcher": {"href": "https://publications.scilifelab.se/researcher/c1d13b9d68534df3a8a271742b55b240.json"}}, {"family": "Stein", "given": "Lincoln D", "initials": "LD"}, {"family": "Puente", "given": "Xose S", "initials": "XS", "orcid": "0000-0001-9525-1483", "researcher": {"href": "https://publications.scilifelab.se/researcher/3c757bd329184ea2a2aa9183802fefb1.json"}}, {"family": "Campo", "given": "El\u00edas", "initials": "E", "orcid": "0000-0001-9850-9793", "researcher": {"href": "https://publications.scilifelab.se/researcher/5642afaa4ed648dfabe66194e42bc01b.json"}}], "type": "journal article", "published": "2025-09-00", "journal": {"title": "Leukemia", "issn": "1476-5551", "volume": "39", "issue": "9", "pages": "2076-2086", "issn-l": "0887-6924"}, "abstract": "Recurrent mutations in the third base of U1 spliceosomal RNA responsible for marked splicing and expression abnormalities have been described in chronic lymphocytic leukemia (CLL) and some solid tumors. However, the clinical significance of these mutations in large and independent CLL cohorts as well as their presence in other B-cell neoplasms is unknown. Here we characterized U1 mutations in 1670 CLL and 363 mature B-cell lymphomas. We confirmed that the g.3A>C U1 mutation is found in 3.5% of CLL, which conferred rapid disease progression independently of the main biological and clinical prognostic markers of the disease. Additionally, a recurrent g.9C>T mutation was found in 1.5% of CLL causing downstream splicing alterations and associated with adverse prognosis. We also identified a g.4C>T mutation in 10% of diffuse large B-cell lymphomas of the germinal center subtype and a g.7A>G mutation in 30% of EBV-negative Burkitt lymphomas, both of which altered the splicing pattern of multiple genes. This study reveals novel, recurrent, and tumor-specific U1 mutations in mature B-cell neoplasms with biological and prognostic implications, thus establishing U1 as a novel pan-B-cell malignancy driver gene.", "doi": "10.1038/s41375-025-02667-7", "pmid": "40588565", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12380619"}, {"db": "pii", "key": "10.1038/s41375-025-02667-7"}], "notes": [], "created": "2025-09-08T07:17:22.103Z", "modified": "2025-09-08T07:17:23.018Z"}, {"entity": "publication", "iuid": "6091da69a89748ddb71ea83d5824cd31", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6091da69a89748ddb71ea83d5824cd31.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6091da69a89748ddb71ea83d5824cd31"}}, "title": "Whole genome transcriptional analysis of intestinal biopsies and blood cells indicate genes involved in antioxidant defense systems, amino acid metabolism and antigen presentation in the pathogenesis of celiac disease.", "authors": [{"family": "Torinsson Naluai", "given": "\u00c5sa", "initials": "\u00c5", "orcid": "0000-0002-0504-6492", "researcher": {"href": "https://publications.scilifelab.se/researcher/bcf3474dc7054c598cbe3a195deb8a1b.json"}}, {"family": "Sabbag", "given": "Shafir", "initials": "S"}, {"family": "Abrahamsson", "given": "Sanna", "initials": "S"}, {"family": "Gudj\u00f3nsd\u00f3ttir", "given": "Audur H", "initials": "AH"}, {"family": "Arnell", "given": "Henrik", "initials": "H"}, {"family": "Agardh", "given": "Daniel", "initials": "D"}], "type": "journal article", "published": "2025-08-29", "journal": {"title": "BMC Med", "issn": "1741-7015", "volume": "23", "issue": "1", "pages": "507", "issn-l": "1741-7015"}, "abstract": "Celiac disease is associated with HLA-risk haplotypes, but non-HLA genes and environmental factors are also linked to disease susceptibility. In this study, we explore the molecular pathways involved in celiac disease by analyzing the differential expression of genes in both the gut and peripheral blood across various celiac disease phenotypes.\n\nWhole genome RNA sequencing was performed on 283 samples from intestinal mucosa and peripheral blood from 72 cases with either active, potential, or treated celiac disease and 73 disease controls. Enrichr pathway analysis of top differentially expressed genes was performed.\n\nOverall, 7565 genes in intestinal biopsies and 542 genes in blood samples were differentially expressed between cases and controls. Compared with controls, immunoglobulin heavy variable 5-51 (IGHV5-51) (p = 1.05 \u00d7 10-14) and tissue transglutaminase (TGM2) (p = 5.29 \u00d7 10-10), encoding for TG2, the main autoantigen in celiac disease, were two of the top up-regulated genes in intestinal biopsies from celiac cases. TGM2 was also slightly upregulated in blood cells from cases with active disease compared with controls (p = 0.05). The topmost differentially expressed genes in peripheral blood were HLA-DQB1, HLA-DQB2, and GSTM1. Among pathways identified containing transcriptionally differentiated genes were antioxidant defense systems (e.g., nuclear factor (erythroid-derived 2)-like 2 (Nrf2), glutathione, ergothioneine, and peroxisome metabolism), as well as MHC class 1 antigen presentation, amino acid transport, mTORC1, bilirubin and lipid metabolism, liver homeostasis, the complement system, and interferon signaling.\n\nDifferentially expressed genes in cases and controls indicate crosstalk between molecular pathways involved in antioxidant defense, immune regulation, and nutrient signaling in the pathogenesis of celiac disease.", "doi": "10.1186/s12916-025-04261-1", "pmid": "40883722", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12398127"}, {"db": "pii", "key": "10.1186/s12916-025-04261-1"}], "notes": [], "created": "2025-09-08T07:11:35.688Z", "modified": "2025-09-18T07:36:17.364Z"}, {"entity": "publication", "iuid": "a820631626024f32811c8031777bf540", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a820631626024f32811c8031777bf540.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a820631626024f32811c8031777bf540"}}, "title": "Combinatorial DNMTs and EZH2 inhibition reprograms the H3K27me3 and DNAme-mediated onco-epigenome to suppress multiple myeloma proliferation.", "authors": [{"family": "Atienza P\u00e1rraga", "given": "Alba", "initials": "A"}, {"family": "Nylund", "given": "Patrick", "initials": "P", "orcid": "0000-0002-1274-4010", "researcher": {"href": "https://publications.scilifelab.se/researcher/683976ea3c094b198998dabb0d433f4b.json"}}, {"family": "Diamanti", "given": "Klev", "initials": "K", "orcid": "0000-0002-4922-8415", "researcher": {"href": "https://publications.scilifelab.se/researcher/b71560391b294bb5a344b9c6cabfc956.json"}}, {"family": "Garrido-Zabala", "given": "Berta", "initials": "B"}, {"family": "Tziola", "given": "Stefania Iliana", "initials": "SI"}, {"family": "Vasquez", "given": "Louella", "initials": "L", "orcid": "0000-0002-5758-6036", "researcher": {"href": "https://publications.scilifelab.se/researcher/0479eadb09d44ece8523730e1e0fd0b1.json"}}, {"family": "Pyl", "given": "Paul Theodor", "initials": "PT", "orcid": "0000-0002-7651-883X", "researcher": {"href": "https://publications.scilifelab.se/researcher/a69051a0275c442c8c0d5621b4000929.json"}}, {"family": "Raykova", "given": "Doroteya", "initials": "D", "orcid": "0000-0001-6452-2199", "researcher": {"href": "https://publications.scilifelab.se/researcher/0a81c40491e349178167f148f2351875.json"}}, {"family": "Skaftason", "given": "Aron", "initials": "A"}, {"family": "Ma", "given": "Anqi", "initials": "A", "orcid": "0000-0002-9293-4753", "researcher": {"href": "https://publications.scilifelab.se/researcher/67c70ee5b7bd4136a74d7605ec7b1614.json"}}, {"family": "Jin", "given": "Jian", "initials": "J", "orcid": "0000-0002-3774-1609", "researcher": {"href": "https://publications.scilifelab.se/researcher/ed488bfe2c024a6b874b3b964ce80b97.json"}}, {"family": "Mart\u00edn-Subero", "given": "Jos\u00e9 Ignacio", "initials": "JI", "orcid": "0000-0001-8809-5195", "researcher": {"href": "https://publications.scilifelab.se/researcher/06ccbd6b7051490fb2764ce9da7a418e.json"}}, {"family": "\u00d6berg", "given": "Fredrik", "initials": "F", "orcid": "0000-0003-3609-1197", "researcher": {"href": "https://publications.scilifelab.se/researcher/c68243c8cc754cdb8b380db120f3b771.json"}}, {"family": "De Bruyne", "given": "Elke", "initials": "E", "orcid": "0000-0003-4012-4617", "researcher": {"href": "https://publications.scilifelab.se/researcher/e2715df4e920432c9723d8fdf4ff897b.json"}}, {"family": "Komorowski", "given": "Jan", "initials": "J", "orcid": "0000-0002-0766-8789", "researcher": {"href": "https://publications.scilifelab.se/researcher/b2d1190dfa864e4089c58c864857b114.json"}}, {"family": "Jernberg Wiklund", "given": "Helena", "initials": "H"}, {"family": "Kalushkova", "given": "Antonia", "initials": "A", "orcid": "0000-0003-4535-506X", "researcher": {"href": "https://publications.scilifelab.se/researcher/df89c7522b7b4af3b3cef8555380fe8c.json"}}], "type": "journal article", "published": "2025-08-27", "journal": {"title": "Sci Rep", "issn": "2045-2322", "issn-l": "2045-2322", "volume": "15", "issue": "1", "pages": "31568"}, "abstract": "Comprehensive epigenomic studies in multiple myeloma (MM) that unravel the connections between major epigenetic regulators, their intertwined collaboration and the potential of combinatorial targeting remain limited. Utilizing ChIP-seq, ATAC-seq, RNA-seq, and DNA methylation (DNAme) data, we generated whole-genome chromatin annotations from normal plasma cells and MM patients, revealing epigenomic re-configuration affecting downstream genes involved in tumour growth and survival. Primary MM samples showed global DNA hypomethylation but site-specific hypermethylation was observed at transcription start sites, promoters, and enhancers. Moreover, increased deposition of H3K27me3 was observed in clinically relevant functional chromatin clusters. Combined EZH2 and DNMTs inhibition resulted in extensive epigenomic alterations activating apoptosis and cell cycle genes, leading to increased G2/M arrest and apoptosis in MM cell lines. Our findings provide novel insights into the role of epigenetic gene silencing in MM tumorigenesis and the interplay between the Polycomb repressive complex 2 and DNAme.\r\n\r\nThe online version contains supplementary material available at 10.1038/s41598-025-17093-z.", "doi": "10.1038/s41598-025-17093-z", "pmid": "40866476", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics (NBIS)": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC12391466"}, {"db": "pii", "key": "10.1038/s41598-025-17093-z"}], "notes": [], "created": "2025-09-08T07:11:30.283Z", "modified": "2025-10-06T12:40:33.288Z"}, {"entity": "publication", "iuid": "4ed7da9adac244919a18efaef8b67a03", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4ed7da9adac244919a18efaef8b67a03.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4ed7da9adac244919a18efaef8b67a03"}}, "title": "MALNC: a new mutant NPM1/IDH2R140 and PML-RARA-associated lncRNA with impact on AML cell proliferation, maturation and drug response.", "authors": [{"family": "Cozzi", "given": "Elisabetta", "initials": "E", "orcid": "0009-0003-5311-7974", "researcher": {"href": "https://publications.scilifelab.se/researcher/bb6657fdce5a4c8e99ad05f000ef8de3.json"}}, {"family": "Neddermeyer", "given": "Anne", "initials": "A"}, {"family": "Zhong", "given": "Xiangfu", "initials": "X", "orcid": "0000-0002-1872-1186", "researcher": {"href": "https://publications.scilifelab.se/researcher/b625a888935a42a89d7df3522e249413.json"}}, {"family": "Gamboa-Cede\u00f1o", "given": "Angelica Mar\u00eda", "initials": "AM"}, {"family": "Kanellis", "given": "Dimitris C", "initials": "DC", "orcid": "0000-0001-8690-2010", "researcher": {"href": "https://publications.scilifelab.se/researcher/0921ab7566514fb0a3cd0daf2baabe6e.json"}}, {"family": "\u00d6sterroos", "given": "Albin", "initials": "A"}, {"family": "Bj\u00f6rklund", "given": "My", "initials": "M", "orcid": "0000-0002-2325-6012", "researcher": {"href": "https://publications.scilifelab.se/researcher/3cc743cdb2604ffdbc78303d70985c48.json"}}, {"family": "Struyf", "given": "Nona", "initials": "N"}, {"family": "Karlsson", "given": "Kasper", "initials": "K"}, {"family": "Qu", "given": "Ying", "initials": "Y"}, {"family": "M\u00e5nsson", "given": "Alma", "initials": "A", "orcid": "0009-0006-1982-7712", "researcher": {"href": "https://publications.scilifelab.se/researcher/6ccda3e6f49f43f5bcf5576d7acc16e5.json"}}, {"family": "Pandzic", "given": "Tatjana", "initials": "T"}, {"family": "Bengtz\u00e9n", "given": "Sofia", "initials": "S"}, {"family": "Nilsson", "given": "Christer", "initials": "C", "orcid": "0000-0003-0695-0050", "researcher": {"href": "https://publications.scilifelab.se/researcher/7f78180b33fa48cd86474d5c3cdaa852.json"}}, {"family": "Fiskesund", "given": "Roland", "initials": "R"}, {"family": "Baliakas", "given": "Panagiotis", "initials": "P", "orcid": "0000-0002-5634-7156", "researcher": {"href": "https://publications.scilifelab.se/researcher/17370bd509dc4b1081af5aed9e5117c7.json"}}, {"family": "Erkers", "given": "Tom", "initials": "T"}, {"family": "Bartek", "given": "Jiri", "initials": "J"}, {"family": "Kallioniemi", "given": "Olli-Pekka", "initials": "OP"}, {"family": "Qian", "given": "Hong", "initials": "H"}, {"family": "Lennartsson", "given": "Andreas", "initials": "A"}, {"family": "Lehmann", "given": "S\u00f6ren", "initials": "S"}], "type": "journal article", "published": "2025-08-23", "journal": {"title": "Cancer Gene Ther", "issn": "1476-5500", "issn-l": null}, "abstract": "As the non-coding genome remains poorly characterized in acute myeloid leukemia (AML), we aimed to identify and functionally characterize novel long non-coding RNAs (lncRNAs) relevant to AML biology and treatment. We first identified lncRNAs overexpressed in AML blasts and, among them, discovered a novel transcript, which we named myeloid and AML-associated intergenic long non-coding RNA (MALNC). MALNC is overexpressed in AML, particularly in cases with the PML-RARA fusion or IDH2R140/NPM1 co-mutations, and is associated with a distinct gene expression profile. Functional studies showed that MALNC knockout impairs AML cell proliferation and colony formation, enhances ATRA-induced differentiation, and sensitizes cells to arsenic trioxide. Transcriptomic analysis revealed that MALNC loss alters the expression of retinoic acid pathway genes, and chromatin binding studies showed that MALNC binds to genes related to the retinoic acid and Rho GTPase pathways. In conclusion, we have identified MALNC as a novel lncRNA that promotes leukemic cell proliferation, counteracts ATRA-induced differentiation, and modulates drug sensitivity in AML.", "doi": "10.1038/s41417-025-00954-0", "pmid": "40849353", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41417-025-00954-0"}], "notes": [], "created": "2025-09-08T07:03:20.085Z", "modified": "2025-11-14T11:06:29.062Z"}, {"entity": "publication", "iuid": "5736722e01b74b29baf8fe43d4ce6819", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5736722e01b74b29baf8fe43d4ce6819.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5736722e01b74b29baf8fe43d4ce6819"}}, "title": "RNA-seq analysis identifies key genes enhancing hoof strength to withstand barefoot racing in Standardbred trotters.", "authors": [{"family": "Schwochow", "given": "Doreen", "initials": "D"}, {"family": "Alameddine", "given": "Asmaa", "initials": "A"}, {"family": "Sp\u00f6rndly-Nees", "given": "Ellinor", "initials": "E"}, {"family": "Montigny", "given": "Mathilde", "initials": "M"}, {"family": "Naboulsi", "given": "Rakan", "initials": "R", "orcid": "0000-0002-3610-4341", "researcher": {"href": "https://publications.scilifelab.se/researcher/ae740ff060a5499fa477891138e95117.json"}}, {"family": "Jansson", "given": "Anna", "initials": "A"}, {"family": "Niazi", "given": "Adnan", "initials": "A", "orcid": "0000-0003-0311-5279", "researcher": {"href": "https://publications.scilifelab.se/researcher/c9e07c9891804a60980eb07956a7cd0d.json"}}, {"family": "Lindgren", "given": "Gabriella", "initials": "G", "orcid": "0000-0001-6046-9669", "researcher": {"href": "https://publications.scilifelab.se/researcher/a050dea8e99c47fabac28c14fe4daabb.json"}}], "type": "journal article", "published": "2025-08-18", "journal": {"title": "BMC Genomics", "issn": "1471-2164", "volume": "26", "issue": "1", "pages": "751", "issn-l": "1471-2164"}, "abstract": "Racing without protective shoes is common in the Swedish harness racing industry, as it can enhance horses' performance on the track. Trainers typically decide whether a horse will race barefoot based on practical experience rather than objective measures. However, this practice can sometimes lead to excessive hoof wear, posing potential welfare concerns for racing horses. Gene expression differences may help reveal the underlying genetic mechanisms associated with different phenotypic traits. To explore an objective measure for assessing which horses are best suited for barefoot racing, we conducted a polyA-selected RNA-seq experiment on tissue from the growth zone at the coronary band of the hoof. This experiment compared tissues from Standardbred trotters capable of repeatedly racing barefoot without injury (n = 11) to those that could not (n = 7). By combining stringent phenotyping with racing records and trainer interviews, we aimed to elucidate the biological factors related to hoof strength in barefoot racing, focusing on differential abundant genes.\n\nThe RNA-seq analysis identified five significantly downregulated genes in horses capable of competing barefoot across consecutive races. These genes are associated with various biological processes relevant for hoof strength: ACCS, IRX2 and TRAPPAC6A contribute to enhancing the structural integrity of the hoof; MT2A regulates its metal homeostasis and SLC35F3 likely influences local vasoconstriction in the hoof. These gene findings suggest a coordinated genetic basis for structural reinforcement and physiological support of the hoof, which may be critical for sustaining performance under barefoot conditions.\n\nOur findings suggest that the ability of Standardbred trotters to race barefoot in consecutive events is reflected in distinct gene expression patterns, underscoring a genetic basis for hoof strength. This supports further genome-wide scans aimed at identifying genetic markers for hoof durability in these horses. The focused design of our study- comparing horses that could consistently race barefoot with those that could not- enabled us to isolate a select group of genes involved in diverse aspects of hoof biology essential for quality and resilience of horse hooves. This insight could ultimately be applied to augment both the performance and wellbeing of equine athletes across disciplines.", "doi": "10.1186/s12864-025-11814-4", "pmid": "40826322", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12363045"}, {"db": "pii", "key": "10.1186/s12864-025-11814-4"}], "notes": [], "created": "2025-09-08T07:04:42.067Z", "modified": "2025-09-09T13:14:43.091Z"}, {"entity": "publication", "iuid": "4cb1f3bbbd73476d85743dd1a3b24932", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4cb1f3bbbd73476d85743dd1a3b24932.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4cb1f3bbbd73476d85743dd1a3b24932"}}, "title": "Early germline sequestration in a basidiomycete fungus.", "authors": [{"family": "Thor\u00e9n", "given": "Markus Hiltunen", "initials": "MH", "orcid": "0000-0002-8880-872X", "researcher": {"href": "https://publications.scilifelab.se/researcher/77b54361528b4c7c8f5122d91d58b36d.json"}}, {"family": "Olsson", "given": "Boel", "initials": "B", "orcid": "0009-0006-4157-2664", "researcher": {"href": "https://publications.scilifelab.se/researcher/219a75999b65464ca3d405ac20898743.json"}}, {"family": "Vonk", "given": "Peter Jan", "initials": "PJ", "orcid": "0000-0001-5325-7430", "researcher": {"href": "https://publications.scilifelab.se/researcher/d5684212a1f5478cab0943d5064e74a7.json"}}, {"family": "Siljestam", "given": "Mattias", "initials": "M", "orcid": "0000-0002-3720-4926", "researcher": {"href": "https://publications.scilifelab.se/researcher/653d5e0ec2bc4925a19db2697ad61a2d.json"}}, {"family": "Reimeg\u00e5rd", "given": "Johan", "initials": "J", "orcid": "0000-0003-1518-2014", "researcher": {"href": "https://publications.scilifelab.se/researcher/db7ebacfd8764a988ee41f2e5ab23e50.json"}}, {"family": "Ryberg", "given": "Martin", "initials": "M", "orcid": "0000-0002-6795-4349", "researcher": {"href": "https://publications.scilifelab.se/researcher/c0a8578a1ace4105be91ec8116c84365.json"}}, {"family": "Johannesson", "given": "Hanna", "initials": "H", "orcid": "0000-0001-6359-9856", "researcher": {"href": "https://publications.scilifelab.se/researcher/36e8fe278e01470e8cddaaccc5dad596.json"}}], "type": "journal article", "published": "2025-08-14", "journal": {"title": "Science", "issn": "1095-9203", "issn-l": "0036-8075", "volume": "389", "issue": "6761", "pages": "720-723"}, "abstract": "In sexual organisms, inheritance of new mutations is highly dependent on the timing of germline definition. Here, we used the fairy ring-forming fungus Marasmius oreades to challenge the general assumption of a late germline separation in the Fungi. We collected mushrooms from different parts of rings over a 7-year period and identified new mutations in different tissues by whole-genome sequencing. We found evidence that fertile and sterile tissues had accumulated different mutations, suggesting that the germ line, destined for spore production, is already defined in the mycelium in this species. Moreover, the germ line carried fewer mutations than sterile tissues, indicating a lower mutation rate. Our findings suggest that early germline sequestration is more widespread than previously considered across multicellular life.", "doi": "10.1126/science.adu8580", "pmid": "40811541", "labels": {"Bioinformatics (NBIS)": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support and Infrastructure": "Collaborative"}, "xrefs": [], "notes": [], "created": "2025-08-29T12:41:10.841Z", "modified": "2025-11-21T13:14:48.967Z"}, {"entity": "publication", "iuid": "f6b93bc63d7447ab8768a84e8c6aa42a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f6b93bc63d7447ab8768a84e8c6aa42a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f6b93bc63d7447ab8768a84e8c6aa42a"}}, "title": "Systems analysis of clinical malaria reveals proteomic perturbation and innate-adaptive crosstalk linked to disease severity.", "authors": [{"family": "Lautenbach", "given": "Maximilian Julius", "initials": "MJ"}, {"family": "Wyss", "given": "Katja", "initials": "K"}, {"family": "Yman", "given": "Victor", "initials": "V"}, {"family": "Foroogh", "given": "Fariba", "initials": "F"}, {"family": "Satarvandi", "given": "Donya", "initials": "D"}, {"family": "Mousavian", "given": "Zaynab", "initials": "Z"}, {"family": "Sond\u00e9n", "given": "Klara", "initials": "K"}, {"family": "Wang", "given": "Jun", "initials": "J"}, {"family": "\u00c1lvez", "given": "Mar\u00eda Bueno", "initials": "MB"}, {"family": "Bergstr\u00f6m", "given": "Sofia", "initials": "S"}, {"family": "Nilsson", "given": "Peter", "initials": "P"}, {"family": "Edfors", "given": "Fredrik", "initials": "F"}, {"family": "Brodin", "given": "Petter", "initials": "P"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M"}, {"family": "Sundling", "given": "Christopher", "initials": "C"}, {"family": "F\u00e4rnert", "given": "Anna", "initials": "A"}], "type": "journal article", "published": "2025-08-12", "journal": {"title": "Immunity", "issn": "1097-4180", "issn-l": "1074-7613", "volume": "58", "issue": "8", "pages": "2120-2136.e5"}, "abstract": "Malaria presents with varying degrees of severity. To improve clinical management and prevention, it is crucial to understand the pathogenesis and host response. We analyzed 1,463 plasma proteins during and after acute Plasmodium falciparum malaria in adult travelers and linked responses to peripheral immune cells by integrating with single-cell RNA sequencing (RNA-seq) data from a subset of donors. We identified extensive perturbations in over 250 proteins with diverse origins, including many not previously analyzed in malaria patients, such as hormones, circulating receptors, and intracellular or membrane-bound proteins from affected tissues. The protein profiles clustered participants according to disease severity, enabling the identification of a compressed 11-protein signature enriched in severe malaria. Conceptually, this study advances our understanding of malaria by linking systemic proteomic changes to immune cell communication and organ-specific responses. This resource, which includes an interactive platform to explore data, opens new avenues for hypothesis generation, biomarker discovery, and therapeutic target identification.", "doi": "10.1016/j.immuni.2025.06.014", "pmid": "40664217", "labels": {"Affinity Proteomics Stockholm": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "Affinity Proteomics Uppsala": "Service", "NGI Proteomics": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "S1074-7613(25)00283-3"}], "notes": [], "created": "2025-11-17T08:54:30.240Z", "modified": "2025-11-26T11:07:57.819Z"}, {"entity": "publication", "iuid": "741f4c91234245268da4ddfa1e0b9efa", "links": {"self": {"href": "https://publications.scilifelab.se/publication/741f4c91234245268da4ddfa1e0b9efa.json"}, "display": {"href": "https://publications.scilifelab.se/publication/741f4c91234245268da4ddfa1e0b9efa"}}, "title": "Lrig3-deficient mice exhibit strain-specific alterations in liver fat accumulation, intestinal morphology, and middle ear inflammation.", "authors": [{"family": "Herdenberg", "given": "Carl", "initials": "C"}, {"family": "Henriksson", "given": "Roger", "initials": "R"}, {"family": "Hedman", "given": "H\u00e5kan", "initials": "H", "orcid": "0000-0001-6891-6996", "researcher": {"href": "https://publications.scilifelab.se/researcher/6b1b2d57a55e415aa17acbd0318a019e.json"}}, {"family": "Rondahl", "given": "Veronica", "initials": "V"}], "type": "journal article", "published": "2025-08-10", "journal": {"title": "Gene", "issn": "1879-0038", "issn-l": "0378-1119", "volume": "960", "issue": null, "pages": "149539"}, "abstract": "The transmembrane protein leucine-rich repeats and immunoglobulin-like domains 3 (LRIG3) regulates fat metabolism and bone morphogenetic protein (BMP) signaling. Lrig3-deficient mice exhibit impaired development of the snout and the inner ear lateral canal, neural defects, and cardiac hypertrophy in adulthood. However, no thorough and unbiased analysis of the physiological functions of Lrig3 has previously been performed. To address this knowledge gap, we performed histopathological examination of 42 tissues and organs from 1-year-old female C57BL/6JBomTac and 129S1-U mice with different Lrig3 genotypes. Among the scored pathologies, three were significantly associated with Lrig3 genotype: spontaneous macrovesicular hepatocellular degeneration (hepatocellular steatosis) was less prevalent in Lrig3-deficient C57BL/6JBomTac mice, whereas dilated or flaccid ileum and otitis media were more common in Lrig3-deficient 129S1-U mice. To further investigate hepatic steatosis phenotypes, 8-week-old C57BL/6JBomTac mice of both sexes and different Lrig3 genotypes were subjected to consuming a high-fat diet (HFD) for 8 weeks. The HFD regimen led to relatively few cases of hepatocellular steatosis, with no significant differences among the genotypes; however, female Lrig3-deficient mice presented reduced microvesicular hepatocellular degeneration compared with their wild-type littermates. This study revealed that Lrig3 regulates liver fat accumulation, intestinal morphology, and middle ear inflammation in a mouse strain-dependent manner.", "doi": "10.1016/j.gene.2025.149539", "pmid": "40320098", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Service", "Bioinformatics Support and Infrastructure": "Service", "Bioinformatics Support, Infrastructure and Training": "Service"}, "xrefs": [{"db": "pii", "key": "S0378-1119(25)00327-0"}], "notes": [], "created": "2025-09-08T07:06:55.862Z", "modified": "2025-11-19T13:14:56.377Z"}, {"entity": "publication", "iuid": "ab9b4fd3312a411fa7600da6cc9fc651", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ab9b4fd3312a411fa7600da6cc9fc651.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ab9b4fd3312a411fa7600da6cc9fc651"}}, "title": "Precise mapping of single-stranded DNA breaks by sequence-templated erroneous DNA polymerase end-labelling.", "authors": [{"family": "Wenson", "given": "Leonie", "initials": "L", "orcid": "0000-0002-1864-1258", "researcher": {"href": "https://publications.scilifelab.se/researcher/989e0534adbd426386cec5526c5e9668.json"}}, {"family": "Heldin", "given": "Johan", "initials": "J", "orcid": "0000-0002-0915-5303", "researcher": {"href": "https://publications.scilifelab.se/researcher/d8a546798d014cd3a44537ae5db9f889.json"}}, {"family": "Martin", "given": "Marcel", "initials": "M", "orcid": "0000-0002-0680-200X", "researcher": {"href": "https://publications.scilifelab.se/researcher/132afd4fea2e4e86bdf43708c8f49907.json"}}, {"family": "Erbilgin", "given": "Y\u00fccel", "initials": "Y"}, {"family": "Salman", "given": "Bar\u0131\u015f", "initials": "B", "orcid": "0000-0002-7657-8576", "researcher": {"href": "https://publications.scilifelab.se/researcher/eb919f7fcc794c8898fe800056d42f38.json"}}, {"family": "Sundqvist", "given": "Anders", "initials": "A"}, {"family": "Schaal", "given": "Wesley", "initials": "W", "orcid": "0000-0001-6770-0878", "researcher": {"href": "https://publications.scilifelab.se/researcher/ab184845a24f4effb22ec2b338ab8960.json"}}, {"family": "Sandbaumh\u00fcter", "given": "Friederike A", "initials": "FA"}, {"family": "Jansson", "given": "Erik T", "initials": "ET"}, {"family": "Chen", "given": "Xingqi", "initials": "X", "orcid": "0000-0002-5657-2839", "researcher": {"href": "https://publications.scilifelab.se/researcher/ef7ddc09e57745909175e41ac2d1b647.json"}}, {"family": "Davidsson", "given": "Anton", "initials": "A"}, {"family": "Stenerl\u00f6w", "given": "Bo", "initials": "B", "orcid": "0000-0001-8878-8071", "researcher": {"href": "https://publications.scilifelab.se/researcher/22437ff9315d43089232926973feb0d2.json"}}, {"family": "Espinoza", "given": "Jaime A", "initials": "JA", "orcid": "0000-0002-0731-2715", "researcher": {"href": "https://publications.scilifelab.se/researcher/3cdf2cd80f5b4f87adf6d936b6390ee8.json"}}, {"family": "Lindstr\u00f6m", "given": "Mikael", "initials": "M", "orcid": "0000-0003-1148-8497", "researcher": {"href": "https://publications.scilifelab.se/researcher/5aa942fbfbee4257a129b3e7888f5b6d.json"}}, {"family": "Lennartsson", "given": "Johan", "initials": "J"}, {"family": "Spjuth", "given": "Ola", "initials": "O", "orcid": "0000-0002-8083-2864", "researcher": {"href": "https://publications.scilifelab.se/researcher/605dbd52684d4e54ae4150a9933abe6e.json"}}, {"family": "S\u00f6derberg", "given": "Ola", "initials": "O", "orcid": "0000-0003-2883-1925", "researcher": {"href": "https://publications.scilifelab.se/researcher/68df823efa304c0b9962684ac1515808.json"}}], "type": "journal article", "published": "2025-08-04", "journal": {"title": "Nat Commun", "issn": "2041-1723", "issn-l": "2041-1723", "volume": "16", "issue": "1", "pages": "7130"}, "abstract": "The ability to analyze whether DNA contains lesions is essential in identifying mutagenic substances. Currently, the detection of single-stranded DNA breaks (SSBs) lacks precision. To address this limitation, we develop a method for sequence-templated erroneous end-labelling sequencing (STEEL-seq), which enables the mapping of SSBs. The method requires a highly error-prone DNA polymerase, so we engineer a chimeric DNA polymerase, Sloppymerase, capable of replicating DNA in the absence of one nucleotide. Following the omission of a specific nucleotide (e.g., dATP) from the reaction mixture, Sloppymerase introduces mismatches directly downstream of SSBs at positions where deoxyadenosine should occur. This mismatch pattern, coupled with the retention of sequence information flanking these sites, ensures that the identified hits are bona fide SSBs. STEEL-seq is compatible with a variety of sequencing technologies, as demonstrated using Sanger, Illumina, PacBio, and Nanopore systems. Using STEEL-seq, we determine the SSB/base pair frequency in the human genome to range between 0.7 and 3.8 \u00d7 10-6 with an enrichment in active promoter regions.", "doi": "10.1038/s41467-025-62512-4", "pmid": "40759655", "labels": {"NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics (NBIS)": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12322144"}, {"db": "pii", "key": "10.1038/s41467-025-62512-4"}], "notes": [], "created": "2025-08-19T13:16:23.958Z", "modified": "2025-11-28T10:45:45.544Z"}, {"entity": "publication", "iuid": "06ca672ce48846a38877306910ec4cd1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/06ca672ce48846a38877306910ec4cd1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/06ca672ce48846a38877306910ec4cd1"}}, "title": "Small\u2010scale thermal habitat variability may not determine seagrass resilience to climate change", "authors": [{"family": "Hattich", "given": "Giannina S I", "initials": "GSI", "orcid": "0000-0003-4660-7759", "researcher": {"href": "https://publications.scilifelab.se/researcher/86fec49ce8324a27aa3da020810cd115.json"}}, {"family": "Jahnke", "given": "Marlene", "initials": "M", "orcid": "0000-0001-7262-315X", "researcher": {"href": "https://publications.scilifelab.se/researcher/88ddc399062a4cc792c36feb725f3ecd.json"}}, {"family": "Enge", "given": "Swantje", "initials": "S", "orcid": "0000-0003-4292-0051", "researcher": {"href": "https://publications.scilifelab.se/researcher/d92a4e95bf294c34855b27f30ba39dce.json"}}, {"family": "Niemi", "given": "Niklas", "initials": "N", "orcid": "0009-0008-8279-4049", "researcher": {"href": "https://publications.scilifelab.se/researcher/65c382595e5140b18c6ffa7b504f3434.json"}}, {"family": "Bernal\u2010G\u00f3mez", "given": "Maru", "initials": "M", "orcid": "0009-0006-0275-6620", "researcher": {"href": "https://publications.scilifelab.se/researcher/09f54c2d6291411c87843cf10056e32d.json"}}, {"family": "De Wit", "given": "Pierre", "initials": "P", "orcid": "0000-0003-4709-3438", "researcher": {"href": "https://publications.scilifelab.se/researcher/95b69d4724ce4b69819c0a1578cd56eb.json"}}, {"family": "Havenhand", "given": "Jonathan N", "initials": "JN", "orcid": "0000-0003-0253-3428", "researcher": {"href": "https://publications.scilifelab.se/researcher/8d1c6ad9fb0a40418db6e99f127ea8ab.json"}}, {"family": "Pansch", "given": "Christian", "initials": "C", "orcid": "0000-0001-8442-4502", "researcher": {"href": "https://publications.scilifelab.se/researcher/50129df0120e441081efa1a9649ffbd5.json"}}], "type": "journal-article", "published": "2025-08-00", "journal": {"title": "Limnol Oceanogr", "issn": "0024-3590", "volume": "70", "issue": "8", "pages": "2039-2052", "issn-l": null}, "abstract": null, "doi": "10.1002/lno.70049", "pmid": null, "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2025-09-08T07:11:32.834Z", "modified": "2025-11-14T11:05:36.890Z"}, {"entity": "publication", "iuid": "f94b305344964e2abd50b277f36990ad", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f94b305344964e2abd50b277f36990ad.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f94b305344964e2abd50b277f36990ad"}}, "title": "Mast Cell Phenotypic Heterogeneity Impacts the Interplay with Pathogenic Salmonella Typhimurium Bacteria.", "authors": [{"family": "von Beek", "given": "Christopher", "initials": "C", "orcid": "0000-0001-6310-7583", "researcher": {"href": "https://publications.scilifelab.se/researcher/a3ea7730832f4f45ae6583076d90418a.json"}}, {"family": "Prensa", "given": "Grisna I", "initials": "GI", "orcid": "0009-0002-7101-7224", "researcher": {"href": "https://publications.scilifelab.se/researcher/3d030d78925948d993999b66e1959acc.json"}}, {"family": "Andersson", "given": "Julia H M", "initials": "JHM"}, {"family": "Pejler", "given": "Gunnar", "initials": "G", "orcid": "0000-0002-6779-391X", "researcher": {"href": "https://publications.scilifelab.se/researcher/97b2d5f8dec04bc3b7631370d77a2236.json"}}, {"family": "Sellin", "given": "Mikael E", "initials": "ME", "orcid": "0000-0002-8355-0803", "researcher": {"href": "https://publications.scilifelab.se/researcher/f797357bcd3d4447bff96c20873dd500.json"}}], "type": "journal article", "published": "2025-08-00", "journal": {"title": "Eur. J. Immunol.", "issn": "1521-4141", "volume": "55", "issue": "8", "pages": "e70040", "issn-l": "0014-2980"}, "abstract": "Mast cells (MCs) lodge within barrier tissues and respond to infectious microbes. Recent work demonstrated that MCs differentiate their cytokine response to extracellular versus invasive Gram-negative enterobacteria by a two-step activation mechanism that integrates Toll-like-receptor (TLR) sensing with signals elicited by type-III-secretion-system (TTSS) effectors during bacterial invasion. However, multiple MC subtypes exist, and it remains unclear how their phenotypic heterogeneity impacts microbial interactions. We find that murine MCs maintained in IL-3, or differentiated toward a connective-tissue phenotype (CT-MCs), respond potently to the enteropathogen Salmonella enterica Typhimurium (S.Tm) through two-step activation, with the TLR component explained by functional TLR4 and TLR2. By contrast, murine mucosal mast cells (M-MCs) express insignificant levels of these TLRs, therefore being unresponsive to extracellular S.Tm, but still mounting a response to invasive bacteria. Following invasion, MC granule maintenance by serglycin restricts S.Tm vacuolar and cytosolic colonization. Notably, this has no impact on the cytokine release from infected MCs, thus uncoupling S.Tm\u00b4s intracellular life-cycle from the MC cytokine response. Finally, human LUVA MCs employ a variant of two-step activation where TLR2/6 signaling combines with the TTSS-elicited signals. Together, this study explains how MC subtypes can respond differently to S.Tm-infection depending on their TLR expression and granule features.", "doi": "10.1002/eji.70040", "pmid": "40838737", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12369454"}], "notes": [], "created": "2025-09-08T07:06:53.513Z", "modified": "2025-09-09T13:13:50.740Z"}, {"entity": "publication", "iuid": "3b9b5a866e2a4139b03c9bbe033fc083", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3b9b5a866e2a4139b03c9bbe033fc083.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3b9b5a866e2a4139b03c9bbe033fc083"}}, "title": "Landscape connectivity and genetic structure of animal populations in urban ponds", "authors": [{"family": "Yildirim", "given": "Yeserin", "initials": "Y"}, {"family": "Hyseni", "given": "Chaz", "initials": "C", "orcid": "0000-0003-2567-8013", "researcher": {"href": "https://publications.scilifelab.se/researcher/7327304d59cb41a7a97cdcba953f9cdc.json"}}, {"family": "Heino", "given": "Jani", "initials": "J"}, {"family": "Bini", "given": "Luis Mauricio", "initials": "LM", "orcid": "0000-0003-3398-9399", "researcher": {"href": "https://publications.scilifelab.se/researcher/490cfde8f1824571a07f21bf11ea61f0.json"}}, {"family": "H\u00f6glund", "given": "Jacob", "initials": "J"}, {"family": "Johansson", "given": "Frank", "initials": "F", "orcid": "0000-0001-5160-9543", "researcher": {"href": "https://publications.scilifelab.se/researcher/0667c14b327f44fd8a802acd9c3f1fb2.json"}}], "type": "journal-article", "published": "2025-08-00", "journal": {"title": "Conserv Genet", "issn": "1566-0621", "volume": "26", "issue": "4", "pages": "703-714", "issn-l": null}, "abstract": null, "doi": "10.1007/s10592-025-01697-z", "pmid": null, "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [], "notes": [], "created": "2025-09-08T07:17:17.339Z", "modified": "2025-09-09T13:13:41.822Z"}, {"entity": "publication", "iuid": "952ed8e7e59d4100b61d6cf634d568fd", "links": {"self": {"href": "https://publications.scilifelab.se/publication/952ed8e7e59d4100b61d6cf634d568fd.json"}, "display": {"href": "https://publications.scilifelab.se/publication/952ed8e7e59d4100b61d6cf634d568fd"}}, "title": "Genetics of monozygotic twins reveals the impact of environmental sensitivity on psychiatric and neurodevelopmental phenotypes.", "authors": [{"family": "Assary", "given": "Elham", "initials": "E", "orcid": "0000-0001-9788-0478", "researcher": {"href": "https://publications.scilifelab.se/researcher/b4b6d4805e24466a860f5366c30d7ea8.json"}}, {"family": "Coleman", "given": "Jonathan R I", "initials": "JRI", "orcid": "0000-0002-6759-0944", "researcher": {"href": "https://publications.scilifelab.se/researcher/91f9f96c887447918926b36de9cfc820.json"}}, {"family": "Hemani", "given": "Gibran", "initials": "G", "orcid": "0000-0003-0920-1055", "researcher": {"href": "https://publications.scilifelab.se/researcher/cd71462e306f446bae17d8991b97b24e.json"}}, {"family": "van de Weijer", "given": "Margot P", "initials": "MP", "orcid": "0000-0001-9720-9481", "researcher": {"href": "https://publications.scilifelab.se/researcher/92d34b4941224694adccc703a15696dc.json"}}, {"family": "Howe", "given": "Laurence J", "initials": "LJ"}, {"family": "Palviainen", "given": "Teemu", "initials": "T", "orcid": "0000-0002-7847-8384", "researcher": {"href": "https://publications.scilifelab.se/researcher/bcbc4c92052b4819b5d7d821c0c421b0.json"}}, {"family": "Grasby", "given": "Katrina L", "initials": "KL", "orcid": "0000-0001-8539-0228", "researcher": {"href": "https://publications.scilifelab.se/researcher/a8e9d35817bc460ea594b892e5d2030e.json"}}, {"family": "Ahlskog", "given": "Rafael", "initials": "R"}, {"family": "Nygaard", "given": "Marianne", "initials": "M", "orcid": "0000-0003-0703-2665", "researcher": {"href": "https://publications.scilifelab.se/researcher/1d68eda16735460d81993dc39006d5a5.json"}}, {"family": "Cheesman", "given": "Rosa", "initials": "R", "orcid": "0000-0002-6543-0402", "researcher": {"href": "https://publications.scilifelab.se/researcher/b4c5f583a67b418cb5535f55e74a453e.json"}}, {"family": "Lim", "given": "Kai", "initials": "K"}, {"family": "Reynolds", "given": "Chandra A", "initials": "CA"}, {"family": "Ordo\u00f1ana", "given": "Juan R", "initials": "JR", "orcid": "0000-0001-7779-6017", "researcher": {"href": "https://publications.scilifelab.se/researcher/68390af477eb46efadef77a93cc2d5c1.json"}}, {"family": "Colodro-Conde", "given": "Lucia", "initials": "L", "orcid": "0000-0002-9004-364X", "researcher": {"href": "https://publications.scilifelab.se/researcher/a3d04cc447a34470a5063ae581eb9030.json"}}, {"family": "Gordon", "given": "Scott", "initials": "S", "orcid": "0000-0001-7623-328X", "researcher": {"href": "https://publications.scilifelab.se/researcher/8815739662214e75b60f71f0b1ca58a6.json"}}, {"family": "Madrid-Valero", "given": "Juan J", "initials": "JJ", "orcid": "0000-0002-3450-1159", "researcher": {"href": "https://publications.scilifelab.se/researcher/168d9ef0279a4cd792ffc3dafbc45293.json"}}, {"family": "Thalamuthu", "given": "Anbupalam", "initials": "A", "orcid": "0000-0002-7114-1260", "researcher": {"href": "https://publications.scilifelab.se/researcher/440c1694c55e4092a30a69dc495e47d9.json"}}, {"family": "Hottenga", "given": "Jouke-Jan", "initials": "JJ", "orcid": "0000-0002-5668-2368", "researcher": {"href": "https://publications.scilifelab.se/researcher/75553b594b1f4255833de730f7f7d170.json"}}, {"family": "Mengel-From", "given": "Jonas", "initials": "J", "orcid": "0000-0003-1573-8908", "researcher": {"href": "https://publications.scilifelab.se/researcher/d4dbeb78e51b441399c96921567e636f.json"}}, {"family": "Armstrong", "given": "Nicola J", "initials": "NJ", "orcid": "0000-0002-4477-293X", "researcher": {"href": "https://publications.scilifelab.se/researcher/de6e46b360454a4f8185cfa7d4ac7134.json"}}, {"family": "Sachdev", "given": "Perminder S", "initials": "PS", "orcid": "0000-0002-9595-3220", "researcher": {"href": "https://publications.scilifelab.se/researcher/7ec82937a4354f4c8247bcce974f4771.json"}}, {"family": "Lee", "given": "Teresa", "initials": "T"}, {"family": "Brodaty", "given": "Henry", "initials": "H", "orcid": "0000-0001-9487-6617", "researcher": {"href": "https://publications.scilifelab.se/researcher/fa888d67cbac4c5db0782146e17e53e0.json"}}, {"family": "Trollor", "given": "Julian N", "initials": "JN", "orcid": "0000-0002-7685-2977", "researcher": {"href": "https://publications.scilifelab.se/researcher/7b1bbca91f8345d8a1d36e1eacb18613.json"}}, {"family": "Wright", "given": "Margaret", "initials": "M", "orcid": "0000-0001-7133-4970", "researcher": {"href": "https://publications.scilifelab.se/researcher/da35d18966cb418ba5207c85b040ae98.json"}}, {"family": "Ames", "given": "David", "initials": "D"}, {"family": "Catts", "given": "Vibeke S", "initials": "VS", "orcid": "0000-0002-9892-0547", "researcher": {"href": "https://publications.scilifelab.se/researcher/2abf66f90553491f82b01293572b5ec7.json"}}, {"family": "Latvala", "given": "Antti", "initials": "A"}, {"family": "Within Family Consortium", "given": "", "initials": ""}, {"family": "Vuoksimaa", "given": "Eero", "initials": "E"}, {"family": "Mallard", "given": "Travis", "initials": "T", "orcid": "0000-0002-3265-3001", "researcher": {"href": "https://publications.scilifelab.se/researcher/de1d5003d2c641129c1f6518787bf606.json"}}, {"family": "Paige Harden", "given": "K", "initials": "K", "orcid": "0000-0002-1557-6737", "researcher": {"href": "https://publications.scilifelab.se/researcher/ed28dc61f14a48828402ba8db84d7062.json"}}, {"family": "Tucker-Drob", "given": "Elliot M", "initials": "EM", "orcid": "0000-0001-5599-6237", "researcher": {"href": "https://publications.scilifelab.se/researcher/3057f100241341d5becce265f1b983f5.json"}}, {"family": "Oskarsson", "given": "Sven", "initials": "S", "orcid": "0000-0001-8698-2866", "researcher": {"href": "https://publications.scilifelab.se/researcher/892fdebfc99b44249b90fe801db41436.json"}}, {"family": "Hammond", "given": "Christopher J", "initials": "CJ", "orcid": "0000-0002-3227-2620", "researcher": {"href": "https://publications.scilifelab.se/researcher/f17349aecfab4cb2b9b376b53c6e97aa.json"}}, {"family": "Christensen", "given": "Kaare", "initials": "K", "orcid": "0000-0002-5429-5292", "researcher": {"href": "https://publications.scilifelab.se/researcher/e79ea43d09544efc95351b52ac682910.json"}}, {"family": "Taylor", "given": "Mark", "initials": "M"}, {"family": "Lundstr\u00f6m", "given": "Sebastian", "initials": "S", "orcid": "0000-0001-7235-8499", "researcher": {"href": "https://publications.scilifelab.se/researcher/f0e069eb1cd349c4b05c11eded6dca5e.json"}}, {"family": "Larsson", "given": "Henrik", "initials": "H", "orcid": "0000-0002-6851-3297", "researcher": {"href": "https://publications.scilifelab.se/researcher/21f2cca2f6b74c5393c0fc33bcf15ee6.json"}}, {"family": "Karlsson", "given": "Robert", "initials": "R", "orcid": "0000-0002-8949-2587", "researcher": {"href": "https://publications.scilifelab.se/researcher/9df14bf33f3342408d624caa70d45b7c.json"}}, {"family": "Pedersen", "given": "Nancy L", "initials": "NL"}, {"family": "Mather", "given": "Karen A", "initials": "KA", "orcid": "0000-0003-4143-8941", "researcher": {"href": "https://publications.scilifelab.se/researcher/ec0c7f15235d4be4848b56025d5ff4f0.json"}}, {"family": "Medland", "given": "Sarah E", "initials": "SE", "orcid": "0000-0003-1382-380X", "researcher": {"href": "https://publications.scilifelab.se/researcher/da1f0230a912425c9237830be85aa642.json"}}, {"family": "Boomsma", "given": "Dorret I", "initials": "DI", "orcid": "0000-0002-7099-7972", "researcher": {"href": "https://publications.scilifelab.se/researcher/4b66ab2525fd4a468e7a4ad14c955cb4.json"}}, {"family": "Martin", "given": "Nicholas G", "initials": "NG", "orcid": "0000-0003-4069-8020", "researcher": {"href": "https://publications.scilifelab.se/researcher/1b445e5935f74fd6a71b2e92a9dac176.json"}}, {"family": "Plomin", "given": "Robert", "initials": "R", "orcid": "0000-0002-0756-3629", "researcher": {"href": "https://publications.scilifelab.se/researcher/26e3ca0c39ff4a5087146d5125e0190f.json"}}, {"family": "Bartels", "given": "Meike", "initials": "M", "orcid": "0000-0002-9667-7555", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a91c095e993411b99e81e21f40d8597.json"}}, {"family": "Lichtenstein", "given": "Paul", "initials": "P", "orcid": "0000-0003-3037-5287", "researcher": {"href": "https://publications.scilifelab.se/researcher/4db67c51837b4cdfa18cacbc3fca1173.json"}}, {"family": "Kaprio", "given": "Jaakko", "initials": "J", "orcid": "0000-0002-3716-2455", "researcher": {"href": "https://publications.scilifelab.se/researcher/814d362333844b72a70cba9ebcf61e6f.json"}}, {"family": "Eley", "given": "Thalia C", "initials": "TC", "orcid": "0000-0001-6458-0700", "researcher": {"href": "https://publications.scilifelab.se/researcher/a5eb736ac79d451c82ed6c18414ccad4.json"}}, {"family": "Davies", "given": "Neil M", "initials": "NM", "orcid": "0000-0002-2460-0508", "researcher": {"href": "https://publications.scilifelab.se/researcher/2ab6ffbb98594ea69b9fee350cc221e2.json"}}, {"family": "Munroe", "given": "Patricia B", "initials": "PB", "orcid": "0000-0002-4176-2947", "researcher": {"href": "https://publications.scilifelab.se/researcher/657544a7f921459f926aae5cd0e2065c.json"}}, {"family": "Keers", "given": "Robert", "initials": "R"}], "type": "journal article", "published": "2025-08-00", "journal": {"title": "Nat Hum Behav", "issn": "2397-3374", "volume": "9", "issue": "8", "pages": "1683-1696", "issn-l": null}, "abstract": "Individual sensitivity to environmental exposures may be genetically influenced. This genotype-by-environment interplay implies differences in phenotypic variance across genotypes, but these variants have proven challenging to detect. Genome-wide association studies of monozygotic twin differences are conducted through family-based variance analyses, which are more robust to the systemic biases that impact population-based methods. We combined data from 21,792 monozygotic twins (10,896 pairs) from 11 studies to conduct one of the largest genome-wide association study meta-analyses of monozygotic phenotypic differences, in children, adolescents and adults separately, for seven psychiatric and neurodevelopmental phenotypes: attention deficit hyperactivity disorder symptoms, autistic traits, anxiety and depression symptoms, psychotic-like experiences, neuroticism and wellbeing. The proportions of phenotypic variance explained by single-nucleotide polymorphisms in these phenotypes were estimated (h2 = 0-18%), but were imprecise. We identified 13 genome-wide significant associations (single-nucleotide polymorphisms, genes and gene sets), including genes related to stress reactivity for depression, growth factor-related genes for autistic traits and catecholamine uptake-related genes for psychotic-like experiences. This is the largest genetic study of monozygotic twins to date by an order of magnitude, evidencing an alternative method to study the genetic architecture of environmental sensitivity. The statistical power was limited for some analyses, calling for better-powered future studies.", "doi": "10.1038/s41562-025-02193-7", "pmid": "40494901", "labels": {"NGI SNP genotyping": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12367547"}, {"db": "pii", "key": "10.1038/s41562-025-02193-7"}], "notes": [], "created": "2025-09-08T11:34:10.493Z", "modified": "2025-09-08T11:34:12.043Z"}, {"entity": "publication", "iuid": "1d0370becf604d269d8bc287ea19cd6b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1d0370becf604d269d8bc287ea19cd6b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1d0370becf604d269d8bc287ea19cd6b"}}, "title": "Genetic diversity and structure among Acropora austera populations in Mozambique suggest low resilience potential of one of the world\u2019s most charismatic coral reefs", "authors": [{"family": "Duvane", "given": "Jossias Alberto", "initials": "JA", "orcid": "0009-0008-6595-3415", "researcher": {"href": "https://publications.scilifelab.se/researcher/d23044e5482b4936bb376823b8dee593.json"}}, {"family": "Dupont", "given": "Sam", "initials": "S"}, {"family": "Sola", "given": "Erwan", "initials": "E"}, {"family": "Ortega-Martinez", "given": "Olga", "initials": "O"}, {"family": "Pereyra", "given": "Ricardo T", "initials": "RT"}], "type": "journal-article", "published": "2025-08-00", "journal": {"title": "Coral Reefs", "issn": "0722-4028", "volume": "44", "issue": "4", "pages": "1185-1195", "issn-l": null}, "abstract": null, "doi": "10.1007/s00338-025-02679-w", "pmid": null, "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [], "notes": [], "created": "2025-09-08T07:17:08.995Z", "modified": "2025-09-08T07:17:09.074Z"}, {"entity": "publication", "iuid": "c0b630a30a1a46ce900790a05a054996", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c0b630a30a1a46ce900790a05a054996.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c0b630a30a1a46ce900790a05a054996"}}, "title": "Assessing Sperm Quality Parameters in Mass\u2010Spawning Norwegian Arctic Charr", "authors": [{"family": "Kurta", "given": "Khrystyna", "initials": "K", "orcid": "0000-0002-9852-1896", "researcher": {"href": "https://publications.scilifelab.se/researcher/3ba96d1e78654b6992ef1c25035e93da.json"}}, {"family": "Beir\u00e3o", "given": "Jos\u00e9", "initials": "J"}, {"family": "Thomason", "given": "Benjamin", "initials": "B"}, {"family": "Palaiokostas", "given": "Christos", "initials": "C", "orcid": "0000-0002-4480-4612", "researcher": {"href": "https://publications.scilifelab.se/researcher/a1d6c65f53a8434cb1d5dd4c7bf5d444.json"}}], "type": "journal-article", "published": "2025-08-00", "journal": {"title": "Aquaculture Fish &amp; Fisheries", "issn": "2693-8847", "volume": "5", "issue": "4", "issn-l": null}, "abstract": null, "doi": "10.1002/aff2.70111", "pmid": null, "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [], "notes": [], "created": "2025-09-08T07:02:14.701Z", "modified": "2025-09-09T13:12:28.648Z"}, {"entity": "publication", "iuid": "56d7b9a10ca7456c955235973fcb394e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/56d7b9a10ca7456c955235973fcb394e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/56d7b9a10ca7456c955235973fcb394e"}}, "title": "An east\u2013west distribution of genetic diversity in Nordic populations of caraway (Carum carvi L.) and its consequences for conservation prioritisation", "authors": [{"family": "de Haro Reyes", "given": "Bernardo", "initials": "B", "orcid": "0000-0003-0871-094X", "researcher": {"href": "https://publications.scilifelab.se/researcher/bebf9f96b8ae43d38df1dc8a4f3ac389.json"}}, {"family": "Palm\u00e9", "given": "Anna", "initials": "A", "orcid": "0000-0002-8012-8359", "researcher": {"href": "https://publications.scilifelab.se/researcher/fa8ff1168d27459e9b02b7c59afa94f0.json"}}, {"family": "Fitzgerald", "given": "Heli", "initials": "H", "orcid": "0000-0002-6754-6409", "researcher": {"href": "https://publications.scilifelab.se/researcher/79bdf20a416b49509431dd29201d28f2.json"}}, {"family": "G\u00f6ransson", "given": "Magnus", "initials": "M", "orcid": "0000-0002-0081-2207", "researcher": {"href": "https://publications.scilifelab.se/researcher/13cca49312994a8fa45dc1fb7db8a42f.json"}}, {"family": "Lyytik\u00e4inen", "given": "Virva", "initials": "V", "orcid": "0009-0006-0207-9789", "researcher": {"href": "https://publications.scilifelab.se/researcher/315e8b253f184ca081297937e28c5225.json"}}, {"family": "Madsen", "given": "Bjarke", "initials": "B", "orcid": "0000-0002-4490-8710", "researcher": {"href": "https://publications.scilifelab.se/researcher/c8a2e6641fec437f8624b6125d907bdd.json"}}, {"family": "Normand", "given": "Signe", "initials": "S", "orcid": "0000-0002-8782-4154", "researcher": {"href": "https://publications.scilifelab.se/researcher/c676988310824f518a646427dfed6600.json"}}, {"family": "Thorbj\u00f6rnsson", "given": "Hj\u00f6rtur", "initials": "H", "orcid": "0000-0003-1768-3699", "researcher": {"href": "https://publications.scilifelab.se/researcher/98e074fa60a24b3aa9ffcb54c238db8f.json"}}, {"family": "Treier", "given": "Urs Albert", "initials": "UA", "orcid": "0000-0003-4027-739X", "researcher": {"href": "https://publications.scilifelab.se/researcher/985ba0c9228a43f1a1132383266b7579.json"}}, {"family": "Hagenblad", "given": "Jenny", "initials": "J", "orcid": "0000-0002-9850-5546", "researcher": {"href": "https://publications.scilifelab.se/researcher/f8d1a751682448a3b6485cb67c6474f0.json"}}], "type": "journal-article", "published": "2025-08-00", "journal": {"title": "Conserv Genet", "issn": "1566-0621", "volume": "26", "issue": "4", "pages": "771-785", "issn-l": null}, "abstract": null, "doi": "10.1007/s10592-025-01702-5", "pmid": null, "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2025-09-08T11:30:05.435Z", "modified": "2025-11-14T11:05:47.156Z"}, {"entity": "publication", "iuid": "94bc601b34d44e4c92d9c87e8a71600f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/94bc601b34d44e4c92d9c87e8a71600f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/94bc601b34d44e4c92d9c87e8a71600f"}}, "title": "Sex-Biased Gene Expression Under Sexually Antagonistic and Sex-Limited Selection.", "authors": [{"family": "Wiberg", "given": "R Axel W", "initials": "RAW", "orcid": "0000-0002-8074-8670", "researcher": {"href": "https://publications.scilifelab.se/researcher/6e9fd2f8f36a4be4a40b87ce2b65133c.json"}}, {"family": "Zwoinska", "given": "Martyna K", "initials": "MK", "orcid": "0000-0003-3356-7284", "researcher": {"href": "https://publications.scilifelab.se/researcher/8f8ceb1ef19c4089bf685928da01b9e8.json"}}, {"family": "Kaufmann", "given": "Philipp", "initials": "P", "orcid": "0000-0002-7164-6867", "researcher": {"href": "https://publications.scilifelab.se/researcher/4214ade17fff4c30a690c13c43623ee7.json"}}, {"family": "Howie", "given": "James M", "initials": "JM", "orcid": "0000-0001-7142-5100", "researcher": {"href": "https://publications.scilifelab.se/researcher/c1e0979df2194651916b36b39b11064f.json"}}, {"family": "Immonen", "given": "Elina", "initials": "E", "orcid": "0000-0003-1121-6950", "researcher": {"href": "https://publications.scilifelab.se/researcher/f6c9af5588c64dfdacba192b65524d43.json"}}], "type": "journal article", "published": "2025-07-30", "journal": {"title": "Mol. Biol. Evol.", "issn": "1537-1719", "volume": "42", "issue": "8", "issn-l": "0737-4038"}, "abstract": "Sex differences in gene expression are ubiquitous, evolve quickly, and are expected to underlie phenotypic sexual dimorphism (SD). Despite long-standing interest, the impact of sex-specific selection on the transcriptome remains poorly understood. Here, we test fundamental questions on the role of constraints on gene expression evolution arising from the mode of selection and genetic architecture. We also test the relationship between sex-biased expression and evolved SD. We assess these using body size selection lines in the seed beetle, Callosobruchus maculatus, that have evolved variation in SD in response to either sex-limited (SL) or sexually antagonistic (SA). We find that sex differences in the phenotypic responses and expression changes are generally well aligned. SL selection, despite a phenotypic response similar to SA selection in males, but not in females, resulted in a more extensive expression differentiation and increase of sex-biased expression than SA selection. These patterns show that SA selection imposes a transcriptomic constraint and is not required for sex-bias to evolve. Sex-biased transcripts show lower cross-sex correlations in expression changes than unbiased transcripts, suggesting greater sex differences in their underlying genetic architecture. Although male-biased transcripts are disproportionately affected when selection targeted males, we find no support for a transcriptome-wide association between sex-bias and SD. In the light of these unique experimental insights into how sex-specific selection on size changes adult transcription, our findings have important implications for inferring selection history and mode from patterns of sex-biased gene expression in natural populations.", "doi": "10.1093/molbev/msaf178", "pmid": "40729508", "labels": {"National Genomics Infrastructure": "Service", "NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12371189"}, {"db": "pii", "key": "8217438"}], "notes": [], "created": "2025-11-07T07:27:03.269Z", "modified": "2025-11-28T10:50:04.075Z"}, {"entity": "publication", "iuid": "3f3eeca95ed34ac385bdad9bbf4f1a2f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3f3eeca95ed34ac385bdad9bbf4f1a2f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3f3eeca95ed34ac385bdad9bbf4f1a2f"}}, "title": "Predicting immune responsiveness in ER-positive breast cancer for personalized therapy: a population-based study.", "authors": [{"family": "Stenmark Tullberg", "given": "Axel", "initials": "A"}, {"family": "Woxlin", "given": "Sara", "initials": "S"}, {"family": "Sj\u00f6lin", "given": "Filippa", "initials": "F"}, {"family": "Ittner", "given": "Ella", "initials": "E"}, {"family": "Kov\u00e0cs", "given": "Anik\u00f2", "initials": "A"}, {"family": "Helou", "given": "Khalil", "initials": "K"}, {"family": "Holmberg", "given": "Erik", "initials": "E"}, {"family": "Karlsson", "given": "Per", "initials": "P"}], "type": "journal article", "published": "2025-07-23", "journal": {"title": "NPJ Precis Oncol", "issn": "2397-768X", "volume": "9", "issue": "1", "pages": "250", "issn-l": null}, "abstract": "The immune system's role in estrogen receptor (ER)-positive breast cancer is poorly understood. A population-based cohort of 428 breast cancer patients with clinical and molecular data was analyzed to assess how immune biomarkers can inform treatment decisions. Tumor-intrinsic immune responsiveness and local immune infiltration were quantified, and epithelial cell states were derived using EcoTyper. The interaction between ProliferativeIndex and Immunescore predicted risk of local recurrence in ER-positive tumors (HR 0.56, 95% CI 0.36-0.88, p = 0.012). EcoTyper identified two epithelial cell states, S04 and S05, with distinct immunomodulatory properties. S04 tumors showed higher proliferation, enrichment for M1 macrophages, CD8 effector T-cells, and plasma cells, alongside hypomethylation of immune-related pathways and hypermethylation of the PI3K signaling pathway. In contrast, S05-enriched tumors were associated with fibroblast activation, immune exclusion, and enrichment for glycosylation-related pathways. These findings suggest that epithelial cell states shape immune responsiveness in ER-positive breast cancer and may inform biomarker-driven treatment strategies.", "doi": "10.1038/s41698-025-01035-z", "pmid": "40702082", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12287262"}, {"db": "pii", "key": "10.1038/s41698-025-01035-z"}], "notes": [], "created": "2025-09-08T07:07:03.551Z", "modified": "2025-09-08T07:07:03.584Z"}, {"entity": "publication", "iuid": "5c371c3254f24f45930def1fa3ba5c42", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5c371c3254f24f45930def1fa3ba5c42.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5c371c3254f24f45930def1fa3ba5c42"}}, "title": "Wide-scale geographical analysis of genetic ancestry in the South African Coloured population.", "authors": [{"family": "Lankheet", "given": "Imke", "initials": "I"}, {"family": "Hammar\u00e9n", "given": "Rickard", "initials": "R", "orcid": "0000-0001-9017-591X", "researcher": {"href": "https://publications.scilifelab.se/researcher/01a7b62a04c14b99bd73fb436006e4ff.json"}}, {"family": "Alva Caballero", "given": "Luc\u00eda Ximena", "initials": "LX"}, {"family": "Larena", "given": "Maximilian", "initials": "M", "orcid": "0000-0002-8799-7645", "researcher": {"href": "https://publications.scilifelab.se/researcher/5d580f1f3e584c809f5f22d7355f154f.json"}}, {"family": "Malmstr\u00f6m", "given": "Helena", "initials": "H", "orcid": "0000-0002-6456-8055", "researcher": {"href": "https://publications.scilifelab.se/researcher/3b3397b2842142bea34c222f6683c0eb.json"}}, {"family": "Jolly", "given": "Cecile", "initials": "C"}, {"family": "Soodyall", "given": "Himla", "initials": "H"}, {"family": "de Jongh", "given": "Michael", "initials": "M"}, {"family": "Schlebusch", "given": "Carina", "initials": "C", "orcid": "0000-0002-8160-9621", "researcher": {"href": "https://publications.scilifelab.se/researcher/682f10853c1145649b8c76680605dd9b.json"}}], "type": "journal article", "published": "2025-07-22", "journal": {"title": "BMC Biol.", "issn": "1741-7007", "volume": "23", "issue": "1", "pages": "219", "issn-l": "1741-7007"}, "abstract": "The South African Coloured (SAC) population, a prominent admixed population in South Africa, reflects centuries of migration, admixture, and historical segregation. Descendants of local Khoe-San and Bantu-speaking populations, European settlers, and enslaved individuals from Africa and Asia, SAC individuals embody diverse ancestries. This study investigates the genetic makeup of SAC individuals, utilizing autosomal genotypes, mitochondrial DNA and Y-chromosome data. We analyse new genotype data for 125 SAC individuals from seven locations.\n\nOur analysis, based on a dataset comprising 356 SAC individuals from 22 geographic locations, revealed significant regional variations in ancestry. Khoe-San ancestry predominates in 14 locations, highlighting its lasting influence. Inland regions exhibit higher proportions of Khoe-San ancestry, eastern regions show more Bantu-speaker/West African ancestry, and western/coastal areas, particularly around Cape Town, display increased Asian ancestry. Additionally, sex-biased admixture ratios show male-biased admixture from East Africans and Europeans, and female-biased admixture from Khoe-San populations, which is supported by mitochondrial and Y-chromosome data.\n\nThe observed patterns of significant regional variation in ancestry reflect historical migrations and settlement patterns. This research underscores the importance of studying the SAC population to understand South Africa's historical migrations, providing insights into the complex genetic heritage of South Africans.", "doi": "10.1186/s12915-025-02317-5", "pmid": "40696318", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service", "NGI SNP genotyping": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12281806"}, {"db": "pii", "key": "10.1186/s12915-025-02317-5"}], "notes": [], "created": "2025-08-19T13:34:50.043Z", "modified": "2025-11-14T11:08:46.149Z"}, {"entity": "publication", "iuid": "ec61d27d2c1246fd953c84e68a7f1129", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ec61d27d2c1246fd953c84e68a7f1129.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ec61d27d2c1246fd953c84e68a7f1129"}}, "title": "Interplay between antipredator behavior, parasitism, and gut microbiome in wild stickleback populations.", "authors": [{"family": "Varg", "given": "Javier Edo", "initials": "JE", "orcid": "0000-0002-7895-4563", "researcher": {"href": "https://publications.scilifelab.se/researcher/72cb1019516e49f7b8f39b18924babc2.json"}}, {"family": "Brealey", "given": "Jaelle C", "initials": "JC", "orcid": "0000-0001-7068-2017", "researcher": {"href": "https://publications.scilifelab.se/researcher/eeb2930d582f4483afc1f5bd52e37818.json"}}, {"family": "Benha\u00efm", "given": "David", "initials": "D"}, {"family": "Losada-Germain", "given": "Rafael", "initials": "R"}, {"family": "Boughman", "given": "Janette W", "initials": "JW"}], "type": "journal article", "published": "2025-07-19", "journal": {"title": "NPJ Biofilms Microbiomes", "issn": "2055-5008", "volume": "11", "issue": "1", "pages": "138", "issn-l": "2055-5008"}, "abstract": "The impact of microbial composition on stress-related behavior in aquatic organisms is poorly understood. This study explored the link between antipredator behavior, parasitism, and the gut microbiome in wild stickleback from two lakes: clear, spring-fed Galtab\u00f3l and turbid, glacial-fed \u00deristikla. Behavioral analysis revealed differences between populations, with each exhibiting unique baseline behaviors. Microbiome analysis showed that a small proportion of its variation was explained by population, likely reflecting differences in lake environments. Only the marine genus Pseudoalteromonas abundance differed between populations. Our findings suggest that behavior and microbiome correlations may primarily reflect environmental adaptations and parasite status rather than direct gut-brain interactions. However, some tentative evidence suggests a potential innate connection between some antipredator behavior and microbiome composition. The study highlights the complexity of the gut-brain axis in wild populations and suggests future research directions, including experimental manipulations to uncover causal relationships between microbiome composition and behavior.", "doi": "10.1038/s41522-025-00758-y", "pmid": "40683872", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12276351"}, {"db": "pii", "key": "10.1038/s41522-025-00758-y"}], "notes": [], "created": "2025-09-08T11:37:13.990Z", "modified": "2025-09-09T13:13:05.326Z"}, {"entity": "publication", "iuid": "3a670a7d749a49c1bc72990a94337d2a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3a670a7d749a49c1bc72990a94337d2a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3a670a7d749a49c1bc72990a94337d2a"}}, "title": "Sequencing airborne DNA to monitor crop pathogens and pests.", "authors": [{"family": "Mikko", "given": "Amanda", "initials": "A"}, {"family": "Villegas", "given": "Jose Antonio", "initials": "JA"}, {"family": "Svensson", "given": "Daniel", "initials": "D"}, {"family": "Karlsson", "given": "Edvin", "initials": "E"}, {"family": "Esseen", "given": "Per-Anders", "initials": "PA"}, {"family": "Albrectsen", "given": "Benedicte Riber", "initials": "BR"}, {"family": "Lundin", "given": "Ola", "initials": "O"}, {"family": "Forsman", "given": "Mats", "initials": "M"}, {"family": "Berlin", "given": "Anna", "initials": "A"}, {"family": "Stenberg", "given": "Per", "initials": "P", "orcid": "0000-0003-4738-4788", "researcher": {"href": "https://publications.scilifelab.se/researcher/3e9b9949cf994f6c93d60261eb530d1b.json"}}], "type": "journal article", "published": "2025-07-18", "journal": {"title": "iScience", "issn": "2589-0042", "pages": "112912", "volume": "28", "issue": "7", "issn-l": "2589-0042"}, "abstract": "Crop pests and diseases increasingly challenge the global food system. To prepare for and detect outbreaks, surveillance plays an important role. Traditional monitoring methods are often organism-specific, making large-scale monitoring of crop pathogens and pests impractical. We here investigate the potential for using shotgun sequencing of airborne eDNA for large-scale surveillance of crop pathogens and pests. We show that it is possible to detect DNA from all types of organisms in air, and that DNA can be classified down to species level. However, the accuracy of the identification is highly dependent on the quality of reference genomes of both the pathogens or pests, and their close relatives present in the region. Finally, we find that observed degree of crop damages correlate with amount of DNA from crop pathogens and pests in air, showing the promise of this approach for surveillance of all types of crop pathogens and pests.", "doi": "10.1016/j.isci.2025.112912", "pmid": "40678541", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12269458"}, {"db": "pii", "key": "S2589-0042(25)01173-3"}], "notes": [], "created": "2025-06-30T07:24:39.046Z", "modified": "2025-11-14T11:06:13.683Z"}, {"entity": "publication", "iuid": "d936680b828c47f8a2753c7de07ce0de", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d936680b828c47f8a2753c7de07ce0de.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d936680b828c47f8a2753c7de07ce0de"}}, "title": "DNA Methylation Reflects Cis-Genetic Differentiation Across the European Crow Hybrid Zone.", "authors": [{"family": "Merondun", "given": "Justin", "initials": "J", "orcid": "0000-0001-5077-4096", "researcher": {"href": "https://publications.scilifelab.se/researcher/38e6336366e1418685f36244f39ecde6.json"}}, {"family": "Wolf", "given": "Jochen B W", "initials": "JBW", "orcid": "0000-0002-2958-5183", "researcher": {"href": "https://publications.scilifelab.se/researcher/6c4445d760a64905a9ea6d8664f6a32d.json"}}], "type": "journal article", "published": "2025-07-10", "journal": {"title": "Mol. Ecol.", "issn": "1365-294X", "issn-l": "0962-1083", "volume": "34", "issue": "21", "pages": "e70026"}, "abstract": "Chromatin modifications provide a substrate for epigenetic variation with evolutionary potential. To quantify the contribution of this layer of variation during speciation in crows, we leveraged genome and methylome sequencing data from an incipient avian species: all-black carrion crows, grey-coated hooded crows, and their hybrids. Combining controlled experimentation under common garden conditions and sampling of natural genetic variation across the hybrid zone, we show that 5mC methylation variation was largely explained by genome properties and the ontogenetic programme of the organism. Taxonomically related methylation divergence clustered in intergenic space, with the only genomic region of strongly elevated genetic differentiation encoding the diagnostic colour contrast between taxa. We conclude that methylation variation with relevance to speciation largely follows cis-genetic polymorphism in this system and does not constitute an autonomous axis of evolution.", "doi": "10.1111/mec.70026", "pmid": "40637207", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [], "notes": [], "created": "2025-09-08T06:59:29.504Z", "modified": "2025-11-03T08:42:37.319Z"}, {"entity": "publication", "iuid": "0711daac3c544b8fb60416da8e9cb152", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0711daac3c544b8fb60416da8e9cb152.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0711daac3c544b8fb60416da8e9cb152"}}, "title": "Bladder cancer subtypes exhibit limited plasticity across different microenvironments and in metastases.", "authors": [{"family": "Bernardo", "given": "Carina", "initials": "C"}, {"family": "Chattopadhyay", "given": "Subhayan", "initials": "S"}, {"family": "Andersson", "given": "Natalie", "initials": "N"}, {"family": "Eriksson", "given": "Pontus", "initials": "P"}, {"family": "Medle", "given": "Benjamin", "initials": "B"}, {"family": "Tran", "given": "Lena", "initials": "L"}, {"family": "Dain Marzouka", "given": "Nour Al", "initials": "NA"}, {"family": "Mattsson", "given": "Adam", "initials": "A"}, {"family": "Zadoroznyj", "given": "Aymeric", "initials": "A"}, {"family": "Larsson", "given": "Malin", "initials": "M"}, {"family": "Liedberg", "given": "Fredrik", "initials": "F"}, {"family": "H\u00f6glund", "given": "Mattias", "initials": "M"}, {"family": "Sj\u00f6dahl", "given": "Gottfrid", "initials": "G"}], "type": "journal article", "published": "2025-07-02", "journal": {"title": "Exp Hematol Oncol", "issn": "2162-3619", "volume": "14", "issue": "1", "pages": "91", "issn-l": null}, "abstract": "Transcriptomic and genomic analyses of bladder cancer (BC) reveal a highly diverse disease stratified into molecular subtypes with distinct molecular features and biological behaviors. Intratumor heterogeneity (ITH) and plasticity can significantly impact diagnosis and patient management, yet their extent in BC remains highly debated. Here, we investigated whether the three main bladder cancer subtypes maintain or alter their identity in response to changes in the microenvironment and during metastatic colonization.\n\nSeven patient-derived xenograft (PDX) models representing the major BC subtypes were propagated into three distinct tissue microenvironments: subcutaneous, mammary fat pad and under the kidney capsule. Metastatic lesions were generated via systemic injection of tumor cells. Tumor samples were analysed using RNA- and exome sequencing, SNP-arrays and histopathology to assess subtype fidelity, genomic evolution, and clonal dynamics.\n\nA comprehensive, longitudinal multiomics analysis showed that tumors consistently maintain their molecular subtype, as well as their transcriptomic and genomic profiles, across different environments. No evidence of emerging ITH or subtype transitions was observed, regardless of the microenvironment. The transcriptomic adaptations observed in metastases and different implantation sites are limited and are associated primarily with hypoxia, epithelial-mesenchymal transition (EMT), and invasion.\n\nOur results suggest that invasive bladder cancers have a strong intrinsic tumor identity that is not easily reprogrammed by the microenvironment.", "doi": "10.1186/s40164-025-00682-z", "pmid": "40605119", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics (NBIS)": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "NGI Short read": "Service", "NGI SNP genotyping": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Clinical Genomics Lund": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12225047"}, {"db": "pii", "key": "10.1186/s40164-025-00682-z"}], "notes": [], "created": "2025-08-22T08:26:48.445Z", "modified": "2025-11-12T06:56:23.529Z"}, {"entity": "publication", "iuid": "a934d3358dd642a89a636f574a2204fb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a934d3358dd642a89a636f574a2204fb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a934d3358dd642a89a636f574a2204fb"}}, "title": "Associations between carotid artery intima-media thickness, traditional risk factors and proteins", "authors": [{"family": "Lind", "given": "Lars", "initials": "L"}, {"family": "Zheng", "given": "Rui", "initials": "R"}], "type": "journal-article", "published": "2025-07-02", "journal": {"title": "npj Cardiovasc Health", "issn": "2948-2836", "issn-l": null, "volume": "2", "issue": "1", "pages": null}, "abstract": null, "doi": "10.1038/s44325-025-00073-7", "pmid": null, "labels": {"Affinity Proteomics Uppsala": "Service", "National Genomics Infrastructure": "Service", "NGI Proteomics": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [], "notes": [], "created": "2025-11-25T19:18:59.510Z", "modified": "2025-11-26T11:05:15.077Z"}, {"entity": "publication", "iuid": "cc07bc3e7dbc4945b766931b0ee2f31a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/cc07bc3e7dbc4945b766931b0ee2f31a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/cc07bc3e7dbc4945b766931b0ee2f31a"}}, "title": "The interplay of genetics and fatty acid metabolism: exploring their impact on metabolic syndrome in Swedish men.", "authors": [{"family": "Oskarsdottir", "given": "Harpa", "initials": "H"}, {"family": "Palsson", "given": "Arnar", "initials": "A"}, {"family": "Olafsdottir", "given": "Erla B", "initials": "EB"}, {"family": "Giedraitis", "given": "Vilmantas", "initials": "V"}, {"family": "Mohammad", "given": "Salahuddin", "initials": "S"}, {"family": "Ris\u00e9rus", "given": "Ulf", "initials": "U"}, {"family": "Schi\u00f6th", "given": "Helgi B", "initials": "HB"}, {"family": "Skuladottir", "given": "Gudrun V", "initials": "GV"}, {"family": "Mwinyi", "given": "Jessica", "initials": "J"}], "type": "journal article", "published": "2025-07-01", "journal": {"title": "Nutr J", "issn": "1475-2891", "volume": "24", "issue": "1", "pages": "99", "issn-l": "1475-2891"}, "abstract": "Genetic risk variants for obesity and metabolic syndrome (MetS) have been identified, but their link to relevant metabolic health parameters warrants further attention. This study aimed to investigate the extent to which single-nucleotide polymorphisms (SNPs) associated with obesity are linked to changes in fatty acid (FA) profiles in serum cholesteryl esters, lipid metabolism, and MetS risk.\n\nData from the Uppsala Longitudinal Study of Adult Men (ULSAM), conducted in men at age 50 (N = 1973) and age 70 (N = 982), were used to investigate SNPs associated with body mass index (BMI) in genome-wide association studies with metabolic parameters at age 50. The significant SNPs and associated lipid parameters were then used as predictors of MetS over a 20-year follow-up period, at age 70 in binary regression models.\n\nThe two genes, the brain-derived neurotrophic factor gene (BDNF) (rs7103411) and the fat mass and obesity-associated gene (FTO) (rs1558902), together with delta-5-desaturase (D5D) activity, 20:5n-3 in serum cholesteryl esters (CE), fasting blood glucose, abdominal skinfold thickness, apolipoprotein-B, and high-density lipoprotein cholesterol (HDL-C) at age 50, significantly predicted the risk of MetS at age 70.\n\nThe findings suggest a considerable contribution of the SNPs BDNF rs7103411, FTO rs1558902, and ETV5 rs9816226, along with low D5D activities and serum levels of HDL-C in men at age 50, to the risk for MetS 20 years later.", "doi": "10.1186/s12937-025-01168-8", "pmid": "40598589", "labels": {"NGI SNP genotyping": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12210471"}, {"db": "pii", "key": "10.1186/s12937-025-01168-8"}], "notes": [], "created": "2025-09-08T07:04:09.137Z", "modified": "2025-09-08T07:04:09.166Z"}, {"entity": "publication", "iuid": "1402afcac4d540aca64003dddf86e9be", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1402afcac4d540aca64003dddf86e9be.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1402afcac4d540aca64003dddf86e9be"}}, "title": "A high polygenic risk score is associated with SSA/SSB antibody positivity and early onset in primary Sj\u00f6gren's disease.", "authors": [{"family": "Fugmann", "given": "Cecilia", "initials": "C", "orcid": "0009-0005-6078-8826", "researcher": {"href": "https://publications.scilifelab.se/researcher/afc6666ee2204df6b3f8f84f58f89c81.json"}}, {"family": "Reid", "given": "Sarah", "initials": "S"}, {"family": "Pucholt", "given": "Pascal", "initials": "P", "orcid": "0000-0003-3342-1373", "researcher": {"href": "https://publications.scilifelab.se/researcher/61a214ff2d494b568cb6da944e858acf.json"}}, {"family": "Kvarnstr\u00f6m", "given": "Marika", "initials": "M"}, {"family": "Bj\u00f6rk", "given": "Albin", "initials": "A"}, {"family": "Mofors", "given": "Johannes", "initials": "J", "orcid": "0000-0003-1873-7169", "researcher": {"href": "https://publications.scilifelab.se/researcher/4db00a3d9a5b49e9b86cec83a76bbfe2.json"}}, {"family": "Sj\u00f6wall", "given": "Christopher", "initials": "C", "orcid": "0000-0003-0900-2048", "researcher": {"href": "https://publications.scilifelab.se/researcher/fe4dd47b8ca1436e8a26fdea33f5e7f6.json"}}, {"family": "Eriksson", "given": "Per", "initials": "P"}, {"family": "Olsson", "given": "Peter", "initials": "P"}, {"family": "Mandl", "given": "Thomas", "initials": "T", "orcid": "0000-0002-7143-7088", "researcher": {"href": "https://publications.scilifelab.se/researcher/b72a91b349c148c9b9b59028d079217d.json"}}, {"family": "Forsblad-d'Elia", "given": "Helena", "initials": "H", "orcid": "0000-0001-7871-5303", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a0765b2c9d64087bd9ad36bd473968e.json"}}, {"family": "Magnusson Bucher", "given": "Sara", "initials": "S"}, {"family": "Johnsen", "given": "Svein Joar", "initials": "SJ", "orcid": "0000-0002-1591-9250", "researcher": {"href": "https://publications.scilifelab.se/researcher/1fcaa1c5f1164f9d87e856a6eafb9e2c.json"}}, {"family": "Norheim", "given": "Katrine Br\u00e6kke", "initials": "KB"}, {"family": "Appel", "given": "Silke", "initials": "S", "orcid": "0000-0002-2199-2315", "researcher": {"href": "https://publications.scilifelab.se/researcher/eebec3871f18492b9f5047fd5add422b.json"}}, {"family": "Hammenfors", "given": "Daniel", "initials": "D"}, {"family": "Jensen", "given": "Janicke Liaaen", "initials": "JL", "orcid": "0000-0003-4276-9611", "researcher": {"href": "https://publications.scilifelab.se/researcher/773434ab6d4845d187376dd8cc972d8b.json"}}, {"family": "Palm", "given": "\u00d8yvind", "initials": "\u00d8"}, {"family": "Omdal", "given": "Roald", "initials": "R"}, {"family": "Jonsson", "given": "Roland", "initials": "R", "orcid": "0000-0002-9588-0260", "researcher": {"href": "https://publications.scilifelab.se/researcher/f6edb43a7da34bf9af85c876b1b8974a.json"}}, {"family": "Baecklund", "given": "Eva", "initials": "E", "orcid": "0000-0001-5033-0188", "researcher": {"href": "https://publications.scilifelab.se/researcher/203b156cd5b3427aac72efeb47a89c96.json"}}, {"family": "Wahren-Herlenius", "given": "Marie", "initials": "M", "orcid": "0000-0002-0915-7245", "researcher": {"href": "https://publications.scilifelab.se/researcher/a8451e7f5e6e4e4da0bace3dfafaeb38.json"}}, {"family": "Leonard", "given": "Dag", "initials": "D", "orcid": "0000-0002-6275-7282", "researcher": {"href": "https://publications.scilifelab.se/researcher/42ed25c2f495484db4757f4fef51abae.json"}}, {"family": "Imgenberg-Kreuz", "given": "Juliana", "initials": "J", "orcid": "0000-0002-7230-8990", "researcher": {"href": "https://publications.scilifelab.se/researcher/5d4c2f630d484ee780c2c12aaabdb939.json"}}, {"family": "Nordmark", "given": "Gunnel", "initials": "G", "orcid": "0000-0002-3829-7431", "researcher": {"href": "https://publications.scilifelab.se/researcher/188fda53498740dbb007441cc94bb1ad.json"}}], "type": "journal article", "published": "2025-07-01", "journal": {"title": "Rheumatology (Oxford)", "issn": "1462-0332", "volume": "64", "issue": "7", "pages": "4341-4346", "issn-l": "1462-0324"}, "abstract": "To calculate a polygenic risk score (PRS) based on single nucleotide variants (SNVs) previously associated with primary Sj\u00f6gren's disease (SjD) with genome-wide significance and determine the genetic risk for SjD stratified by antibodies, sex and age at diagnosis.\n\nPatients with SjD (n = 1065) were genotyped using Illumina OmniExpressExome chip. Control genotype data were available (n = 7742). Two PRSs were constructed, one including HLA gene variants (n = 21 SNVs), and one without HLA (n = 18 SNVs). High PRS quartile (Q4) individuals were compared with low PRS (Q1-3).\n\nA high PRS was associated with SSA antibody-positive SjD (OR 9.16, 95% CI 7.75-10.85, P = 3.7 \u00d7 10-146), and strengthened in SjD positive for both SSA/SSB antibodies (OR 13.67, 95% CI 10.88-17.32, P = 4.6 \u00d7 10-108). High PRS classified SSA/SSB antibody-positive SjD with very good accuracy (AUC 0.86). PRS without HLA showed a weaker association with SSA/SSB positive SjD (OR 2.09, 95% CI 1.71-2.55, P = 6.4 \u00d7 10-13). Antibody negative SjD displayed a PRS similar to controls. Patients in the high PRS quartile were significantly younger at diagnosis, 48.9 \u00b1 14.9 vs 53.4 \u00b1 13.4 years in the low PRS quartiles (Q1-3), P = 2.2 \u00d7 10-6, and presented higher frequencies of ANA, SSA and SSA/SSB antibodies, P < 1 \u00d7 10-5.\n\nA high PRS is associated with SSA/SSB antibody positivity and early disease onset, both largely attributed to the weight of the HLA alleles. Integration of PRS with other biomarkers applied to clinical phenotypes could be a useful tool for disease risk stratification and treatment decisions.", "doi": "10.1093/rheumatology/keae693", "pmid": "39693120", "labels": {"NGI SNP genotyping": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12212914"}, {"db": "pii", "key": "7927842"}], "notes": [], "created": "2025-07-02T12:44:52.822Z", "modified": "2025-11-14T11:07:58.575Z"}, {"entity": "publication", "iuid": "109d08b7139947779a648f3aea19ed7a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/109d08b7139947779a648f3aea19ed7a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/109d08b7139947779a648f3aea19ed7a"}}, "title": "Genetic structure and diversity of the declining orchid Gymnadenia conopsea in Scandinavia: implications for conservation and management", "authors": [{"family": "S\u00f6derquist", "given": "Linus", "initials": "L", "orcid": "0000-0002-9894-4119", "researcher": {"href": "https://publications.scilifelab.se/researcher/6a0c370d6402423284ea40a2f51179ae.json"}}, {"family": "Joffard", "given": "Nina", "initials": "N", "orcid": "0000-0003-3712-6080", "researcher": {"href": "https://publications.scilifelab.se/researcher/fae9d351d1d14a129908a73c37ff5728.json"}}, {"family": "Scofield", "given": "Douglas G", "initials": "DG", "orcid": "0000-0001-5235-6461", "researcher": {"href": "https://publications.scilifelab.se/researcher/62a8063a48a446a7947d55f9900894a6.json"}}, {"family": "Milesi", "given": "Pascal", "initials": "P", "orcid": "0000-0001-8580-4291", "researcher": {"href": "https://publications.scilifelab.se/researcher/1f59e048cc6a4159a1829885b370d978.json"}}, {"family": "Karrenberg", "given": "Sophie", "initials": "S", "orcid": "0000-0002-7146-588X", "researcher": {"href": "https://publications.scilifelab.se/researcher/3a982636b44f4b93b7ec0bd64e5d6bfb.json"}}, {"family": "Sletvold", "given": "Nina", "initials": "N", "orcid": "0000-0002-9868-3449", "researcher": {"href": "https://publications.scilifelab.se/researcher/e342483c6e3f44c29453f9bc5ce5bb05.json"}}], "type": "journal-article", "published": "2025-07-00", "journal": {"title": "Ecography", "issn": "0906-7590", "volume": "2025", "issue": "7", "issn-l": null}, "abstract": null, "doi": "10.1111/ecog.07628", "pmid": null, "labels": {"NGI SNP genotyping": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2025-09-08T11:33:58.539Z", "modified": "2025-11-28T10:51:06.434Z"}, {"entity": "publication", "iuid": "3f5a358c368e430a9e7513509782e6dd", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3f5a358c368e430a9e7513509782e6dd.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3f5a358c368e430a9e7513509782e6dd"}}, "title": "Genetic markers associated with bone strength and density in Rhode Island Red laying hens.", "authors": [{"family": "Yue", "given": "Qiaoxian", "initials": "Q"}, {"family": "Johnsson", "given": "Martin", "initials": "M"}, {"family": "Wilson", "given": "Peter W", "initials": "PW"}, {"family": "Andersson", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Schmutz", "given": "Matthias", "initials": "M"}, {"family": "Benavides", "given": "Cristina", "initials": "C"}, {"family": "Dominguez-Gasca", "given": "Nazaret", "initials": "N"}, {"family": "Sanchez-Rodriguez", "given": "Estefania", "initials": "E"}, {"family": "Rodriguez-Navarro", "given": "Alejandro B", "initials": "AB"}, {"family": "Dunn", "given": "Ian C", "initials": "IC"}, {"family": "de Koning", "given": "Dirk-Jan", "initials": "DJ"}], "type": "journal article", "published": "2025-07-00", "journal": {"title": "Poult. Sci.", "issn": "1525-3171", "volume": "104", "issue": "7", "pages": "105246", "issn-l": "0032-5791"}, "abstract": "Damage to the keel bone in commercial laying hens represent one of the greatest welfare issues in laying hens. This study aims to identify the DNA markers and candidate genes for bone strength and density traits in a Rhode Island Red laying hen population. We conducted genome-wide association studies (GWAS) on bone quality traits using a sample of 925 Rhode Island Red laying hens genotyped with a genotyping array consisting of 60 000 DNA markers. With a univariate linear mixed model, we identified 52 suggestive genetic markers located within 28 candidate genes that are associated with the humerus, keel, and tibia strength and density. We also found overlaps between the GWAS results for medullary bone score and tibia strength and density with published quantitative trait loci (QTL) for eggshell effective layer thickness and abdominal fat weight, respectively. Heritability estimates for the humerus stiffness, tibia stiffness, medullary bone score and minor bone diameter ranged from 0.21 to 0.34. Annotation term enrichment analysis of genes within 2 Megabases of suggestive markers found that mTOR signalling pathway, tryptophan metabolism, TGF-\u03b2 signalling pathway, and apoptosis were significantly enriched. These loci do not overlap previously published associations, and thus appear to be novel.", "doi": "10.1016/j.psj.2025.105246", "pmid": "40339236", "labels": {"NGI SNP genotyping": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12138422"}, {"db": "pii", "key": "S0032-5791(25)00488-2"}], "notes": [], "created": "2025-09-08T07:15:20.568Z", "modified": "2025-09-08T07:15:20.576Z"}, {"entity": "publication", "iuid": "e5847a1ccb154e33b092ebbb525beec4", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e5847a1ccb154e33b092ebbb525beec4.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e5847a1ccb154e33b092ebbb525beec4"}}, "title": "Genetic and Environmental Effects on Parent-Rated Adaptive Behaviour in Infancy.", "authors": [{"family": "Halkola", "given": "Hanna", "initials": "H", "orcid": "0000-0002-2474-0682", "researcher": {"href": "https://publications.scilifelab.se/researcher/d7f3e7c9f77645678b82928153a60bd1.json"}}, {"family": "Viktorsson", "given": "Charlotte", "initials": "C", "orcid": "0000-0003-2727-2957", "researcher": {"href": "https://publications.scilifelab.se/researcher/465e2969410c4109aaa466735d26002b.json"}}, {"family": "Jones", "given": "Emily J H", "initials": "EJH"}, {"family": "Charman", "given": "Tony", "initials": "T", "orcid": "0000-0003-1993-6549", "researcher": {"href": "https://publications.scilifelab.se/researcher/bec55e31a33d40f688e58a0436ae92c9.json"}}, {"family": "Falck-Ytter", "given": "Terje", "initials": "T"}, {"family": "Bussu", "given": "Giorgia", "initials": "G"}], "type": "journal article", "published": "2025-07-00", "journal": {"title": "Dev Sci", "issn": "1467-7687", "volume": "28", "issue": "4", "pages": "e70041", "issn-l": null}, "abstract": "Adaptive behaviour refers to the everyday skills that individuals are expected to have to function independently, based on their age and societal norms. Currently, we know little about the role of genetic and environmental factors in parent-rated adaptive behaviours in early infancy. The aim of this study was to investigate the aetiological factors that influence individual variability in different adaptive behaviour domains at 5 months, and the degree of genetic and environmental influences that are unique and shared across these domains. We analysed data from the Vineland Adaptive Behaviour Scale (VABS-II) motor domain and combined domain of socialization and communication (social-communication) using a multivariate twin modelling approach. Participants were a community sample of monozygotic and dizygotic twins assessed at 5 months of age (n = 594). The results show high shared environmental influence on both motor (0.67) and social-communication (0.78) domains with 45% shared variance. Both had low, but significant heritability estimates (0.21 and 0.12, respectively) but did not share genetic variance. No statistically significant associations were found between polygenic scores for autism, ADHD, schizophrenia, depression, and bipolar disorder, and either of the adaptive behaviours measured here. Our results highlight the importance of shared environmental factors in the development of social-communication and motor skills in infancy, whether it is through social interaction with caregivers, or the stimuli and opportunities presented at home. SUMMARY: During development structural arm length representation is underestimated, while the functional arm length representation is overestimated. Underestimation of structural arm length is driven by an underestimation of hand length, as forearm length is accurate. Structural hand length is underestimated, supporting that underestimation of hand length is a characteristic of human body representation. The opposite pattern of results between structural and functional arm representation suggests the existence of multiple independent representations of the body.", "doi": "10.1111/desc.70041", "pmid": "40537989", "labels": {"NGI SNP genotyping": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12179425"}], "notes": [], "created": "2025-09-08T11:34:03.298Z", "modified": "2025-09-08T11:34:03.476Z"}, {"entity": "publication", "iuid": "e0d1dc8451a44076825e43da0bc8506c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e0d1dc8451a44076825e43da0bc8506c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e0d1dc8451a44076825e43da0bc8506c"}}, "title": "Ex vivo drug responses and molecular profiles of 597 pediatric acute lymphoblastic leukemia patients.", "authors": [{"family": "Enblad", "given": "Anna Pia", "initials": "AP"}, {"family": "Krali", "given": "Olga", "initials": "O"}, {"family": "Gezelius", "given": "Henrik", "initials": "H"}, {"family": "Lundmark", "given": "Anders", "initials": "A"}, {"family": "Blom", "given": "Kristin", "initials": "K"}, {"family": "Andersson", "given": "Claes", "initials": "C"}, {"family": "Palle", "given": "Josefine", "initials": "J"}, {"family": "Frost", "given": "Britt-Marie", "initials": "BM"}, {"family": "Ryh\u00e4nen", "given": "Samppa", "initials": "S"}, {"family": "Fl\u00e6gstad", "given": "Trond", "initials": "T"}, {"family": "J\u00f3nsson", "given": "\u00d3lafur G", "initials": "\u00d3G"}, {"family": "Schmiegelow", "given": "Kjeld", "initials": "K"}, {"family": "Heyman", "given": "Mats", "initials": "M"}, {"family": "Harila", "given": "Arja", "initials": "A"}, {"family": "Nygren", "given": "Peter", "initials": "P"}, {"family": "Larsson", "given": "Rolf", "initials": "R"}, {"family": "L\u00f6nnerholm", "given": "Gudmar", "initials": "G"}, {"family": "Nordlund", "given": "Jessica", "initials": "J", "orcid": "0000-0001-8699-9959", "researcher": {"href": "https://publications.scilifelab.se/researcher/ddf48c9262134821bcc6ce1180049753.json"}}], "type": "journal article", "published": "2025-07-00", "journal": {"title": "Hemasphere", "issn": "2572-9241", "volume": "9", "issue": "7", "pages": "e70176", "issn-l": null}, "abstract": "Ex vivo drug response profiling is emerging as a valuable tool for identifying drug resistance mechanisms and advancing precision medicine in hematological cancers. However, the functional impact of dysregulation of the epigenome and transcriptome in this context remains poorly understood. In this study, we combined ex vivo drug sensitivity profiling with transcriptomic and epigenomic analyses in diagnostic samples from 597 pediatric B-cell precursor acute lymphoblastic leukemia (BCP-ALL) patients. Ex vivo resistance to antimetabolites (e.g., cytarabine, thioguanine), glucocorticoids (e.g., dexamethasone, prednisolone), and doxorubicin was independently associated with reduced relapse-free survival (P < 0.05). Molecular profiling identified pretreatment DNA methylation and gene expression patterns distinguishing resistant from sensitive cases, revealing key drug resistance signatures. These included aberrant expression of genes related to heme metabolism (e.g., ATPV06A) and KRAS signaling (e.g., GS02). Notably, we also observed atypical expression of genes usually restricted to T cells and other immune cells (e.g., ITK) in resistant BCP-ALL cells. Our findings demonstrate that ex vivo drug response patterns are predictive of clinical outcomes and reflect intrinsic molecular states associated with drug tolerance. This integrative multi-omics approach highlights potential therapeutic targets and underscores the value of functional precision medicine in identifying treatment vulnerabilities in pediatric ALL.", "doi": "10.1002/hem3.70176", "pmid": "40727946", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12301861"}, {"db": "pii", "key": "HEM370176"}], "notes": [], "created": "2025-09-08T07:17:19.785Z", "modified": "2025-11-28T10:40:21.057Z"}, {"entity": "publication", "iuid": "d7516c3dcf1d40f885a03f6e3f2e3c26", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d7516c3dcf1d40f885a03f6e3f2e3c26.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d7516c3dcf1d40f885a03f6e3f2e3c26"}}, "title": "Genomic Analysis of Trichotillomania.", "authors": [{"family": "Halvorsen", "given": "Matthew W", "initials": "MW"}, {"family": "Garrett", "given": "Melanie E", "initials": "ME"}, {"family": "Cuccaro", "given": "Michael L", "initials": "ML"}, {"family": "Ashley-Koch", "given": "Allison E", "initials": "AE"}, {"family": "Crowley", "given": "James J", "initials": "JJ"}], "type": "journal article", "published": "2025-06-13", "journal": {"title": "Am. J. Med. Genet. B Neuropsychiatr. Genet.", "issn": "1552-485X", "pages": "e33035", "issn-l": "1552-4841"}, "abstract": "Trichotillomania (TTM) is a psychiatric condition in which people feel an overwhelming urge to pull out their hair, resulting in noticeable hair loss and significant distress. Twin and family studies suggest that TTM is at least partly genetic, but no genome-wide analyses have been completed. To fill the gap in this field, we have conducted a case-control study of genotype array data from 101 European ancestry TTM cases and 488 ancestry-matched unaffected controls. TTM cases were ascertained in the United States through web-based recruitment, patient support groups, and conferences organized by the Trichotillomania Learning Center. Following clinical confirmation of a TTM diagnosis, patients completed self-report assessments of frequency and duration of hair pulling, other psychiatric symptoms, and family history. Unaffected controls were also ascertained in the United States and were matched to cases by ancestry. In the first formal genome-wide association study of TTM, we did not identify any common variants with a genome-wide significant (p < 5 \u00d7 10-8) association level with case status. We found that cases carry a higher load of common polygenic risk for psychiatric disorders (p = 0.008). We also detected copy number variants previously associated with neuropsychiatric disorders (specifically, deletions in NRXN1, CSMD1, and 15q11.2). These results further support genetics' role in the etiology of TTM and suggest that larger studies are likely to identify risk variation and, ultimately, specific risk genes associated with the condition.", "doi": "10.1002/ajmg.b.33035", "pmid": "40511557", "labels": {"NGI SNP genotyping": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "mid", "key": "NIHMS2090990"}, {"db": "pmc", "key": "PMC12354282"}], "notes": [], "created": "2025-09-08T07:02:43.198Z", "modified": "2025-09-08T07:02:43.211Z"}, {"entity": "publication", "iuid": "5993e1e4e51044008a8a228e19ce6f0b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5993e1e4e51044008a8a228e19ce6f0b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5993e1e4e51044008a8a228e19ce6f0b"}}, "title": "Deep plasma proteomics identifies and validates an eight-protein biomarker panel that separate benign from malignant tumors in ovarian cancer.", "authors": [{"family": "Moskov", "given": "Mikaela", "initials": "M"}, {"family": "Hedlund Lindberg", "given": "Julia", "initials": "J"}, {"family": "Lycke", "given": "Maria", "initials": "M"}, {"family": "Ivansson", "given": "Emma", "initials": "E", "orcid": "0000-0002-4630-1576", "researcher": {"href": "https://publications.scilifelab.se/researcher/1d2acd6a50fe49178f424c55df0a6b51.json"}}, {"family": "Gyllensten", "given": "Ulf", "initials": "U", "orcid": "0000-0002-6316-3355", "researcher": {"href": "https://publications.scilifelab.se/researcher/e8739f0f42c44019ab88a49db350a4f2.json"}}, {"family": "Sundfeldt", "given": "Karin", "initials": "K"}, {"family": "St\u00e5lberg", "given": "Karin", "initials": "K", "orcid": "0000-0001-5527-8796", "researcher": {"href": "https://publications.scilifelab.se/researcher/47a9c8e243994dccb4730266b0431d6d.json"}}, {"family": "Enroth", "given": "Stefan", "initials": "S", "orcid": "0000-0002-5056-9137", "researcher": {"href": "https://publications.scilifelab.se/researcher/16bb97ef16ee49f3ae0c7ea0495fd971.json"}}], "type": "journal article", "published": "2025-06-12", "journal": {"title": "Commun Med (Lond)", "issn": "2730-664X", "volume": "5", "issue": "1", "pages": "230", "issn-l": null}, "abstract": "Ovarian cancer has the highest mortality of all gynecological cancers and surgery is commonly used as final diagnostic. Available literature indicates that women with benign tumors could often be conservatively managed, but accurate molecular tests are needed for triaging when gold-standard imaging techniques are inconclusive or lacking.\n\nHere, we analyzed 5416 plasma proteins in two independent cohorts (N1 = 171, N2 = 233) with women surgically diagnosed with benign or malignant tumors. Using one cohort as discovery, we compared protein levels of benign tumors with early stage (I-II), late stage (III-IV) or any stage (I-IV) ovarian cancer and trained risk-score reporting multivariate models including a fixed cut-off for malignancy. Associations and model performance was then evaluated in the replication cohort.\n\nWe identify 327 biomarker associations, corresponding to 191 unique proteins, and replicate 326 (99.7%). By comparing the 191 proteins with their corresponding tumor gene expression we find that only 11% (21/191) have significant correlation. Through analyzes of protein-protein correlation networks, we find that 62 of the 191 proteins have high correlation with at least one other protein, suggesting that many of the associations are secondary effects. In the replication cohort, our model has areas under the curve (AUC = 0.96) corresponding to 97% sensitivity at 68% specificity. For early-stage tumors, we estimate the sensitivity to 91% at a specificity of 68% as compared to 85% and 54% for CA-125 alone.\n\nOur results indicates that up to one third of benign cases can be identified by molecular measures thereby reducing the need for diagnostic surgery.", "doi": "10.1038/s43856-025-00945-0", "pmid": "40506476", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12162877"}, {"db": "pii", "key": "10.1038/s43856-025-00945-0"}], "notes": [], "created": "2025-09-08T07:17:14.990Z", "modified": "2025-11-14T11:07:27.366Z"}, {"entity": "publication", "iuid": "43c900f054f54ac892c881ee00972405", "links": {"self": {"href": "https://publications.scilifelab.se/publication/43c900f054f54ac892c881ee00972405.json"}, "display": {"href": "https://publications.scilifelab.se/publication/43c900f054f54ac892c881ee00972405"}}, "title": "Genomic insights into antimicrobial resistance and virulence of E. coli in central Ethiopia: a one health approach.", "authors": [{"family": "Chekole", "given": "Wagaw Sendeku", "initials": "WS"}, {"family": "Potgieter", "given": "Lizel", "initials": "L"}, {"family": "Adamu", "given": "Haileeyesus", "initials": "H"}, {"family": "Sternberg-Lewerin", "given": "Susanna", "initials": "S"}, {"family": "Tessema", "given": "Tesfaye Sisay", "initials": "TS"}, {"family": "Magnusson", "given": "Ulf", "initials": "U"}], "type": "journal article", "published": "2025-06-10", "journal": {"title": "Front Microbiol", "issn": "1664-302X", "volume": "16", "pages": "1597580", "issn-l": "1664-302X"}, "abstract": "Antimicrobial resistance is a global threat causing millions of deaths annually. The study aimed to identify antibiotic resistance genes (ARGs), mobile genetic elements (MGEs), and virulence genes (VGs) and track their dissemination among E. coli isolates. Seventy-seven isolates from calves, environments, and human sources were studied. The study involved WGS sequencing, bacterial strains characterized; pan genome, multi-locus sequence typing, and serotyping using O-, and H-typing. The ARGs, VGs, and MGEs were identified using ABRicate against selected respective databases. A maximum likelihood SNP (single nucleotide polymorphism) tree was constructed and visualized with an interactive tree of life (IToL). Descriptive statistics were used to analyze the data. Seventy-seven of the isolates were identified as E. coli, later grouped into 5 clades and four known phylogroups. ST10 and O16:H48 were most prevalent in 12 and 42 isolates, respectively. There were about 106 unique ARGs detected between 1.3% and 91.9%, with 57 detected in 40% of isolates. In terms of ARGs, the most common were bla-ampH (90.9%), bla-AmpC1 (89.6%), tet(A) (84.4%), mdf(A) (81.8%), aph(3\")-Ib (79%), sul2 (79%), aph(6)-Id (75%), and bla-PBP (70%). It was found that 95 percent (96/106) of ARGs came from at least two sources. The majority of detected ARGs exhibited high concordance between phenotypic resistance and ARGs profiles (JSI \u2265 0.5). In eight isolates, mutations in the gyrA (3) and par-C/E (5) genes led to ciprofloxacin and nalidixic acid resistance. The most common co-occurrences of ARG and MGE were Tn3 with bla-TEM-105 (34), Int1 with sul1 (13), and dhfr7 (11). Meanwhile, the most frequently detected VGs (n \u2265 71 isolates) included elfA-G, fimB-I, hcpA-C, espL, ibeC, entA, fepA-C, ompA, ecpA-E, fepD, fes, and ibeB. Nearly, 88.3% (128/1450) VGs were shared in isolates from at least two sources. ETEC (53.2%), EAEC (22.1%), and STEC (14.3%) were the three most frequently predicted pathotypes. Despite significant ST diversity, ARGs and VGs showed an extensive distribution among the study groups. These findings suggest limited clonal transmission of isolates. In comparison, the wide distribution of ARGs and VGs may be attributed to horizontal gene transfer driven by similar antibiotic selection pressures in the study area.", "doi": "10.3389/fmicb.2025.1597580", "pmid": "40556891", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12185407"}], "notes": [], "created": "2025-09-08T07:13:07.348Z", "modified": "2025-09-08T07:13:07.354Z"}, {"entity": "publication", "iuid": "cbd3115766d1403b90d47770ed1ebec6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/cbd3115766d1403b90d47770ed1ebec6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/cbd3115766d1403b90d47770ed1ebec6"}}, "title": "Metagenomic insights into the complex viral composition of the enteric RNA virome in healthy and diarrheic calves from Ethiopia.", "authors": [{"family": "Bergholm", "given": "Julia", "initials": "J"}, {"family": "Tessema", "given": "Tesfaye Sisay", "initials": "TS"}, {"family": "Blomstr\u00f6m", "given": "Anne-Lie", "initials": "AL"}, {"family": "Berg", "given": "Mikael", "initials": "M"}], "type": "journal article", "published": "2025-06-07", "journal": {"title": "Virol J", "issn": "1743-422X", "volume": "22", "issue": "1", "pages": "188", "issn-l": "1743-422X"}, "abstract": "Viruses and the virome have received increased attention in the context of calf diarrhea and with the advancement of high-throughput sequencing the detection and discovery of viruses has been improved. Calf diarrhea, being the main contributor to calf morbidity and mortality, is a major issue within the livestock sector in Ethiopia. However, studies on viruses and the virome in calves is lacking in the country. Therefore, we utilized viral metagenomics to investigate the diversity of RNA viruses in healthy and diarrheic calves from central Ethiopia.\n\nFecal material from 47 calves were collected, pooled, and sequenced using Illumina. Following sequencing, the virome composition and individual viral sequences were investigated using bioinformatic analysis.\n\nThe metagenomic analysis revealed the presence of several RNA viruses, including rotavirus and bovine coronavirus, known causative agents in calf diarrhea. In addition, several enteric RNA viruses that have not been detected in cattle in Ethiopia previously, such as norovirus, nebovirus, astrovirus, torovirus, kobuvirus, enterovirus, boosepivirus and hunnivirus were identified. Furthermore, a highly divergent viral sequence, which we gave the working name suluvirus, was found. Suluvirus showed a similar genome structure to viruses within the Picornaviridae family and phylogenetic analysis showed that it clusters with crohiviruses. However, due to its very divergent amino acid sequence, we propose that suluvirus represent either a new genus within the Picornaviridae or a new species within crohiviruses.\n\nTo our knowledge, this is the first characterization of the RNA virome in Ethiopian cattle and the study revealed multiple RNA viruses circulating in both diarrheic and healthy calves, as well as a putative novel virus, suluvirus. Our study highlights that viral metagenomics is a powerful tool in understanding the divergence of viruses and their possible association to calf diarrhea, enabling characterization of known viruses as well as discovery of novel viruses.", "doi": "10.1186/s12985-025-02821-8", "pmid": "40483486", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12145588"}, {"db": "pii", "key": "10.1186/s12985-025-02821-8"}, {"db": "BioProject", "key": "PRJNA1224038"}, {"db": "SRA", "key": "PRJNA1224038"}, {"db": "GENBANK", "key": "PV076094-PV076105."}, {"db": "GENBANK", "key": "PV053516"}, {"db": "GENBANK", "key": "PV061389-PV061398"}], "notes": [], "created": "2025-06-09T05:48:13.273Z", "modified": "2025-11-14T11:08:51.197Z"}, {"entity": "publication", "iuid": "5677316fa2684bbba44365a528fe26fb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5677316fa2684bbba44365a528fe26fb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5677316fa2684bbba44365a528fe26fb"}}, "title": "Three-dimensional cell-cell interactions promote direct reprogramming of patient fibroblasts into functional and transplantable neurons.", "authors": [{"family": "Kajtez", "given": "Janko", "initials": "J", "orcid": "0000-0001-9997-2325", "researcher": {"href": "https://publications.scilifelab.se/researcher/5b3315d47d804d8cb1dc7f6ff2b31731.json"}}, {"family": "Laurin", "given": "Kerstin", "initials": "K", "orcid": "0000-0002-3267-1111", "researcher": {"href": "https://publications.scilifelab.se/researcher/9fabb942c9c540de9e23f5e79018535c.json"}}, {"family": "Nilsson", "given": "Fredrik", "initials": "F"}, {"family": "Bruzelius", "given": "Andreas", "initials": "A"}, {"family": "Cepeda-Prado", "given": "Efrain", "initials": "E", "orcid": "0000-0001-9781-3742", "researcher": {"href": "https://publications.scilifelab.se/researcher/f0ee87e59e144bd6b8a0cce5b1e29194.json"}}, {"family": "Birtele", "given": "Marcella", "initials": "M", "orcid": "0000-0003-2123-6453", "researcher": {"href": "https://publications.scilifelab.se/researcher/5597264e465b4396b0016336b46a7fb1.json"}}, {"family": "Barker", "given": "Roger A", "initials": "RA", "orcid": "0000-0001-8843-7730", "researcher": {"href": "https://publications.scilifelab.se/researcher/125769a66f77471da6266577717a6395.json"}}, {"family": "Herborg", "given": "Freja", "initials": "F", "orcid": "0000-0002-0159-4598", "researcher": {"href": "https://publications.scilifelab.se/researcher/3ab2173b0ed34bf48a77880e33146a05.json"}}, {"family": "Rylander Ottosson", "given": "Daniella", "initials": "D", "orcid": "0000-0002-9270-3576", "researcher": {"href": "https://publications.scilifelab.se/researcher/0d5ebb28287f4725b41a4bbf981d0e40.json"}}, {"family": "Storm", "given": "Petter", "initials": "P", "orcid": "0000-0002-7655-3731", "researcher": {"href": "https://publications.scilifelab.se/researcher/f5af5462a2c04920bb43120d429ac386.json"}}, {"family": "Fiorenzano", "given": "Alessandro", "initials": "A", "orcid": "0000-0003-2478-5941", "researcher": {"href": "https://publications.scilifelab.se/researcher/5a17c87028884ff8b5bf3da42a0d63fe.json"}}, {"family": "Habekost", "given": "Mette", "initials": "M", "orcid": "0000-0002-5987-2909", "researcher": {"href": "https://publications.scilifelab.se/researcher/f50503763ece48ba851a3031aade3256.json"}}, {"family": "Parmar", "given": "Malin", "initials": "M", "orcid": "0000-0001-5002-4199", "researcher": {"href": "https://publications.scilifelab.se/researcher/c48b5aaff3bc4832a96fda4f2cf127cb.json"}}], "type": "journal article", "published": "2025-06-06", "journal": {"title": "Sci Adv", "issn": "2375-2548", "volume": "11", "issue": "23", "pages": "eadq7855", "issn-l": "2375-2548"}, "abstract": "Direct reprogramming of somatic cells into induced neurons (iNs) has become an attractive strategy for the generation of patient-specific neurons for disease modeling and regenerative neuroscience. To this end, adult human dermal fibroblasts (hDFs) present one of the most relevant cell sources. However, iNs generated from adult hDFs using two-dimensional cultures are difficult to maintain in vitro and face challenges in survival upon transplantation into the adult brain, thus imposing constraints on biomedical applications of iN technology. Here, we present a platform for direct in vitro reprogramming of adult hDFs inside three-dimensional suspension microcultures (3D-iNs). We show that the 3D environment favors neuronal over fibroblast cellular identity to yield more robust conversion into functional neurons with extended culturing span. The 3D reprogramming approach also provides a platform for fusion into induced assembloids. 3D-iNs can be gently harvested and transplanted into the adult rodent brain to reproducibly generate neuron-rich grafts, thus eliminating a major bottleneck in the direct reprogramming field.", "doi": "10.1126/sciadv.adq7855", "pmid": "40479059", "labels": {"NGI SNP genotyping": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12143395"}], "notes": [], "created": "2025-09-08T07:10:49.448Z", "modified": "2025-09-08T07:10:50.125Z"}, {"entity": "publication", "iuid": "aeb9fc21fabb4b8f8b5a91ef25b0c7a8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/aeb9fc21fabb4b8f8b5a91ef25b0c7a8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/aeb9fc21fabb4b8f8b5a91ef25b0c7a8"}}, "title": "Antimicrobial resistance and serotype distribution of Salmonella spp. isolated from fresh foods in Cambodia.", "authors": [{"family": "Huoy", "given": "Laingshun", "initials": "L", "orcid": "0000-0002-0194-4754", "researcher": {"href": "https://publications.scilifelab.se/researcher/6683581dbb2448008f33711ca1ada131.json"}}, {"family": "Nasirzadeh", "given": "Leila", "initials": "L", "orcid": "0000-0003-0282-1227", "researcher": {"href": "https://publications.scilifelab.se/researcher/d9465e8d872740a083579657d96bb431.json"}}, {"family": "Phan", "given": "Kongkea", "initials": "K", "orcid": "0000-0003-2965-8415", "researcher": {"href": "https://publications.scilifelab.se/researcher/0826a7f731ac490b84b1e6823b9cedb5.json"}}, {"family": "Tieng", "given": "Siteng", "initials": "S", "orcid": "0000-0002-9037-6671", "researcher": {"href": "https://publications.scilifelab.se/researcher/fd94295461f642cca1a44b46e4b923a2.json"}}, {"family": "Sternberg-Lewerin", "given": "Susanna", "initials": "S", "orcid": "0000-0001-7907-8377", "researcher": {"href": "https://publications.scilifelab.se/researcher/41bff7b199434422b316875f399f5ebe.json"}}, {"family": "Bongcam-Rudloff", "given": "Erik", "initials": "E", "orcid": "0000-0002-1947-8288", "researcher": {"href": "https://publications.scilifelab.se/researcher/6970ca57259d498588ecf9e1ad28a9b0.json"}}, {"family": "Boqvist", "given": "Sofia", "initials": "S", "orcid": "0000-0002-8072-7132", "researcher": {"href": "https://publications.scilifelab.se/researcher/04e91c7a79164ce88c1a2aeaed836ca7.json"}}], "type": "journal article", "published": "2025-06-02", "journal": {"title": "J Appl Microbiol", "issn": "1365-2672", "volume": "136", "issue": "6", "issn-l": "1364-5072"}, "abstract": "To determine the Salmonella serotype distribution, antimicrobial resistance profiles, and antimicrobial resistance genes (ARGs) in food samples obtained from local markets in a low-income urban setting and nearby farms in Cambodia.\n\nOne hundred and thirty-nine Salmonella isolates from various food sources were tested for antibiotic susceptibility using a panel of 12 antibiotics, and 81 selected Salmonella isolates were further sequenced for serotype distribution and ARG identification. The results showed that 71% (99/139) of the isolates exhibited resistance to at least one antibiotic, with 39% (39/99) classified as multidrug-resistant (MDR). The highest resistance was observed against azithromycin (37%), followed by oxytetracycline (35%). A total of 32 serotypes were identified, with the six most common being S. Corvallis (7%), S. Haifa (6%), S. Weltevreden (6%), S. Agona (5%), S. Kentucky (5%), and S. Livingstone (5%). A broad range of ARGs was observed across multiple antibiotic classes, including macrolides, aminoglycosides, tetracyclines, phenicols, fluoroquinolones, sulfonamide-trimethoprim, beta-lactams, and MDR genes.\n\nThe results highlight the potential role of fresh food products in the widespread dissemination of Salmonella strains resistant to multiple antibiotics.", "doi": "10.1093/jambio/lxaf137", "pmid": "40459912", "labels": {"Clinical Genomics Link\u00f6ping": "Collaborative", "Clinical Genomics": "Collaborative", "NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pii", "key": "8155881"}], "notes": [], "created": "2025-06-04T12:59:02.555Z", "modified": "2025-09-08T06:59:27.016Z"}, {"entity": "publication", "iuid": "19d4f0ca29364061b137e9116162d5d2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/19d4f0ca29364061b137e9116162d5d2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/19d4f0ca29364061b137e9116162d5d2"}}, "title": "Genetically Determined Inflammation-Related Proteins in Asthma and Type-2 Signatures.", "authors": [{"family": "Hernandez-Pacheco", "given": "Natalia", "initials": "N", "orcid": "0000-0002-6313-1847", "researcher": {"href": "https://publications.scilifelab.se/researcher/833e75515e024830b827806684d61126.json"}}, {"family": "Bj\u00f6rkander", "given": "Sophia", "initials": "S", "orcid": "0000-0002-4600-2883", "researcher": {"href": "https://publications.scilifelab.se/researcher/310af30b841741a790046af03a3cee6d.json"}}, {"family": "Merid", "given": "Simon Kebede", "initials": "SK", "orcid": "0000-0001-5974-7676", "researcher": {"href": "https://publications.scilifelab.se/researcher/c7a04c6538814b089994c7a822ecf07f.json"}}, {"family": "Kere", "given": "Maura", "initials": "M", "orcid": "0000-0002-5725-2773", "researcher": {"href": "https://publications.scilifelab.se/researcher/2d213ed52d084d79a7a87e09a3688d01.json"}}, {"family": "Kumar", "given": "Ashish", "initials": "A", "orcid": "0000-0002-7075-5930", "researcher": {"href": "https://publications.scilifelab.se/researcher/de86e6bb6d154c2db787a769da96323b.json"}}, {"family": "Klevebro", "given": "Susanna", "initials": "S", "orcid": "0000-0002-1261-6502", "researcher": {"href": "https://publications.scilifelab.se/researcher/2cace10c20c847f6a04259937e74891e.json"}}, {"family": "Mogensen", "given": "Ida", "initials": "I", "orcid": "0000-0002-0198-2718", "researcher": {"href": "https://publications.scilifelab.se/researcher/a8e3b914932c4470ba02ff73278972c8.json"}}, {"family": "Ekstr\u00f6m", "given": "Sandra", "initials": "S", "orcid": "0000-0002-2060-8190", "researcher": {"href": "https://publications.scilifelab.se/researcher/d813a2fda4fc410cb5db71c62af9d0ea.json"}}, {"family": "Janson", "given": "Christer", "initials": "C", "orcid": "0000-0001-5093-6980", "researcher": {"href": "https://publications.scilifelab.se/researcher/bae457d633714159a73704f9ebe7bfa6.json"}}, {"family": "Palmberg", "given": "Lena", "initials": "L", "orcid": "0000-0001-5650-4484", "researcher": {"href": "https://publications.scilifelab.se/researcher/c77734a210e146dbaadc33363eaaaa6f.json"}}, {"family": "van Hage", "given": "Marianne", "initials": "M", "orcid": "0000-0003-3091-1596", "researcher": {"href": "https://publications.scilifelab.se/researcher/2e9a55cd378c46d5a1fc6b4694423849.json"}}, {"family": "M\u00e4larstig", "given": "Anders", "initials": "A", "orcid": "0000-0003-2608-1358", "researcher": {"href": "https://publications.scilifelab.se/researcher/e70c845d32264b448e0b4631b826be6d.json"}}, {"family": "Merritt", "given": "Anne-Sophie", "initials": "AS", "orcid": "0000-0002-4497-1779", "researcher": {"href": "https://publications.scilifelab.se/researcher/c9a96b69dc76435a83ea3dc089a5b657.json"}}, {"family": "Pershagen", "given": "G\u00f6ran", "initials": "G", "orcid": "0000-0002-9701-1130", "researcher": {"href": "https://publications.scilifelab.se/researcher/9d97eee1803d4ce3a85c1fcb423c75d9.json"}}, {"family": "Bergstr\u00f6m", "given": "Anna", "initials": "A", "orcid": "0000-0002-7981-6314", "researcher": {"href": "https://publications.scilifelab.se/researcher/70d058e4d5bc49d7a3c958950c9d4e6d.json"}}, {"family": "Kull", "given": "Inger", "initials": "I", "orcid": "0000-0001-6096-3771", "researcher": {"href": "https://publications.scilifelab.se/researcher/7f248045358c4711b1d10d7b9fe9649c.json"}}, {"family": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications.scilifelab.se/researcher/aba5822711b246b397fffacb7ae403b3.json"}}, {"family": "Mel\u00e9n", "given": "Erik", "initials": "E", "orcid": "0000-0002-8248-0663", "researcher": {"href": "https://publications.scilifelab.se/researcher/3af5a23ba0a847778eea300f745cb143.json"}}], "type": "journal article", "published": "2025-06-00", "journal": {"title": "Allergy", "issn": "1398-9995", "volume": "80", "issue": "6", "pages": "1702-1714", "issn-l": "0105-4538"}, "abstract": "Protein quantitative trait loci (pQTLs) remain underexplored in asthma but might provide valuable insights into the underlying molecular mechanisms. This study aimed to investigate associations between genetic variation and inflammation-related plasma proteins and to assess differences in the levels of genetically determined proteins in subjects with signatures of type-2 inflammation and/or asthma.\n\nA pQTL mapping of 92 inflammation-related plasma proteins was conducted in young adults from the Swedish BAMSE cohort (n = 1538). Replication of sentinel pQTLs was attempted, and the overlap and colocalization of pQTLs with expression quantitative trait loci (eQTLs) were investigated using publicly available data. Proteins with significant pQTLs were tested for association with type-2 signatures defined as high levels of fractional exhaled nitric oxide, blood eosinophils, and/or sensitization to airborne allergens in subjects with or without asthma in BAMSE.\n\nForty-five sentinel pQTLs (33 cis, 12 trans) for 39 inflammation-related proteins were identified (p \u2264 7.14 \u00d7 10-11), and a high proportion of these were validated in independent populations. A high likelihood for colocalization of cis-pQTLs and cis-eQTLs was observed for 19 proteins in different tissues. Six of the 39 circulating proteins with significant pQTLs were associated with type-2 signatures and/or asthma, and matrix metalloproteinase-10 (MMP-10) showed the most significant associations.\n\nThese findings underscore the existence of a genetic component influencing the plasma levels of proteins involved in inflammatory processes, including MMP-10, which is suggested to have a role in high type-2 inflammation in asthma subjects.", "doi": "10.1111/all.16608", "pmid": "40464643", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service", "Affinity Proteomics Uppsala": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12186602"}], "notes": [], "created": "2025-09-08T07:17:11.553Z", "modified": "2025-11-25T19:21:03.863Z"}, {"entity": "publication", "iuid": "2a2ca50ec2b44ca99ee63649522c4aaf", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2a2ca50ec2b44ca99ee63649522c4aaf.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2a2ca50ec2b44ca99ee63649522c4aaf"}}, "title": "Diel Bacterioplankton Community Dynamics Under Contrasting Light Regimes.", "authors": [{"family": "Papadopoulou", "given": "Sofia", "initials": "S", "orcid": "0000-0001-7315-3671", "researcher": {"href": "https://publications.scilifelab.se/researcher/5f6cb7f8c28f4e0fbc030ee7311c6078.json"}}, {"family": "Linkhorst", "given": "Annika", "initials": "A", "orcid": "0000-0002-3609-5107", "researcher": {"href": "https://publications.scilifelab.se/researcher/0ba8c037d8ba4defbfa03364e2e264e7.json"}}, {"family": "Balmonte", "given": "John Paul", "initials": "JP", "orcid": "0000-0001-5571-4893", "researcher": {"href": "https://publications.scilifelab.se/researcher/b3949f1396414e15a27c85460886d7ac.json"}}, {"family": "Csit\u00e1ri", "given": "Bianka", "initials": "B", "orcid": "0000-0002-5219-5829", "researcher": {"href": "https://publications.scilifelab.se/researcher/72ae1be693ac4900987f70a21a271494.json"}}, {"family": "Felf\u00f6ldi", "given": "Tam\u00e1s", "initials": "T", "orcid": "0000-0003-2009-2478", "researcher": {"href": "https://publications.scilifelab.se/researcher/3a452e1d353649bc860f59485fc8bf03.json"}}, {"family": "M\u00e1rton", "given": "Zsuzsanna", "initials": "Z", "orcid": "0000-0002-7420-5039", "researcher": {"href": "https://publications.scilifelab.se/researcher/631b674f8b91403e95b1bbc8383fd8a8.json"}}, {"family": "Mershad", "given": "Maliheh", "initials": "M", "orcid": "0000-0002-1108-6888", "researcher": {"href": "https://publications.scilifelab.se/researcher/d3eca2f7212a4c67bd7b251fa93848e1.json"}}, {"family": "Szab\u00f3", "given": "Attila", "initials": "A", "orcid": "0000-0002-7777-8166", "researcher": {"href": "https://publications.scilifelab.se/researcher/78425c54e73b4bc1bf8c8b900224d41d.json"}}, {"family": "Torstensson", "given": "Anders", "initials": "A", "orcid": "0000-0002-8283-656X", "researcher": {"href": "https://publications.scilifelab.se/researcher/352fd53b3b584caa95ee5ff4405498cf.json"}}, {"family": "Bertilsson", "given": "Stefan", "initials": "S", "orcid": "0000-0002-4265-1835", "researcher": {"href": "https://publications.scilifelab.se/researcher/2c17765c2a9f4383b5383138d11ae93f.json"}}, {"family": "Sz\u00e9kely", "given": "Anna J", "initials": "AJ", "orcid": "0000-0001-8063-7156", "researcher": {"href": "https://publications.scilifelab.se/researcher/c9b2d69cfd6a4f41a978b38ddf66c8d5.json"}}], "type": "journal article", "published": "2025-06-00", "journal": {"title": "Environ Microbiol Rep", "issn": "1758-2229", "issn-l": "1758-2229", "volume": "17", "issue": "3", "pages": "e70099"}, "abstract": "In the Boreal region, extreme seasonal variations in day-night length expose communities to dynamic light and temperature fluctuations. Freshwater bacterioplankton, representing key ecosystem components, faces climate-driven shifts; yet the fixed day-length patterns determined by latitude underscore the importance of studying light's role in predicting ecosystem responses. We investigated bacterial community composition in a brown peat bog and a clear oligotrophic lake across seasons with contrasting light regimes: the summer solstice (> 20 h of daylight) and the autumn equinox (equal day-night length). Using amplicon sequencing of 16S rRNA transcripts, alongside measurements of physicochemical parameters, organic matter characterisation and dissolved carbon dioxide and methane gas measurements, we found no diel cycling in the lake during either period or in the peat bog near the summer solstice. However, the structure of bacterial peat bog communities exhibited cyclic changes over diel cycles at the autumn equinox. Twelve amplicon sequence variants, including both phototrophic and heterotrophic taxa, increased in abundance at all measured morning sampling times. These findings provide valuable insights into the diel patterns of boreal lentic habitats and their bacterioplankton communities, highlighting the absence of diel fluctuations in some systems and seasons, while revealing cyclic dynamics in others, driven by conditionally rare taxa.", "doi": "10.1111/1758-2229.70099", "pmid": "40344486", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": null, "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12061850"}], "notes": [], "created": "2025-05-12T05:46:12.949Z", "modified": "2025-11-28T10:50:46.010Z"}, {"entity": "publication", "iuid": "3cba993176914d9489704b83ceb80532", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3cba993176914d9489704b83ceb80532.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3cba993176914d9489704b83ceb80532"}}, "title": "Defining short linear motif binding determinants by phage display-based deep mutational scanning.", "authors": [{"family": "Benz", "given": "Caroline", "initials": "C"}, {"family": "Maassen", "given": "Lars", "initials": "L"}, {"family": "Simonetti", "given": "Leandro", "initials": "L"}, {"family": "Mihalic", "given": "Filip", "initials": "F", "orcid": "0000-0002-6840-2319", "researcher": {"href": "https://publications.scilifelab.se/researcher/5f57a961e98e4e15b1b96ec8efc95d4f.json"}}, {"family": "Lindqvist", "given": "Richard", "initials": "R"}, {"family": "Tsitsa", "given": "Ifigenia", "initials": "I", "orcid": "0000-0001-8154-5528", "researcher": {"href": "https://publications.scilifelab.se/researcher/9afb0faf7a4c435cbba2b4aa63b99b51.json"}}, {"family": "Konstantinou", "given": "Aimiliani", "initials": "A"}, {"family": "Jemth", "given": "Per", "initials": "P", "orcid": "0000-0003-1516-7228", "researcher": {"href": "https://publications.scilifelab.se/researcher/91bb46ceba74462498354a328886b982.json"}}, {"family": "\u00d6verby", "given": "Anna K", "initials": "AK"}, {"family": "Davey", "given": "Norman E", "initials": "NE"}, {"family": "Ivarsson", "given": "Ylva", "initials": "Y", "orcid": "0000-0002-7081-3846", "researcher": {"href": "https://publications.scilifelab.se/researcher/f51534acce8c4214a55a3e7387850d53.json"}}], "type": "journal article", "published": "2025-06-00", "journal": {"title": "Protein Sci.", "issn": "1469-896X", "volume": "34", "issue": "6", "pages": "e70174", "issn-l": "0961-8368"}, "abstract": "Deep mutational scanning (DMS) has emerged as a powerful approach for evaluating the effects of mutations on binding or function. Here, we developed a DMS by phage display protocol to define the specificity determinants of short linear motifs (SLiMs) binding to peptide-binding domains. We first designed a benchmarking DMS library to evaluate the performance of the approach on well-known ligands for 11 different peptide-binding domains, including the talin-1 PTB domain, the G3BP1 NTF2 domain, and the MDM2 SWIB domain. Comparison with a set of reference motifs from the eukaryotic linear motif (ELM) database confirmed that the DMS by phage display analysis correctly identifies known motif binding determinants and provides novel insights into specificity determinants, including defining a non-canonical talin-1 PTB binding motif with a putative extended conformation. A second DMS library was designed, aiming to provide information on the binding determinants for 19 SLiM-based interactions between human and SARS-CoV-2 proteins. The analysis confirmed the affinity determining residues of viral peptides binding to host proteins and refined the consensus motifs in human peptides binding to five domains from SARS-CoV-2 proteins, including the non-structural protein (NSP) 9. The DMS analysis further pinpointed mutations that increased the affinity of ligands for NSP3 and NSP9. An affinity-improved cell-permeable NSP9-binding peptide was found to exert stronger antiviral effects than the wild-type peptide. Our study demonstrates that DMS by phage display can efficiently be multiplexed and applied to refine binding determinants and shows how the results can guide peptide-engineering efforts.", "doi": "10.1002/pro.70174", "pmid": "40411416", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12102759"}], "notes": [], "created": "2025-09-08T11:37:16.206Z", "modified": "2025-11-21T18:30:05.510Z"}, {"entity": "publication", "iuid": "92e3372715cf4361b696885f895c9243", "links": {"self": {"href": "https://publications.scilifelab.se/publication/92e3372715cf4361b696885f895c9243.json"}, "display": {"href": "https://publications.scilifelab.se/publication/92e3372715cf4361b696885f895c9243"}}, "title": "Comprehensive transcriptome assessment in PBMCs of post-COVID patients at a median follow-up of 28 months after a mild COVID infection reveals upregulation of JAK/STAT signaling and a prolonged immune response.", "authors": [{"family": "Fineschi", "given": "Serena", "initials": "S"}, {"family": "Klar", "given": "Joakim", "initials": "J"}, {"family": "Lopez Egido", "given": "Juan Ramon", "initials": "JR"}, {"family": "Schuster", "given": "Jens", "initials": "J"}, {"family": "Bergquist", "given": "Jonas", "initials": "J"}, {"family": "Kaden", "given": "Ren\u00e9", "initials": "R"}, {"family": "Dahl", "given": "Niklas", "initials": "N"}], "type": "journal article", "published": "2025-05-30", "journal": {"title": "Front Immunol", "issn": "1664-3224", "volume": "16", "pages": "1589589", "issn-l": "1664-3224"}, "abstract": "Post-acute sequelae of SARS-CoV-2 infection (PASC), also known as post-COVID-19 condition (here abbreviated as post-COVID) is an escalating global health issue. The aim of our study was to investigate the mechanisms and clinical manifestations of post-COVID following a mild SARS-CoV-2 infection.\n\nWe analyzed the gene expression profile in PBMCs from 60 middle-aged post-COVID patients and 50 age-matched controls at a median time of 28 months following a mild SARS-CoV-2 infection. The clinical assessments included intensity of post-COVID symptoms, physical and mental fatigue, depression and anxiety. Sixty-seven participants performed a mild exertion ergometer test with assessment of lactate concentrations. Transcriptome analysis was performed on mRNA selected by poly-A enrichment and SARS-CoV-2 RNA fragments were analyzed using the ARTIC protocol.\n\nWe identified 463 differentially expressed transcripts in PBMCs, of which 324 were upregulated and 129 downregulated in post-COVID patients. Upregulated genes in post-COVID individuals were enriched for processes involving JAK-STAT signaling, negative regulation of ubiquitination, IL9 signaling, and negative regulation of viral process, suggesting chronic inflammation. Downregulated genes were enriched for processes involving mitochondrial ATP synthesis, and oxidative phosphorylation, suggesting mitochondrial dysfunction. No SARS-CoV-2 gene fragments were detected in PBMCs of patients with post-COVID and no IFN genes were found differentially expressed in post-COVID patients. Post-COVID was associated with elevated lactate levels in blood, both at rest and after a short recovery phase following exertion, suggesting increased anaerobic activity in skeletal muscles. We did not find differences in the transcriptional profiles or clinical manifestations when comparing patients who contracted the infection from early SARS-CoV-2 variants with those who contracted the infection during the period when the Omicron variant was prevalent.\n\nOur findings highlight molecular changes compatible with a persistent immune response in PBMCs of post-COVID subjects at a median follow-up of 28 months after a mild infection, supporting the hypothesis that post-COVID is a chronic inflammatory condition. The upregulation of JAK/STAT signaling suggests a potential therapeutic target in post-COVID.", "doi": "10.3389/fimmu.2025.1589589", "pmid": "40519915", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Clinical Genomics Uppsala": "Collaborative", "Clinical Genomics": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC12162955"}], "notes": [], "created": "2025-06-18T07:32:51.275Z", "modified": "2025-11-26T14:14:30.711Z"}, {"entity": "publication", "iuid": "5b6d8c72800145a294f1fab88be77e43", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5b6d8c72800145a294f1fab88be77e43.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5b6d8c72800145a294f1fab88be77e43"}}, "title": "Selection for Tameness in Red Junglefowl Recapitulates Genetic Loci Associated With Domestication-Related Brain Composition.", "authors": [{"family": "Guerrero-Bosagna", "given": "Carlos", "initials": "C"}, {"family": "P\u00e9rtille", "given": "F\u00e1bio", "initials": "F"}, {"family": "Moradinour", "given": "Zahra", "initials": "Z"}, {"family": "Katajama", "given": "Rebecca", "initials": "R"}, {"family": "Martin Cerezo", "given": "Maria Luisa", "initials": "ML", "orcid": "0000-0003-3952-2853", "researcher": {"href": "https://publications.scilifelab.se/researcher/53e025902fc04455ad70a33ba146c003.json"}}, {"family": "Henriksen", "given": "Rie", "initials": "R"}, {"family": "Jensen", "given": "Per", "initials": "P"}, {"family": "Wright", "given": "Dominic", "initials": "D", "orcid": "0000-0003-2329-2635", "researcher": {"href": "https://publications.scilifelab.se/researcher/6447b896ea3b453ab10136b5f44ae241.json"}}], "type": "journal article", "published": "2025-05-19", "journal": {"title": "Mol. Ecol.", "issn": "1365-294X", "pages": "e17788", "issn-l": "0962-1083"}, "abstract": "Domestication involves huge phenotypic shifts via strong directional selection. The resulting changes, often termed the Domestication Syndrome, typically encompass numerous traits; however, the most universal of these are changes in reduced fear of humans (tameness) and brain composition. To assess how early domestication selection may have focused on tameness and its interaction with brain composition, a Red Junglefowl (Gallus gallus) population (the wild progenitor of the domestic chicken) was used to create two lines bidirectionally selected for fear of humans over eight generations of selection. These selection lines were then used to make an intercross population. Using a combination of genome-wide mapping in the intercross and between-line analysis of the selection lines, we show that the genetic loci for tameness co-localise with genetic loci for brain composition and anxiety behaviour. Furthermore, the detected loci for brain composition also co-localise with brain composition loci identified in a separate wild \u00d7 domestic intercross. These results indicate that tameness and brain composition are either pleiotropic or genetically linked, and that tameness selection appears to recapitulate the same loci that have been selected by domestication itself. Therefore, selection for increased tameness could be the initial selection pressure driving the core of the domestication syndrome.", "doi": "10.1111/mec.17788", "pmid": "40386851", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics (NBIS)": "Service", "Bioinformatics Long-term Support WABI": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2025-09-08T11:37:29.894Z", "modified": "2025-11-28T10:51:37.135Z"}, {"entity": "publication", "iuid": "d87a1093323d4610a405b3a7a6fcc248", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d87a1093323d4610a405b3a7a6fcc248.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d87a1093323d4610a405b3a7a6fcc248"}}, "title": "Brain tumors induce immunoregulatory dendritic cells in draining lymph nodes that can be targeted by OX40 agonist treatment.", "authors": [{"family": "Badillo-Godinez", "given": "Oscar", "initials": "O", "orcid": "0000-0002-3840-9448", "researcher": {"href": "https://publications.scilifelab.se/researcher/3a36cfe85dec4e5099c4fb754f8c4b7e.json"}}, {"family": "Niemi", "given": "Jenni", "initials": "J"}, {"family": "Helfridsson", "given": "Liam", "initials": "L"}, {"family": "Karimi", "given": "Shokoufeh", "initials": "S"}, {"family": "Ramachandran", "given": "Mohanraj", "initials": "M"}, {"family": "Mangukiya", "given": "Hitesh Bhagavanbhai", "initials": "HB", "orcid": "0000-0002-8460-4850", "researcher": {"href": "https://publications.scilifelab.se/researcher/d32958c394c749d19d7444dac9fe6c3b.json"}}, {"family": "Nelander", "given": "Sven", "initials": "S"}, {"family": "Hellstr\u00f6m", "given": "Mats", "initials": "M"}], "type": "journal article", "published": "2025-05-19", "journal": {"title": "J Immunother Cancer", "issn": "2051-1426", "volume": "13", "issue": "5", "issn-l": null}, "abstract": "Primary and metastatic brain tumors have a poor prognosis, partly owing to the unique characteristics of the central nervous system (CNS) and tumor immune microenvironment (TIME). One distinct feature of the CNS TIME is the limited infiltration and activation of dendritic cells (DCs). The impact of CNS versus non-CNS TIME can be assessed by injecting tumor cells from the same model, either subcutaneously (peripherally) or into the brain. Subcutaneous tumors drain into the tumor-draining lymph nodes in the skin (TdLN-p), whereas brain tumors drain into the deep cervical TdLN (TdLN-c). We previously showed that CNS tumors that are not responsive to immune checkpoint inhibition become responsive when grown peripherally, and that non-responsiveness correlates with a tolerogenic immune response in the local TIME and TdLN-c.\n\nIn this study, we investigated the immunoregulatory potential of cervical DCs (DC-c) compared with that of peripheral DCs (DC-p) using high-resolution flow cytometry, single-cell RNA sequencing, and ex vivo and in vivo functional characterization of TdLNs from mouse models of glioma and lymphoma.\n\nOur analysis revealed that DC-c promoted regulatory T-cell expansion and poorly cytotoxic CD8+ T cells compared with DC-p. Furthermore, we identified OX40 (Tnfrsf4) as a modulator of immunoregulatory DC-c function and found that its antitumor effect depended on lymphocyte trafficking and the DC transcription factor Batf3. CCR7+OX40+ DCs were efficient in antigen processing and presentation, and OX40 agonists further enhanced DC activation. In TIME, the CCR7+OX40+ DCs expressed OX40L, and blocking it promoted Treg formation ex vivo.\n\nOur findings highlight the unique immunoregulatory functions of DC-c in TdLNs and suggest the importance of OX40 signaling through direct effects on CCR7+OX40+ DCs and indirect effects on T cells.", "doi": "10.1136/jitc-2025-011548", "pmid": "40389372", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12090865"}, {"db": "pii", "key": "jitc-2025-011548"}], "notes": [], "created": "2025-09-08T07:10:13.442Z", "modified": "2025-09-08T07:10:13.516Z"}, {"entity": "publication", "iuid": "5adffdb972b34ba1ad08ce191ce10297", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5adffdb972b34ba1ad08ce191ce10297.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5adffdb972b34ba1ad08ce191ce10297"}}, "title": "Revised phylogeny of mouflon based on expanded sampling of mitogenomes.", "authors": [{"family": "Mereu", "given": "Paolo", "initials": "P", "orcid": "0000-0001-6615-4828", "researcher": {"href": "https://publications.scilifelab.se/researcher/422d206c68a94124a43bed3c4db41999.json"}}, {"family": "Pirastru", "given": "Monica", "initials": "M"}, {"family": "Morell Miranda", "given": "Pedro", "initials": "P", "orcid": "0000-0001-7678-9691", "researcher": {"href": "https://publications.scilifelab.se/researcher/b3a48ddd9e9b491ea55ec2ac0bd4328f.json"}}, {"family": "Ata\u011f", "given": "G\u00f6zde", "initials": "G"}, {"family": "Ba\u015fak Vural", "given": "K\u0131v\u0131lc\u0131m", "initials": "K"}, {"family": "Wilkens", "given": "Barbara", "initials": "B"}, {"family": "Rodrigues Soares", "given": "Andr\u00e9 Elias", "initials": "AE"}, {"family": "Kaptan", "given": "Damla", "initials": "D", "orcid": "0000-0001-7953-1354", "researcher": {"href": "https://publications.scilifelab.se/researcher/d969faa7d65045298f3ef289d849dfe8.json"}}, {"family": "Zedda", "given": "Marco", "initials": "M", "orcid": "0000-0003-2347-9264", "researcher": {"href": "https://publications.scilifelab.se/researcher/0108c75581c44c61a3f1bcaa0728e77a.json"}}, {"family": "Columbano", "given": "Nicol\u00f2", "initials": "N", "orcid": "0000-0003-2201-8773", "researcher": {"href": "https://publications.scilifelab.se/researcher/b39bcac149fd4b8ca83c833bf86da2f7.json"}}, {"family": "Barbato", "given": "Mario", "initials": "M", "orcid": "0000-0002-7203-1549", "researcher": {"href": "https://publications.scilifelab.se/researcher/2cf7e142b2894c9f8e3249dda9bc6728.json"}}, {"family": "Naitana", "given": "Salvatore", "initials": "S"}, {"family": "Hadjisterkotis", "given": "Eleftherios", "initials": "E"}, {"family": "Somel", "given": "Mehmet", "initials": "M"}, {"family": "\u00d6zer", "given": "F\u00fcsun", "initials": "F", "orcid": "0000-0003-0443-5805", "researcher": {"href": "https://publications.scilifelab.se/researcher/676b684e50e04c7686e5ddfd1b9c41a1.json"}}, {"family": "G\u00fcnther", "given": "Torsten", "initials": "T", "orcid": "0000-0001-9460-390X", "researcher": {"href": "https://publications.scilifelab.se/researcher/84159bff82a64a938bcff107f550c901.json"}}, {"family": "Leoni", "given": "Giovanni Giuseppe", "initials": "GG"}], "type": "journal article", "published": "2025-05-14", "journal": {"title": "PLoS ONE", "issn": "1932-6203", "volume": "20", "issue": "5", "pages": "e0323354", "issn-l": "1932-6203"}, "abstract": "Mouflons are flagship species of the Mediterranean islands where they persist. Once thought to be the remnants of a European wild sheep population, archaeology suggests they were introduced by humans to the islands of Cyprus in the Early Neolithic (~10,000 years ago) and later to Corsica and Sardinia. Their status as truly wild animals remains a subject of debate. To investigate the phylogenetic relationship between these island populations and other domestic and wild sheep from the Mediterranean region, we sequenced 50 mitogenomes of mouflons from Sardinia and Corsica, and modern and ancient Sardinian domestic sheep. A total of 68 additional publicly available mitogenomes were included in the comparative analysis and used to reconstruct the phylogeny of sheep and its closest wild relative, the mouflon (Ovis gmelini). Our study analyzed the evolutionary relationships within the C-E-X and haplogroup B clusters, showing that: a) Cyprus mouflons are more related to Anatolian and Iranian mouflons belonging to the wild haplogroup X, which seems to be basal to the domestic C and E haplogroups; b) Corsican and Sardinian mouflon arise from basal lineages associated with the early European expansion of domestic sheep. These results highlight the phylogenetic distinctiveness of the mouflon populations from the Mediterranean islands, suggesting a revision of their systematic classification and an update of the nomenclature for Sardinian and Corsican mouflons from the current status of subspecies of domestic sheep (Ovis aries musimon) to subspecies of their wild relatives (Ovis gmelini musimon) which would facilitate conservation efforts.", "doi": "10.1371/journal.pone.0323354", "pmid": "40367058", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Ancient DNA": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12077669"}, {"db": "pii", "key": "PONE-D-25-02476"}], "notes": [], "created": "2025-09-08T07:03:22.964Z", "modified": "2025-11-14T11:09:06.543Z"}, {"entity": "publication", "iuid": "9f220d0577d84d8fa3e6281e3aa1f84d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9f220d0577d84d8fa3e6281e3aa1f84d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9f220d0577d84d8fa3e6281e3aa1f84d"}}, "title": "Maternal asthma and newborn DNA methylation.", "authors": [{"family": "Pedersen", "given": "Casper-Emil Tingskov", "initials": "CT"}, {"family": "Hoang", "given": "Thanh T", "initials": "TT"}, {"family": "Jin", "given": "Jianping", "initials": "J"}, {"family": "Starnawska", "given": "Anna", "initials": "A"}, {"family": "Granell", "given": "Raquel", "initials": "R"}, {"family": "Elliott", "given": "Hannah R", "initials": "HR"}, {"family": "Huels", "given": "Anke", "initials": "A"}, {"family": "Zar", "given": "Heather J", "initials": "HJ"}, {"family": "Stein", "given": "Dan J", "initials": "DJ"}, {"family": "Zhang", "given": "Yining", "initials": "Y"}, {"family": "Dekker", "given": "Herman T den", "initials": "HTD"}, {"family": "Duijts", "given": "Liesbeth", "initials": "L"}, {"family": "Felix", "given": "Janine F", "initials": "JF"}, {"family": "Sang\u00fcesa", "given": "J\u00falia", "initials": "J"}, {"family": "Bustamante", "given": "Mariona", "initials": "M"}, {"family": "Casas", "given": "Maribel", "initials": "M"}, {"family": "Vrijheid", "given": "Martine", "initials": "M"}, {"family": "Kadalayil", "given": "Latha", "initials": "L"}, {"family": "Rezwan", "given": "Faisal I", "initials": "FI"}, {"family": "Arshad", "given": "Hasan", "initials": "H"}, {"family": "Holloway", "given": "John W", "initials": "JW"}, {"family": "R\u00f6der", "given": "Stefan", "initials": "S"}, {"family": "Zenclussen", "given": "Ana C", "initials": "AC"}, {"family": "Herberth", "given": "Gunda", "initials": "G"}, {"family": "Staunstrup", "given": "Nicklas Heine", "initials": "NH"}, {"family": "Horsdal", "given": "Henriette Thisted", "initials": "HT"}, {"family": "Mill", "given": "Jonathan", "initials": "J"}, {"family": "Hannon", "given": "Eilis", "initials": "E"}, {"family": "iPSYCH-MINERvA Group", "given": "", "initials": ""}, {"family": "Annesi-Maesano", "given": "Isabella", "initials": "I"}, {"family": "Pesce", "given": "Giancarlo", "initials": "G"}, {"family": "Ba\u00efz", "given": "Nour", "initials": "N"}, {"family": "Heude", "given": "Barbara", "initials": "B"}, {"family": "Hosseinian-Mohazzab", "given": "Sahra", "initials": "S"}, {"family": "Breton", "given": "Carrie V", "initials": "CV"}, {"family": "Harlid", "given": "Sophia", "initials": "S"}, {"family": "Harbs", "given": "Justin", "initials": "J"}, {"family": "Domellof", "given": "Magnus", "initials": "M"}, {"family": "West", "given": "Christina", "initials": "C"}, {"family": "Yeung", "given": "Edwina", "initials": "E"}, {"family": "Zeng", "given": "Xuehuo", "initials": "X"}, {"family": "Nystad", "given": "Wenche", "initials": "W"}, {"family": "H\u00e5berg", "given": "Siri E", "initials": "SE"}, {"family": "Magnus", "given": "Maria C", "initials": "MC"}, {"family": "Schendel", "given": "Diana", "initials": "D"}, {"family": "London", "given": "Stephanie J", "initials": "SJ"}, {"family": "B\u00f8nnelykke", "given": "Klaus", "initials": "K"}], "type": "journal article", "published": "2025-05-10", "journal": {"title": "Clin Epigenetics", "issn": "1868-7083", "volume": "17", "issue": "1", "pages": "79", "issn-l": "1868-7075"}, "abstract": "Prenatal exposure to maternal asthma may influence DNA methylation patterns in offspring, potentially affecting their susceptibility to later diseases including asthma.\n\nTo investigate the relationship between parental asthma and newborn blood DNA methylation.\n\nEpigenome-wide association analyses were conducted in 13 cohorts on 7433 newborns with blood methylation data from the Illumina450K or EPIC array. We used fixed effects meta-analyses to identify differentially methylated CpGs (DMCs) and comb-p to identify differentially methylated regions (DMRs) associated with maternal asthma during pregnancy and maternal asthma ever. Paternal asthma was analyzed for comparison. Models were adjusted for covariates and cell-type composition. We examined whether implicated sites related to gene expression analyses in publicly available data for childhood blood and adult lung.\n\nWe identified 27 CpGs associated with maternal asthma during pregnancy at False Discovery Rate < 0.05 but none for maternal asthma ever. Two distinct CpGs were associated with paternal asthma. We observed 5 DMRs associated with maternal asthma during pregnancy 3 associated with maternal asthma ever and 13 DMRs associated with paternal asthma. Gene expression analysis using data in blood from 832 children and lung from 424 adults showed associations between identified DMCs using maternal asthma and expression of several genes, including HLA genes and HOXA5, previously implicated in asthma or lung function.\n\nParental asthma, especially maternal asthma during pregnancy, may be associated with alterations in newborn DNA methylation. These findings might shed light on underlying mechanisms for asthma susceptibility.", "doi": "10.1186/s13148-025-01858-4", "pmid": "40349045", "labels": {"NGI SNP genotyping": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12065361"}, {"db": "pii", "key": "10.1186/s13148-025-01858-4"}], "notes": [], "created": "2025-09-08T07:15:22.753Z", "modified": "2025-09-08T07:15:22.764Z"}, {"entity": "publication", "iuid": "188369759b0648d5ae25d06f97ae8ef1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/188369759b0648d5ae25d06f97ae8ef1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/188369759b0648d5ae25d06f97ae8ef1"}}, "title": "CpG island methylator phenotype classification improves risk assessment in pediatric T-cell acute lymphoblastic leukemia.", "authors": [{"family": "Sch\u00e4fer Hackenhaar", "given": "Fernanda", "initials": "F", "orcid": "0000-0002-9395-2216", "researcher": {"href": "https://publications.scilifelab.se/researcher/6ac3981903a34a4d855647822d5339d1.json"}}, {"family": "Refhagen", "given": "Nina", "initials": "N"}, {"family": "Hagleitner", "given": "Melanie", "initials": "M"}, {"family": "van Leeuwen", "given": "Frank", "initials": "F", "orcid": "0000-0003-1107-6513", "researcher": {"href": "https://publications.scilifelab.se/researcher/97425d5c32d14c86b3b8414b24f6a387.json"}}, {"family": "Marquart", "given": "Hanne Vibeke", "initials": "HV", "orcid": "0000-0001-9740-6522", "researcher": {"href": "https://publications.scilifelab.se/researcher/c9476b7116154ea9990d7c61c675c794.json"}}, {"family": "Madsen", "given": "Hans Ole", "initials": "HO"}, {"family": "Landfors", "given": "Mattias", "initials": "M", "orcid": "0000-0003-3974-4245", "researcher": {"href": "https://publications.scilifelab.se/researcher/7e2393ca69324818ac8bcb976da908be.json"}}, {"family": "Osterman", "given": "Pia", "initials": "P"}, {"family": "Schmiegelow", "given": "Kjeld", "initials": "K"}, {"family": "Flaegstad", "given": "Trond", "initials": "T"}, {"family": "J\u00f3nsson", "given": "\u00d3lafur", "initials": "\u00d3"}, {"family": "Kanerva", "given": "Jukka", "initials": "J"}, {"family": "Abrahamsson", "given": "Jonas", "initials": "J"}, {"family": "Heyman", "given": "Mats", "initials": "M", "orcid": "0000-0001-7637-1949", "researcher": {"href": "https://publications.scilifelab.se/researcher/d810139e533a4c2493e62b3e03bb9623.json"}}, {"family": "Nor\u00e9n Nystr\u00f6m", "given": "Ulrika", "initials": "U", "orcid": "0000-0001-5606-5442", "researcher": {"href": "https://publications.scilifelab.se/researcher/03f7a89bc35d4e72b4b2c0d4252b69f0.json"}}, {"family": "Hultdin", "given": "Magnus", "initials": "M"}, {"family": "Degerman", "given": "Sofie", "initials": "S", "orcid": "0000-0002-2783-0712", "researcher": {"href": "https://publications.scilifelab.se/researcher/8611162e883645f59195c4221199967f.json"}}], "type": "journal article", "published": "2025-05-08", "journal": {"title": "Blood", "issn": "1528-0020", "volume": "145", "issue": "19", "pages": "2161-2178", "issn-l": "0006-4971"}, "abstract": "Current intensive treatment of pediatric T-cell acute lymphoblastic leukemia (T-ALL) has substantial side effects, highlighting a need for novel biomarkers to improve risk stratification. Canonical biomarkers, such as genetics and immunophenotype, are largely not used in pediatric T-ALL stratification. This study aimed to validate the prognostic relevance of DNA methylation CpG island methylator phenotype (CIMP) risk stratification in 2 pediatric T-ALL patient cohorts: the Nordic Society of Paediatric Haematology (NOPHO) ALL2008 T-ALL study cohort (n = 192) and the Dutch Childhood Oncology Group (DCOG) ALL-10/ALL-11 validation cohorts (n = 156). Both cohorts revealed that combining CIMP classification at diagnosis with measurable residual disease (MRD) at treatment day 29 (D29) or 33 (D33) significantly improved outcome prediction. The poor prognosis subgroup, characterized by CIMP low/D29 or D33 MRD \u2265 0.1%, had a cumulative incidence of relapse (pCIR5yr) of 29% and 23% and overall survival (pOS5yr) of 59.7% and 65.4%, in NOPHO and DCOG, respectively. Conversely, a good prognosis subgroup was also identified representing CIMP high/D29 or D33 MRD < 0.1% with pCIR5yr of 0% and 3.4% and pOS5yr of 98.2% and 94.8%, in NOPHO and DCOG, respectively. For NOPHO, MRD was also evaluated on D15, and the relapse prediction accuracy of CIMP/D29 MRD (0.79) and CIMP/D15 MRD (0.75) classification was comparable, indicating potential for earlier stratification. The evaluation of the biology behind the CIMP subgroups revealed associations with transcriptome profiles, genomic aberrations, and mitotic history, suggesting distinct routes for leukemia development. In conclusion, integrating MRD assessment with the novel CIMP biomarker has the potential to improve risk stratification in pediatric T-ALL and guide future therapeutic decisions.", "doi": "10.1182/blood.2024026027", "pmid": "39841000", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pii", "key": "535228"}], "notes": [], "created": "2025-05-12T06:17:29.072Z", "modified": "2025-05-12T06:17:30.354Z"}, {"entity": "publication", "iuid": "592bb323bd1c4346b9df99f55f08eb97", "links": {"self": {"href": "https://publications.scilifelab.se/publication/592bb323bd1c4346b9df99f55f08eb97.json"}, "display": {"href": "https://publications.scilifelab.se/publication/592bb323bd1c4346b9df99f55f08eb97"}}, "title": "Elucidation of short linear motif-based interactions of the MIT and rhodanese domains of the ubiquitin-specific protease 8.", "authors": [{"family": "Konstantinou", "given": "Aimiliani", "initials": "A"}, {"family": "Varga", "given": "Julia K", "initials": "JK"}, {"family": "C\u00f3rdova-P\u00e9rez", "given": "Alicia", "initials": "A"}, {"family": "Simonetti", "given": "Leandro", "initials": "L"}, {"family": "Gomez-Lucas", "given": "Lidia", "initials": "L"}, {"family": "Schueler-Furman", "given": "Ora", "initials": "O"}, {"family": "Davey", "given": "Norman E", "initials": "NE"}, {"family": "Kulathu", "given": "Yogesh", "initials": "Y"}, {"family": "Ivarsson", "given": "Ylva", "initials": "Y"}], "type": "journal article", "published": "2025-05-06", "journal": {"title": "Biol. Direct", "issn": "1745-6150", "volume": "20", "issue": "1", "pages": "59", "issn-l": "1745-6150"}, "abstract": "Ubiquitin-specific protease 8 (USP8) is a deubiquitinating enzyme with essential functions in protein trafficking and stability. It is a multidomain protein, with an N-terminal MIT (microtubule interacting and trafficking) domain, followed by a non-catalytic rhodanese (Rhod) domain, a long intrinsically disordered region, and a C-terminal catalytic domain. The N-terminal MIT domain of USP8 is known to mediate protein-protein interactions through binding to short linear motifs. The non-catalytic Rhod domain is also involved in protein-protein interactions, however detailed insights into these interactions remain limited. In this study we explore the short linear motif-based interactions of the MIT and Rhod domains of USP8 using a combination of proteomic peptide-phage display, peptide arrays and deep mutational scanning. We show that the MIT domain can bind ligands with a general [DE][LIF]x{2,3}R[FYIL]xxL[LV] consensus motif. We uncover that the rhodanese domain of USP8 is a peptide-binding domain, and define two distinct binding motifs (Rx[LI]xGxxxPxxL and G[LV][DE][IM]WExKxxxLxE) for this domain by deep mutational scanning of two different peptide ligands. Using the motif information, we predict binding sites within known USP8 interactors and substrates and validate interactions through peptide array analysis. Our findings demonstrate that both the USP8 MIT and rhodanese domains are peptide-binding domains that can be bound by degenerate and distinct binding motifs. The detailed information on the peptide binding preference of the two N-terminal domains of USP8 provide novel insights into the molecular recognition events that underlie the function of this essential deubiquitinating enzyme.", "doi": "10.1186/s13062-025-00638-7", "pmid": "40329301", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12057046"}, {"db": "pii", "key": "10.1186/s13062-025-00638-7"}], "notes": [], "created": "2025-09-08T11:30:02.875Z", "modified": "2025-09-08T11:30:02.896Z"}, {"entity": "publication", "iuid": "54e65a8ce2c94cf5ac271086444360f9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/54e65a8ce2c94cf5ac271086444360f9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/54e65a8ce2c94cf5ac271086444360f9"}}, "title": "Sperm DNA methylation landscape and its links to male fertility in a non-model teleost using EM-seq.", "authors": [{"family": "Pappas", "given": "Fotis", "initials": "F", "orcid": "0000-0003-3696-5069", "researcher": {"href": "https://publications.scilifelab.se/researcher/238d355f0f5f4dd798fdc7f58d4c5a41.json"}}, {"family": "Johnsson", "given": "Martin", "initials": "M", "orcid": "0000-0003-1262-4585", "researcher": {"href": "https://publications.scilifelab.se/researcher/02b768197c08422aaad526f35c526eaf.json"}}, {"family": "Andersson", "given": "G\u00f6ran", "initials": "G", "orcid": "0000-0001-5131-3144", "researcher": {"href": "https://publications.scilifelab.se/researcher/39ce81c314db47c8ad63c3ed38dffcb3.json"}}, {"family": "Debes", "given": "Paul V", "initials": "PV", "orcid": "0000-0003-4491-9564", "researcher": {"href": "https://publications.scilifelab.se/researcher/e1887c01f5b343e19e398b3fcd96ba14.json"}}, {"family": "Palaiokostas", "given": "Christos", "initials": "C", "orcid": "0000-0002-4480-4612", "researcher": {"href": "https://publications.scilifelab.se/researcher/a1d6c65f53a8434cb1d5dd4c7bf5d444.json"}}], "type": "journal article", "published": "2025-05-00", "journal": {"title": "Heredity (Edinb)", "issn": "1365-2540", "volume": "134", "issue": "5", "pages": "293-305", "issn-l": "0018-067X"}, "abstract": "Differential DNA methylation due to epigenetic phenomena is crucial in regulating gene expression. Understanding the consequences of such differential expression on sperm quality parameters may provide insights into the underlying mechanisms of male reproductive success. Nonetheless, male fertility in fish remains understudied despite its critical importance to overall reproductive success in nature and captivity. This study investigated the DNA methylation landscape in spermatozoa of domesticated Arctic charr (Salvelinus alpinus) and its associations with sperm quality parameters. Computer assisted-semen analysis (CASA) was performed in 47 sperm samples of farmed Arctic charr, followed by enzymatic methylation sequencing (EM-seq). Our results showed that the DNA of Arctic charr sperm is highly methylated (mean value of ~86%), though variations were observed in genomic features involved in gene regulation. Methylation at variable CpG sites exhibited regional correlation decaying by physical distance, while methylation similarities among individuals were strongly coupled with genetic variation and mirrored pedigree structure. Comethylation network analyses for promoters, CpG islands and first introns revealed genomic modules significantly correlated with sperm quality traits (p < 0.05; Bonferroni adjusted), with distinct patterns suggesting a resource trade-off between sperm concentration and kinematics. Furthermore, annotation and gene-set enrichment analysis highlighted biological mechanisms related to spermatogenesis, cytoskeletal regulation, and mitochondrial function, all vital to sperm physiology. These findings suggest that DNA methylation is a critical and fundamental factor influencing male fertility in Arctic charr, providing insights into the underlying mechanisms of male reproductive success.", "doi": "10.1038/s41437-025-00756-y", "pmid": "40097595", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12056074"}, {"db": "pii", "key": "10.1038/s41437-025-00756-y"}], "notes": [], "created": "2025-09-08T06:59:19.759Z", "modified": "2025-11-14T11:06:34.293Z"}, {"entity": "publication", "iuid": "2db32f8194a7438484ff5bbd2844c22e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2db32f8194a7438484ff5bbd2844c22e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2db32f8194a7438484ff5bbd2844c22e"}}, "title": "Mutational signatures and kataegis in pediatric B-cell precursor acute lymphoblastic leukemia.", "authors": [{"family": "Gunnarsson", "given": "Rebeqa", "initials": "R", "orcid": "0000-0002-2283-786X", "researcher": {"href": "https://publications.scilifelab.se/researcher/12601745d2c74562bf83d22879f212eb.json"}}, {"family": "Yang", "given": "Minjun", "initials": "M", "orcid": "0000-0002-3324-1498", "researcher": {"href": "https://publications.scilifelab.se/researcher/62822d0b9c6c4a01a53829b9b05443ba.json"}}, {"family": "Biloglav", "given": "Andrea", "initials": "A"}, {"family": "Lundin-Str\u00f6m", "given": "Kristina B", "initials": "KB"}, {"family": "Lilljebj\u00f6rn", "given": "Henrik", "initials": "H"}, {"family": "Castor", "given": "Anders", "initials": "A"}, {"family": "Fioretos", "given": "Thoas", "initials": "T"}, {"family": "Olsson-Arvidsson", "given": "Linda", "initials": "L"}, {"family": "Paulsson", "given": "Kajsa", "initials": "K"}, {"family": "Johansson", "given": "Bertil", "initials": "B"}], "type": "letter", "published": "2025-05-00", "journal": {"title": "Hemasphere", "issn": "2572-9241", "volume": "9", "issue": "5", "pages": "e70136", "issn-l": null}, "abstract": null, "doi": "10.1002/hem3.70136", "pmid": "40395431", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12088958"}, {"db": "pii", "key": "HEM370136"}, {"db": "figshare", "key": "10.6084/m9.figshare.28053263"}], "notes": [], "created": "2025-09-08T07:07:08.984Z", "modified": "2025-09-08T07:07:09.087Z"}, {"entity": "publication", "iuid": "102255837dfd43148aaedb132eaadffa", "links": {"self": {"href": "https://publications.scilifelab.se/publication/102255837dfd43148aaedb132eaadffa.json"}, "display": {"href": "https://publications.scilifelab.se/publication/102255837dfd43148aaedb132eaadffa"}}, "title": "Genome-wide association study of direct oral anticoagulants and their relation to bleeding.", "authors": [{"family": "Attelind", "given": "Sofia", "initials": "S", "orcid": "0000-0002-7631-7376", "researcher": {"href": "https://publications.scilifelab.se/researcher/1544b43ea7d14369a4fb6de3174a1d00.json"}}, {"family": "Eriksson", "given": "Niclas", "initials": "N", "orcid": "0000-0002-2152-4343", "researcher": {"href": "https://publications.scilifelab.se/researcher/64611a83caba46d597f45371b77de26b.json"}}, {"family": "Wadelius", "given": "Mia", "initials": "M", "orcid": "0000-0002-6368-2622", "researcher": {"href": "https://publications.scilifelab.se/researcher/ec07b9869a1f4b77b734c5dc567dc630.json"}}, {"family": "Hallberg", "given": "P\u00e4r", "initials": "P", "orcid": "0000-0003-3465-3280", "researcher": {"href": "https://publications.scilifelab.se/researcher/968cb3fe072d4ed09739e8be6668d168.json"}}], "type": "journal article", "published": "2025-05-00", "journal": {"title": "Eur J Clin Pharmacol", "issn": "1432-1041", "volume": "81", "issue": "5", "pages": "771-783", "issn-l": null}, "abstract": "Direct oral anticoagulants (DOACs) are used to prevent and treat thromboembolic events in adults. We aimed to investigate whether pharmacogenomic variation contributes to the risk of bleeding during DOAC treatment.\n\nCases were recruited from reports of bleeding sent to the Swedish Medical Products Agency (n = 129, 60% men, 93% Swedish, 89% on factor Xa inhibitors) and compared with population controls (n = 4891) and a subset matched for exposure to DOACs (n = 353). We performed a genome-wide association study, with analyses of candidate single nucleotide polymorphisms (SNPs) and candidate gene set analyses.\n\nForty-four cases had major, 37 minor, and 48 clinically relevant non-major (CRNM) bleeding. When cases were compared with matched controls, BAIAP2L2 rs142001534 was significantly associated with any bleeding and major/CRNM bleeding (P = 4.66 \u00d7 10-8 and P = 3.28 \u00d7 10-8, respectively). The candidate SNP CYP3A5 rs776746 was significantly associated with major and major/CRNM bleeding (P = 0.00020 and P = 0.00025, respectively), and ABCG2 rs2231142 was nominally associated with any bleeding (P = 0.01499). Rare coding variants in the candidate gene VWF were significantly associated with any bleeding (P = 0.00296).\n\nBAIAP2L2, CYP3A5, ABCG2, and VWF may be associated with bleeding in DOAC-treated patients. The risk estimates of the candidate variants in CYP3A5 and ABCG2 were in the same direction as in previous studies. The Von Willebrand Factor gene (VWF) is linked to hereditary bleeding disorders, while there is no previous evidence of bleeding associated with BAIAP2L2.", "doi": "10.1007/s00228-025-03821-x", "pmid": "40116934", "labels": {"NGI SNP genotyping": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12003525"}, {"db": "pii", "key": "10.1007/s00228-025-03821-x"}], "notes": [], "created": "2025-09-08T11:34:07.950Z", "modified": "2025-09-08T11:34:08.131Z"}, {"entity": "publication", "iuid": "cc91895d782a4623b95f8d39c736a4cf", "links": {"self": {"href": "https://publications.scilifelab.se/publication/cc91895d782a4623b95f8d39c736a4cf.json"}, "display": {"href": "https://publications.scilifelab.se/publication/cc91895d782a4623b95f8d39c736a4cf"}}, "title": "Error Reduction in Leukemia Machine Learning Classification With Conformal Prediction.", "authors": [{"family": "Lysenkova Wiklander", "given": "Mariya", "initials": "M", "orcid": "0000-0002-0012-2310", "researcher": {"href": "https://publications.scilifelab.se/researcher/48850e5606b9470caa6b130286055388.json"}}, {"family": "Zachariah", "given": "Dave", "initials": "D", "orcid": "0000-0002-6698-0166", "researcher": {"href": "https://publications.scilifelab.se/researcher/cdf118819f654f32ad53f994e83c227d.json"}}, {"family": "Krali", "given": "Olga", "initials": "O", "orcid": "0000-0002-6436-9531", "researcher": {"href": "https://publications.scilifelab.se/researcher/14a6e2f99d3b4758a10af78b93777779.json"}}, {"family": "Nordlund", "given": "Jessica", "initials": "J", "orcid": "0000-0001-8699-9959", "researcher": {"href": "https://publications.scilifelab.se/researcher/ddf48c9262134821bcc6ce1180049753.json"}}], "type": "journal article", "published": "2025-05-00", "journal": {"title": "JCO Clin Cancer Inform", "issn": "2473-4276", "volume": "9", "pages": "e2400324", "issn-l": null}, "abstract": "Recent advances in machine learning have led to the development of classifiers that predict molecular subtypes of acute lymphoblastic leukemia (ALL) using RNA-sequencing (RNA-seq) data. Although these models have shown promising results, they often lack robust performance guarantees. The aim of this study was three-fold: to quantify the uncertainty of these classifiers, to provide prediction sets that control the false-negative rate (FNR), and to perform implicit error reduction by transforming incorrect predictions into uncertain predictions.\n\nConformal prediction (CP) is a distribution-agnostic framework for generating statistically calibrated prediction sets whose size reflects model uncertainty. In this study, we applied an extension called conformal risk control to three RNA-seq ALL subtype classifiers. Leveraging RNA-seq data from 1,227 patient samples taken at diagnosis, we developed a multiclass conformal predictor ALLCoP, which generates statistically guaranteed FNR-controlled prediction sets.\n\nALLCoP was able to create prediction sets with specified FNR tolerances ranging from 7.5% to 30%. In a validation cohort, ALLCoP successfully reduced the FNR of the ALLIUM RNA-seq ALL subtype classifier from 8.95% to 3.5%. For patients whose subtype was not previously known, the use of ALLCoP was able to reduce the occurrence of empty predictions from 37% to 17%. Notably, up to 34% of the multiple-class prediction sets included the PAX5alt subtype, suggesting that increased prediction set size may reflect secondary aberrations and biological complexity, contributing to classifier uncertainty. Finally, ALLCoP was validated on two additional RNA-seq ALL subtype classifiers, ALLSorts and ALLCatchR.\n\nOur results highlight the potential of CP in enhancing the use of oncologic RNA-seq subtyping classifiers and also in uncovering additional molecular aberrations of potential clinical importance.", "doi": "10.1200/CCI-24-00324", "pmid": "40435436", "labels": {"National Genomics Infrastructure": "Service", "NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12133051"}], "notes": [], "created": "2025-11-07T07:27:00.813Z", "modified": "2025-11-14T11:08:56.250Z"}, {"entity": "publication", "iuid": "c98d5ccd590e4c039a3d963c2cbb2bd1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c98d5ccd590e4c039a3d963c2cbb2bd1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c98d5ccd590e4c039a3d963c2cbb2bd1"}}, "title": "Disruption-induced changes in syntrophic propionate and acetate oxidation: flocculation, cell proximity, and microbial activity.", "authors": [{"family": "Weng", "given": "Nils", "initials": "N"}, {"family": "Najafabadi", "given": "Hossein Nadali", "initials": "HN"}, {"family": "Westerholm", "given": "Maria", "initials": "M"}], "type": "journal article", "published": "2025-04-19", "journal": {"title": "Biotechnol Biofuels Bioprod", "issn": "2731-3654", "issn-l": null, "volume": "18", "issue": "1", "pages": "45"}, "abstract": "Syntrophic propionate- and acetate-oxidising bacteria (SPOB and SAOB) play a crucial role in biogas production, particularly under high ammonia conditions that are common in anaerobic degradation of protein-rich waste streams. These bacteria rely on close interactions with hydrogenotrophic methanogens to facilitate interspecies electron transfer and maintain thermodynamic feasibility. However, the impact of mixing-induced disruption of these essential syntrophic interactions in biogas systems remains largely unexplored. This study investigates how magnetic stirring and orbital shaking influence degradation dynamics, microbial community composition, and gene expression in syntrophic enrichment communities under high-ammonia conditions.\r\n\r\nStirring significantly delayed the initiation of propionate degradation in one culture and completely inhibited it in the other two parallel cultures, whereas acetate degradation was less affected. Computational fluid dynamics modelling revealed that stirring generated higher shear rates (~ 20 s-1) and uniform cell distribution, while shaking led to lower shear rates and cell accumulation at the bottom of the culture bottle. Visual observations confirmed that stirring inhibited floc formation, while shaking promoted larger flocs compared to the static control condition, which formed smaller flocs and a sheet-like biofilm. Microbial community analysis identified substrate type and degradation progress as primary drivers of community structure, with motion displaying minimal influence. However, metatranscriptomic analysis revealed that motion-induced gene downregulation was associated with motility, surface sensing, and biofilm formation in SAOB and another bacterial species expressing genes for the glycine synthase reductase pathway. Stirring also suppressed oxalate-formate antiporter expression in SPOB, suggesting its dependence on spatial proximity for this energy-conserving mechanism. The strongest gene expression changes of stirring were observed in methanogens, indicating a coupling of the first and last steps of hydrogenotrophic methanogenesis, likely an adaptive strategy for efficient energy conservation. Other downregulated genes included ferrous iron transporters and electron transfer-associated enzymes.\r\n\r\nThis study highlights that stirring critically disrupts the initial syntrophic connection between SPOB and methanogens, whereas SAOB communities exhibit greater tolerance to shear stress and disruptive conditions that inhibits aggregate formation. These findings emphasize the importance of carefully managing mixing regimes, especially when attempting to reactivate ammonia-tolerant syntrophic propionate degraders in biogas systems experiencing rapid propionate accumulation under high-ammonia conditions.", "doi": "10.1186/s13068-025-02644-3", "pmid": "40253350", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pmc", "key": "PMC12008871"}, {"db": "pii", "key": "10.1186/s13068-025-02644-3"}], "notes": [], "created": "2025-09-08T11:37:37.001Z", "modified": "2025-10-08T15:40:18.553Z"}, {"entity": "publication", "iuid": "5693c08391ae49c7a5b87864c53e6f34", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5693c08391ae49c7a5b87864c53e6f34.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5693c08391ae49c7a5b87864c53e6f34"}}, "title": "Nuclear AGO2 supports influenza A virus replication through type-I interferon regulation.", "authors": [{"family": "Huang", "given": "Hsiang-Chi", "initials": "HC"}, {"family": "Fong", "given": "Michelle", "initials": "M"}, {"family": "Nowak", "given": "Iwona", "initials": "I"}, {"family": "Shcherbinina", "given": "Evgeniia", "initials": "E"}, {"family": "Lobo", "given": "Vivian", "initials": "V"}, {"family": "Besavilla", "given": "Danica F", "initials": "DF"}, {"family": "Huynh", "given": "Hang T", "initials": "HT"}, {"family": "Sch\u00f6n", "given": "Karin", "initials": "K"}, {"family": "Westholm", "given": "Jakub O", "initials": "JO"}, {"family": "Fernandez", "given": "Carola", "initials": "C"}, {"family": "Patel", "given": "Angana A H", "initials": "AAH"}, {"family": "Wiel", "given": "Clotilde", "initials": "C"}, {"family": "Sayin", "given": "Volkan I", "initials": "VI"}, {"family": "Anastasakis", "given": "Dimitrios G", "initials": "DG"}, {"family": "Angeletti", "given": "Davide", "initials": "D", "orcid": "0000-0002-5256-1972", "researcher": {"href": "https://publications.scilifelab.se/researcher/ae59c12bf82b4ad9a8d9ad8603d03d9c.json"}}, {"family": "Sarshad", "given": "Aishe A", "initials": "AA", "orcid": "0000-0001-7153-5959", "researcher": {"href": "https://publications.scilifelab.se/researcher/42c62bd8dbe34b5da39de17d6a2a06ab.json"}}], "type": "journal article", "published": "2025-04-10", "journal": {"title": "Nucleic Acids Res.", "issn": "1362-4962", "issn-l": "0305-1048", "volume": "53", "issue": "7", "pages": null}, "abstract": "The role of Argonaute (AGO) proteins and the RNA interference (RNAi) machinery in mammalian antiviral response has been debated. Therefore, we set out to investigate how mammalian RNAi impacts influenza A virus (IAV) infection. We reveal that IAV infection triggers nuclear accumulation of AGO2, which is directly facilitated by p53 activation. Mechanistically, we show that IAV induces nuclear AGO2 targeting of TRIM71and type-I interferon-pathway genes for silencing. Accordingly, Tp53-/- mice do not accumulate nuclear AGO2 and demonstrate decreased susceptibility to IAV infection. Hence, the RNAi machinery is highjacked by the virus to evade the immune system and support viral replication. Furthermore, the FDA-approved drug, arsenic trioxide, prevents p53 nuclear translocation, increases interferon response and decreases viral replication in vitro and in a mouse model in vivo. Our data indicate that targeting the AGO2:p53-mediated silencing of innate immunity may offer a promising strategy to mitigate viral infections.", "doi": "10.1093/nar/gkaf268", "pmid": "40219968", "labels": {"Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics (NBIS)": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11992678"}, {"db": "pii", "key": "8112696"}], "notes": [], "created": "2025-04-16T07:03:31.301Z", "modified": "2025-09-08T11:29:59.901Z"}, {"entity": "publication", "iuid": "59b7b1a3171445408a05b3c342c2dc3b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/59b7b1a3171445408a05b3c342c2dc3b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/59b7b1a3171445408a05b3c342c2dc3b"}}, "title": "Genome-wide comparison reveals large structural variants in cassava landraces.", "authors": [{"family": "Landi", "given": "Michael", "initials": "M"}, {"family": "Carluccio", "given": "Anna Vittoria", "initials": "AV"}, {"family": "Shah", "given": "Trushar", "initials": "T"}, {"family": "Niazi", "given": "Adnan", "initials": "A"}, {"family": "Stavolone", "given": "Livia", "initials": "L"}, {"family": "Falquet", "given": "Laurent", "initials": "L"}, {"family": "Gisel", "given": "Andreas", "initials": "A"}, {"family": "Bongcam-Rudloff", "given": "Erik", "initials": "E"}], "type": "journal article", "published": "2025-04-10", "journal": {"title": "BMC Genomics", "issn": "1471-2164", "volume": "26", "issue": "1", "pages": "362", "issn-l": "1471-2164"}, "abstract": "Structural variants (SVs) are critical for plant genomic diversity and phenotypic variation. This study investigates a large, 9.7 Mbp highly repetitive segment on chromosome 12 of TMEB117, a region not previously characterized in cassava (Manihot esculenta Crantz). We aim to explore its presence and variability across multiple cassava landraces, providing insights into its genomic significance and potential implications.\n\nWe validated the presence of the 9.7 Mbp segment in the TMEB117 genome, distinguishing it from other published cassava genome assemblies. By mapping short-read sequencing data from 16 cassava landraces to TMEB117 chromosome 12, we observed variability in read mapping, suggesting that while all genotypes contain the insertion region, some exhibit missing segments or sequence differences. Further analysis revealed two unique genes associated with deacetylase activity, HDA14 and SRT2, within the insertion. Additionally, the MUDR-Mutator transposable element was significantly overrepresented in this region.\n\nThis study uncovers a large structural variant in the TMEB117 cassava genome, highlighting its variability among different genotypes. The enrichment of HDA14 and SRT2 genes and the MUDR-Mutator elements within the insertion suggests potential functional significance, though further research is needed to explore this. These findings provide important insights into the role of structural variations in shaping cassava genomic diversity.", "doi": "10.1186/s12864-025-11523-y", "pmid": "40211122", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11987339"}, {"db": "pii", "key": "10.1186/s12864-025-11523-y"}], "notes": [], "created": "2025-09-08T06:59:22.722Z", "modified": "2025-09-08T06:59:22.728Z"}, {"entity": "publication", "iuid": "a624b6ccad7b449fa079200d5b4a545f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a624b6ccad7b449fa079200d5b4a545f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a624b6ccad7b449fa079200d5b4a545f"}}, "title": "Genetic influence of a STAU2 frameshift mutation and RELN regulatory elements on performance in Icelandic horses.", "authors": [{"family": "Sigur\u00f0ard\u00f3ttir", "given": "Hei\u00f0r\u00fan", "initials": "H"}, {"family": "Eriksson", "given": "Susanne", "initials": "S"}, {"family": "Niazi", "given": "Adnan", "initials": "A"}, {"family": "Rhodin", "given": "Marie", "initials": "M"}, {"family": "Albertsd\u00f3ttir", "given": "Elsa", "initials": "E"}, {"family": "Kristjansson", "given": "Thorvaldur", "initials": "T"}, {"family": "Lindgren", "given": "Gabriella", "initials": "G"}], "type": "journal article", "published": "2025-04-04", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "15", "issue": "1", "pages": "11641", "issn-l": "2045-2322"}, "abstract": "Selection for performance in horse breeding benefits from precise genetic insights at a molecular level, but knowledge remains limited. This study used whole-genome sequences of 39 elite and non-elite Icelandic horses to identify candidate causal variants linked to previously identified haplotypes in the STAU2 and RELN genes affecting pace and other gaits. A frameshift variant in linkage disequilibrium with the previously identified haplotypes in the STAU2 gene (r2 = 0.85) was identified within a predicted STAU2 transcript. This variant alters the amino acid sequence and introduces a premature stop codon but does not appear harmful or disease-causing and is potentially unique to equine biology. A large portion of the RELN haplotype overlapped with an H3K27me3 modification mark, suggesting a regulatory role of this region. Despite the small sample size, the RELN haplotype's effects were validated for t\u00f6lt, trot, and canter/gallop. Additionally, the RELN haplotype significantly influenced the age at which horses were presented for breeding field tests, indicating a potential role of the region in precocity and trainability. Functional experiments are needed to further investigate the regions' influences on biological processes and their potential impact on horse performance.", "doi": "10.1038/s41598-025-95593-8", "pmid": "40185812", "labels": {"National Genomics Infrastructure": "Service", "NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11971302"}, {"db": "pii", "key": "10.1038/s41598-025-95593-8"}], "notes": [], "created": "2025-11-07T07:27:05.828Z", "modified": "2025-11-14T11:07:06.654Z"}, {"entity": "publication", "iuid": "49398b063f5d4500a3dd373382da546a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/49398b063f5d4500a3dd373382da546a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/49398b063f5d4500a3dd373382da546a"}}, "title": "A genome-wide association study of imaging-defined atherosclerosis.", "authors": [{"family": "Gummesson", "given": "Anders", "initials": "A", "orcid": "0000-0003-0024-960X", "researcher": {"href": "https://publications.scilifelab.se/researcher/cb164de27f2846328bb675876922a5fe.json"}}, {"family": "Lundmark", "given": "Per", "initials": "P", "orcid": "0009-0006-2334-8802", "researcher": {"href": "https://publications.scilifelab.se/researcher/f30b1a2e60d646c4a0cc0be06ffe77dd.json"}}, {"family": "Chen", "given": "Qiao Sen", "initials": "QS", "orcid": "0000-0002-5864-7574", "researcher": {"href": "https://publications.scilifelab.se/researcher/84dde05e01624f07a374810c1086f20a.json"}}, {"family": "Bj\u00f6rnson", "given": "Elias", "initials": "E"}, {"family": "Dekkers", "given": "Koen F", "initials": "KF", "orcid": "0000-0002-4074-7235", "researcher": {"href": "https://publications.scilifelab.se/researcher/ee8d56ef781e42d5b6f21b551054a3e7.json"}}, {"family": "Hammar", "given": "Ulf", "initials": "U"}, {"family": "Adiels", "given": "Martin", "initials": "M"}, {"family": "Wang", "given": "Yunzhang", "initials": "Y", "orcid": "0000-0003-1165-3595", "researcher": {"href": "https://publications.scilifelab.se/researcher/2869602ee77944d2b1a736638a76bb3a.json"}}, {"family": "Andersson", "given": "Therese", "initials": "T"}, {"family": "Bergstr\u00f6m", "given": "G\u00f6ran", "initials": "G", "orcid": "0000-0003-4289-5722", "researcher": {"href": "https://publications.scilifelab.se/researcher/fbc3ade3079e4265ad42ed1be485bc24.json"}}, {"family": "Carlh\u00e4ll", "given": "Carl-Johan", "initials": "CJ"}, {"family": "Erlinge", "given": "David", "initials": "D"}, {"family": "Jernberg", "given": "Tomas", "initials": "T"}, {"family": "Landfors", "given": "Fredrik", "initials": "F", "orcid": "0000-0002-5695-2276", "researcher": {"href": "https://publications.scilifelab.se/researcher/d85f85dce6c548fd9f36ac1540c9aff3.json"}}, {"family": "Lind", "given": "Lars", "initials": "L"}, {"family": "Mannila", "given": "Maria", "initials": "M", "orcid": "0000-0001-6189-2901", "researcher": {"href": "https://publications.scilifelab.se/researcher/786397ffc6a54d3e8c54f5493fbb7aa2.json"}}, {"family": "Melander", "given": "Olle", "initials": "O"}, {"family": "Pirazzi", "given": "Carlo", "initials": "C"}, {"family": "Sundstr\u00f6m", "given": "Johan", "initials": "J"}, {"family": "\u00d6stgren", "given": "Carl Johan", "initials": "CJ", "orcid": "0000-0003-1617-3179", "researcher": {"href": "https://publications.scilifelab.se/researcher/d4b5d952d50c4801aa88c0c9ae0d5813.json"}}, {"family": "Gunnarsson", "given": "Cecilia", "initials": "C", "orcid": "0000-0001-9474-6820", "researcher": {"href": "https://publications.scilifelab.se/researcher/ed1a42fede5f4f6d87c20d6bb9f694de.json"}}, {"family": "Orho-Melander", "given": "Marju", "initials": "M", "orcid": "0000-0002-3578-2503", "researcher": {"href": "https://publications.scilifelab.se/researcher/7e54fbe6f0fc4eed93108b382e1b2952.json"}}, {"family": "S\u00f6derberg", "given": "Stefan", "initials": "S", "orcid": "0000-0001-9225-1306", "researcher": {"href": "https://publications.scilifelab.se/researcher/b13944767ad9446e885ce32ca88afebd.json"}}, {"family": "Fall", "given": "Tove", "initials": "T", "orcid": "0000-0003-2071-5866", "researcher": {"href": "https://publications.scilifelab.se/researcher/4ed3f066719f43b291743a8bdaf3d2a0.json"}}, {"family": "Gigante", "given": "Bruna", "initials": "B", "orcid": "0000-0003-4508-7990", "researcher": {"href": "https://publications.scilifelab.se/researcher/3ac1bdc52e3241ea9eb5645f603229a3.json"}}], "type": "journal article", "published": "2025-03-31", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "16", "issue": "1", "pages": "2266", "issn-l": "2041-1723"}, "abstract": "Imaging-defined atherosclerosis represents an intermediate phenotype of atherosclerotic cardiovascular disease (ASCVD). Genome-wide association studies (GWAS) on directly measured coronary plaques using coronary computed tomography angiography (CCTA) are scarce. In the so far largest population-based cohort with CCTA data, we performed a GWAS on coronary plaque burden as determined by the segment involvement score (SIS) in 24,811 European individuals. We identified 20 significant independent genetic markers for SIS, three of which were found in loci not implicated in ASCVD before. Further GWAS on coronary artery calcification showed similar results to that of SIS, whereas a GWAS on ultrasound-assessed carotid plaques identified both shared and non-shared loci with SIS. In two-sample Mendelian randomization studies using SIS-associated markers in UK Biobank and CARDIoGRAMplusC4D, one extra coronary segment with atherosclerosis corresponded to 1.8-fold increased odds of myocardial infarction. This GWAS data can aid future studies of causal pathways in ASCVD.", "doi": "10.1038/s41467-025-57457-7", "pmid": "40164586", "labels": {"NGI SNP genotyping": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11958696"}, {"db": "pii", "key": "10.1038/s41467-025-57457-7"}], "notes": [], "created": "2025-05-12T05:48:37.162Z", "modified": "2025-11-14T11:06:44.446Z"}, {"entity": "publication", "iuid": "647d53b18b37408db896d3a565fec76c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/647d53b18b37408db896d3a565fec76c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/647d53b18b37408db896d3a565fec76c"}}, "title": "The DNA methylation landscape of primary triple-negative breast cancer.", "authors": [{"family": "Aine", "given": "Mattias", "initials": "M", "orcid": "0000-0002-0851-5952", "researcher": {"href": "https://publications.scilifelab.se/researcher/ec863fc84b064759b355272fa1be61ff.json"}}, {"family": "Nacer", "given": "Deborah F", "initials": "DF", "orcid": "0000-0002-7117-1371", "researcher": {"href": "https://publications.scilifelab.se/researcher/e484e25cfdf64d27842357355409dbfc.json"}}, {"family": "Arbajian", "given": "Elsa", "initials": "E", "orcid": "0000-0002-1484-0073", "researcher": {"href": "https://publications.scilifelab.se/researcher/e9615e08a1a04fada47e805c27a29c61.json"}}, {"family": "Veerla", "given": "Srinivas", "initials": "S", "orcid": "0000-0001-7328-6239", "researcher": {"href": "https://publications.scilifelab.se/researcher/c203a0b3112f4f499ccc79db3e47b303.json"}}, {"family": "Karlsson", "given": "Anna", "initials": "A", "orcid": "0000-0001-6974-5965", "researcher": {"href": "https://publications.scilifelab.se/researcher/016d7daf94304064a461e0df719112c5.json"}}, {"family": "H\u00e4kkinen", "given": "Jari", "initials": "J", "orcid": "0000-0002-8466-9179", "researcher": {"href": "https://publications.scilifelab.se/researcher/9b8605b9a7c74b20986146f020cf4b8f.json"}}, {"family": "Johansson", "given": "Henrik J", "initials": "HJ", "orcid": "0000-0003-4729-4205", "researcher": {"href": "https://publications.scilifelab.se/researcher/18aebf211fa640f48a7c8d860c168e5a.json"}}, {"family": "Rosengren", "given": "Frida", "initials": "F"}, {"family": "Vallon-Christersson", "given": "Johan", "initials": "J", "orcid": "0000-0002-2195-0385", "researcher": {"href": "https://publications.scilifelab.se/researcher/648fa1d04cb640858fe3534d04cd04d1.json"}}, {"family": "Borg", "given": "\u00c5ke", "initials": "\u00c5", "orcid": "0000-0002-5793-132X", "researcher": {"href": "https://publications.scilifelab.se/researcher/127501d4e0854d14a4120acee9042bb7.json"}}, {"family": "Staaf", "given": "Johan", "initials": "J", "orcid": "0000-0001-5254-5115", "researcher": {"href": "https://publications.scilifelab.se/researcher/07acbd7f211e4809a8195e2ccf5faf57.json"}}], "type": "journal article", "published": "2025-03-28", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "16", "issue": "1", "pages": "3041", "issn-l": "2041-1723"}, "abstract": "Triple-negative breast cancer (TNBC) is a clinically challenging and molecularly heterogenous breast cancer subgroup. Here, we investigate the DNA methylation landscape of TNBC. By analyzing tumor methylome profiles and accounting for the genomic context of CpG methylation, we divide TNBC into two epigenetic subtypes corresponding to a Basal and a non-Basal group, in which characteristic transcriptional patterns are correlated with DNA methylation of distal regulatory elements and epigenetic regulation of key steroid response genes and developmental transcription factors. Further subdivision of the Basal and non-Basal subtypes identifies subgroups transcending genetic and proposed TNBC mRNA subtypes, demonstrating widely differing immunological microenvironments, putative epigenetically-mediated immune evasion strategies, and a specific metabolic gene network in older patients that may be epigenetically regulated. Our study attempts to target the epigenetic backbone of TNBC, an approach that may inform future studies regarding tumor origins and the role of the microenvironment in shaping the cancer epigenome.", "doi": "10.1038/s41467-025-58158-x", "pmid": "40155623", "labels": {"Clinical Genomics Lund": "Service", "NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11953470"}, {"db": "pii", "key": "10.1038/s41467-025-58158-x"}], "notes": [], "created": "2025-04-14T12:30:37.267Z", "modified": "2025-09-08T06:57:25.392Z"}, {"entity": "publication", "iuid": "a2b369b29d704e429e7d6fc25ebcdee7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a2b369b29d704e429e7d6fc25ebcdee7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a2b369b29d704e429e7d6fc25ebcdee7"}}, "title": "Genetic Origins of the Kiritimati Population from Central-Eastern Micronesia.", "authors": [{"family": "Larena", "given": "Maximilian", "initials": "M", "orcid": "0000-0002-8799-7645", "researcher": {"href": "https://publications.scilifelab.se/researcher/5d580f1f3e584c809f5f22d7355f154f.json"}}, {"family": "Chowdhury", "given": "Afifa Enam", "initials": "AE", "orcid": "0009-0000-8509-0276", "researcher": {"href": "https://publications.scilifelab.se/researcher/4d3db9785b2f47fd93c5d4a23d8b2ced.json"}}, {"family": "Kels", "given": "Ma Junaliah Tuazon", "initials": "MJT", "orcid": "0000-0002-8730-1062", "researcher": {"href": "https://publications.scilifelab.se/researcher/083b0316d97f4be3a43126d01f9a173e.json"}}, {"family": "T\u00e4tte", "given": "Kai", "initials": "K", "orcid": "0000-0002-4753-8954", "researcher": {"href": "https://publications.scilifelab.se/researcher/d44e6836c0144dac85f38f1054520e44.json"}}, {"family": "Metspalu", "given": "Mait", "initials": "M", "orcid": "0000-0003-3099-9161", "researcher": {"href": "https://publications.scilifelab.se/researcher/0557a5b67af948ee8e47473a8ee621d7.json"}}, {"family": "Schlebusch", "given": "Carina M", "initials": "CM", "orcid": "0000-0002-8160-9621", "researcher": {"href": "https://publications.scilifelab.se/researcher/682f10853c1145649b8c76680605dd9b.json"}}, {"family": "Garcia-Bertrand", "given": "Ralph", "initials": "R", "orcid": "0000-0003-3011-9822", "researcher": {"href": "https://publications.scilifelab.se/researcher/7e0cd4c1175c444c912c1a6db7f44665.json"}}, {"family": "Herrera", "given": "Rene J", "initials": "RJ", "orcid": "0000-0002-5119-4381", "researcher": {"href": "https://publications.scilifelab.se/researcher/8cd8305c817e4adabe92faeebb02fe6e.json"}}], "type": "journal article", "published": "2025-03-06", "journal": {"title": "Genome Biol Evol", "issn": "1759-6653", "volume": "17", "issue": "3", "issn-l": "1759-6653"}, "abstract": "The migration of Austronesian-speaking populations through Oceania has intrigued researchers for decades. The Kiribati islands, situated along the boundaries of Micronesia and Polynesia, provide a crucial link in this migration. We analyzed the genome-wide data of the Kiritimati population of Kiribati to uncover their genetic origins and connections with other Oceanian groups. Our study reveals that the Kiritimati population primarily exhibits Remote Oceanian-related ancestry associated with ancient Lapita and present-day Polynesian populations. In addition, our identity-by-descent analysis identifies populations from the coastal southern Philippines as their closest relatives in Island Southeast Asia. The genetic links between Kiritimati, ancient Lapita, and modern Polynesians underscore the shared ancestry and continuous gene flow across these regions. This genetic continuity and ongoing links are supported by linguistic and cultural evidence, illustrating a complex history of migration and admixture in Oceania.", "doi": "10.1093/gbe/evaf046", "pmid": "40065639", "labels": {"NGI SNP genotyping": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11937891"}, {"db": "pii", "key": "8069057"}], "notes": [], "created": "2025-09-08T07:15:27.954Z", "modified": "2025-11-14T11:07:53.391Z"}, {"entity": "publication", "iuid": "59ebc9f2f08d46dcafe5fe8d76317dbf", "links": {"self": {"href": "https://publications.scilifelab.se/publication/59ebc9f2f08d46dcafe5fe8d76317dbf.json"}, "display": {"href": "https://publications.scilifelab.se/publication/59ebc9f2f08d46dcafe5fe8d76317dbf"}}, "title": "Genomic characterization of the HER2-enriched intrinsic molecular subtype in primary ER-positive HER2-negative breast cancer.", "authors": [{"family": "Hohmann", "given": "Lennart", "initials": "L", "orcid": "0000-0002-0281-7140", "researcher": {"href": "https://publications.scilifelab.se/researcher/b605a3b893a24a238b5bb6eddd27b672.json"}}, {"family": "Sigurjonsdottir", "given": "Kristin", "initials": "K"}, {"family": "Campos", "given": "Ana Bosch", "initials": "AB"}, {"family": "Nacer", "given": "Deborah F", "initials": "DF", "orcid": "0000-0002-7117-1371", "researcher": {"href": "https://publications.scilifelab.se/researcher/e484e25cfdf64d27842357355409dbfc.json"}}, {"family": "Veerla", "given": "Srinivas", "initials": "S", "orcid": "0000-0001-7328-6239", "researcher": {"href": "https://publications.scilifelab.se/researcher/c203a0b3112f4f499ccc79db3e47b303.json"}}, {"family": "Rosengren", "given": "Frida", "initials": "F"}, {"family": "Reddy", "given": "Poojaswini Thimmaraya", "initials": "PT", "orcid": "0009-0009-7743-4986", "researcher": {"href": "https://publications.scilifelab.se/researcher/868440eeaf364b28aa186eb24b37e2d8.json"}}, {"family": "H\u00e4kkinen", "given": "Jari", "initials": "J", "orcid": "0000-0002-8466-9179", "researcher": {"href": "https://publications.scilifelab.se/researcher/9b8605b9a7c74b20986146f020cf4b8f.json"}}, {"family": "Nordborg", "given": "Nicklas", "initials": "N"}, {"family": "Vallon-Christersson", "given": "Johan", "initials": "J", "orcid": "0000-0002-2195-0385", "researcher": {"href": "https://publications.scilifelab.se/researcher/648fa1d04cb640858fe3534d04cd04d1.json"}}, {"family": "Memari", "given": "Yasin", "initials": "Y"}, {"family": "Black", "given": "Daniella", "initials": "D"}, {"family": "Bowden", "given": "Ramsay", "initials": "R", "orcid": "0000-0003-1138-4452", "researcher": {"href": "https://publications.scilifelab.se/researcher/0b6effa9663145dabd83b3ced199385c.json"}}, {"family": "Davies", "given": "Helen R", "initials": "HR", "orcid": "0000-0001-6381-3664", "researcher": {"href": "https://publications.scilifelab.se/researcher/e02b6738c9e140858456e24cef5d6b42.json"}}, {"family": "Borg", "given": "\u00c5ke", "initials": "\u00c5", "orcid": "0000-0002-5793-132X", "researcher": {"href": "https://publications.scilifelab.se/researcher/127501d4e0854d14a4120acee9042bb7.json"}}, {"family": "Nik-Zainal", "given": "Serena", "initials": "S", "orcid": "0000-0001-5054-1727", "researcher": {"href": "https://publications.scilifelab.se/researcher/af746cf472144e1699ee12fa08921c1d.json"}}, {"family": "Staaf", "given": "Johan", "initials": "J", "orcid": "0000-0001-5254-5115", "researcher": {"href": "https://publications.scilifelab.se/researcher/07acbd7f211e4809a8195e2ccf5faf57.json"}}], "type": "journal article", "published": "2025-03-05", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "16", "issue": "1", "pages": "2208", "issn-l": "2041-1723"}, "abstract": "ER-positive/HER2-negative (ERpHER2n) breast cancer classified as PAM50 HER2-enriched (ERpHER2n-HER2E) represents a small high-risk patient subgroup. In this study, we investigate genomic, transcriptomic, and clinical features of ERpHER2n-HER2E breast tumors using two primary ERpHER2n cohorts comprising a total of 5640 patients. We show that ERpHER2n-HER2E tumors exhibit aggressive clinical features and poorer clinical outcomes compared to Luminal A and Luminal B tumors. Furthermore, ERpHER2n-HER2E breast cancer does not consist of misclassified or HER2-low cases, has little impact of ERBB2, is highly proliferative and less ER dependent than other luminal subtypes. It is not an obvious biological entity but is nevertheless associated with potentially targetable molecular features, notably a high immune response and high FGFR4 expression. Strikingly, molecular features that define the HER2E subtype in luminal disease are also consistent in HER2-positive disease, including an epigenetic mechanism for high FGFR4 expression in breast cancer.", "doi": "10.1038/s41467-025-57419-z", "pmid": "40044693", "labels": {"NGI SNP genotyping": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11882987"}, {"db": "pii", "key": "10.1038/s41467-025-57419-z"}], "notes": [], "created": "2025-09-08T07:15:25.268Z", "modified": "2025-09-08T07:15:25.630Z"}, {"entity": "publication", "iuid": "4f4d1f7839b6467eb6f4d7b6b2564378", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4f4d1f7839b6467eb6f4d7b6b2564378.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4f4d1f7839b6467eb6f4d7b6b2564378"}}, "title": "Genomic prediction of bone strength in laying hens using different sources of information.", "authors": [{"family": "Sallam", "given": "M", "initials": "M"}, {"family": "Wall", "given": "H", "initials": "H"}, {"family": "Wilson", "given": "P W", "initials": "PW"}, {"family": "Andersson", "given": "B", "initials": "B"}, {"family": "Schmutz", "given": "M", "initials": "M"}, {"family": "Benavides", "given": "C", "initials": "C"}, {"family": "Checa", "given": "M", "initials": "M"}, {"family": "Sanchez-Rodriguez", "given": "E", "initials": "E"}, {"family": "Rodriguez-Navarro", "given": "A B", "initials": "AB"}, {"family": "Kindmark", "given": "A", "initials": "A"}, {"family": "Dunn", "given": "I C", "initials": "IC"}, {"family": "de Koning", "given": "D-J", "initials": "DJ"}, {"family": "Johnsson", "given": "M", "initials": "M"}], "type": "journal article", "published": "2025-03-00", "journal": {"title": "Animal", "issn": "1751-732X", "volume": "19", "issue": "3", "pages": "101452", "issn-l": null}, "abstract": "Bone damage in laying hens remains a significant welfare concern in the egg industry. Breeding companies rely on selective cross-breeding of purebred birds to produce commercial hybrids, which farmers raise for table-egg production. Genomic prediction is a potential tool to improve bone quality in laying hens. Because commercial layers are crossbred and kept in different environments than pure lines, the question arises whether to use within-line purebred selection or whether to use crossbred data. While selection based on pure line data is common, achieving optimal bone strength in hybrids may require incorporating hybrid data to account for heterosis and housing-specific effects. This study aims to evaluate how combining pure line and hybrid data could affect the accuracy of breeding values for bone strength. Genotypes and phenotypes were available from two types of white hybrids (Bovans White and Lohmann Selected Leghorn Classic) housed in two housing systems (furnished cages and floor housing). This resulted in four hybrid-housing combinations (n \u223c 220 for each). Tibia strength and genotypes for pure breeding lines of White Leghorn (WL, n = 947) and Rhode Island Red (RIR, n = 924) were also included. Each of the hybrid-housing combinations and pure lines was fitted separately into (1) single-trait Genomic Best Linear Unbiased Prediction (GBLUP), then simultaneously via multitrait GBLUP, (2) within hybrids across housing, (3) across hybrids within housing, (4) across hybrids and housing, (5) the latter in combination with WL and/or RIR data. Including hybrid data slightly increased the accuracy of the genomic estimated breeding value (GEBV) of other hybrids, but not that of pure lines. Pure line data increased the GEBV accuracy of hybrids over and above that of combining hybrid information. Combining data from two pure lines improved the GEBV accuracy of both. In comparison to the combination of data across lines and/or houses, combining tibia strength and BW within-lines increased tibia strength GEBV accuracy. The maximum GEBV accuracy obtained for tibia strength ranged from 0.42 to 0.65 for hybrids and from 0.63 to 0.78 for pure lines. Further study is required to test whether modelling the interactions of genotype by environment could help to breed hybrids for specific housing systems.", "doi": "10.1016/j.animal.2025.101452", "pmid": "40043590", "labels": {"NGI SNP genotyping": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pii", "key": "S1751-7311(25)00035-7"}], "notes": [], "created": "2025-09-08T06:53:11.259Z", "modified": "2025-09-08T06:53:11.308Z"}, {"entity": "publication", "iuid": "94b833e1cf11498a8be10d219e3db160", "links": {"self": {"href": "https://publications.scilifelab.se/publication/94b833e1cf11498a8be10d219e3db160.json"}, "display": {"href": "https://publications.scilifelab.se/publication/94b833e1cf11498a8be10d219e3db160"}}, "title": "Genome Sequence Resources from Three Isolates of the Apple Canker Pathogen Neonectria ditissima Infecting Forest Trees", "authors": [{"family": "Bourras", "given": "Salim", "initials": "S", "orcid": "0000-0003-0855-5433", "researcher": {"href": "https://publications.scilifelab.se/researcher/c6b49cf30d404c7ab7bbbe30bda39d1c.json"}}, {"family": "V\u00e9l\u00ebz", "given": "Heriberto", "initials": "H"}, {"family": "Ihrmark", "given": "Katarina", "initials": "K"}, {"family": "Corrales Guti\u00e9rrez", "given": "Miguel \u00c1ngel", "initials": "M\u00c1"}, {"family": "Elfstrand", "given": "Malin", "initials": "M", "orcid": "0000-0002-0214-5284", "researcher": {"href": "https://publications.scilifelab.se/researcher/2957dac173f4495a9245f0d8a9750606.json"}}, {"family": "Garkava-Gustavsson", "given": "Larisa", "initials": "L"}, {"family": "Falk", "given": "Kerstin Dalman", "initials": "KD"}], "type": "journal-article", "published": "2025-03-00", "journal": {"title": "PhytoFrontiers\u2122", "issn": "2690-5442", "volume": "5", "issue": "1", "pages": "117-119", "issn-l": null}, "abstract": null, "doi": "10.1094/phytofr-05-24-0055-a", "pmid": null, "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [], "notes": [], "created": "2025-09-08T06:54:44.172Z", "modified": "2025-09-08T06:54:44.391Z"}, {"entity": "publication", "iuid": "5e9bfb4d2aac4d3b827631ccd1bfd299", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5e9bfb4d2aac4d3b827631ccd1bfd299.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5e9bfb4d2aac4d3b827631ccd1bfd299"}}, "title": "Human adaptation in the Andes Mountains", "authors": [{"family": "De Loma", "given": "Jessica", "initials": "J"}, {"family": "Vicente", "given": "M\u00e1rio", "initials": "M"}, {"family": "Tirado", "given": "Noemi", "initials": "N"}, {"family": "Ascui", "given": "Franz", "initials": "F"}, {"family": "Parada", "given": "Luis A", "initials": "LA"}, {"family": "Gardon", "given": "Jacques", "initials": "J"}, {"family": "Schlebusch", "given": "Carina", "initials": "C"}, {"family": "Broberg", "given": "Karin", "initials": "K"}], "type": "journal-article", "published": "2025-02-28", "journal": {"title": "Hum Popul Genet Genom", "issn": "2770-5005", "issn-l": null, "volume": null, "issue": null, "pages": null}, "abstract": null, "doi": "10.47248/hpgg2505010002", "pmid": null, "labels": {"NGI SNP genotyping": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics (NBIS)": "Service", "Bioinformatics Long-term Support WABI": "Service", "Bioinformatics Support, Infrastructure and Training": "Service"}, "xrefs": [], "notes": [], "created": "2025-09-08T06:53:08.875Z", "modified": "2025-11-19T08:10:24.832Z"}, {"entity": "publication", "iuid": "42d2bb44130c40a9a57616496fc17474", "links": {"self": {"href": "https://publications.scilifelab.se/publication/42d2bb44130c40a9a57616496fc17474.json"}, "display": {"href": "https://publications.scilifelab.se/publication/42d2bb44130c40a9a57616496fc17474"}}, "title": "Yellow barley xan-m mutants are deficient in the motor unit SECA1 of the SEC1 translocase system.", "authors": [{"family": "Stuart", "given": "David", "initials": "D"}, {"family": "Ivanova", "given": "Anastasiia", "initials": "A"}, {"family": "Zakhrabekova", "given": "Shakhira", "initials": "S"}, {"family": "Hansson", "given": "Mats", "initials": "M", "orcid": "0000-0002-0168-9968", "researcher": {"href": "https://publications.scilifelab.se/researcher/63440c24a3874af18614b26ac550e5cc.json"}}], "type": "journal article", "published": "2025-02-26", "journal": {"title": "Planta", "issn": "1432-2048", "volume": "261", "issue": "4", "pages": "68", "issn-l": "0032-0935"}, "abstract": "Chloroplast protein transport depends on the SEC1 translocase. Barley xan-m mutants, deficient in SECA1, lack chlorophyll and die as seedlings. Their yellow phenotype indicates that carotenoid chemistry is less SEC1-dependent. Chloroplast proteins encoded by genes located in the cell nucleus need to be transported across up to three chloroplast membranes to find its correct location. SEC1 is one of the major translocase systems. In plants, SEC1 consists of three proteins (SECA1, SECY1 and SECE1) and transports substrate proteins over the thylakoid membrane. SECA1 is an ATPase that delivers the substrate protein to the SECY1-SECE1 channel. In the present study, we analyzed five allelic barley xan-m mutants, which had been isolated between 1925 and 1957. The mutants belong to a larger collection of barley mutants deficient in chlorophyll biosynthesis and chloroplast development. Mutations in the xan-m gene are recessive and result in a yellow phenotype due to lack of chlorophyll and presence of carotenoids. Mutant seedlings die after approximately 10 days. We identified the defective gene in the xan-m mutants by a variant of bulk segregant analysis. The gene xan-m is an orthologue of SECA1 in Arabidopsis. Previously, only genes related to chlorophyll biosynthesis have been identified in the collection of barley xan mutants. The yellow phenotype of the mutants demonstrates that proteins responsible for carotenoid biosynthesis and storage are not or less dependent on an intact SEC1 translocase.", "doi": "10.1007/s00425-025-04654-9", "pmid": "40009246", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11865152"}, {"db": "pii", "key": "10.1007/s00425-025-04654-9"}], "notes": [], "created": "2025-09-08T06:54:56.835Z", "modified": "2025-11-14T11:05:42.039Z"}, {"entity": "publication", "iuid": "31cc2ec2f8a34c93b6d17050bec2d830", "links": {"self": {"href": "https://publications.scilifelab.se/publication/31cc2ec2f8a34c93b6d17050bec2d830.json"}, "display": {"href": "https://publications.scilifelab.se/publication/31cc2ec2f8a34c93b6d17050bec2d830"}}, "title": "Single-cell analysis of aplastic anemia reveals a convergence of NK and NK-like CD8+ T cells with a disease-associated TCR signature.", "authors": [{"family": "Lundgren", "given": "Sofie", "initials": "S", "orcid": "0000-0003-3146-9816", "researcher": {"href": "https://publications.scilifelab.se/researcher/3838050baa4847c5ad8edcd02b3b54e2.json"}}, {"family": "Huuhtanen", "given": "Jani", "initials": "J", "orcid": "0000-0003-2750-4033", "researcher": {"href": "https://publications.scilifelab.se/researcher/f982fef263e644799e27df3f31083d6c.json"}}, {"family": "Ker\u00e4nen", "given": "Mikko", "initials": "M", "orcid": "0000-0001-8027-499X", "researcher": {"href": "https://publications.scilifelab.se/researcher/065055dc206c4749b64c08e7414875b1.json"}}, {"family": "Feng", "given": "Xingmin", "initials": "X", "orcid": "0000-0001-8018-2366", "researcher": {"href": "https://publications.scilifelab.se/researcher/ecf564243b464d919b534c054c6e5fee.json"}}, {"family": "Patel", "given": "Bhavisha A", "initials": "BA", "orcid": "0000-0002-2974-7701", "researcher": {"href": "https://publications.scilifelab.se/researcher/8f42376804c4437fb68895915f369d39.json"}}, {"family": "Ryland", "given": "Georgina L", "initials": "GL", "orcid": "0000-0002-4990-0961", "researcher": {"href": "https://publications.scilifelab.se/researcher/891952aec8b442e1af79388838e73e05.json"}}, {"family": "Fox", "given": "Lucy C", "initials": "LC", "orcid": "0000-0002-3855-8232", "researcher": {"href": "https://publications.scilifelab.se/researcher/827f9263f0734c7ab1b757bc35758862.json"}}, {"family": "Bravo-Perez", "given": "Carlos", "initials": "C", "orcid": "0000-0001-9794-7847", "researcher": {"href": "https://publications.scilifelab.se/researcher/4260758112534ceba7efe94660a0a43e.json"}}, {"family": "Clemente", "given": "Michael", "initials": "M"}, {"family": "Kerr", "given": "Cassandra", "initials": "C"}, {"family": "Walldin", "given": "Gunilla", "initials": "G", "orcid": "0009-0005-6663-6540", "researcher": {"href": "https://publications.scilifelab.se/researcher/24fb888d0212421eaa2353ed6cc31ac7.json"}}, {"family": "Dufva", "given": "Olli", "initials": "O"}, {"family": "Zaimoku", "given": "Yoshitaka", "initials": "Y", "orcid": "0000-0002-4108-5245", "researcher": {"href": "https://publications.scilifelab.se/researcher/f9bc97e77a35491197fa901757bd92f0.json"}}, {"family": "Tuononen", "given": "Tiina", "initials": "T", "orcid": "0009-0007-6677-3064", "researcher": {"href": "https://publications.scilifelab.se/researcher/b2c764c4bf7746fc9c6c468a51a5db52.json"}}, {"family": "Myllym\u00e4ki", "given": "Mikko", "initials": "M", "orcid": "0000-0002-8194-7356", "researcher": {"href": "https://publications.scilifelab.se/researcher/071c21748567437393dfb1b7c3bedad4.json"}}, {"family": "Ebeling", "given": "Freja", "initials": "F", "orcid": "0000-0002-7921-089X", "researcher": {"href": "https://publications.scilifelab.se/researcher/5318f08e1aff4e988f961f1c7806d1bb.json"}}, {"family": "Jokinen", "given": "Emmi", "initials": "E", "orcid": "0000-0002-0060-6868", "researcher": {"href": "https://publications.scilifelab.se/researcher/8392afc052914d47ab93466ba898cbc8.json"}}, {"family": "Heinonen", "given": "Markus", "initials": "M", "orcid": "0000-0002-7741-2279", "researcher": {"href": "https://publications.scilifelab.se/researcher/8733ddf664b2445188aed518dab08873.json"}}, {"family": "Kasanen", "given": "Tiina", "initials": "T", "orcid": "0000-0002-5408-1948", "researcher": {"href": "https://publications.scilifelab.se/researcher/06fb270832244566bfc649d43f7e718c.json"}}, {"family": "Klievink", "given": "Jay", "initials": "J", "orcid": "0000-0002-4081-5840", "researcher": {"href": "https://publications.scilifelab.se/researcher/fdad6fd259c749a5b3a770ae47c770cf.json"}}, {"family": "L\u00e4hteenm\u00e4ki", "given": "Hanna", "initials": "H", "orcid": "0000-0001-6773-2677", "researcher": {"href": "https://publications.scilifelab.se/researcher/e0cb9da3e4cb4430a779d4d4185e6652.json"}}, {"family": "Jaatinen", "given": "Taina", "initials": "T", "orcid": "0000-0001-7783-6189", "researcher": {"href": "https://publications.scilifelab.se/researcher/3b981dc2e49a4731abc5ac1ee7bbfecf.json"}}, {"family": "Kyt\u00f6l\u00e4", "given": "Sari", "initials": "S", "orcid": "0000-0003-1649-8993", "researcher": {"href": "https://publications.scilifelab.se/researcher/a8e0b29c15c24626b529b3b1cab1ca1a.json"}}, {"family": "Siitonen", "given": "Sanna", "initials": "S", "orcid": "0009-0001-2241-6731", "researcher": {"href": "https://publications.scilifelab.se/researcher/5c6a7c0c04f3451086c3b32d74da6ffa.json"}}, {"family": "Dulau-Florea", "given": "Alina", "initials": "A", "orcid": "0000-0003-3512-4946", "researcher": {"href": "https://publications.scilifelab.se/researcher/480fa59b41ab400d8eca304bf23c3332.json"}}, {"family": "Braylan", "given": "Raul", "initials": "R", "orcid": "0000-0001-6733-5161", "researcher": {"href": "https://publications.scilifelab.se/researcher/d1ec596e60c542238a5ada29bb62fc51.json"}}, {"family": "Hein\u00e4niemi", "given": "Merja", "initials": "M", "orcid": "0000-0001-6190-3439", "researcher": {"href": "https://publications.scilifelab.se/researcher/be7efa5a7c9a4da18b397a07ebd8d9ec.json"}}, {"family": "Nakao", "given": "Shinji", "initials": "S", "orcid": "0000-0002-9674-624X", "researcher": {"href": "https://publications.scilifelab.se/researcher/ab2d147043454ff2b403f70bd60136e6.json"}}, {"family": "Hellstr\u00f6m-Lindberg", "given": "Eva", "initials": "E", "orcid": "0000-0002-7839-3743", "researcher": {"href": "https://publications.scilifelab.se/researcher/6bf8d52e24234fa8b348ad08f58d1d48.json"}}, {"family": "Maciejewski", "given": "Jaroslaw P", "initials": "JP"}, {"family": "Blombery", "given": "Piers", "initials": "P"}, {"family": "Young", "given": "Neal S", "initials": "NS"}, {"family": "L\u00e4hdesm\u00e4ki", "given": "Harri", "initials": "H"}, {"family": "Mustjoki", "given": "Satu", "initials": "S", "orcid": "0000-0002-0816-8241", "researcher": {"href": "https://publications.scilifelab.se/researcher/03cdbac477284e7093121bc3d35a6dfb.json"}}], "type": "journal article", "published": "2025-02-26", "journal": {"title": "Sci Transl Med", "issn": "1946-6242", "volume": "17", "issue": "787", "pages": "eadl6758", "issn-l": "1946-6234"}, "abstract": "Immune aplastic anemia (AA) is a life-threatening bone marrow failure disorder driven by an autoimmune T cell attack against hematopoietic stem and progenitor cells (HSPCs). However, the exact autoantigen targets and role of other immune cells in the pathogenesis of AA are unknown. Here, we analyzed a cohort of 218 patients with AA using single-cell RNA and T cell receptor (TCR) \u03b1\u03b2 sequencing, TCR\u03b2 sequencing, flow cytometry, and plasma cytokine profiling. We identified natural killer (NK) cells and CD8+ terminally differentiated effector T (TEMRA) cells expressing NK receptors with AA-associated TCR\u03b2 motifs as the most dysregulated immune cell populations in AA bone marrow. Functional coculture experiments using primary HSPCs and immune cells showed that NK cells cannot kill HSPCs alone but may sensitize HSPCs to CD8+ T cell-mediated killing through production of interferons. Furthermore, HSPCs induced activation of T cell clones with CD8+ TEMRA NK-like phenotype in coculture. Our results reveal a convergent phenotype of innate and adaptive immune cells that may drive AA.", "doi": "10.1126/scitranslmed.adl6758", "pmid": "40009697", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [], "notes": [], "created": "2025-09-08T11:37:23.304Z", "modified": "2025-09-08T11:37:24.704Z"}, {"entity": "publication", "iuid": "229f504c7e6941e88c6f4ae750d0bbcf", "links": {"self": {"href": "https://publications.scilifelab.se/publication/229f504c7e6941e88c6f4ae750d0bbcf.json"}, "display": {"href": "https://publications.scilifelab.se/publication/229f504c7e6941e88c6f4ae750d0bbcf"}}, "title": "Digital sequencing is improved by using structured unique molecular identifiers.", "authors": [{"family": "Micallef", "given": "Peter", "initials": "P"}, {"family": "Santamar\u00eda", "given": "Manuel Luna", "initials": "ML"}, {"family": "Escobar", "given": "Mandy", "initials": "M"}, {"family": "Andersson", "given": "Daniel", "initials": "D"}, {"family": "\u00d6sterlund", "given": "Tobias", "initials": "T"}, {"family": "Mouhanna", "given": "Pia", "initials": "P"}, {"family": "Filges", "given": "Stefan", "initials": "S"}, {"family": "Johansson", "given": "Gustav", "initials": "G"}, {"family": "Fagman", "given": "Henrik", "initials": "H"}, {"family": "Vannas", "given": "Christoffer", "initials": "C"}, {"family": "St\u00e5hlberg", "given": "Anders", "initials": "A", "orcid": "0000-0003-4243-0191", "researcher": {"href": "https://publications.scilifelab.se/researcher/05306b130d6543eea88a4f518085981e.json"}}], "type": "journal article", "published": "2025-02-25", "journal": {"title": "Genome Biol.", "issn": "1474-760X", "volume": "26", "issue": "1", "pages": "37", "issn-l": "1474-7596"}, "abstract": "Digital sequencing uses unique molecular identifiers (UMIs) to correct for polymerase induced errors and amplification biases. Here, we design 19 different structured UMIs to minimize the capacity of primers to form non-specific PCR products during library construction using SiMSen-Seq, a PCR-based digital sequencing approach with flexible multiplexing capabilities suitable for tumor-informed mutation analysis. All structured UMI designs demonstrate enhanced assay performance compared with an unstructured reference UMI. The best performing structured UMI design shows significant improvements in all tested aspects of assay and sequencing performance with the ability to reliable detect low variant allele frequencies.", "doi": "10.1186/s13059-025-03504-x", "pmid": "40001095", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11853513"}, {"db": "pii", "key": "10.1186/s13059-025-03504-x"}], "notes": [], "created": "2025-09-08T06:54:47.020Z", "modified": "2025-09-08T06:54:47.088Z"}, {"entity": "publication", "iuid": "7de26605147e4edb8845e6c78bddd3aa", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7de26605147e4edb8845e6c78bddd3aa.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7de26605147e4edb8845e6c78bddd3aa"}}, "title": "DNA methylation patterns contribute to changes of cellular differentiation pathways in leukocytes with LOY from patients with Alzheimer\u00b4s disease.", "authors": [{"family": "J\u0105kalski", "given": "Marcin", "initials": "M", "orcid": "0000-0002-5481-9148", "researcher": {"href": "https://publications.scilifelab.se/researcher/e4411ec776b94c89b0444bd8d49672ca.json"}}, {"family": "Bruhn-Olszewska", "given": "Bo\u017cena", "initials": "B", "orcid": "0000-0003-2141-0247", "researcher": {"href": "https://publications.scilifelab.se/researcher/0fa96509bbe94834858aee3c16d41b97.json"}}, {"family": "Rychlicka-Buniowska", "given": "Edyta", "initials": "E"}, {"family": "Davies", "given": "Hanna", "initials": "H"}, {"family": "Sarkisyan", "given": "Daniil", "initials": "D"}, {"family": "Siedlar", "given": "Maciej", "initials": "M"}, {"family": "Baran", "given": "Jaros\u0142aw", "initials": "J"}, {"family": "W\u0119glarczyk", "given": "Kazimierz", "initials": "K"}, {"family": "Jaszczynski", "given": "Janusz", "initials": "J"}, {"family": "Ry\u015b", "given": "Janusz", "initials": "J"}, {"family": "Gedraitis", "given": "Vilmantas", "initials": "V"}, {"family": "Filipowicz", "given": "Natalia", "initials": "N"}, {"family": "Klich-R\u0105czka", "given": "Alicja", "initials": "A"}, {"family": "Kilander", "given": "Lena", "initials": "L"}, {"family": "Ingelsson", "given": "Martin", "initials": "M"}, {"family": "Dumanski", "given": "Jan P", "initials": "JP", "orcid": "0000-0002-1489-1452", "researcher": {"href": "https://publications.scilifelab.se/researcher/15b14282209342cfa9c82cdbf02999f6.json"}}], "type": "journal article", "published": "2025-02-25", "journal": {"title": "Cell. Mol. Life Sci.", "issn": "1420-9071", "volume": "82", "issue": "1", "pages": "93", "issn-l": "1420-682X"}, "abstract": "Alzheimer's disease (AD) is a common and increasing societal problem due to the extending human lifespan. In males, loss of chromosome Y (LOY) in leukocytes is strongly associated with AD. We studied here DNA methylation and RNA expression in sorted monocytes and granulocytes with and without LOY from male AD patients. Through multi-omic analysis, we identified new candidate genes along with those previously associated with AD. Global analyses of DNA methylation in samples with LOY vs. normal state showed that hypomethylation dominated both in granulocytes and monocytes. Our findings highlight LOY-related differences in DNA methylation that occur in gene regulatory regions. Specifically, we observed alterations in key genes involved in leukocyte differentiation: FLI1, involved in early hematopoiesis; RUNX1, essential for blood cell development; RARA, regulating gene expression in response to retinoic acid; CANX, crucial for protein folding; CEBPB, a transcription factor important for immune responses; and MYADM, implicated in cell adhesion and migration. Moreover, protein-protein interaction analysis in granulocytes identified that products of two of these genes, CANX and CEBPB, are key hub proteins. This research underscores the potential of multi-omic approach in pure hematopoietic cell populations to uncover the molecular underpinnings of AD. Finally, our results link previous analysis showing impact of LOY on leukocyte differentiation, LOY-associated transcriptional dysregulation and GWAS studies of LOY.", "doi": "10.1007/s00018-025-05618-8", "pmid": "39998604", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "NGI SNP genotyping": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11861481"}, {"db": "pii", "key": "10.1007/s00018-025-05618-8"}], "notes": [], "created": "2025-09-08T06:57:22.526Z", "modified": "2025-09-08T07:12:23.743Z"}, {"entity": "publication", "iuid": "e09133a40d7145b18f9bb8facb4dc96c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e09133a40d7145b18f9bb8facb4dc96c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e09133a40d7145b18f9bb8facb4dc96c"}}, "title": "Comprehensive Gene Expression Analysis in Papillary Thyroid Carcinoma Reveals a Transcriptional Profile Associated with Reduced Radioiodine Avidity.", "authors": [{"family": "Condello", "given": "Vincenzo", "initials": "V", "orcid": "0000-0003-4569-5398", "researcher": {"href": "https://publications.scilifelab.se/researcher/09be613118f743bd992bba237b61ceb4.json"}}, {"family": "Marchettini", "given": "Carlotta", "initials": "C"}, {"family": "Ihre-Lundgren", "given": "Catharina", "initials": "C"}, {"family": "Nilsson", "given": "Joachim N", "initials": "JN", "orcid": "0000-0001-7496-9189", "researcher": {"href": "https://publications.scilifelab.se/researcher/47b5460e0a2444c49675506d7f028784.json"}}, {"family": "Juhlin", "given": "C Christofer", "initials": "CC", "orcid": "0000-0002-5945-9081", "researcher": {"href": "https://publications.scilifelab.se/researcher/bb660e24421749d4acaaf6e9a90042f8.json"}}], "type": "journal article", "published": "2025-02-21", "journal": {"title": "Endocr. Pathol.", "issn": "1559-0097", "volume": "36", "issue": "1", "pages": "4", "issn-l": "1046-3976"}, "abstract": "Papillary thyroid carcinoma (PTC) is the most common form of well-differentiated thyroid cancer (WDTC) and generally has a favorable prognosis. However, subsets of these tumors can metastasize, leading to aggressive disease progression and poorer clinical outcomes. Radioactive iodine (RAI) therapy is routinely given in the adjuvant setting following thyroidectomy and lymph node dissection for WDTC. Nevertheless, its therapeutic efficacy is limited to tumors with high iodine avidity. Early post-surgical classification of thyroid cancers as either iodine-avid or refractory is crucial for enabling more personalized and effective treatment strategies. In this study, we aimed to identify transcriptomic determinants associated with RAI refractoriness (RAI-R) to improve prognostication. We collected clinicopathologic data and conducted RNA-seq on 36 tissue samples (18 high-avidity and 18 low-avidity), each uniquely characterized by ex vivo iodine concentration measurements taken directly from surgical specimens. Whole-transcriptomic analysis identified 63 differentially expressed genes, with six (S100A4, CRTC2, ANO1, WWTR1, DEPTOR, MT1G) showing consistent deregulation. The expression of ANO1, an established iodine transporter at the apical membrane of the thyroid follicular cells, correlated significantly with iodine avidity (r = 0.54). Validation via RT-qPCR confirmed differential expression trends. Gene ontology and pathway enrichment analyses highlighted thyroid hormone synthesis, PI3K-AKT, and MAPK signaling pathways as key regulators of RAI avidity. A refined multivariate predictive model incorporating ANO1 mRNA expression, histological subtypes, and sample type demonstrated strong predictive performance (adjusted R2 = 0.55). These findings suggest ANO1 as a promising biomarker for predicting iodine avidity in thyroid cancer.", "doi": "10.1007/s12022-025-09849-0", "pmid": "39982585", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11845550"}, {"db": "pii", "key": "10.1007/s12022-025-09849-0"}], "notes": [], "created": "2025-05-12T05:46:47.965Z", "modified": "2025-09-08T07:13:03.100Z"}, {"entity": "publication", "iuid": "d9bc92127ecf49ce8f19dabdd5e631a1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d9bc92127ecf49ce8f19dabdd5e631a1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d9bc92127ecf49ce8f19dabdd5e631a1"}}, "title": "Age-Dependent Pleomorphism in Mycobacterium monacense Cultures.", "authors": [{"family": "Ramesh", "given": "Malavika", "initials": "M", "orcid": "0000-0002-2353-0237", "researcher": {"href": "https://publications.scilifelab.se/researcher/e679c292f1904ecbb1dece92d5513d26.json"}}, {"family": "Behra", "given": "Phani Rama Krishna", "initials": "PRK", "orcid": "0000-0002-8810-6066", "researcher": {"href": "https://publications.scilifelab.se/researcher/711dae7f552146ac95d209bc8efab54e.json"}}, {"family": "Pettersson", "given": "B M Fredrik", "initials": "BMF", "orcid": "0009-0006-8579-4023", "researcher": {"href": "https://publications.scilifelab.se/researcher/e5d1d0f6732d4dee869861d57ce02cd7.json"}}, {"family": "Dasgupta", "given": "Santanu", "initials": "S"}, {"family": "Kirsebom", "given": "Leif A", "initials": "LA", "orcid": "0000-0002-5092-512X", "researcher": {"href": "https://publications.scilifelab.se/researcher/e80849a89d0043b0b4daff9804c67332.json"}}], "type": "journal article", "published": "2025-02-20", "journal": {"title": "Microorganisms", "issn": "2076-2607", "volume": "13", "issue": "3", "issn-l": "2076-2607"}, "abstract": "Changes in cell shape have been shown to be an integral part of the mycobacterial life cycle; however, systematic investigations into its patterns of pleomorphic behaviour in connection with stages or conditions of growth are scarce. We have studied the complete growth cycle of Mycobacterium monacense cultures, a Non-Tuberculous Mycobacterium (NTM), in solid as well as in liquid media. We provide data showing changes in cell shape from rod to coccoid and occurrence of refractive cells ranging from Phase Grey to phase Bright (PGB) in appearance upon ageing. Changes in cell shape could be correlated to the bi-phasic nature of the growth curves for M. monacense (and the NTM Mycobacterium boenickei) as measured by the absorbance of liquid cultures while growth measured by colony-forming units (CFU) on solid media showed a uniform exponential growth. Based on the complete M. monacense genome we identified genes involved in cell morphology, and analyses of their mRNA levels revealed changes at different stages of growth. One gene, dnaK_3 (encoding a chaperone), showed significantly increased transcript levels in stationary phase cells relative to exponentially growing cells. Based on protein domain architecture, we identified that the DnaK_3 N-terminus domain is an MreB-like homolog. Endogenous overexpression of M. monacense dnaK_3 in M. monacense was unsuccessful (appears to be lethal) while exogenous overexpression in Mycobacterium marinum resulted in morphological changes with an impact on the frequency of appearance of PGB cells. However, the introduction of an anti-sense \"gene\" targeting the M. marinum dnaK_3 did not show significant effects. Using dnaK_3-lacZ reporter constructs we also provide data suggesting that the morphological differences could be due to differences in the regulation of dnaK_3 in the two species. Together these data suggest that, although its regulation may vary between mycobacterial species, the dnaK_3 might have a direct or indirect role in the processes influencing mycobacterial cell shape.", "doi": "10.3390/microorganisms13030475", "pmid": "40142368", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service", "NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11946739"}, {"db": "pii", "key": "microorganisms13030475"}], "notes": [], "created": "2025-08-19T13:27:17.755Z", "modified": "2025-09-08T07:17:25.329Z"}, {"entity": "publication", "iuid": "db0102f308044e068375eaab4e78dc48", "links": {"self": {"href": "https://publications.scilifelab.se/publication/db0102f308044e068375eaab4e78dc48.json"}, "display": {"href": "https://publications.scilifelab.se/publication/db0102f308044e068375eaab4e78dc48"}}, "title": "An Evolutionary Mosaic Challenges Traditional Monitoring of a Foundation Species in a Coastal Environment-The Baltic Fucus vesiculosus.", "authors": [{"family": "Pereyra", "given": "Ricardo T", "initials": "RT"}, {"family": "Kinnby", "given": "Alexandra", "initials": "A"}, {"family": "Le Moan", "given": "Alan", "initials": "A", "orcid": "0000-0002-9124-6844", "researcher": {"href": "https://publications.scilifelab.se/researcher/609a745ce1fb42fea85cc8d55db25acf.json"}}, {"family": "Ortega-Martinez", "given": "Olga", "initials": "O"}, {"family": "Jonsson", "given": "Per R", "initials": "PR"}, {"family": "Piarulli", "given": "Stefania", "initials": "S"}, {"family": "Pinder", "given": "Matthew I M", "initials": "MIM", "orcid": "0000-0003-4407-0214", "researcher": {"href": "https://publications.scilifelab.se/researcher/ca6d9f52178249f3995c3d276fbc2728.json"}}, {"family": "T\u00f6pel", "given": "Mats", "initials": "M"}, {"family": "De Wit", "given": "Pierre", "initials": "P", "orcid": "0000-0003-4709-3438", "researcher": {"href": "https://publications.scilifelab.se/researcher/95b69d4724ce4b69819c0a1578cd56eb.json"}}, {"family": "Andr\u00e9", "given": "Carl", "initials": "C"}, {"family": "Knutsen", "given": "Halvor", "initials": "H", "orcid": "0000-0002-7627-7634", "researcher": {"href": "https://publications.scilifelab.se/researcher/a822f994fed046018a713105bc5e03a0.json"}}, {"family": "Johannesson", "given": "Kerstin", "initials": "K", "orcid": "0000-0003-0176-7986", "researcher": {"href": "https://publications.scilifelab.se/researcher/a376951d80cd405183f4ff8606df8bbc.json"}}], "type": "journal article", "published": "2025-02-17", "journal": {"title": "Mol. Ecol.", "issn": "1365-294X", "pages": "e17699", "issn-l": "0962-1083"}, "abstract": "During periods of environmental change, genetic diversity in foundation species is critical for ecosystem function and resilience, but it remains overlooked in environmental monitoring. In the Baltic Sea, a key species for monitoring is the brown seaweed Fucus vesiculosus, which forms sublittoral 3D habitats providing shelter and food for fish and invertebrates. Ecological distribution models predict a significant loss of Baltic F. vesiculosus due to ocean warming, unless populations can adapt. Genetic variation and recombination during sexual reproduction are essential for adaptation, but studies have revealed large-scale clonal reproduction within the Baltic Sea. We analysed genome-wide single nucleotide polymorphism (SNP) data from the east Atlantic, the \"Transition zone,\" and the Baltic Sea, and found a mosaic of divergent lineages in the Baltic Sea, contrasting an outside dominance of a few genetic groups. We determined that the previously described endemic species Fucus radicans is predominantly a large female clone of F. vesiculosus in its northern Baltic distribution. In the two Estonian sites, however, individuals earlier referred to as F. radicans are sexually and reproductively isolated from Baltic F. vesiculosus, revealing a separate lineage that may have diverged long before the formation of the Baltic Sea. Monitoring Baltic Fucus without considering this genetic complexity will fail to prioritise populations with adaptive potential to new climate conditions. From our genomic data, we can extract informative and diagnostic genetic markers that differentiate major genetic entities. Such a SNP panel will provide a straightforward tool for spatial and temporal monitoring and informing management decisions and actions.", "doi": "10.1111/mec.17699", "pmid": "39957665", "labels": {"National Genomics Infrastructure": "Service", "NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [], "notes": [], "created": "2025-11-07T07:26:56.214Z", "modified": "2025-11-07T07:26:56.376Z"}, {"entity": "publication", "iuid": "12fa1b73f76d40158b12fc385a35aa1f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/12fa1b73f76d40158b12fc385a35aa1f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/12fa1b73f76d40158b12fc385a35aa1f"}}, "title": "Methodological aspects of investigating the resistome in pig farm environments.", "authors": [{"family": "Ladyhina", "given": "Valeriia", "initials": "V"}, {"family": "Rajala", "given": "Elisabeth", "initials": "E"}, {"family": "Sternberg-Lewerin", "given": "Susanna", "initials": "S"}, {"family": "Nasirzadeh", "given": "Leila", "initials": "L"}, {"family": "Bongcam-Rudloff", "given": "Erik", "initials": "E", "orcid": "0000-0002-1947-8288", "researcher": {"href": "https://publications.scilifelab.se/researcher/6970ca57259d498588ecf9e1ad28a9b0.json"}}, {"family": "Dicksved", "given": "Johan", "initials": "J"}], "type": "journal article", "published": "2025-02-13", "journal": {"title": "J Microbiol Methods", "issn": "1872-8359", "issn-l": null, "volume": "230-231", "issue": null, "pages": "107103"}, "abstract": "A typical One Health issue, antimicrobial resistance (AMR) development and its spread among people, animals, and the environment attracts significant research attention. The animal sector is one of the major contributors to the development and dissemination of AMR and accounts for more than 50 % of global antibiotics usage. The use of antibiotics exerts a selective pressure for resistant bacteria in the exposed microbiome, but many questions about the epidemiology of AMR in farm environments remain unanswered. This is connected to several methodological challenges and limitations, such as inconsistent sampling methods, complexity of farm environment samples and the lack of standardized protocols for sample collection, processing and bioinformatical analysis. In this project, we combined metagenomics and bioinformatics to optimise the methodology for reproducible research on the resistome in complex samples from the indoor farm environment. The work included optimizing sample collection, transportation, and storage, as well as DNA extraction, sequencing, and bioinformatic analysis, such as metagenome assembly and antibiotic resistance gene (ARG) detection. Our studies suggest that the current most optimal and cost-effective pipeline for ARG search should be based on Illumina sequencing of sock sample material at high depth (at least 25 M 250 bp PE for AMR gene families and 43 M for gene variants). We present a computational analysis utilizing MEGAHIT assembly to balance the identification of bacteria carrying ARGs with the potential loss of diversity and abundance of resistance genes. Our findings indicate that searching against multiple ARG databases is essential for detecting the highest diversity of ARGs.", "doi": "10.1016/j.mimet.2025.107103", "pmid": "39954816", "labels": {"Clinical Genomics Link\u00f6ping": "Collaborative", "Clinical Genomics": "Collaborative", "NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pii", "key": "S0167-7012(25)00019-3"}], "notes": [], "created": "2025-03-18T07:11:00.806Z", "modified": "2025-09-08T07:13:09.538Z"}, {"entity": "publication", "iuid": "67fe70a7254545e7b2be4a509f5ff479", "links": {"self": {"href": "https://publications.scilifelab.se/publication/67fe70a7254545e7b2be4a509f5ff479.json"}, "display": {"href": "https://publications.scilifelab.se/publication/67fe70a7254545e7b2be4a509f5ff479"}}, "title": "Functionally characterizing obesity-susceptibility genes using CRISPR/Cas9, in vivo imaging and deep learning.", "authors": [{"family": "Mazzaferro", "given": "Eugenia", "initials": "E"}, {"family": "Mujica", "given": "Endrina", "initials": "E"}, {"family": "Zhang", "given": "Hanqing", "initials": "H"}, {"family": "Emmanouilidou", "given": "Anastasia", "initials": "A"}, {"family": "Jenseit", "given": "Anne", "initials": "A"}, {"family": "Evcimen", "given": "Bade", "initials": "B"}, {"family": "Metzendorf", "given": "Christoph", "initials": "C"}, {"family": "Dethlefsen", "given": "Olga", "initials": "O"}, {"family": "Loos", "given": "Ruth Jf", "initials": "RJ"}, {"family": "Vienberg", "given": "Sara Gry", "initials": "SG"}, {"family": "Larsson", "given": "Anders", "initials": "A"}, {"family": "Allalou", "given": "Amin", "initials": "A"}, {"family": "den Hoed", "given": "Marcel", "initials": "M"}], "type": "journal article", "published": "2025-02-13", "journal": {"title": "Sci Rep", "issn": "2045-2322", "issn-l": "2045-2322", "volume": "15", "issue": "1", "pages": "5408"}, "abstract": "Hundreds of loci have been robustly associated with obesity-related traits, but functional characterization of candidate genes remains a bottleneck. Aiming to systematically characterize candidate genes for a role in accumulation of lipids in adipocytes and other cardiometabolic traits, we developed a pipeline using CRISPR/Cas9, non-invasive, semi-automated fluorescence imaging and deep learning-based image analysis in live zebrafish larvae. Results from a dietary intervention show that 5 days of overfeeding is sufficient to increase the odds of lipid accumulation in adipocytes by 10 days post-fertilization (dpf, n = 275). However, subsequent experiments show that across 12 to 16 established obesity genes, 10 dpf is too early to detect an effect of CRISPR/Cas9-induced mutations on lipid accumulation in adipocytes (n = 1014), and effects on food intake at 8 dpf (n = 1127) are inconsistent with earlier results from mammals. Despite this, we observe effects of CRISPR/Cas9-induced mutations on ectopic accumulation of lipids in the vasculature (sh2b1 and sim1b) and liver (bdnf); as well as on body size (pcsk1, pomca, irs1); whole-body LDLc and/or total cholesterol content (irs2b and sh2b1); and pancreatic beta cell traits and/or glucose content (pcsk1, pomca, and sim1a). Taken together, our results illustrate that CRISPR/Cas9- and image-based experiments in zebrafish larvae can highlight direct effects of obesity genes on cardiometabolic traits, unconfounded by their - not yet apparent - effect on excess adiposity.", "doi": "10.1038/s41598-025-89823-2", "pmid": "39948378", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics (NBIS)": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11825957"}, {"db": "pii", "key": "10.1038/s41598-025-89823-2"}], "notes": [], "created": "2025-09-08T11:37:27.351Z", "modified": "2025-11-28T10:47:20.122Z"}, {"entity": "publication", "iuid": "ab8fa0c345a2433995ebac47f3ad0b58", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ab8fa0c345a2433995ebac47f3ad0b58.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ab8fa0c345a2433995ebac47f3ad0b58"}}, "title": "Rare and common single nucleotide variants in childhood-onset systemic lupus erythematosus.", "authors": [{"family": "Sayadi", "given": "Ahmed", "initials": "A", "orcid": "0000-0002-5662-9145", "researcher": {"href": "https://publications.scilifelab.se/researcher/0f74f301499b4f888e0ac7c5161ae161.json"}}, {"family": "Sandling", "given": "Johanna K", "initials": "JK", "orcid": "0000-0003-1382-2321", "researcher": {"href": "https://publications.scilifelab.se/researcher/9c7bae5a05ac47eeac96547ca7336767.json"}}, {"family": "Eloranta", "given": "Maija-Leena", "initials": "ML", "orcid": "0000-0002-8454-1351", "researcher": {"href": "https://publications.scilifelab.se/researcher/d162e060954d420e825884f254886dcd.json"}}, {"family": "ImmunoArray Development Consortium", "given": "", "initials": ""}, {"family": "DISSECT Consortium", "given": "", "initials": ""}, {"family": "J\u00f6nsen", "given": "Andreas", "initials": "A"}, {"family": "Gunnarsson", "given": "Iva", "initials": "I"}, {"family": "Rantap\u00e4\u00e4-Dahlqvist", "given": "Solbritt", "initials": "S", "orcid": "0000-0001-8259-3863", "researcher": {"href": "https://publications.scilifelab.se/researcher/dfca4bfdcf3946fda64397d3b7debc59.json"}}, {"family": "Sj\u00f6wall", "given": "Christopher", "initials": "C", "orcid": "0000-0003-0900-2048", "researcher": {"href": "https://publications.scilifelab.se/researcher/fe4dd47b8ca1436e8a26fdea33f5e7f6.json"}}, {"family": "Bengtsson", "given": "Anders A", "initials": "AA"}, {"family": "Svenungsson", "given": "Elisabet", "initials": "E", "orcid": "0000-0003-3396-3244", "researcher": {"href": "https://publications.scilifelab.se/researcher/0ab5989c3c604a96bf42b1b6f90434a0.json"}}, {"family": "Lindblad-Toh", "given": "Kerstin", "initials": "K", "orcid": "0000-0001-8338-0253", "researcher": {"href": "https://publications.scilifelab.se/researcher/e0063145f7d6476f80ab42f94833f4cf.json"}}, {"family": "Leonard", "given": "Dag", "initials": "D", "orcid": "0000-0002-6275-7282", "researcher": {"href": "https://publications.scilifelab.se/researcher/42ed25c2f495484db4757f4fef51abae.json"}}, {"family": "R\u00f6nnblom", "given": "Lars", "initials": "L", "orcid": "0000-0001-9403-6503", "researcher": {"href": "https://publications.scilifelab.se/researcher/053ed3b657124a1bab3a78dc685556e6.json"}}, {"family": " DISSECT Consortium", "given": "", "initials": ""}], "type": "journal article", "published": "2025-02-11", "journal": {"title": "Lupus Sci Med", "issn": "2053-8790", "volume": "12", "issue": "1", "issn-l": "2053-8790"}, "abstract": "SLE is a systemic autoimmune disease with a large number of common risk gene variants, but several rare gene variants can cause monogenic SLE. The relationship between common and rare variants in SLE is unclear. We therefore investigated the occurrence of rare deleterious variants in patients with childhood-onset SLE (cSLE) and adult-onset SLE (aSLE) and compared the frequency of these variants with their individual SLE polygenic risk score (PRS).\n\nTargeted sequencing of 1832 gene regions, including coding regions of 31 genes associated with monogenic SLE, was performed in 958 patients with SLE and 1026 healthy individuals. A total of 116 patients with SLE had disease onset before the age of 18 (cSLE). An SLE common variant PRS was created from 37 SLE genome-wide association study single nucleotide variants (SNVs).\n\nRare coding deleterious SNVs (RD SNVs) were observed in 23 of the monogenic SLE-associated genes. Six per cent of patients with cSLE, compared with 3.2% of controls and 4.6% of patients with aSLE, carried rare deleterious alleles. In cSLE, RD SNVs were observed in the C1S, DDX58, IFIH1, IKZF1, RNASEH2A and C8A genes. A PRS analysis showed that patients with cSLE with any of these gene variants had a similar average PRS as control individuals.\n\nRD SNVs were observed in a small proportion of cSLE and carriers of these RD SNVs had a PRS similar to healthy individuals, suggesting the importance of rare coding heterozygous variants in driving disease risk in a subset of children with SLE.", "doi": "10.1136/lupus-2024-001436", "pmid": "39933823", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pii", "key": "12/1/e001436"}], "notes": [], "created": "2025-02-12T13:49:33.306Z", "modified": "2025-03-24T08:21:29.400Z"}, {"entity": "publication", "iuid": "ae26270a2c64410591f4cbb23c632b69", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ae26270a2c64410591f4cbb23c632b69.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ae26270a2c64410591f4cbb23c632b69"}}, "title": "In vivo regulation of the monocyte phenotype by Mycobacterium marinum and the ESX-1 type VII secretion system.", "authors": [{"family": "Munke", "given": "Kristina", "initials": "K"}, {"family": "Wulff", "given": "Line", "initials": "L"}, {"family": "Lienard", "given": "Julia", "initials": "J"}, {"family": "Carlsson", "given": "Fredric", "initials": "F"}, {"family": "Agace", "given": "William W", "initials": "WW"}], "type": "journal article", "published": "2025-02-07", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "15", "issue": "1", "pages": "4545", "issn-l": "2045-2322"}, "abstract": "Pathogenic mycobacteria require the conserved ESX-1 type VII secretion system to cause disease. In a murine Mycobacterium marinum infection model we previously demonstrated that infiltrating monocytes and neutrophils represent the major bacteria-harbouring cell populations in infected tissue. In the current study we use this model, in combination with scRNA sequencing, to assess the impact of M. marinum infection on the transcriptional profile of infiltrating Ly6C\u207aMHCII\u207a monocytes in vivo. Our findings demonstrate that infection of infiltrating monocytes with M. marinum alters their cytokine expression profile, induces glycolytic metabolism, hypoxia-mediated signaling, nitric oxide synthesis, tissue remodeling, and suppresses responsiveness to IFN\u03b3. We further show that the transcriptional response of bystander monocytes is influenced by ESX-1-dependent mechanisms, including a reduced responsiveness to IFN\u03b3. These findings suggest that mycobacterial infection has pleiotropic effects on monocyte phenotype, with potential implications in bacterial growth restriction and granuloma formation.", "doi": "10.1038/s41598-025-88212-z", "pmid": "39915532", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11802795"}, {"db": "pii", "key": "10.1038/s41598-025-88212-z"}], "notes": [], "created": "2025-09-08T11:29:57.395Z", "modified": "2025-09-08T11:29:57.400Z"}, {"entity": "publication", "iuid": "05dfc96807f64f37a3917f85f1198b7e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/05dfc96807f64f37a3917f85f1198b7e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/05dfc96807f64f37a3917f85f1198b7e"}}, "title": "Whole genome sequencing in early onset advanced heart failure.", "authors": [{"family": "Linn\u00e9r", "given": "Erik", "initials": "E", "orcid": "0009-0004-6961-8957", "researcher": {"href": "https://publications.scilifelab.se/researcher/666959db0ed3435ab374dcbd50cb9925.json"}}, {"family": "Czuba", "given": "Tomasz", "initials": "T"}, {"family": "Gidl\u00f6f", "given": "Olof", "initials": "O", "orcid": "0000-0002-7402-3139", "researcher": {"href": "https://publications.scilifelab.se/researcher/83f5453e507041b995e0d69a74540c24.json"}}, {"family": "Lundgren", "given": "Jakob", "initials": "J", "orcid": "0000-0001-9338-2906", "researcher": {"href": "https://publications.scilifelab.se/researcher/c929a6ea1c6f4975ad0ec84da3a32f5e.json"}}, {"family": "Bollano", "given": "Entela", "initials": "E", "orcid": "0000-0003-3341-2434", "researcher": {"href": "https://publications.scilifelab.se/researcher/f486393025c0406bbf6c397b7d1b6f05.json"}}, {"family": "Hellberg", "given": "Maria", "initials": "M"}, {"family": "Celik", "given": "Selvi", "initials": "S", "orcid": "0000-0001-7032-3444", "researcher": {"href": "https://publications.scilifelab.se/researcher/5da057ac725d4fb0bdbaddbc06a8ea64.json"}}, {"family": "Pimpalwar", "given": "Neha", "initials": "N"}, {"family": "Rentzsch", "given": "Philipp", "initials": "P", "orcid": "0000-0002-0413-7974", "researcher": {"href": "https://publications.scilifelab.se/researcher/372fb956b5634de493dd639dae9e8158.json"}}, {"family": "Martorella", "given": "Molly", "initials": "M", "orcid": "0000-0002-3306-6650", "researcher": {"href": "https://publications.scilifelab.se/researcher/64e0f833822b463b9736178d9a25c861.json"}}, {"family": "Gummesson", "given": "Anders", "initials": "A", "orcid": "0000-0003-0024-960X", "researcher": {"href": "https://publications.scilifelab.se/researcher/cb164de27f2846328bb675876922a5fe.json"}}, {"family": "Melander", "given": "Olle", "initials": "O", "orcid": "0000-0002-2581-484X", "researcher": {"href": "https://publications.scilifelab.se/researcher/868a7e41aa054097a85575aa1d9658cc.json"}}, {"family": "Albinsson", "given": "Sebastian", "initials": "S", "orcid": "0000-0001-6936-3967", "researcher": {"href": "https://publications.scilifelab.se/researcher/ac577769c2d44ac7bd8ccc28f69045de.json"}}, {"family": "Dellgren", "given": "G\u00f6ran", "initials": "G", "orcid": "0000-0003-4961-9704", "researcher": {"href": "https://publications.scilifelab.se/researcher/2d5ee559ab58458197bab1d119a50824.json"}}, {"family": "Bor\u00e9n", "given": "Jan", "initials": "J", "orcid": "0000-0003-0786-8091", "researcher": {"href": "https://publications.scilifelab.se/researcher/1e85f6d287ce4c60a7b35b287efb4f79.json"}}, {"family": "Jeppsson", "given": "Anders", "initials": "A", "orcid": "0000-0003-2356-2295", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ec361c8c3f84b25a44213af77f4ac31.json"}}, {"family": "Lumbers", "given": "R Thomas", "initials": "RT", "orcid": "0000-0002-9077-4741", "researcher": {"href": "https://publications.scilifelab.se/researcher/a53e4d6591db481f881ec6046d54535b.json"}}, {"family": "Shah", "given": "Sonia", "initials": "S", "orcid": "0000-0001-5860-4526", "researcher": {"href": "https://publications.scilifelab.se/researcher/c6a8568b3cae476199b27818eeb19e4d.json"}}, {"family": "Nilsson", "given": "Johan", "initials": "J", "orcid": "0000-0001-6860-6090", "researcher": {"href": "https://publications.scilifelab.se/researcher/c07e3381e15b4806b77d1b575e4ddca2.json"}}, {"family": "Natarajan", "given": "Pradeep", "initials": "P", "orcid": "0000-0001-8402-7435", "researcher": {"href": "https://publications.scilifelab.se/researcher/85de5f6926c94fbd96bbc9428b6a384f.json"}}, {"family": "Lappalainen", "given": "Tuuli", "initials": "T", "orcid": "0000-0002-7746-8109", "researcher": {"href": "https://publications.scilifelab.se/researcher/a1f81f8a2e6f4f11ad4504746492fc41.json"}}, {"family": "Levin", "given": "Malin", "initials": "M", "orcid": "0000-0003-1069-5275", "researcher": {"href": "https://publications.scilifelab.se/researcher/8d251e6a73fb49bcbd930f7ec8bd274c.json"}}, {"family": "Ehrencrona", "given": "Hans", "initials": "H", "orcid": "0000-0002-5589-3622", "researcher": {"href": "https://publications.scilifelab.se/researcher/7b89608a8ce941c3b9911630b4ff9720.json"}}, {"family": "Smith", "given": "J Gustav", "initials": "JG", "orcid": "0000-0001-6285-9935", "researcher": {"href": "https://publications.scilifelab.se/researcher/26e50df6bb7f4194a52546dbd5652e84.json"}}], "type": "journal article", "published": "2025-02-05", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "15", "issue": "1", "pages": "4306", "issn-l": "2045-2322"}, "abstract": "The genetic contributions to early onset heart failure (HF) are incompletely understood. Genetic testing in advanced HF patients undergoing heart transplantation (HTx) may yield clinical benefits, but data is limited. We performed deep-coverage whole genome sequencing (WGS) in 102 Swedish HTx recipients. Gene lists were compiled through a systematic literature review. Variants were prioritized for pathogenicity and classified manually. We also compared polygenic HF risk scores to a population-based cohort. We found a pathogenic (LP/P) variant in 34 individuals (34%). Testing yield was highest in hypertrophic (63% LP/P carriers), dilated (40%) and arrhythmogenic right ventricular (33%) cardiomyopathy and lower in ischemic cardiomyopathy (10%). A family history was more common in LP/P variant carriers than in non-carriers but was present in less than half of carriers (44% vs 13%, P < 0.001), whereas age was similar. Polygenic risk scores were similar in HTx recipients and the population cohort. In conclusion, we observed a high prevalence of pathogenic cardiomyopathy gene variants in individuals with early-onset advanced HF, which could not accurately be ruled out by family history and age. In contrast, we did not observe higher polygenic risk scores in early onset advanced HF cases than in the general population.", "doi": "10.1038/s41598-025-88465-8", "pmid": "39910139", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11799378"}, {"db": "pii", "key": "10.1038/s41598-025-88465-8"}], "notes": [], "created": "2025-02-11T07:01:17.258Z", "modified": "2025-02-11T07:01:20.425Z"}, {"entity": "publication", "iuid": "874f1c17b7aa431f977a1f680546f059", "links": {"self": {"href": "https://publications.scilifelab.se/publication/874f1c17b7aa431f977a1f680546f059.json"}, "display": {"href": "https://publications.scilifelab.se/publication/874f1c17b7aa431f977a1f680546f059"}}, "title": "Reducing methane emissions by developing low-fumarate high-ethanol eco-friendly rice.", "authors": [{"family": "Jin", "given": "Yunkai", "initials": "Y"}, {"family": "Liu", "given": "Tong", "initials": "T"}, {"family": "Hu", "given": "Jia", "initials": "J"}, {"family": "Sun", "given": "Kai", "initials": "K"}, {"family": "Xue", "given": "Lihong", "initials": "L"}, {"family": "Bettembourg", "given": "Mathilde", "initials": "M"}, {"family": "Bedada", "given": "Girma", "initials": "G"}, {"family": "Hou", "given": "Pengfu", "initials": "P"}, {"family": "Hao", "given": "Peiying", "initials": "P"}, {"family": "Tang", "given": "Jintian", "initials": "J"}, {"family": "Ye", "given": "Zihong", "initials": "Z"}, {"family": "Liu", "given": "Chunlin", "initials": "C"}, {"family": "Li", "given": "Peng", "initials": "P"}, {"family": "Pan", "given": "Aihu", "initials": "A"}, {"family": "Weng", "given": "Lushui", "initials": "L"}, {"family": "Xiao", "given": "Guoying", "initials": "G"}, {"family": "Moazzami", "given": "Ali A", "initials": "AA"}, {"family": "Yu", "given": "Xiaoping", "initials": "X"}, {"family": "Wu", "given": "Jun", "initials": "J"}, {"family": "Schn\u00fcrer", "given": "Anna", "initials": "A"}, {"family": "Sun", "given": "Chuanxin", "initials": "C"}], "type": "journal article", "published": "2025-02-03", "journal": {"title": "Mol Plant", "issn": "1752-9867", "issn-l": "1674-2052", "volume": "18", "issue": "2", "pages": "333-349"}, "abstract": "Methane in rice paddies is mainly produced by methanogenic communities feeding on carbon from root exudates and debris. However, the dominant root secretion governing methane emissions is not yet identified after decades of studies, even though secreted carbohydrates and organic acids have been shown to contribute to methane emissions. In this study, we discovered that fumarate and ethanol are two major rice-orchestrated secretions and play a key role in regulating methane emissions. Fumarate released in the rhizosphere is metabolized by microorganisms, supporting the growth of methanogenic archaea that produce methane as an end carbon product, while ethanol mitigates methane emissions through inhibition of methanogenic activity and growth as well as reducing fumarate synthesis in the rice root. Furthermore, we elucidated the route of fumarate metabolism in the anoxic rhizospheric zone. We found that fumarate in the rice root is produced from acetate via propionate and succinate, and when released into soil directly is oxidized to propionate before conversion via acetate into methane as the end product. The knowledge on fumarate and ethanol metabolism in rice was then used for hybrid breeding of new rice varieties with the property of low methane emission. Cultivation of these novel rice lines or employing our findings for rice cultivation managements showed up to 70% reductions in methane production from seven paddy field sites during 3 years of cultivation trials. Taken together, these findings offer great possibilities for effective mitigation of the global climatic impact of rice cultivation.", "doi": "10.1016/j.molp.2025.01.008", "pmid": "39904305", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics (NBIS)": "Service", "Bioinformatics Support and Infrastructure": "Service", "Bioinformatics Support, Infrastructure and Training": "Service"}, "xrefs": [{"db": "pii", "key": "S1674-2052(25)00029-2"}], "notes": [], "created": "2025-09-08T11:37:21.068Z", "modified": "2025-11-21T12:24:20.380Z"}, {"entity": "publication", "iuid": "ce8b106b6f714fb9af54bf212eb1a45f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ce8b106b6f714fb9af54bf212eb1a45f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ce8b106b6f714fb9af54bf212eb1a45f"}}, "title": "Dissociable genetic influences on eye movements during abstract versus naturalistic social scene viewing in infancy.", "authors": [{"family": "Portugal", "given": "Ana Maria", "initials": "AM"}, {"family": "Taylor", "given": "Mark J", "initials": "MJ"}, {"family": "Tammimies", "given": "Kristiina", "initials": "K"}, {"family": "Ronald", "given": "Angelica", "initials": "A"}, {"family": "Falck-Ytter", "given": "Terje", "initials": "T"}], "type": "journal article", "published": "2025-02-03", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "15", "issue": "1", "pages": "4100", "issn-l": "2045-2322"}, "abstract": "Eye-movement metrics like fixation location and duration are increasingly being used in infancy research. We tested whether fixation durations during meaningful social stimulus viewing involve common or different familial influences than fixation durations during viewing of abstract stimulus. We analysed the duration of fixations, and the allocation of fixations to face and motion, from 536 dizygotic and monozygotic 5-month-old twins in: naturalistic scenes including low- and high-level social features, and abstract scenes only having low-level features. We observed significant genetic influences in both conditions (h2naturalistic = 0.30, 95% confidence interval (CI) 0.14 to 0.44; h2abstract = 0.25, 95% CI 0.09 to 0.39), while shared environmental influences were negligible. Although some genetic influences were shared between the two conditions, unique genetic factors were linked to naturalistic scene viewing, indicating that fixation durations index different phenomena dependent on the context. Heritability for face looking was moderate (h2 = 0.19, 95% CI 0.03 to 0.34), and no familial influences were found for motion looking. Exploratory polygenic score analyses revealed no significant associations with fixation measures. This study underscores the dissociable genetic influences on infants' visual exploration of abstract versus naturalistic stimuli and the importance of considering context when interpreting eye-tracking data.", "doi": "10.1038/s41598-024-83557-3", "pmid": "39900629", "labels": {"NGI SNP genotyping": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11791049"}, {"db": "pii", "key": "10.1038/s41598-024-83557-3"}], "notes": [], "created": "2025-09-08T11:34:00.982Z", "modified": "2025-11-14T11:07:01.444Z"}, {"entity": "publication", "iuid": "5959d8a1ef54451098a8e6ac640e7442", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5959d8a1ef54451098a8e6ac640e7442.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5959d8a1ef54451098a8e6ac640e7442"}}, "title": "Unraveling the Genetics of Shared Clinical and Serological Manifestations in Patients With Systemic Inflammatory Autoimmune Diseases.", "authors": [{"family": "Bianchi", "given": "Matteo", "initials": "M", "orcid": "0000-0003-3394-6495", "researcher": {"href": "https://publications.scilifelab.se/researcher/d645ef0e04a245f0ac9e7d7498b2bd69.json"}}, {"family": "Kozyrev", "given": "Sergey V", "initials": "SV", "orcid": "0000-0001-6209-4100", "researcher": {"href": "https://publications.scilifelab.se/researcher/b6be89ad73a14d66a3b9439efc9c4099.json"}}, {"family": "Notarnicola", "given": "Antonella", "initials": "A", "orcid": "0000-0003-0272-2931", "researcher": {"href": "https://publications.scilifelab.se/researcher/42411ecc60cd4357930ff0e978b3fcd8.json"}}, {"family": "Sandling", "given": "Johanna K", "initials": "JK"}, {"family": "Pettersson", "given": "Mats", "initials": "M"}, {"family": "Leonard", "given": "Dag", "initials": "D"}, {"family": "Sj\u00f6wall", "given": "Christopher", "initials": "C", "orcid": "0000-0003-0900-2048", "researcher": {"href": "https://publications.scilifelab.se/researcher/fe4dd47b8ca1436e8a26fdea33f5e7f6.json"}}, {"family": "Gunnarsson", "given": "Iva", "initials": "I"}, {"family": "Rantap\u00e4\u00e4-Dahlqvist", "given": "Solbritt", "initials": "S", "orcid": "0000-0001-8259-3863", "researcher": {"href": "https://publications.scilifelab.se/researcher/dfca4bfdcf3946fda64397d3b7debc59.json"}}, {"family": "Bengtsson", "given": "Anders A", "initials": "AA"}, {"family": "J\u00f6nsen", "given": "Andreas", "initials": "A"}, {"family": "Svenungsson", "given": "Elisabet", "initials": "E", "orcid": "0000-0003-3396-3244", "researcher": {"href": "https://publications.scilifelab.se/researcher/0ab5989c3c604a96bf42b1b6f90434a0.json"}}, {"family": "Enocsson", "given": "Helena", "initials": "H", "orcid": "0000-0002-2125-2931", "researcher": {"href": "https://publications.scilifelab.se/researcher/e34f7f45437c404da069fe0e83bf11f6.json"}}, {"family": "Kvarnstr\u00f6m", "given": "Marika", "initials": "M"}, {"family": "Forsblad-d'Elia", "given": "Helena", "initials": "H"}, {"family": "Bucher", "given": "Sara Magnusson", "initials": "SM"}, {"family": "Norheim", "given": "Katrine B", "initials": "KB"}, {"family": "Baecklund", "given": "Eva", "initials": "E"}, {"family": "Jonsson", "given": "Roland", "initials": "R"}, {"family": "Hammenfors", "given": "Daniel", "initials": "D"}, {"family": "Eriksson", "given": "Per", "initials": "P"}, {"family": "Mandl", "given": "Thomas", "initials": "T"}, {"family": "Omdal", "given": "Roald", "initials": "R"}, {"family": "Padyukov", "given": "Leonid", "initials": "L"}, {"family": "Andersson", "given": "Helena", "initials": "H"}, {"family": "Molberg", "given": "\u00d8yvind", "initials": "\u00d8"}, {"family": "Diederichsen", "given": "Louise Pyndt", "initials": "LP"}, {"family": "Syv\u00e4nen", "given": "Ann-Christine", "initials": "AC"}, {"family": "Wahren-Herlenius", "given": "Marie", "initials": "M", "orcid": "0000-0002-0915-7245", "researcher": {"href": "https://publications.scilifelab.se/researcher/a8451e7f5e6e4e4da0bace3dfafaeb38.json"}}, {"family": "Nordmark", "given": "Gunnel", "initials": "G", "orcid": "0000-0002-3829-7431", "researcher": {"href": "https://publications.scilifelab.se/researcher/188fda53498740dbb007441cc94bb1ad.json"}}, {"family": "Lundberg", "given": "Ingrid E", "initials": "IE", "orcid": "0000-0002-6068-9212", "researcher": {"href": "https://publications.scilifelab.se/researcher/40f6c8e761a944b78e67f0e04453f78b.json"}}, {"family": "R\u00f6nnblom", "given": "Lars", "initials": "L"}, {"family": "Lindblad-Toh", "given": "Kerstin", "initials": "K"}, {"family": "with the DISSECT consortium and the ImmunoArray consortium", "given": "", "initials": ""}], "type": "journal article", "published": "2025-02-00", "journal": {"title": "Arthritis & rheumatology (Hoboken, N.J.)", "issn": "2326-5205", "volume": "77", "issue": "2", "pages": "212-225", "issn-l": "2326-5191"}, "abstract": "Systemic inflammatory autoimmune diseases (SIADs) such as systemic lupus erythematosus (SLE), primary Sj\u00f6gren disease (pSS), and idiopathic inflammatory myopathies (myositis) are complex conditions characterized by shared circulating autoantibodies and clinical manifestations, including skin rashes, among others. This study was aimed at elucidating the genetics underlying these common features.\n\nWe performed targeted DNA sequencing of coding and regulatory regions from approximately 1,900 immune-related genes in a large cohort of 2,292 well-characterized Scandinavian patients with SIADs with SLE, pSS, and myositis as well as 1,252 controls. A gene-based functionally weighted genetic score for aggregate testing of all genetic variants, including rare variants, was complemented by in silico functional analyses and in vitro reporter experiments.\n\nCase-control association analysis detected known and potentially novel genetic loci in agreement with previous genetic and transcriptomics findings linked to the SIAD autoimmune background. Intriguingly, case-case comparisons between patient subgroups with and without specific autoantibodies revealed that the subgroups defined by antinuclear antibodies and anti-double-stranded DNA antibodies have unique genetic profiles reflecting their heterogeneity. When focusing on clinical features, we overall showed that dual-specificity phosphatase 1 (DUSP1) protective genetic variants lead to increased gene expression and potentially to anti-inflammatory effects on the SIAD-associated skin phenotype. This is consistent with recent genetic findings on eczema and with the previously reported down-regulation of the MAPK signaling-related gene DUSP1 in other skin disorders.\n\nTogether, this suggests common molecular mechanisms potentially underlying overlapping clinical manifestations shared among different disorders and informs clinical heterogeneity, which could be translated to improve disease diagnostic and treatment, also in more generalized disease frameworks.", "doi": "10.1002/art.42988", "pmid": "39284741", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "Service", "Bioinformatics Support for Computational Resources": "Service", "NGI SNP genotyping": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11782108"}], "notes": [], "created": "2024-11-12T11:40:11.189Z", "modified": "2025-09-08T06:50:36.661Z"}, {"entity": "publication", "iuid": "c8f5dbcb52864b11a987807b315f87ed", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c8f5dbcb52864b11a987807b315f87ed.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c8f5dbcb52864b11a987807b315f87ed"}}, "title": "RNA Sequencing Reveals the Long Non-Coding RNA Signature in Psoriasis Keratinocytes and Identifies CYDAER as a Long Non-Coding RNA Regulating Epidermal Differentiation.", "authors": [{"family": "Freisenhausen", "given": "Jan Cedric", "initials": "JC", "orcid": "0000-0002-3078-0365", "researcher": {"href": "https://publications.scilifelab.se/researcher/74f596e44f3d4dd78d499469c9f0b04e.json"}}, {"family": "Luo", "given": "Longlong", "initials": "L", "orcid": "0000-0002-5931-0666", "researcher": {"href": "https://publications.scilifelab.se/researcher/aa6310dd902342b4a74bac1efd4090c0.json"}}, {"family": "Kelemen", "given": "Evelyn", "initials": "E", "orcid": "0000-0002-8357-790X", "researcher": {"href": "https://publications.scilifelab.se/researcher/8f1c75b553304176b8cafa84815421e8.json"}}, {"family": "Elton", "given": "Jonathan", "initials": "J", "orcid": "0000-0003-4919-8065", "researcher": {"href": "https://publications.scilifelab.se/researcher/22bf1246696541abafd2c2ad902a3b84.json"}}, {"family": "Skoog", "given": "Viktor", "initials": "V", "orcid": "0009-0005-8862-1534", "researcher": {"href": "https://publications.scilifelab.se/researcher/160d22c12c9743e193a47f6ded86b7ad.json"}}, {"family": "Pivarcsi", "given": "Andor", "initials": "A", "orcid": "0000-0003-2196-1102", "researcher": {"href": "https://publications.scilifelab.se/researcher/77ca870317234573a3da5dffb24bb268.json"}}, {"family": "Sonkoly", "given": "Enik\u00f6", "initials": "E", "orcid": "0000-0002-4909-5413", "researcher": {"href": "https://publications.scilifelab.se/researcher/5c1ce318445d4b2bb586ac1f8ed8ed87.json"}}], "type": "journal article", "published": "2025-02-00", "journal": {"title": "Exp. Dermatol.", "issn": "1600-0625", "volume": "34", "issue": "2", "pages": "e70054", "issn-l": "0906-6705"}, "abstract": "Psoriasis is a common chronic inflammatory skin disease determined by genetic and environmental factors, resulting in the activation of IL-23/IL-17-mediated immune response, epidermal hyperproliferation, and keratinocyte activation. Long non-coding RNAs (lncRNAs) are non-protein-coding transcripts > 500 nucleotides with diverse regulatory functions; their role in epidermal dysfunction in psoriasis is poorly understood. To identify epidermal transcripts with potential roles in psoriasis, including lncRNAs, we performed RNA sequencing on keratinocytes from psoriasis and healthy skin. We identified 889 differentially expressed lncRNAs, many of which with yet unknown functions. RP11-295G20.2 was identified as a lncRNA significantly induced in psoriasis keratinocytes, and this was verified by qRT-PCR and by single-molecule in situ hybridisation. Analysis of subcellular fractions of epidermis revealed a cytoplasmic localisation in line with results of single molecule in situ hybridisation. We report that RP11-295G20.2 has a skin-enriched expression, and within skin it is mainly expressed in suprabasal epidermal layers. Moreover, RP11-295G20.2 is induced by the key psoriasis cytokine IL-17A and shows a dynamic regulation during keratinocyte differentiation with upregulation during early differentiation and downregulation in the late stage. Knockdown of RP11-295G20.2 in keratinocytes promotes terminal differentiation. Based on our findings, we named RP11-295G20.2 Cytoplasmic Differentiation-Associated Epidermal RNA, CYDAER. In summary, our study provides a comprehensive characterisation of the non-coding RNA landscape of psoriasis keratinocytes and identifies CYDAER as a skin-enriched lncRNA regulating keratinocyte differentiation. Our data suggest that overexpression of CYDAER may contribute to altered differentiation in psoriatic epidermis.", "doi": "10.1111/exd.70054", "pmid": "39953783", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11829188"}], "notes": [], "created": "2025-09-08T06:52:12.448Z", "modified": "2025-09-08T06:52:13.267Z"}, {"entity": "publication", "iuid": "5327a3ebdfe244b481789f7baf594301", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5327a3ebdfe244b481789f7baf594301.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5327a3ebdfe244b481789f7baf594301"}}, "title": "Pain in idiopathic scoliosis not associated with known genetic variants for pain.", "authors": [{"family": "Cheng", "given": "Tian", "initials": "T", "orcid": "0000-0001-5013-6473", "researcher": {"href": "https://publications.scilifelab.se/researcher/b65aa57c2cae41ed8b5d808377eca30d.json"}}, {"family": "Diarbakerli", "given": "Elias", "initials": "E"}, {"family": "Simony", "given": "Ane", "initials": "A"}, {"family": "\u00d8sterheden Andersen", "given": "Mikkel", "initials": "M"}, {"family": "Danielsson", "given": "Aina", "initials": "A"}, {"family": "Kere", "given": "Juha", "initials": "J"}, {"family": "Einarsdottir", "given": "Elisabet", "initials": "E"}, {"family": "Gerdhem", "given": "Paul", "initials": "P"}], "type": "journal article", "published": "2025-02-00", "journal": {"title": "Pain Rep", "issn": "2471-2531", "issn-l": null, "volume": "10", "issue": "1", "pages": "e1227"}, "abstract": "Back pain is common in idiopathic scoliosis. The aim of this study was to study known genetic variants associated with pain in individuals with idiopathic scoliosis.\r\n\r\nWe included 1442 individuals with juvenile or adolescent idiopathic scoliosis from Sweden and Denmark. Single nucleotide variants (SNV) genotyping was performed on 37 SNVs. Pain was assessed using 2 questionnaires. The mean pain domain score on the Scoliosis Research Society 22 revised questionnaire (SRS-22r) ranging between 1 (worst) and 5 (best) was dichotomized into a \"back pain group\" (score <4) and a \"no back pain group\" (score \u22654). The EuroQol 5-dimensions (EQ-5D) 3 level pain domain was dichotomized into a \"no pain group\" and a \"pain group.\" Odds ratios were used to describe the associations.\r\n\r\nBased on the SRS-22r pain domain scores, 456 individuals (32%) reported back pain. Based on the EQ-5D questionnaire, 813 individuals (56%) reported moderate or extreme pain/discomfort. The odds ratio for the associations between the selected genetic variants and back pain or pain in general as measured with SRS-22r and EQ-5D-3L ranged between 0.88 to 1.17 and 0.86 to 1.16, with P-values ranging between 0.08 to 0.99 and 0.08 to 0.95.\r\n\r\nThis study suggests that known genetic variants associated with pain do not play a significant role in the development of pain in individuals with idiopathic scoliosis.", "doi": "10.1097/PR9.0000000000001227", "pmid": "39713503", "labels": {"NGI SNP genotyping": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics (NBIS)": null, "Bioinformatics Long-term Support WABI": "Service", "Bioinformatics Support, Infrastructure and Training": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11661741"}, {"db": "pii", "key": "PAINREPORTS-D-23-0205"}], "notes": [], "created": "2025-09-08T07:06:06.228Z", "modified": "2025-11-19T08:43:57.611Z"}, {"entity": "publication", "iuid": "9458971190ee41e099e40121d1866819", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9458971190ee41e099e40121d1866819.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9458971190ee41e099e40121d1866819"}}, "title": "Impact of excess sugar on the whole genome DNA methylation pattern in human sperm.", "authors": [{"family": "J\u00f6nsson", "given": "Josefine", "initials": "J", "orcid": "0000-0003-0709-2828", "researcher": {"href": "https://publications.scilifelab.se/researcher/9a4b2eb9eef5496eb27e76fc9fca120a.json"}}, {"family": "Perfilyev", "given": "Alexander", "initials": "A"}, {"family": "Kugelberg", "given": "Unn", "initials": "U"}, {"family": "Skog", "given": "Signe", "initials": "S"}, {"family": "Lindstr\u00f6m", "given": "Axel", "initials": "A"}, {"family": "Ruhrmann", "given": "Sabrina", "initials": "S"}, {"family": "Ofori", "given": "Jones K", "initials": "JK"}, {"family": "Bacos", "given": "Karl", "initials": "K"}, {"family": "R\u00f6nn", "given": "Tina", "initials": "T"}, {"family": "\u00d6st", "given": "Anita", "initials": "A"}, {"family": "Ling", "given": "Charlotte", "initials": "C", "orcid": "0000-0003-0587-7154", "researcher": {"href": "https://publications.scilifelab.se/researcher/dd7c1ea934034c4db99f31a5a9b04691.json"}}], "type": "journal article", "published": "2025-02-00", "journal": {"title": "Epigenomics", "issn": "1750-192X", "volume": "17", "issue": "2", "pages": "89-104", "issn-l": null}, "abstract": "Dietary factors may regulate the epigenome. We aimed to explore whether a diet intervention, including excess sugar, affects the methylome in human sperm, and to describe the sperm methylome. We used Whole Genome Bisulfite Sequencing (WGBS) to analyze DNA methylation in sperm taken at three time points from 15 males during a diet intervention; i) at baseline, ii) after one week on a standardized diet, and iii) after an additional week on a high-sugar diet providing 150% of their estimated total energy expenditure.\n\nWe identified seven nominal diet-associated differentially methylated regions in sperm (p < 0.05). The diet was nominally associated with methylation of 143 sites linked to fertility (e.g. AHRR, GNAS, and HDAC4), 313 sites in imprinted genes (e.g. GLIS3, PEG10, PEG3, and SNURF), and 42 sites in top 1%-expressed genes (e.g. CHD2) (p < 0.05). In sperm, 3'UTRs and introns had the highest levels of methylation, while 5'UTRs and CpG islands had the lowest levels. Non-expressed genes in human sperm were hypomethylated in exons compared with transcribed genes.\n\nIn human sperm, DNA methylation levels were linked to gene expression, and excess sugar had modest effects on methylation on imprinted and highly expressed genes, and genes affecting fertility.", "doi": "10.1080/17501911.2024.2439782", "pmid": "39707713", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "Service"}, "xrefs": [], "notes": [], "created": "2025-02-03T07:41:54.349Z", "modified": "2025-02-03T07:41:54.880Z"}, {"entity": "publication", "iuid": "b7086e5f716e435090388237fe0eaeb5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b7086e5f716e435090388237fe0eaeb5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b7086e5f716e435090388237fe0eaeb5"}}, "title": "Lack of ST2 aggravates glioma invasiveness, vascular abnormality, and immune suppression.", "authors": [{"family": "Wicher", "given": "Grzegorz", "initials": "G"}, {"family": "Roy", "given": "Ananya", "initials": "A"}, {"family": "Vaccaro", "given": "Alessandra", "initials": "A"}, {"family": "Vemuri", "given": "Kalyani", "initials": "K"}, {"family": "Ramachandran", "given": "Mohanraj", "initials": "M"}, {"family": "Olofsson", "given": "Tommie", "initials": "T"}, {"family": "Imbria", "given": "Rebeca-Noemi", "initials": "RN"}, {"family": "Belting", "given": "Mattias", "initials": "M"}, {"family": "Nilsson", "given": "Gunnar", "initials": "G"}, {"family": "Dimberg", "given": "Anna", "initials": "A"}, {"family": "Forsberg-Nilsson", "given": "Karin", "initials": "K", "orcid": "0000-0003-0692-6245", "researcher": {"href": "https://publications.scilifelab.se/researcher/5da04859250141a0a7271a69c7da9176.json"}}], "type": "journal article", "published": "2025-01-27", "journal": {"title": "Neurooncol Adv", "issn": "2632-2498", "volume": "7", "issue": "1", "pages": "vdaf010", "issn-l": null}, "abstract": "Glioblastoma (GBM) is the most common primary malignant brain tumor in adults, characterized by aggressive growth and a dismal prognosis. Interleukin-33 (IL-33) and its receptor ST2 have emerged as regulators of glioma growth, but their exact function in tumorigenesis has not been deciphered. Indeed, previous studies on IL-33 in cancer have yielded somewhat opposing results as to whether it is pro- or anti-tumorigenic.\n\nIL-33 expression was assessed in a GBM tissue microarray and public databases. As in vivo models we used orthotopic xenografts of patient-derived GBM cells, and syngenic models with grafted mouse glioma cells.\n\nWe analyzed the role of IL-33 and its receptor ST2 in nonmalignant cells of the glioma microenvironment and found that IL-33 levels are increased in cells surrounding the tumor. Protein complexes of IL-33 and ST2 are mainly found outside of the tumor core. The IL-33-producing cells consist primarily of oligodendrocytes. To determine the function of IL-33 in the tumor microenvironment, we used mice lacking the ST2 receptor. When glioma cells were grafted to ST2-deficient mouse brains, the resulting tumors exhibited a more invasive growth pattern, and are associated with poorer survival, compared to wild-type mice. Tumors in ST2-deficient hosts are more invasive, with increased expression of extracellular matrix remodeling enzymes and enhanced tumor angiogenesis. Furthermore, the absence of ST2 leads to a more immunosuppressive environment.\n\nOur findings reveal that glia-derived IL-33 and its receptor ST2 participate in modulating tumor invasiveness, tumor vasculature, and immunosuppression in glioma.", "doi": "10.1093/noajnl/vdaf010", "pmid": "39931535", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11808570"}, {"db": "pii", "key": "vdaf010"}], "notes": [], "created": "2025-09-08T11:37:18.675Z", "modified": "2025-09-08T11:37:18.685Z"}, {"entity": "publication", "iuid": "694184d0fedc41c3ba78ea06f31e7668", "links": {"self": {"href": "https://publications.scilifelab.se/publication/694184d0fedc41c3ba78ea06f31e7668.json"}, "display": {"href": "https://publications.scilifelab.se/publication/694184d0fedc41c3ba78ea06f31e7668"}}, "title": "Exploring a pico-well based scRNA-seq method (HIVE) for simplified processing of equine bronchoalveolar lavage cells.", "authors": [{"family": "Fegraeus", "given": "Kim", "initials": "K"}, {"family": "Riihim\u00e4ki", "given": "Miia", "initials": "M"}, {"family": "Nordlund", "given": "Jessica", "initials": "J"}, {"family": "Akula", "given": "Srinivas", "initials": "S"}, {"family": "Wernersson", "given": "Sara", "initials": "S", "orcid": "0000-0003-3067-7875", "researcher": {"href": "https://publications.scilifelab.se/researcher/6d03168eb2f54a91897b5b738e2c5137.json"}}, {"family": "Raine", "given": "Amanda", "initials": "A", "orcid": "0000-0002-2775-6516", "researcher": {"href": "https://publications.scilifelab.se/researcher/a97b7df8379f42f0a412fb7c234a6c70.json"}}], "type": "journal article", "published": "2025-01-24", "journal": {"title": "PLoS ONE", "issn": "1932-6203", "volume": "20", "issue": "1", "pages": "e0317343", "issn-l": "1932-6203"}, "abstract": "Single-cell RNA sequencing (scRNA-seq) is a valuable tool for investigating cellular heterogeneity in diseases such as equine asthma (EA). This study evaluates the HIVE\u2122 scRNA-seq method, a pico-well-based technology, for processing bronchoalveolar lavage (BAL) cells from horses with EA. The HIVE method offers practical advantages, including compatibility with both field and clinical settings, as well as a gentle workflow suited for handling sensitive cells. Our results show that the major cell types in equine BAL were successfully identified; however, the proportions of T cells and macrophages deviated from cytological expectations, with macrophages being overrepresented and T cells underrepresented. Despite these limitations, the HIVE method confirmed previously identified T cell and macrophage subpopulations and defined other BAL cell subsets. However, compared to previous studies T helper subsets were less clearly defined. Additionally, consistent with previous scRNA-seq studies, the HIVE method detected fewer granulocytes and mast cells than anticipated in the total BAL samples. Nevertheless, applying the method to purified mast cells recovered an expected number of cells. A small set of eosinophils were also detected which have not been characterized in earlier studies. In summary these findings suggest that while the HIVE method shows promise for certain applications, further optimization is needed to improve the accuracy of cell type representation, particularly for granulocytes and mast cells, in BAL samples.", "doi": "10.1371/journal.pone.0317343", "pmid": "39854349", "labels": {"NGI Short read": "Technology development", "NGI Uppsala (SNP&SEQ Technology Platform)": "Technology development", "National Genomics Infrastructure": "Technology development", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11760581"}, {"db": "pii", "key": "PONE-D-24-13492"}], "notes": [], "created": "2025-05-12T05:47:24.783Z", "modified": "2025-11-14T11:09:01.384Z"}, {"entity": "publication", "iuid": "0729e1b65266450092168ec789fee122", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0729e1b65266450092168ec789fee122.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0729e1b65266450092168ec789fee122"}}, "title": "Life-history adaptation under climate warming magnifies the agricultural footprint of a cosmopolitan insect pest.", "authors": [{"family": "Burc", "given": "Estelle", "initials": "E"}, {"family": "Girard-Tercieux", "given": "Camille", "initials": "C"}, {"family": "Metz", "given": "Moa", "initials": "M"}, {"family": "Cazaux", "given": "Elise", "initials": "E"}, {"family": "Baur", "given": "Julian", "initials": "J", "orcid": "0000-0002-4739-2756", "researcher": {"href": "https://publications.scilifelab.se/researcher/7e69e394b67145188a77f90365f3fe15.json"}}, {"family": "Koppik", "given": "Mareike", "initials": "M"}, {"family": "R\u00eago", "given": "Alexandre", "initials": "A"}, {"family": "Hart", "given": "Alex F", "initials": "AF"}, {"family": "Berger", "given": "David", "initials": "D", "orcid": "0000-0003-0196-6109", "researcher": {"href": "https://publications.scilifelab.se/researcher/c788f99e9df4435587f7e991eae4311e.json"}}], "type": "journal article", "published": "2025-01-18", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "16", "issue": "1", "pages": "827", "issn-l": "2041-1723"}, "abstract": "Climate change is affecting population growth rates of ectothermic pests with potentially dire consequences for agriculture and global food security. However, current projection models of pest impact typically overlook the potential for rapid genetic adaptation, making current forecasts uncertain. Here, we predict how climate change adaptation in life-history traits of insect pests affects their growth rates and impact on agricultural yields by unifying thermodynamics with classic theory on resource acquisition and allocation trade-offs between foraging, reproduction, and maintenance. Our model predicts that warming temperatures will favour resource allocation towards maintenance coupled with increased resource acquisition through larval foraging, and the evolution of this life-history strategy results in both increased population growth rates and per capita host consumption, causing a double-blow on agricultural yields. We find support for these predictions by studying thermal adaptation in life-history traits and gene expression in the wide-spread insect pest, Callosobruchus maculatus; with 5 years of evolution under experimental warming causing an almost two-fold increase in its predicted agricultural footprint. These results show that pest adaptation can offset current projections of agricultural impact and emphasize the need for integrating a mechanistic understanding of life-history evolution into forecasts of pest impact under climate change.", "doi": "10.1038/s41467-025-56177-2", "pmid": "39827176", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11743133"}, {"db": "pii", "key": "10.1038/s41467-025-56177-2"}], "notes": [], "created": "2025-09-08T11:37:34.656Z", "modified": "2025-09-08T11:37:34.821Z"}, {"entity": "publication", "iuid": "6c276021592e42bf829461a46e283293", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6c276021592e42bf829461a46e283293.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6c276021592e42bf829461a46e283293"}}, "title": "Airway MMP-12 and DNA methylation in COPD: an integrative approach.", "authors": [{"family": "Eriksson Str\u00f6m", "given": "Jonas", "initials": "J"}, {"family": "Kebede Merid", "given": "Simon", "initials": "S"}, {"family": "Linder", "given": "Robert", "initials": "R"}, {"family": "Pourazar", "given": "Jamshid", "initials": "J"}, {"family": "Lindberg", "given": "Anne", "initials": "A"}, {"family": "Mel\u00e9n", "given": "Erik", "initials": "E"}, {"family": "Behndig", "given": "Annelie F", "initials": "AF"}], "type": "journal article", "published": "2025-01-10", "journal": {"title": "Respir. Res.", "issn": "1465-993X", "volume": "26", "issue": "1", "pages": "10", "issn-l": "1465-9921"}, "abstract": "In COPD, the balance between matrix metalloproteinases (MMPs) and their natural inhibitors [tissue inhibitors of metalloproteinases (TIMPs)] is shifted towards excessive degradation, reflected in bronchoalveolar lavage (BAL) as increased MMP concentrations. Because of their critical role in lung homeostasis, MMP activity is tightly regulated, but to what extent this regulation occurs through epigenetic mechanisms remains unknown.\n\nTo explore the interplay between MMPs, TIMPs, and DNA methylation (DNAm) we (1) analysed MMP-9, -12, and TIMP-1 concentrations in BAL fluid, and profiled DNAm in BAL cells from 18 COPD and 30 control subjects, (2) estimated protein-COPD relationships using multivariable regression, (3) identified protein quantitative trait methylation loci (pQTMs) with COPD as a potential modifier in a separate interaction model, and (4) integrated significant interactions with a previous COPD GWAS meta-analysis.\n\nCOPD was associated with higher levels of BAL MMP-12 (p = 0.016) but not with MMP-9 or TIMP-1. Further examination of MMP-12 identified association with DNAm at 34 loci (pQTMs), with TGFBR2 (p = 2.25 \u00d7 10-10) and THBS4 (p = 1.11 \u00d7 10-9) among the top ten pQTM genes. The interaction model identified 66 sites where the DNAm-MMP-12 association was significantly different in COPD compared to controls. Of these, one was colocalized with SNPs previously associated with COPD.\n\nOur findings indicate that airway MMP-12 may partially be regulated by epigenetic mechanisms and that this regulation is disrupted in COPD. Furthermore, integration with COPD GWAS data suggests that this dysregulation is influenced by a combination of environmental factors, disease processes, and genetics, with the latter potentially playing a lesser role.", "doi": "10.1186/s12931-024-03088-3", "pmid": "39794761", "labels": {"NGI SNP genotyping": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11724436"}, {"db": "pii", "key": "10.1186/s12931-024-03088-3"}], "notes": [], "created": "2025-09-08T11:34:14.781Z", "modified": "2025-09-08T11:34:14.809Z"}, {"entity": "publication", "iuid": "fd23b37917bf4c6f8b0bb095abb3235d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/fd23b37917bf4c6f8b0bb095abb3235d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/fd23b37917bf4c6f8b0bb095abb3235d"}}, "title": "The type of environment has a greater impact on the larval microbiota of Anopheles arabiensis than on the microbiota of their breeding water.", "authors": [{"family": "Assentato", "given": "Lorenzo", "initials": "L", "orcid": "0000-0003-3699-0483", "researcher": {"href": "https://publications.scilifelab.se/researcher/69a8069f62434b128fb5837b139dbb56.json"}}, {"family": "Nilsson", "given": "Louise K J", "initials": "LKJ"}, {"family": "Brunius", "given": "Carl", "initials": "C", "orcid": "0000-0003-3957-870X", "researcher": {"href": "https://publications.scilifelab.se/researcher/560a5d14ee83421680058b00df2ac9e2.json"}}, {"family": "Feltelius", "given": "Vilhelm", "initials": "V"}, {"family": "Elleby", "given": "Rasmus", "initials": "R"}, {"family": "Hopkins", "given": "Richard J", "initials": "RJ"}, {"family": "Terenius", "given": "Olle", "initials": "O"}], "type": "journal article", "published": "2025-01-07", "journal": {"title": "FEMS Microbiol. Ecol.", "issn": "1574-6941", "volume": "101", "issue": "1", "issn-l": "0168-6496"}, "abstract": "Mosquito larvae of the genus Anopheles develop entirely in water, frequently visiting the surface for air. The aquatic environment plays a key role in shaping their microbiota, but the connection between environmental characteristics of breeding sites and larval microbiota remains underexplored. This study focuses on Anopheles arabiensis, which inhabits the surface microlayer (SML) of breeding sites, a zone with high particle density. We hypothesized that the SML could allow us to capture the diversity of the surrounding environment, and in turn its influence on the larval microbial communities. To test this, we collected A. arabiensis larvae and SML samples from various breeding sites categorized by environmental features. Our results confirm that breeding site characteristics are significant drivers of the bacterial species present in mosquito larvae. Additionally, we found that the larval micro-environment selectively shapes its microbiota, highlighting a dynamic interplay between environmental and internal factors. Interestingly, specific bacterial families were associated with the presence or absence of larvae in breeding sites, suggesting potential ecological roles. These findings expand our understanding of vector-mosquito microbiota, emphasizing the importance of breeding site features in shaping larval microbial communities and providing a foundation for future research on mosquito ecology and control strategies.", "doi": "10.1093/femsec/fiae161", "pmid": "39694819", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11737318"}, {"db": "pii", "key": "7928135"}], "notes": [], "created": "2025-09-08T11:37:32.415Z", "modified": "2025-09-08T11:37:32.533Z"}, {"entity": "publication", "iuid": "36465c1e65bd499d940371185242fb06", "links": {"self": {"href": "https://publications.scilifelab.se/publication/36465c1e65bd499d940371185242fb06.json"}, "display": {"href": "https://publications.scilifelab.se/publication/36465c1e65bd499d940371185242fb06"}}, "title": "Hydrological regime of a continental river system predicts bacterial macroecological patterns.", "authors": [{"family": "Demeter", "given": "Katalin", "initials": "K", "orcid": "0000-0002-4260-3630", "researcher": {"href": "https://publications.scilifelab.se/researcher/5df5f47af9c9454bbf13ea30dfef4df3.json"}}, {"family": "Savio", "given": "Domenico", "initials": "D", "orcid": "0000-0001-5322-9536", "researcher": {"href": "https://publications.scilifelab.se/researcher/66c6378c7ebf41cca7c709a88fcf27c2.json"}}, {"family": "Kirschner", "given": "Alexander K T", "initials": "AKT", "orcid": "0000-0002-9797-3073", "researcher": {"href": "https://publications.scilifelab.se/researcher/9fb459d6e22e4c39983578abae121f74.json"}}, {"family": "Reischer", "given": "Georg H", "initials": "GH", "orcid": "0000-0002-3962-8685", "researcher": {"href": "https://publications.scilifelab.se/researcher/3f1d9145cd724db1803aae7a6ff3319a.json"}}, {"family": "Kolarevic", "given": "Stoimir", "initials": "S"}, {"family": "Parajka", "given": "Juraj", "initials": "J", "orcid": "0000-0002-1177-5181", "researcher": {"href": "https://publications.scilifelab.se/researcher/2698181b5e734debaeb74650004ed055.json"}}, {"family": "Derx", "given": "Julia", "initials": "J", "orcid": "0000-0002-9931-088X", "researcher": {"href": "https://publications.scilifelab.se/researcher/6845bf4cbe784c41b4efe52b87b887c1.json"}}, {"family": "Jakwerth", "given": "Stefan", "initials": "S"}, {"family": "Wurzbacher", "given": "Christian", "initials": "C", "orcid": "0000-0001-7418-0831", "researcher": {"href": "https://publications.scilifelab.se/researcher/1fed784d185749498b07f7458c9ccfb6.json"}}, {"family": "Blaschke", "given": "Alfred P", "initials": "AP", "orcid": "0000-0001-8617-5802", "researcher": {"href": "https://publications.scilifelab.se/researcher/aa8d81f7cfcc4a82acce9690a4d6cffc.json"}}, {"family": "Mach", "given": "Robert L", "initials": "RL", "orcid": "0000-0003-2375-7244", "researcher": {"href": "https://publications.scilifelab.se/researcher/5a53d6c16f2f4e978764b982ba485e97.json"}}, {"family": "Bl\u00f6schl", "given": "G\u00fcnter", "initials": "G", "orcid": "0000-0003-2227-8225", "researcher": {"href": "https://publications.scilifelab.se/researcher/8791191bfcb041d28768a3cda7206d16.json"}}, {"family": "Farnleitner", "given": "Andreas H", "initials": "AH", "orcid": "0000-0002-0542-5425", "researcher": {"href": "https://publications.scilifelab.se/researcher/7f1019fab4eb42a8896e3aa2c2cced44.json"}}, {"family": "Eiler", "given": "Alexander", "initials": "A", "orcid": "0000-0001-9916-9567", "researcher": {"href": "https://publications.scilifelab.se/researcher/e7286785c9334dcba90273b69f81c018.json"}}], "type": "journal article", "published": "2025-01-02", "journal": {"title": "ISME J", "issn": "1751-7370", "volume": "19", "issue": "1", "issn-l": "1751-7362"}, "abstract": "Modeling bacterial dynamics in large river systems is crucial for predicting continental-scale ecosystem functioning under anthropogenic pressures. Although the River Continuum and Metacommunity concepts have provided theoretical frameworks, quantitative parameters necessary for microbial macroecological models remain scarce. Here, we present results from two whole-river surveys, conducted six years apart along 2600 km of the Danube River. Using bacterial secondary production, cell counts, and 16S ribosomal RNA (rRNA) gene amplicon sequencing, we quantified carbon, cell, phylotype, and diversity turnover along the river. Carbon incorporation per cell declined with water travel time by 6000-21 000 atoms per hour. Bacterial cells multiplied every eight days, resulting in four to six doublings during downstream transport. Growth responses at the level of individual phylotypes differed up to a hundredfold from these bulk community estimates. Bacterial diversity dynamics were dominated by phylotype turnover rather than phylotype loss. Turnover ranged from 0.92 to 0.96 along the river, indicating an almost complete replacement of phylotypes with 2%-11% of headwater-associated amplicon sequence variants (ASVs) persisting under base-flow conditions. Richness declined gradually downstream at a rate of ~0.13 ASVs per hour. Variations in bacterial secondary production, cell abundance, and observed ASVs were best explained by models combining hydrological and water quality parameters, whereas beta diversity followed a gradual development primarily structured by water travel time. Together, these results identify water travel time as the key integrative parameter governing microbial macroecological dynamics along large rivers, with environmental conditions fine-tuning local responses. These models can help predict changes in microbial diversity and functioning under anthropogenic alterations.", "doi": "10.1093/ismejo/wrag013", "pmid": "41626752", "labels": {"National Genomics Infrastructure": "Service", "NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "8454621"}, {"db": "pmc", "key": "PMC12927878"}], "notes": [], "created": "2026-02-24T19:07:12.652Z", "modified": "2026-02-24T19:07:14.084Z"}, {"entity": "publication", "iuid": "c42cf07b07844cabbe0ad109571234eb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c42cf07b07844cabbe0ad109571234eb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c42cf07b07844cabbe0ad109571234eb"}}, "title": "Cellular heterogeneity in metabolism and associated microbiome of a non-model phytoflagellate.", "authors": [{"family": "Jeevannavar", "given": "Aditya", "initials": "A"}, {"family": "Florenza", "given": "Javier", "initials": "J"}, {"family": "Divne", "given": "Anna-Maria", "initials": "A"}, {"family": "Tamminen", "given": "Manu", "initials": "M"}, {"family": "Bertilsson", "given": "Stefan", "initials": "S"}], "type": "journal article", "published": "2025-01-02", "journal": {"title": "ISME J", "issn": "1751-7370", "issn-l": "1751-7362", "volume": "19", "issue": "1", "pages": null}, "abstract": "Single-cell transcriptomics is a key tool for unravelling metabolism and tissue diversity in model organisms. Its potential for elucidating the ecological roles of microeukaryotes, especially non-model ones, remains largely unexplored. This study employed the Smart-seq2 protocol on Ochromonas triangulata, a microeukaryote lacking a reference genome, showcasing how transcriptional states align with two distinct growth phases: a fast-growing phase and a slow-growing phase. Besides the two expected expression clusters, each corresponding to either growth phase, a third transcriptional state was identified across both growth phases. Metabolic mapping revealed a boost of photosynthetic activity in the fast growth over the slow growth stage, as well as downregulation trend in pathways associated with ribosome functioning, CO2 fixation, and carbohydrate catabolism characteristic of the third transcriptional state. In addition, carry-over rRNA reads recapitulated the taxonomic identity of the target while revealing distinct bacterial communities, in co-culture with the eukaryote, each associated with distinct transcriptional states. This study underscores single-cell transcriptomics as a powerful tool for characterizing metabolic states in microeukaryotes without a reference genome, offering insights into unknown physiological states and individual-level interactions with different bacterial taxa. This approach holds broad applicability to describe the ecological roles of environmental microeukaryotes, culture-free, and reference-free, surpassing alternative methods like metagenomics or metatranscriptomics.", "doi": "10.1093/ismejo/wraf046", "pmid": "40057978", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Collaborative", "NGI Single cell": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC11973420"}, {"db": "pii", "key": "8064733"}], "notes": [], "created": "2025-09-08T06:54:54.550Z", "modified": "2025-11-21T14:35:21.491Z"}, {"entity": "publication", "iuid": "56f2be4738414a2bb34f30ee5eda8d1c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/56f2be4738414a2bb34f30ee5eda8d1c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/56f2be4738414a2bb34f30ee5eda8d1c"}}, "title": "Single-cell proteo-transcriptomic profiling reveals altered characteristics of stem and progenitor cells in patients receiving cytoreductive hydroxyurea in early-phase chronic myeloid leukemia.", "authors": [{"family": "Komic", "given": "Hana", "initials": "H"}, {"family": "Nilsson", "given": "Malin S", "initials": "MS"}, {"family": "Wennstr\u00f6m", "given": "Lovisa", "initials": "L"}, {"family": "Bandaru", "given": "Tagore Sanketh", "initials": "TS"}, {"family": "Jaako", "given": "Pekka", "initials": "P"}, {"family": "Hellstrand", "given": "Kristoffer", "initials": "K"}, {"family": "Thor\u00e9n", "given": "Fredrik B", "initials": "FB"}, {"family": "Martner", "given": "Anna", "initials": "A"}], "type": "journal article", "published": "2025-01-01", "journal": {"title": "Haematologica", "issn": "1592-8721", "issn-l": "0390-6078", "volume": "110", "issue": "1", "pages": "117-128"}, "abstract": "Hydroxyurea (HU) is frequently used in the early phase of chronic myeloid leukemia (CML) to achieve cytoreduction prior to tyrosine kinase inhibitor therapy. However, its impact on CML stem and progenitor cells (SPC) remains largely unknown. This study utilized targeted proteo-transcriptomic expression data on 596 genes and 51 surface proteins in 60,000 CD14-CD34+ cells from chronic phase CML patients to determine effects of short-term HU treatment (4-19 days) on CML SPC. Peripheral blood and bone marrow samples were obtained from 17 CML patients eligible for short-term HU treatment (3 patients before and after HU, 7 patients before HU and 7 patients after HU) and subjected to single-cell CITE-sequencing and/or flow cytometry analysis. The analysis revealed enhanced frequencies of hemoglobin-expressing (HBA1, HBA2, HBB) erythroid progenitor cells in blood and bone marrow following HU treatment. In addition, there was an accumulation of cell subsets with S/G2/M phase-related gene and protein expression, likely representing cells arrested in, or progressing slowly through, the cell cycle. The increased frequency of cells in S/G2/M phase after HU was observed already among the most immature leukemic stem cells (LSC), and patients with a large fraction of LSC in the S/G2/M phase showed poor responsiveness to tyrosine kinase inhibitor treatment. We conclude that short-term HU treatment entails differentiation of erythroid progenitor cells and alters the characteristics of LSC in CML. The results imply that studies of LSC and progenitor populations in CML should take effects of initial HU therapy into account.", "doi": "10.3324/haematol.2024.285071", "pmid": "39157872", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "Service", "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pmc", "key": "PMC11694111"}], "notes": [], "created": "2025-02-03T07:42:24.770Z", "modified": "2025-02-28T08:05:18.309Z"}, {"entity": "publication", "iuid": "14530d7aa2004964a747e0dc46f3c5aa", "links": {"self": {"href": "https://publications.scilifelab.se/publication/14530d7aa2004964a747e0dc46f3c5aa.json"}, "display": {"href": "https://publications.scilifelab.se/publication/14530d7aa2004964a747e0dc46f3c5aa"}}, "title": "Can genetic diversity in microalgae species be explained by climate: an overview of metabarcoding with diatoms.", "authors": [{"family": "Kula\u0161", "given": "Antonija", "initials": "A", "orcid": "0000-0003-0619-4697", "researcher": {"href": "https://publications.scilifelab.se/researcher/08acba03d1b445a7b4d0571c287b723b.json"}}, {"family": "Lemonnier", "given": "Clarisse", "initials": "C"}, {"family": "Alric", "given": "Benjamin", "initials": "B"}, {"family": "Kahlert", "given": "Maria", "initials": "M"}, {"family": "Trobajo", "given": "Rosa", "initials": "R"}, {"family": "Udovi\u010d", "given": "Marija Gligora", "initials": "MG"}, {"family": "Rimet", "given": "Fr\u00e9d\u00e9ric", "initials": "F"}], "type": "journal article", "published": "2025-01-00", "journal": {"title": "ISME COMMUN.", "issn": "2730-6151", "volume": "5", "issue": "1", "pages": "ycaf171", "issn-l": null}, "abstract": "Diatoms, a diverse and abundant group of microalgae, play a crucial role in the functioning of rivers, and are widely used as indicators of ecological quality. This microalgae group has an intraspecific genetic diversity that is poorly understood on a global scale. We examined their genetic diversity using metabarcoding data from Nordic to Equatorial rivers (n = 1103 samples). Notably, 61% of genetic variants were endemic to a single climate zone, including 33% from the Equatorial zone. Looking at the genetic diversity within species, one third of the species showed geographic pattern between climate zones and the phylogenetic structure of their communities indicated that they were shaped by environmental filtering. Another third showed no geographic pattern, and their communities were in majority shaped by neutral processes. A final group was between these two situations. Interestingly, no geographic pattern was observed within the same climate zones, even in regions over 10 000 km apart. We conclude that the numerous species showing allopatric diversification between climate zones, would deserve to be separated into new species to improve diatom-based biomonitoring tools. For future studies, expanding geographical sampling coverage, together with using multi-markers or metagenomes approaches would enable to go beyond these results.", "doi": "10.1093/ismeco/ycaf171", "pmid": "41104113", "labels": {"National Genomics Infrastructure": "Service", "NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12527276"}, {"db": "pii", "key": "ycaf171"}], "notes": [], "created": "2025-11-18T15:39:43.663Z", "modified": "2025-11-18T15:39:43.810Z"}, {"entity": "publication", "iuid": "af0d181b15e0476d8f4d1f701ba25a03", "links": {"self": {"href": "https://publications.scilifelab.se/publication/af0d181b15e0476d8f4d1f701ba25a03.json"}, "display": {"href": "https://publications.scilifelab.se/publication/af0d181b15e0476d8f4d1f701ba25a03"}}, "title": "Cord Blood Biomarkers Predict Psoriasis Many Years Before Diagnosis: A Prospective Birth Cohort Study", "authors": [{"family": "Das", "given": "Debojyoti", "initials": "D"}, {"family": "Ludvigsson", "given": "Johnny", "initials": "J"}], "type": "journal-article", "published": "2025-00-00", "journal": {"title": "Arch Clin Biomed Res 2025", "issn": "2572-5017", "issn-l": null, "volume": "9", "issue": "3", "pages": null}, "abstract": null, "doi": "10.26502/acbr.50170452", "pmid": null, "labels": {"Affinity Proteomics Uppsala": "Service", "National Genomics Infrastructure": "Service", "NGI Proteomics": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [], "notes": [], "created": "2025-11-25T19:19:11.236Z", "modified": "2025-11-26T11:08:19.953Z"}, {"entity": "publication", "iuid": "94ab6b3617474bc092224f924b8f0d46", "links": {"self": {"href": "https://publications.scilifelab.se/publication/94ab6b3617474bc092224f924b8f0d46.json"}, "display": {"href": "https://publications.scilifelab.se/publication/94ab6b3617474bc092224f924b8f0d46"}}, "title": "The evolutionary history of metastatic pancreatic neuroendocrine tumours reveals a therapy driven route to high-grade transformation.", "authors": [{"family": "Backman", "given": "Samuel", "initials": "S"}, {"family": "Botling", "given": "Johan", "initials": "J"}, {"family": "Nord", "given": "Helena", "initials": "H", "orcid": "0000-0002-6098-0237", "researcher": {"href": "https://publications.scilifelab.se/researcher/22d8cc445c6b41b4a8488d620995d8c3.json"}}, {"family": "Ghosal", "given": "Suman", "initials": "S"}, {"family": "St\u00e5lberg", "given": "Peter", "initials": "P"}, {"family": "Juhlin", "given": "C Christofer", "initials": "CC", "orcid": "0000-0002-5945-9081", "researcher": {"href": "https://publications.scilifelab.se/researcher/bb660e24421749d4acaaf6e9a90042f8.json"}}, {"family": "Alml\u00f6f", "given": "Jonas", "initials": "J", "orcid": "0000-0002-1211-9821", "researcher": {"href": "https://publications.scilifelab.se/researcher/046904cd12eb4764bd2dcadc876f65d7.json"}}, {"family": "Sundin", "given": "Anders", "initials": "A", "orcid": "0000-0001-6615-2419", "researcher": {"href": "https://publications.scilifelab.se/researcher/b03a78e59f0845c5b68b372f2709dbf0.json"}}, {"family": "Zhang", "given": "Liang", "initials": "L"}, {"family": "Moens", "given": "Lotte", "initials": "L", "orcid": "0000-0002-5347-6526", "researcher": {"href": "https://publications.scilifelab.se/researcher/577b0c2d09e349d89ef8ae73efd8c5f7.json"}}, {"family": "Eriksson", "given": "Barbro", "initials": "B"}, {"family": "Welin", "given": "Staffan", "initials": "S"}, {"family": "Hellman", "given": "Per", "initials": "P"}, {"family": "Skogseid", "given": "Britt", "initials": "B"}, {"family": "Pacak", "given": "Karel", "initials": "K"}, {"family": "Mollazadegan", "given": "Kazhan", "initials": "K"}, {"family": "\u00c5kerstr\u00f6m", "given": "Tobias", "initials": "T"}, {"family": "Crona", "given": "Joakim", "initials": "J", "orcid": "0000-0003-0677-4894", "researcher": {"href": "https://publications.scilifelab.se/researcher/2c601868a0c14b13a01b2868a4fb690e.json"}}], "type": "journal article", "published": "2024-12-00", "journal": {"title": "J. Pathol.", "issn": "1096-9896", "volume": "264", "issue": "4", "pages": "357-370", "issn-l": "0022-3417"}, "abstract": "Tumour evolution with acquisition of more aggressive disease characteristics is a hallmark of disseminated cancer. Metastatic pancreatic neuroendocrine tumours (PanNETs) in particular may progress from a low/intermediate to a high-grade disease. The aim of this work was to understand the molecular mechanisms underlying metastatic progression as well as PanNET transformation from a low/intermediate to a high-grade disease. We performed multi-omics analysis (genome/exome sequencing, total RNA-sequencing and methylation array) of 32 longitudinal samples from six patients with metastatic low/intermediate grade PanNET. The clonal composition of tumour lesions and underlying phylogeny of each patient were determined with bioinformatics analyses. Findings were validated in post-alkylating chemotherapy samples from 24 patients with PanNET using targeted next generation sequencing. We validate the current PanNET evolutionary model with MEN1 inactivation that occurs very early in tumourigenesis. This was followed by pronounced genetic diversity on both spatial and temporal levels, with parallel and convergent tumour evolution involving the ATRX/DAXX and mechanistic target of the rapamycin (mTOR) pathways. Following alkylating chemotherapy treatment, some PanNETs developed mismatch repair deficiency and acquired a hypermutational phenotype. This was validated among 16 patients with PanNET who had high-grade progression after alkylating chemotherapy, of whom eight had a tumour mutational burden >50 (50%). In comparison, among the eight patients who did not show high-grade progression, 0 had a tumour mutational burden >50 (0%; odds ratio 'infinite', 95% confidence interval 1.8 to 'infinite', p = 0.02). Our findings contribute to broaden the understanding of metastatic/high-grade PanNETs and suggests that therapy driven disease evolution is an important hallmark of this disease. \u00a9 2024 The Author(s). The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland. This article has been contributed to by U.S. Government employees and their work is in the public domain in the USA.", "doi": "10.1002/path.6348", "pmid": "39360347", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "NGI SNP genotyping": "Service", "NGI Short read": "Service", "Clinical Genomics Uppsala": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Clinical Genomics": "Collaborative"}, "xrefs": [], "notes": [], "created": "2024-11-12T11:41:11.475Z", "modified": "2025-04-07T07:28:57.040Z"}, {"entity": "publication", "iuid": "ae5f4ce1bcc449d2bd0c22369b2de2a8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ae5f4ce1bcc449d2bd0c22369b2de2a8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ae5f4ce1bcc449d2bd0c22369b2de2a8"}}, "title": "Lifestyle, biological, and genetic factors related to brain iron accumulation across adulthood.", "authors": [{"family": "Gustavsson", "given": "Jonatan", "initials": "J"}, {"family": "I\u0161tv\u00e1nfyov\u00e1", "given": "Zuzana", "initials": "Z"}, {"family": "Papenberg", "given": "Goran", "initials": "G"}, {"family": "Falahati", "given": "Farshad", "initials": "F"}, {"family": "Laukka", "given": "Erika J", "initials": "EJ"}, {"family": "Lehtisalo", "given": "Jenni", "initials": "J"}, {"family": "Mangialasche", "given": "Francesca", "initials": "F"}, {"family": "Kalpouzos", "given": "Gr\u00e9goria", "initials": "G"}], "type": "journal article", "published": "2024-12-00", "journal": {"title": "Neurobiol. Aging", "issn": "1558-1497", "volume": "144", "pages": "56-67", "issn-l": "0197-4580"}, "abstract": "Iron is necessary for many neurobiological mechanisms, but its overaccumulation can be harmful. Factors triggering age-related brain iron accumulation remain largely unknown and longitudinal data are insufficient. We examined associations between brain iron load and accumulation and, blood markers of iron metabolism, cardiovascular health, lifestyle factors (smoking, alcohol use, physical activity, diet), and ApoE status using longitudinal data from the IronAge study (n = 208, age = 20-79, mean follow-up time = 2.75 years). Iron in cortex and basal ganglia was estimated with magnetic resonance imaging using quantitative susceptibility mapping (QSM). Our results showed that (1) higher peripheral iron levels (i.e., composite score of blood iron markers) were related to greater iron load in the basal ganglia; (2) healthier diet was related to higher iron levels in the cortex and basal ganglia, although for the latter the association was significant only in younger adults (age = 20-39); (3) worsening cardiovascular health was related to increased iron accumulation; (4) younger ApoE \u03b54 carriers accumulated more iron in basal ganglia than younger non-carriers. Our results demonstrate that modifiable factors, including lifestyle, cardiovascular, and physiological ones, are linked to age-related brain iron content and accumulation, contributing novel information on potential targets for interventions in preventing brain iron-overload.", "doi": "10.1016/j.neurobiolaging.2024.09.004", "pmid": "39277972", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI SNP genotyping": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pii", "key": "S0197-4580(24)00159-3"}], "notes": [], "created": "2024-10-21T11:16:38.288Z", "modified": "2024-10-21T11:16:38.353Z"}, {"entity": "publication", "iuid": "281525954deb43569a3aeab075748d9c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/281525954deb43569a3aeab075748d9c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/281525954deb43569a3aeab075748d9c"}}, "title": "Genomics of severe and treatment-resistant obsessive-compulsive disorder treated with deep brain stimulation: A preliminary investigation.", "authors": [{"family": "Chen", "given": "Long Long", "initials": "LL"}, {"family": "Naesstr\u00f6m", "given": "Matilda", "initials": "M"}, {"family": "Halvorsen", "given": "Matthew", "initials": "M"}, {"family": "Fytagoridis", "given": "Anders", "initials": "A"}, {"family": "Crowley", "given": "Stephanie B", "initials": "SB"}, {"family": "Mataix-Cols", "given": "David", "initials": "D"}, {"family": "R\u00fcck", "given": "Christian", "initials": "C"}, {"family": "Crowley", "given": "James J", "initials": "JJ", "orcid": "0000-0001-9051-1557", "researcher": {"href": "https://publications.scilifelab.se/researcher/14ecad66262b47dcadebcc8c7e759024.json"}}, {"family": "Pascal", "given": "Diana", "initials": "D"}], "type": "journal article", "published": "2024-12-00", "journal": {"title": "Am. J. Med. Genet. B Neuropsychiatr. Genet.", "issn": "1552-485X", "issn-l": "1552-4841", "volume": "195", "issue": "8", "pages": "e32983"}, "abstract": "Individuals with severe and treatment-resistant obsessive-compulsive disorder (trOCD) represent a small but severely disabled group of patients. Since trOCD cases eligible for deep brain stimulation (DBS) probably comprise the most severe end of the OCD spectrum, we hypothesize that they may be more likely to have a strong genetic contribution to their disorder. Therefore, while the worldwide population of DBS-treated cases may be small (~300), screening these individuals with modern genomic methods may accelerate gene discovery in OCD. As such, we have begun to collect DNA from trOCD cases who qualify for DBS, and here we report results from whole exome sequencing and microarray genotyping of our first five cases. All participants had previously received DBS in the bed nucleus of stria terminalis (BNST), with two patients responding to the surgery and one showing a partial response. Our analyses focused on gene-disruptive rare variants (GDRVs; rare, predicted-deleterious single-nucleotide variants or copy number variants overlapping protein-coding genes). Three of the five cases carried a GDRV, including a missense variant in the ion transporter domain of KCNB1, a deletion at 15q11.2, and a duplication at 15q26.1. The KCNB1 variant (hg19 chr20-47991077-C-T, NM_004975.3:c.1020G>A, p.Met340Ile) causes substitution of methionine for isoleucine in the trans-membrane region of neuronal potassium voltage-gated ion channel KV2.1. This KCNB1 substitution (Met340Ile) is located in a highly constrained region of the protein where other rare missense variants have previously been associated with neurodevelopmental disorders. The patient carrying the Met340Ile variant responded to DBS, which suggests that genetic factors could potentially be predictors of treatment response in DBS for OCD. In sum, we have established a protocol for recruiting and genomically characterizing trOCD cases. Preliminary results suggest that this will be an informative strategy for finding risk genes in OCD.", "doi": "10.1002/ajmg.b.32983", "pmid": "38650085", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "mid", "key": "NIHMS1984060"}, {"db": "pmc", "key": "PMC11493841"}], "notes": "Pre-print available:\r\nDOI: 10.1101/2023.04.15.23288623", "created": "2024-11-12T10:39:23.334Z", "modified": "2024-11-19T10:09:44.036Z"}, {"entity": "publication", "iuid": "ba82c88779c94bd8ae035c075c26214b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ba82c88779c94bd8ae035c075c26214b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ba82c88779c94bd8ae035c075c26214b"}}, "title": "Genomic signals of adaptation to a natural CO2 gradient over a striking microgeographic scale", "authors": [{"family": "Gonz\u00e1lez-Delgado", "given": "Sara", "initials": "S"}, {"family": "P\u00e9rez-Portela", "given": "Roc\u00edo", "initials": "R"}, {"family": "Ortega-Mart\u00ednez", "given": "Olga", "initials": "O", "orcid": "0000-0003-2734-6434", "researcher": {"href": "https://publications.scilifelab.se/researcher/bc84f54ca2cc49bc869cd23adeffc7ac.json"}}, {"family": "Alfonso", "given": "Beatriz", "initials": "B"}, {"family": "Pereyra", "given": "Ricardo T", "initials": "RT"}, {"family": "Hern\u00e1ndez", "given": "Jos\u00e9 Carlos", "initials": "JC"}], "type": "journal-article", "published": "2024-12-00", "journal": {"title": "Marine Pollution Bulletin", "issn": "0025-326X", "volume": "209", "pages": "117225", "issn-l": null}, "abstract": null, "doi": "10.1016/j.marpolbul.2024.117225", "pmid": null, "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "Service"}, "xrefs": [], "notes": [], "created": "2024-11-12T10:38:54.128Z", "modified": "2025-04-07T07:31:21.426Z"}, {"entity": "publication", "iuid": "b63ebec5607f49219d63cb4bcce20f95", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b63ebec5607f49219d63cb4bcce20f95.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b63ebec5607f49219d63cb4bcce20f95"}}, "title": "Genetic diversity insights from population genomics and machine learning tools for Nordic Arctic charr (Salvelinus alpinus) populations", "authors": [{"family": "Palaiokostas", "given": "Christos", "initials": "C", "orcid": "0000-0002-4480-4612", "researcher": {"href": "https://publications.scilifelab.se/researcher/a1d6c65f53a8434cb1d5dd4c7bf5d444.json"}}, {"family": "Kurta", "given": "Khrystyna", "initials": "K"}, {"family": "Pappas", "given": "Fotis", "initials": "F"}, {"family": "Jeuthe", "given": "Henrik", "initials": "H"}, {"family": "Hagen", "given": "\u00d8rjan", "initials": "\u00d8"}, {"family": "Beir\u00e3o", "given": "Jos\u00e9", "initials": "J"}, {"family": "Janhunen", "given": "Matti", "initials": "M"}, {"family": "Kause", "given": "Antti", "initials": "A"}], "type": "journal-article", "published": "2024-12-00", "journal": {"title": "Aquaculture Reports", "issn": "2352-5134", "volume": "39", "pages": "102495", "issn-l": "2352-5134"}, "abstract": null, "doi": "10.1016/j.aqrep.2024.102495", "pmid": null, "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2024-11-12T10:39:01.587Z", "modified": "2025-12-04T19:36:52.855Z"}, {"entity": "publication", "iuid": "9eebd20478a544b7ba6aacefbf1745f3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9eebd20478a544b7ba6aacefbf1745f3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9eebd20478a544b7ba6aacefbf1745f3"}}, "title": "A genome-wide association study in Swedish colorectal cancer patients with gastric- and prostate cancer in relatives.", "authors": [{"family": "Samola Winnberg", "given": "Johanna", "initials": "J"}, {"family": "Vermani", "given": "Litika", "initials": "L"}, {"family": "Liu", "given": "Wen", "initials": "W"}, {"family": "Soller", "given": "Veronika", "initials": "V"}, {"family": "Thutkawkorapin", "given": "Jessada", "initials": "J", "orcid": "0000-0001-9306-844X", "researcher": {"href": "https://publications.scilifelab.se/researcher/fa13464dfebd4c868fe4eb1f0186a41b.json"}}, {"family": "Lindblad", "given": "Mats", "initials": "M"}, {"family": "Lindblom", "given": "Annika", "initials": "A"}], "type": "journal article", "published": "2024-11-14", "journal": {"title": "Hered Cancer Clin Pract", "issn": "1731-2302", "volume": "22", "issue": "1", "pages": "25", "issn-l": null}, "abstract": "A complex inheritance has been suggested in families with colorectal-, gastric- and prostate cancer. Therefore, we conducted a genome-wide association study (GWAS) in colorectal cancer patients, who's relatives had prostate-, and/or gastric cancer.\n\nThe GWAS analysis consisted of 685 cases of colorectal cancer and 4780 healthy controls from Sweden. A sliding window haplotype analysis was conducted using a logistic regression model. Thereafter, we performed sequencing to find candidate variants, finally to be tested in a nested case-control study.\n\nCandidate loci/genes on ten chromosomal regions were suggested with odds ratios between 1.71-3.62 and p-values < 5 \u00d7 10-8 in the analysis. The regions suggested were 1q32.2, 3q29, 4q35.1, 4p15.31, 4q26, 8p23.1, 13q33.3, 13q13.3, 16q23.3 and 22q11.21. All regions, except one on 1q32.2, had protein coding genes, many already shown to be involved in cancer, such as ZDHHC19, SYNPO2, PCYT1A, MYO16, TXNRD2, COMT, and CDH13. Sequencing of DNA from 122 colorectal cancer patients with gastric- and/or prostate cancer in their families was performed to search for candidate variants in the haplotype regions. The identified candidate variants were tested in a nested case-control study of similar colorectal cancer cases and controls. There was some support for an increased risk of colorectal-, gastric-, and/or prostate cancer in all the six loci tested.\n\nThis study demonstrated a proof of principle strategy to identify risk variants found by GWAS, and identified ten candidate loci that could be associated with colorectal, gastric- and prostate cancer.", "doi": "10.1186/s13053-024-00299-z", "pmid": "39543761", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "NGI SNP genotyping": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11562479"}, {"db": "pii", "key": "10.1186/s13053-024-00299-z"}], "notes": [], "created": "2024-11-15T16:33:05.387Z", "modified": "2025-04-07T09:25:52.668Z"}, {"entity": "publication", "iuid": "3b78200d104a464e92c79279e034bb9f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3b78200d104a464e92c79279e034bb9f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3b78200d104a464e92c79279e034bb9f"}}, "title": "Perfluorooctanesulfonic acid (PFOS) induced cancer related DNA methylation alterations in human breast cells: A whole genome methylome study.", "authors": [{"family": "Pierozan", "given": "Paula", "initials": "P"}, {"family": "H\u00f6glund", "given": "Andrey", "initials": "A"}, {"family": "Theodoropoulou", "given": "Eleftheria", "initials": "E"}, {"family": "Karlsson", "given": "Oskar", "initials": "O"}], "type": "journal article", "published": "2024-11-01", "journal": {"title": "Sci. Total Environ.", "issn": "1879-1026", "volume": "949", "pages": "174864", "issn-l": "0048-9697"}, "abstract": "DNA methylation plays a pivotal role in cancer. The ubiquitous contaminant perfluorooctanesulfonic acid (PFOS) has been epidemiologically associated with breast cancer, and can induce proliferation and malignant transformation of normal human breast epithelial cells (MCF-10A), but the information about its effect on DNA methylation is sparse. The aim of this study was to characterize the whole-genome methylome effects of PFOS in our breast cell model and compare the findings with previously demonstrated DNA methylation alterations in breast tumor tissues. The DNA methylation profile was assessed at single CpG resolution in MCF-10A cells treated with 1 \u03bcM PFOS for 72 h by using Enzymatic Methyl sequencing (EM-seq). We found 12,591 differentially methylated CpG-sites and 13,360 differentially methylated 100 bp tiles in the PFOS exposed breast cells. These differentially methylated regions (DMRs) overlapped with 2406 genes of which 494 were long non-coding RNA and 1841 protein coding genes. We identified 339 affected genes that have been shown to display altered DNA methylation in breast cancer tissue and several other genes related to cancer development. This includes hypermethylation of GACAT3, DELEC1, CASC2, LCIIAR, MUC16, SYNE1 and hypomethylation of TTN and KMT2C. DMRs were also found in estrogen receptor genes (ESR1, ESR2, ESRRG, ESRRB, GREB1) and estrogen responsive genes (GPER1, EEIG1, RERG). The gene ontology analysis revealed pathways related to cancer phenotypes such as cell adhesion and growth. These findings improve the understanding of PFOS's potential role in breast cancer and illustrate the value of whole-genome methylome analysis in uncovering mechanisms of chemical effects, identifying biomarker candidates, and strengthening epidemiological associations, potentially impacting risk assessment.", "doi": "10.1016/j.scitotenv.2024.174864", "pmid": "39032741", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Short read": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "S0048-9697(24)05013-7"}], "notes": [], "created": "2024-10-21T11:15:52.243Z", "modified": "2025-02-28T14:12:59.071Z"}, {"entity": "publication", "iuid": "ff82f6f4bfb34c93a66ea6b5c6e6a9f0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ff82f6f4bfb34c93a66ea6b5c6e6a9f0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ff82f6f4bfb34c93a66ea6b5c6e6a9f0"}}, "title": "The non-canonical BAF chromatin remodeling complex is a novel target of spliceosome dysregulation in SF3B1-mutated chronic lymphocytic leukemia.", "authors": [{"family": "H\u00e4gerstrand", "given": "Daniel", "initials": "D", "orcid": "0000-0001-7270-0776", "researcher": {"href": "https://publications.scilifelab.se/researcher/35a683cea1874ac290d91c325a648be8.json"}}, {"family": "Oder", "given": "Bla\u017e", "initials": "B", "orcid": "0000-0001-7984-3104", "researcher": {"href": "https://publications.scilifelab.se/researcher/9851f9fc65fc44aea55d0c1567be7887.json"}}, {"family": "Cortese", "given": "Diego", "initials": "D"}, {"family": "Qu", "given": "Ying", "initials": "Y"}, {"family": "Binzer-Panchal", "given": "Amrei", "initials": "A", "orcid": "0000-0002-0472-0609", "researcher": {"href": "https://publications.scilifelab.se/researcher/9b6fe18ad8f8495a97d9322cac3201da.json"}}, {"family": "\u00d6sterholm", "given": "Cecilia", "initials": "C"}, {"family": "Del Peso Santos", "given": "Teresa", "initials": "T"}, {"family": "Rabbani", "given": "Leily", "initials": "L"}, {"family": "Asl", "given": "Hassan Foroughi", "initials": "HF"}, {"family": "Skaftason", "given": "Aron", "initials": "A"}, {"family": "Ljungstr\u00f6m", "given": "Viktor", "initials": "V"}, {"family": "Lundholm", "given": "August", "initials": "A"}, {"family": "Koutroumani", "given": "Maria", "initials": "M"}, {"family": "Haider", "given": "Zahra", "initials": "Z"}, {"family": "Jylh\u00e4", "given": "Cecilia", "initials": "C"}, {"family": "Mollstedt", "given": "John", "initials": "J"}, {"family": "Mansouri", "given": "Larry", "initials": "L"}, {"family": "Plevova", "given": "Karla", "initials": "K"}, {"family": "Agathangelidis", "given": "Andreas", "initials": "A", "orcid": "0000-0002-8467-7945", "researcher": {"href": "https://publications.scilifelab.se/researcher/79eb64984ac1494094f8c632b18bc793.json"}}, {"family": "Scarf\u00f2", "given": "Lydia", "initials": "L", "orcid": "0000-0002-0844-0989", "researcher": {"href": "https://publications.scilifelab.se/researcher/47c4c336efb24d86b41c872d03836c78.json"}}, {"family": "Armand", "given": "Marine", "initials": "M", "orcid": "0000-0001-8906-3128", "researcher": {"href": "https://publications.scilifelab.se/researcher/8d2e8c325db8415cb723a9718d49ae78.json"}}, {"family": "Muggen", "given": "Alice F", "initials": "AF"}, {"family": "Kay", "given": "Neil E", "initials": "NE", "orcid": "0000-0002-5951-5055", "researcher": {"href": "https://publications.scilifelab.se/researcher/ef074d0fdb0b4070b5216be063317bf8.json"}}, {"family": "Shanafelt", "given": "Tait", "initials": "T"}, {"family": "Rossi", "given": "Davide", "initials": "D"}, {"family": "Orre", "given": "Lukas M", "initials": "LM", "orcid": "0000-0002-0384-1003", "researcher": {"href": "https://publications.scilifelab.se/researcher/7b4e49a93b0143db88059c4d1e9fdc59.json"}}, {"family": "Pospisilova", "given": "Sarka", "initials": "S", "orcid": "0000-0001-7136-2680", "researcher": {"href": "https://publications.scilifelab.se/researcher/241cf7f1344c4016b40dfcf439c0b43d.json"}}, {"family": "Barylyuk", "given": "Konstantin", "initials": "K", "orcid": "0000-0002-3580-0345", "researcher": {"href": "https://publications.scilifelab.se/researcher/f5db39fce380438e82060c586e230ee6.json"}}, {"family": "Davi", "given": "Frederic", "initials": "F"}, {"family": "Vesterlund", "given": "Mattias", "initials": "M", "orcid": "0000-0001-9471-6592", "researcher": {"href": "https://publications.scilifelab.se/researcher/0942e438993b494db2a3db914852c808.json"}}, {"family": "Langerak", "given": "Anton W", "initials": "AW", "orcid": "0000-0002-2078-3220", "researcher": {"href": "https://publications.scilifelab.se/researcher/769a5b06013b43d6af8d3e13804cd50c.json"}}, {"family": "Lehti\u00f6", "given": "Janne", "initials": "J", "orcid": "0000-0002-8100-9562", "researcher": {"href": "https://publications.scilifelab.se/researcher/8406a97bac744a59b1bc951978994581.json"}}, {"family": "Ghia", "given": "Paolo", "initials": "P", "orcid": "0000-0003-3750-7342", "researcher": {"href": "https://publications.scilifelab.se/researcher/46f24783739d44c7b73a1be28c344a35.json"}}, {"family": "Stamatopoulos", "given": "Kostas", "initials": "K", "orcid": "0000-0001-8529-640X", "researcher": {"href": "https://publications.scilifelab.se/researcher/772756566c154559b2c70c8f0f44d1ad.json"}}, {"family": "Sutton", "given": "Lesley-Ann", "initials": "LA"}, {"family": "Rosenquist", "given": "Richard", "initials": "R", "orcid": "0000-0002-0211-8788", "researcher": {"href": "https://publications.scilifelab.se/researcher/b570128e641140fb964ae3241414f510.json"}}], "type": "journal article", "published": "2024-11-00", "journal": {"title": "Leukemia", "issn": "1476-5551", "volume": "38", "issue": "11", "pages": "2429-2442", "issn-l": "0887-6924"}, "abstract": "SF3B1 mutations are recurrent in chronic lymphocytic leukemia (CLL), particularly enriched in clinically aggressive stereotyped subset #2. To investigate their impact, we conducted RNA-sequencing of 18 SF3B1MUT and 17 SF3B1WT subset #2 cases and identified 80 significant alternative splicing events (ASEs). Notable ASEs concerned exon inclusion in the non-canonical BAF (ncBAF) chromatin remodeling complex subunit, BRD9, and splice variants in eight additional ncBAF complex interactors. Long-read RNA-sequencing confirmed the presence of splice variants, and extended analysis of 139 CLL cases corroborated their association with SF3B1 mutations. Overexpression of SF3B1K700E induced exon inclusion in BRD9, resulting in a novel splice isoform with an alternative C-terminus. Protein interactome analysis of the BRD9 splice isoform revealed augmented ncBAF complex interaction, while exhibiting decreased binding of auxiliary proteins, including SPEN, BRCA2, and CHD9. Additionally, integrative multi-omics analysis identified a ncBAF complex-bound gene quartet on chromosome 1 with higher expression levels and more accessible chromatin in SF3B1MUT CLL. Finally, Cancer Dependency Map analysis and BRD9 inhibition displayed BRD9 dependency and sensitivity in cell lines and primary CLL cells. In conclusion, spliceosome dysregulation caused by SF3B1 mutations leads to multiple ASEs and an altered ncBAF complex interactome, highlighting a novel pathobiological mechanism in SF3B1MUT CLL.", "doi": "10.1038/s41375-024-02379-4", "pmid": "39261602", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "Service", "Bioinformatics Support for Computational Resources": "Service", "Global Proteomics and Proteogenomics": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11518989"}, {"db": "pii", "key": "10.1038/s41375-024-02379-4"}], "notes": [], "created": "2024-11-12T10:55:28.718Z", "modified": "2025-02-28T14:13:56.146Z"}, {"entity": "publication", "iuid": "46b3ed67f2a843ca94d9f62dbdd2fa42", "links": {"self": {"href": "https://publications.scilifelab.se/publication/46b3ed67f2a843ca94d9f62dbdd2fa42.json"}, "display": {"href": "https://publications.scilifelab.se/publication/46b3ed67f2a843ca94d9f62dbdd2fa42"}}, "title": "Pushing the boundaries of rare disease diagnostics with the help of the first Undiagnosed Hackathon.", "authors": [{"family": "Delgado-Vega", "given": "Angelica Maria", "initials": "AM", "orcid": "0000-0002-9865-0591", "researcher": {"href": "https://publications.scilifelab.se/researcher/e5e5d5e55948460d964544438d221c34.json"}}, {"family": "Cederroth", "given": "Helene", "initials": "H", "orcid": "0000-0002-5522-3418", "researcher": {"href": "https://publications.scilifelab.se/researcher/bcdb1f50435a4fce8814882e22a69b37.json"}}, {"family": "Taylan", "given": "Fulya", "initials": "F", "orcid": "0000-0002-2907-0235", "researcher": {"href": "https://publications.scilifelab.se/researcher/c250909cc40f42ff9d6e2f640d12451b.json"}}, {"family": "Ekholm", "given": "Katja", "initials": "K", "orcid": "0009-0005-8231-8876", "researcher": {"href": "https://publications.scilifelab.se/researcher/d36170b3e310492f8a3d6a70edbe8f24.json"}}, {"family": "Ek", "given": "Marlene", "initials": "M"}, {"family": "Thonberg", "given": "H\u00e5kan", "initials": "H"}, {"family": "Jemt", "given": "Anders", "initials": "A", "orcid": "0000-0002-2219-0197", "researcher": {"href": "https://publications.scilifelab.se/researcher/5cc562a42048411aa86ded8e0bd90852.json"}}, {"family": "Nilsson", "given": "Daniel", "initials": "D"}, {"family": "Eisfeldt", "given": "Jesper", "initials": "J"}, {"family": "Bilgrav Saether", "given": "Kristine", "initials": "K"}, {"family": "H\u00f6ijer", "given": "Ida", "initials": "I"}, {"family": "Akgun-Dogan", "given": "Ozlem", "initials": "O"}, {"family": "Asano", "given": "Yui", "initials": "Y"}, {"family": "Barakat", "given": "Tahsin Stefan", "initials": "TS", "orcid": "0000-0003-1231-1562", "researcher": {"href": "https://publications.scilifelab.se/researcher/05636291c79b4835a863d66a221025c7.json"}}, {"family": "Batkovskyte", "given": "Dominyka", "initials": "D", "orcid": "0000-0002-0492-1259", "researcher": {"href": "https://publications.scilifelab.se/researcher/017749b78ac540a6b2a36303130606f2.json"}}, {"family": "Baynam", "given": "Gareth", "initials": "G", "orcid": "0000-0003-4920-9553", "researcher": {"href": "https://publications.scilifelab.se/researcher/bd6905ffc70041b980e4398d68eb114c.json"}}, {"family": "Bodamer", "given": "Olaf", "initials": "O", "orcid": "0000-0002-7847-552X", "researcher": {"href": "https://publications.scilifelab.se/researcher/0aa490ac1a9f44c0b73be02898f51212.json"}}, {"family": "Chetruengchai", "given": "Wanna", "initials": "W"}, {"family": "Corcoran", "given": "P\u00e1draic", "initials": "P"}, {"family": "Couse", "given": "Madeline", "initials": "M"}, {"family": "Danis", "given": "Daniel", "initials": "D", "orcid": "0000-0003-0900-3411", "researcher": {"href": "https://publications.scilifelab.se/researcher/6a25afd9229a48968ecb47d2315b964f.json"}}, {"family": "Demidov", "given": "German", "initials": "G", "orcid": "0000-0001-9075-4276", "researcher": {"href": "https://publications.scilifelab.se/researcher/4157231d1af64838a00ee99b9d0e6676.json"}}, {"family": "Dohi", "given": "Eisuke", "initials": "E", "orcid": "0000-0002-5365-4900", "researcher": {"href": "https://publications.scilifelab.se/researcher/248bdd8187cb41899bb49aeb6f22727e.json"}}, {"family": "Erhardsson", "given": "Mattias", "initials": "M", "orcid": "0000-0002-5631-2033", "researcher": {"href": "https://publications.scilifelab.se/researcher/fc48a126473e4b2aa69c704186c52466.json"}}, {"family": "Fernandez-Luna", "given": "Luis", "initials": "L"}, {"family": "Fujiwara", "given": "Toyofumi", "initials": "T"}, {"family": "Garg", "given": "Neha", "initials": "N"}, {"family": "Giugliani", "given": "Roberto", "initials": "R"}, {"family": "Gonzaga-Jauregui", "given": "Claudia", "initials": "C", "orcid": "0000-0002-4667-3679", "researcher": {"href": "https://publications.scilifelab.se/researcher/5ddb6b4197874a1aab306b678a5e8a41.json"}}, {"family": "Grigelioniene", "given": "Giedre", 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"Maya-Gonz\u00e1lez", "given": "Carolina", "initials": "C"}, {"family": "Meyn", "given": "M Stephen", "initials": "MS"}, {"family": "Neethiraj", "given": "Ramprasad", "initials": "R"}, {"family": "Nigro", "given": "Vincenzo", "initials": "V"}, {"family": "Nordgren", "given": "Felix", "initials": "F"}, {"family": "Nordlund", "given": "Jessica", "initials": "J", "orcid": "0000-0001-8699-9959", "researcher": {"href": "https://publications.scilifelab.se/researcher/ddf48c9262134821bcc6ce1180049753.json"}}, {"family": "Orrsj\u00f6", "given": "Sara", "initials": "S", "orcid": "0009-0008-9223-3923", "researcher": {"href": "https://publications.scilifelab.se/researcher/acd6e5385a7b4406b973a3adbed96245.json"}}, {"family": "Ottosson", "given": "Jesper", "initials": "J"}, {"family": "Ozbek", "given": "Ugur", "initials": "U", "orcid": "0000-0001-5319-0547", "researcher": {"href": "https://publications.scilifelab.se/researcher/a9f5f921edb64de6ac115abdd57e55d3.json"}}, {"family": "\u00d6zdemir", "given": "\u00d6zkan", "initials": "\u00d6"}, {"family": "Partin", "given": "Clyde", "initials": "C", "orcid": "0000-0003-3996-9604", "researcher": {"href": "https://publications.scilifelab.se/researcher/20955ec5ea6c4253beccddfdb1120135.json"}}, {"family": "Pearce", "given": "David A", "initials": "DA", "orcid": "0000-0002-0707-063X", "researcher": {"href": "https://publications.scilifelab.se/researcher/a17879050f7949a7b91d266bd5be19da.json"}}, {"family": "Peck", "given": "Raquel", "initials": "R"}, {"family": "Pedersen", "given": "Annie", "initials": "A"}, {"family": "Pettersson", "given": "Maria", "initials": "M"}, {"family": "Pongpanich", "given": "Monnat", "initials": "M"}, {"family": "Posada de la Paz", "given": "Manuel", "initials": "M", "orcid": "0000-0002-8372-4180", "researcher": {"href": "https://publications.scilifelab.se/researcher/2a12ab27c65a464a90606c83769b3a6f.json"}}, {"family": "Ramani", "given": "Arun", "initials": "A"}, {"family": "Romero", "given": "Juan Andres", "initials": "JA"}, {"family": "Romero", "given": "Vanessa I", "initials": "VI"}, {"family": "Rosenquist", "given": "Richard", "initials": "R", "orcid": "0000-0002-0211-8788", "researcher": {"href": "https://publications.scilifelab.se/researcher/b570128e641140fb964ae3241414f510.json"}}, {"family": "Saw", "given": "Aung Min", "initials": "AM"}, {"family": "Spencer", "given": "Matthew", "initials": "M"}, {"family": "Stattin", "given": "Eva-Lena", "initials": "EL"}, {"family": "Srichomthong", "given": "Chalurmpon", "initials": "C"}, {"family": "Tapia-Paez", "given": "Isabel", "initials": "I", "orcid": "0000-0002-0535-4233", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ed50bc3a5034bafbff8ee63e129fb10.json"}}, {"family": "Taruscio", "given": "Domenica", "initials": "D", "orcid": "0000-0001-5403-233X", "researcher": {"href": "https://publications.scilifelab.se/researcher/1cc58bd63f7c43f7834c1c7b98cbc065.json"}}, {"family": "Taylor", "given": "Julie P", "initials": "JP"}, {"family": "Tkemaladze", "given": "Tinatin", "initials": "T", "orcid": "0000-0003-1924-6695", "researcher": {"href": "https://publications.scilifelab.se/researcher/8fd7bba98c164a3ca012971f7b654aeb.json"}}, {"family": "Tully", "given": "Ian", "initials": "I"}, {"family": "T\u00fcmer", "given": "Zeynep", "initials": "Z", "orcid": "0000-0002-4777-5802", "researcher": {"href": "https://publications.scilifelab.se/researcher/9f87998993834fdea81a28997ee1ce76.json"}}, {"family": "van Zelst-Stams", "given": "Wendy A G", "initials": "WAG"}, {"family": "Verloes", "given": "Alain", "initials": "A", "orcid": "0000-0003-4819-0264", "researcher": {"href": "https://publications.scilifelab.se/researcher/1326e4bc6d764442b2fd851888c84f67.json"}}, {"family": "V\u00e4sterviga", "given": "Emma", "initials": "E"}, {"family": "Wang", "given": "Sailan", "initials": "S"}, {"family": "Yang", "given": "Rachel", "initials": "R", "orcid": "0009-0009-4487-6390", "researcher": {"href": "https://publications.scilifelab.se/researcher/85caaf4cb8fb4bc6bac8129b0bed5564.json"}}, {"family": "Yamamoto", "given": "Shinya", "initials": "S", "orcid": "0000-0003-2172-8036", "researcher": {"href": "https://publications.scilifelab.se/researcher/90c060c592574ce58cda8bf0339281d7.json"}}, {"family": "Y\u00e9pez", "given": "Vicente A", "initials": "VA", "orcid": "0000-0001-7916-3643", "researcher": {"href": "https://publications.scilifelab.se/researcher/661e0ca688574056bc9952c2ccdd19a4.json"}}, {"family": "Zhang", "given": "Qing", "initials": "Q"}, {"family": "Shotelersuk", "given": "Vorasuk", "initials": "V", "orcid": "0000-0002-1856-0589", "researcher": {"href": "https://publications.scilifelab.se/researcher/645f2ef9414e4301af16d3fd7841b4a2.json"}}, {"family": "Wiafe", "given": "Samuel Agyei", "initials": "SA"}, {"family": "Alanay", "given": "Yasemin", "initials": "Y"}, {"family": "Botto", "given": "Lorenzo D", "initials": "LD"}, {"family": "Kirmani", "given": "Salman", "initials": "S"}, {"family": "Lumaka", "given": "Aim\u00e9", "initials": "A", "orcid": "0000-0002-5468-8678", "researcher": {"href": "https://publications.scilifelab.se/researcher/604f009096d94902a984f0dcef8ea9a4.json"}}, {"family": "Palmer", "given": "Elizabeth Emma", "initials": "EE", "orcid": "0000-0003-1844-215X", "researcher": {"href": "https://publications.scilifelab.se/researcher/14a2059bb4314217bdf97310285da941.json"}}, {"family": "Puri", "given": "Ratna Dua", "initials": "RD", "orcid": "0000-0003-2694-6147", "researcher": {"href": "https://publications.scilifelab.se/researcher/be27a5b2e8924201be34b890b479878d.json"}}, {"family": "Wirta", "given": "Valtteri", "initials": "V"}, {"family": "Lindstrand", "given": "Anna", "initials": "A", "orcid": "0000-0003-0806-5602", "researcher": {"href": "https://publications.scilifelab.se/researcher/07f3e6152da043d38c7a81974fcf8c23.json"}}, {"family": "Buske", "given": "Orion J", "initials": "OJ", "orcid": "0000-0002-9064-092X", "researcher": {"href": "https://publications.scilifelab.se/researcher/4bff68f288e34d81a1412ce98556d8f2.json"}}, {"family": "Cederroth", "given": "Mikk", "initials": "M"}, {"family": "Nordgren", "given": "Ann", "initials": "A", "orcid": "0000-0003-3285-4281", "researcher": {"href": "https://publications.scilifelab.se/researcher/08e74c6ddc27493696beca0883027cdd.json"}}], "type": "journal article", "published": "2024-11-00", "journal": {"title": "Nat. Genet.", "issn": "1546-1718", "volume": "56", "issue": "11", "pages": "2287-2294", "issn-l": "1061-4036"}, "abstract": "The first-ever Undiagnosed Hackathon was a groundbreaking event held by the Wilhelm Foundation, the Karolinska Undiagnosed Disease Program, and PhenoTips in collaboration with UDNI to solve medical mysteries and advance diagnostics for undiagnosed rare diseases. Nearly 100 healthcare professionals and researchers from 28 countries participated, working intensively for 48 hours to diagnose 10 families with undiagnosed rare diseases. This innovative approach to precision diagnostics highlighted the power of international, multidisciplinary collaboration and patient partnership, yielding promising results for patients seeking answers and benefiting the entire rare diseases community.", "doi": "10.1038/s41588-024-01941-1", "pmid": "39433890", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Collaborative", "National Genomics Infrastructure": "Service", "Clinical Genomics Gothenburg": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service", "NGI Long read": "Service", "Clinical Genomics Stockholm": "Service", "Clinical Genomics Uppsala": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Clinical Genomics": "Service"}, "xrefs": [{"db": "mid", "key": "NIHMS2083970"}, {"db": "pmc", "key": "PMC12198426"}, {"db": "pii", "key": "10.1038/s41588-024-01941-1"}], "notes": [], "created": "2024-10-22T07:24:36.866Z", "modified": "2025-11-20T20:34:52.025Z"}, {"entity": "publication", "iuid": "63f6cd69ef3c4f43981d68e75f2d426a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/63f6cd69ef3c4f43981d68e75f2d426a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/63f6cd69ef3c4f43981d68e75f2d426a"}}, "title": "Genomic and functional characterization of the Atlantic salmon gut microbiome in relation to nutrition and health.", "authors": [{"family": "Vera-Ponce de Le\u00f3n", "given": "Arturo", "initials": "A", "orcid": "0000-0003-4085-5700", "researcher": {"href": "https://publications.scilifelab.se/researcher/bd53e0d4a23147acbf207767ed5f930f.json"}}, {"family": "Hensen", "given": "Tim", "initials": "T"}, {"family": "Hoetzinger", "given": "Matthias", "initials": "M"}, {"family": "Gupta", "given": "Shashank", "initials": "S"}, {"family": "Weston", "given": "Bronson", "initials": "B"}, {"family": "Johnsen", "given": "Sander M", "initials": "SM"}, {"family": "Rasmussen", "given": "Jacob A", "initials": "JA", "orcid": "0000-0002-7710-8912", "researcher": {"href": "https://publications.scilifelab.se/researcher/ce676b0101c645e086c4144f309616f0.json"}}, {"family": "Clausen", "given": "Cecilie Gr\u00f8nlund", "initials": "CG"}, {"family": "Pless", "given": "Louisa", "initials": "L"}, {"family": "Ver\u00edssimo", "given": "Ana Raquel Andrade", "initials": "ARA"}, {"family": "Rudi", "given": "Knut", "initials": "K"}, {"family": "Snipen", "given": "Lars", "initials": "L"}, {"family": "Karlsen", "given": "Christian Ren\u00e9", "initials": "CR"}, {"family": "Limborg", "given": "Morten T", "initials": "MT", "orcid": "0000-0002-7718-6531", "researcher": {"href": "https://publications.scilifelab.se/researcher/ccc405b9a4d44155b2d36b0cb7cf05ce.json"}}, {"family": "Bertilsson", "given": "Stefan", "initials": "S", "orcid": "0000-0002-4265-1835", "researcher": {"href": "https://publications.scilifelab.se/researcher/2c17765c2a9f4383b5383138d11ae93f.json"}}, {"family": "Thiele", "given": "Ines", "initials": "I"}, {"family": "Hvidsten", "given": "Torgeir R", "initials": "TR", "orcid": "0000-0001-6097-2539", "researcher": {"href": "https://publications.scilifelab.se/researcher/987fbb5763c74f6895bee64630528d8d.json"}}, {"family": "Sandve", "given": "Simen R", "initials": "SR"}, {"family": "Pope", "given": "Phillip B", "initials": "PB", "orcid": "0000-0002-2067-4059", "researcher": {"href": "https://publications.scilifelab.se/researcher/606fbc0320664a1890b7b6ad0b5f0d68.json"}}, {"family": "La Rosa", "given": "Sabina Leanti", "initials": "SL", "orcid": "0000-0003-3527-8101", "researcher": {"href": "https://publications.scilifelab.se/researcher/1b9163383f4c437495b90bd8f2fb72df.json"}}], "type": "journal article", "published": "2024-11-00", "journal": {"title": "Nat Microbiol", "issn": "2058-5276", "volume": "9", "issue": "11", "pages": "3059-3074", "issn-l": "2058-5276"}, "abstract": "To ensure sustainable aquaculture, it is essential to understand the path 'from feed to fish', whereby the gut microbiome plays an important role in digestion and metabolism, ultimately influencing host health and growth. Previous work has reported the taxonomic composition of the Atlantic salmon (Salmo salar) gut microbiome; however, functional insights are lacking. Here we present the Salmon Microbial Genome Atlas consisting of 211 high-quality bacterial genomes, recovered by cultivation (n = 131) and gut metagenomics (n = 80) from wild and farmed fish both in freshwater and seawater. Bacterial genomes were taxonomically assigned to 14 different orders, including 35 distinctive genera and 29 previously undescribed species. Using metatranscriptomics, we functionally characterized key bacterial populations, across five phyla, in the salmon gut. This included the ability to degrade diet-derived fibres and release vitamins and other exometabolites with known beneficial effects, which was supported by genome-scale metabolic modelling and in vitro cultivation of selected bacterial species coupled with untargeted metabolomic studies. Together, the Salmon Microbial Genome Atlas provides a genomic and functional resource to enable future studies on salmon nutrition and health.", "doi": "10.1038/s41564-024-01830-7", "pmid": "39402236", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41564-024-01830-7"}], "notes": [], "created": "2024-11-12T10:39:11.102Z", "modified": "2025-02-28T14:15:24.513Z"}, {"entity": "publication", "iuid": "a2fdff49e57d4d3b943d89f689136860", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a2fdff49e57d4d3b943d89f689136860.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a2fdff49e57d4d3b943d89f689136860"}}, "title": "Characterization of Pediatric Acute Myeloid Leukemia With t(7;12)(q36;p13)", "authors": [{"family": "\u00d6stlund", "given": "Anders", "initials": "A"}, {"family": "Waraky", "given": "Ahmed", "initials": "A"}, {"family": "Staffas", "given": "Anna", "initials": "A"}, {"family": "Sj\u00f6gren", "given": "Helene", "initials": "H", "orcid": "0000-0003-2592-1239", "researcher": {"href": "https://publications.scilifelab.se/researcher/3cb19c7d5b8c4611ae0ba909897603ca.json"}}, {"family": "De\u00a0Moerloose", "given": "Barbara", "initials": "B"}, {"family": "Arad\u2010Cohen", "given": "Nira", "initials": "N"}, {"family": "Cheuk", "given": "Daniel", "initials": "D"}, {"family": "Navarro", "given": "Jose Maria Fernandez", "initials": "JMF"}, {"family": "Jahnukainen", "given": "Kirsi", "initials": "K", "orcid": "0000-0001-9296-2028", "researcher": {"href": "https://publications.scilifelab.se/researcher/ec8cc2ae60a245e4807ce50c05273ded.json"}}, {"family": "Kaspers", "given": "Gertjan J L", "initials": "GJL"}, {"family": "Kovalova", "given": "Zhanna", "initials": "Z"}, {"family": "Pasauliene", "given": "Ramune", "initials": "R"}, {"family": "Saks", "given": "Kadri", "initials": "K"}, {"family": "Zeller", "given": "Bernward", "initials": "B"}, {"family": "Nor\u00e9n\u2010Nystr\u00f6m", "given": "Ulrika", "initials": "U"}, {"family": "Hasle", "given": "Henrik", "initials": "H", "orcid": "0000-0003-3976-9231", "researcher": {"href": "https://publications.scilifelab.se/researcher/4bd29fb163f9461d92b50157101bf384.json"}}, {"family": "Fogelstrand", "given": "Linda", "initials": "L", "orcid": "0000-0003-3698-8519", "researcher": {"href": "https://publications.scilifelab.se/researcher/f39ff709aa0646b8ad5e520780a0ad49.json"}}, {"family": "Abrahamsson", "given": "Jonas", "initials": "J", "orcid": "0000-0002-9240-3522", "researcher": {"href": "https://publications.scilifelab.se/researcher/0f3199957bd147ec91bbdc04413f1dba.json"}}, {"family": "Palmqvist", "given": "Lars", "initials": "L", "orcid": "0000-0001-9274-360X", "researcher": {"href": "https://publications.scilifelab.se/researcher/7e50c0057dcb47f39e085b16580806c2.json"}}], "type": "journal-article", "published": "2024-11-00", "journal": {"title": "Genes Chromosomes Cancer", "issn": "1045-2257", "volume": "63", "issue": "11", "pages": "e70003", "issn-l": null}, "abstract": "Acute myeloid leukemia (AML) with t(7;12)(q36;p13) is a recurrent translocation in AML in infants or very young children and was recently included in the World Health Organization (WHO) Classification of Hematolymphoid Tumors. AML with t(7;12) is reported to involve MNX1 and ETV6 signaling; however, the mechanism of leukemogenesis is not well understood, and the presence of MNX1::ETV6 fusion transcripts has only been confirmed in approximately 50% of cases. In contrast, high expression of MNX1 has been seen in all investigated cases. In this study, we investigated the clinical as well as biological characteristics of 12 pediatric AML with t(7;12) and performed whole transcriptome (WTS) and whole genome sequencing (WGS) on six of these. There was no significant difference in event-free survival or overall survival of these t(7;12) AML patients compared with other AML in the same age group. Interestingly, WTS identified several fusion transcripts involving ETV6 but not together with MNX1. WGS identified the genomic breakpoints and revealed that a common fusion partner on chromosome 7 was NOM1. Principal component analysis (PCA) of the WTS data showed that all t(7;12) AML cases cluster together, separate from all other pediatric AML subtypes; all cases had high expression of MNX1, MNX1-AS1, and MNX1-AS2. Hence, t(7;12) AML, despite expressing different fusion transcripts and with varying translocation breakpoints, constitutes a phenotypically homogenous subgroup. This underlines that the leukemia-driving event most likely is ectopic expression of MNX1 and that this therefore should be the defining Classifying criteria of this type of AML.", "doi": "10.1002/gcc.70003", "pmid": "39508359", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "Service"}, "xrefs": [], "notes": [], "created": "2024-11-12T10:38:57.208Z", "modified": "2025-12-04T19:33:55.324Z"}, {"entity": "publication", "iuid": "11ebdd1832a843a5ae22f814817c2e99", "links": {"self": {"href": "https://publications.scilifelab.se/publication/11ebdd1832a843a5ae22f814817c2e99.json"}, "display": {"href": "https://publications.scilifelab.se/publication/11ebdd1832a843a5ae22f814817c2e99"}}, "title": "Epigenome-wide analysis across the development span of pediatric acute lymphoblastic leukemia: backtracking to birth.", "authors": [{"family": "Ghantous", "given": "Akram", "initials": "A"}, {"family": "Nussl\u00e9", "given": "Semira Gonseth", "initials": "SG"}, {"family": "Nassar", "given": "Farah J", "initials": "FJ"}, {"family": "Spitz", "given": "Natalia", "initials": "N"}, {"family": "Novoloaca", "given": "Alexei", "initials": "A"}, {"family": "Krali", "given": "Olga", "initials": "O"}, {"family": "Nickels", "given": "Eric", "initials": "E"}, {"family": "Cahais", "given": "Vincent", "initials": "V"}, {"family": "Cuenin", "given": "Cyrille", "initials": "C"}, {"family": "Roy", "given": "Ritu", "initials": "R"}, {"family": "Li", "given": "Shaobo", "initials": "S"}, {"family": "Caron", "given": "Maxime", "initials": "M"}, {"family": "Lam", "given": "Dilys", "initials": "D"}, {"family": "Fransquet", "given": "Peter Daniel", "initials": "PD"}, {"family": "Casement", "given": "John", "initials": "J"}, {"family": "Strathdee", "given": "Gordon", "initials": "G"}, {"family": "Pearce", "given": "Mark S", "initials": "MS"}, {"family": "Hansen", "given": "Helen M", "initials": "HM"}, {"family": "Lee", "given": "Hwi-Ho", "initials": "H"}, {"family": "Lee", "given": "Yong Sun", "initials": "YS"}, {"family": "de Smith", "given": "Adam J", "initials": "AJ"}, {"family": "Sinnett", "given": "Daniel", "initials": "D"}, {"family": "H\u00e5berg", "given": "Siri Eldevik", "initials": "SE"}, {"family": "McKay", "given": "Jill A", "initials": "JA"}, {"family": "Nordlund", "given": "Jessica", "initials": "J"}, {"family": "Magnus", "given": "Per", "initials": "P"}, {"family": "Dwyer", "given": "Terence", "initials": "T"}, {"family": "Saffery", "given": "Richard", "initials": "R"}, {"family": "Wiemels", "given": "Joseph Leo", "initials": "JL"}, {"family": "Munthe-Kaas", "given": "Monica Cheng", "initials": "MC"}, {"family": "Herceg", "given": "Zdenko", "initials": "Z"}], "type": "journal article", "published": "2024-10-23", "journal": {"title": "Mol. Cancer", "issn": "1476-4598", "issn-l": "1476-4598", "volume": "23", "issue": "1", "pages": "238"}, "abstract": "Cancer is the leading cause of disease-related mortality in children. Causes of leukemia, the most common form, are largely unknown. Growing evidence points to an origin in-utero, when global redistribution of DNA methylation occurs driving tissue differentiation.\r\n\r\nEpigenome-wide DNA methylation was profiled in surrogate (blood) and target (bone marrow) tissues at birth, diagnosis, remission and relapse of pediatric pre-B acute lymphoblastic leukemia (pre-B ALL) patients. Double-blinded analyses was performed between prospective cohorts extending from birth to diagnosis and retrospective studies backtracking from clinical disease to birth. Validation was carried out using independent technologies and populations.\r\n\r\nThe imprinted and immuno-modulating VTRNA2-1 was hypermethylated (FDR<0.05) at birth in nested cases relative to controls in all tested populations (totaling 317 cases and 483 controls), including European and Hispanic ancestries. VTRNA2-1 methylation was stable over follow-up years after birth and across surrogate, target and other tissues (n=5,023 tissues; 30 types). When profiled in leukemic tissues from two clinical cohorts (totaling 644 cases), VTRNA2-1 methylation exhibited higher levels at diagnosis relative to controls, it reset back to normal levels at remission, and then re-increased to above control levels at relapse. Hypermethylation was significantly associated with worse pre-B ALL patient survival and with reduced VTRNA2-1 expression (n=2,294 tissues; 26 types), supporting a functional and translational role for VTRNA2-1 methylation.\r\n\r\nThis study provides proof-of-concept to detect at birth epigenetic precursors of pediatric pre-B ALL. These alterations were reproducible with different technologies, in three continents and in two ethnicities, and can offer biomarkers for early detection and prognosis as well as actionable targets for therapy.", "doi": "10.1186/s12943-024-02118-4", "pmid": "39443995", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "NGI SNP genotyping": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11515509"}, {"db": "pii", "key": "10.1186/s12943-024-02118-4"}], "notes": [], "created": "2024-11-05T18:15:38.335Z", "modified": "2024-11-05T18:18:01.358Z"}, {"entity": "publication", "iuid": "34b3ab08d6fb428d9a51611e76936c20", "links": {"self": {"href": "https://publications.scilifelab.se/publication/34b3ab08d6fb428d9a51611e76936c20.json"}, "display": {"href": "https://publications.scilifelab.se/publication/34b3ab08d6fb428d9a51611e76936c20"}}, "title": "High rate of gene family evolution in proximity to the origin of ectomycorrhizal symbiosis in Inocybaceae.", "authors": [{"family": "Khan", "given": "Faheema Kalsoom", "initials": "FK", "orcid": "0000-0002-4891-953X", "researcher": {"href": "https://publications.scilifelab.se/researcher/f3d13492ee8f4ad1b69ce59f21b09155.json"}}, {"family": "S\u00e1nchez-Garc\u00eda", "given": "Marisol", "initials": "M", "orcid": "0000-0002-0635-6281", "researcher": {"href": "https://publications.scilifelab.se/researcher/5ccb3584fa144e178750ff2fc4666cfe.json"}}, {"family": "Johannesson", "given": "Hanna", "initials": "H", "orcid": "0000-0001-6359-9856", "researcher": {"href": "https://publications.scilifelab.se/researcher/36e8fe278e01470e8cddaaccc5dad596.json"}}, {"family": "Ryberg", "given": "Martin", "initials": "M", "orcid": "0000-0002-6795-4349", "researcher": {"href": "https://publications.scilifelab.se/researcher/c0a8578a1ace4105be91ec8116c84365.json"}}], "type": "journal article", "published": "2024-10-00", "journal": {"title": "New Phytol.", "issn": "1469-8137", "volume": "244", "issue": "1", "pages": "219-234", "issn-l": "0028-646X"}, "abstract": "The genomes of ectomycorrhizal (ECM) fungi have a reduced number of genes encoding Carbohydrate-Active EnZymes (CAZymes), expansions in transposable elements (TEs) and small secreted proteins (SSPs) compared with saprotrophs. Fewer genes for specific peptidases and lipases in ECM fungi are also reported. It is unclear whether these changes occur at the shift to the ECM habit or are more gradual throughout the evolution of ECM lineages. We generated a genomic dataset of 20 species in the ECM lineage Inocybaceae and compared them with six saprotrophic species. Inocybaceae genomes have fewer CAZymes, peptidases, lipases, secondary metabolite clusters and SSPs and higher TE content than their saprotrophic relatives. There was an increase in the rate of gene family evolution along the branch with the transition to the ECM lifestyle. This branch had very high rate of evolution in CAZymes and had the largest number of contractions. Other significant changes along this branch included expansions in transporters, transposons-related genes and communication genes such as fungal kinases. There is a high concentration of changes in proximity to the transition to the ECM lifestyle, which correspond to the identified key changes for the gain of this lifestyle.", "doi": "10.1111/nph.20007", "pmid": "39113397", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2024-09-17T11:56:17.664Z", "modified": "2025-02-28T14:20:41.968Z"}, {"entity": "publication", "iuid": "7a3541f280af4c2284e0b872bff2d2b6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7a3541f280af4c2284e0b872bff2d2b6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7a3541f280af4c2284e0b872bff2d2b6"}}, "title": "Comparative proteomic analyses of potato leaves from field-grown plants grown under extremely long days.", "authors": [{"family": "Resj\u00f6", "given": "Svante", "initials": "S"}, {"family": "Willforss", "given": "Jakob", "initials": "J"}, {"family": "Large", "given": "Annabel", "initials": "A"}, {"family": "Siino", "given": "Valentina", "initials": "V"}, {"family": "Alexandersson", "given": "Erik", "initials": "E"}, {"family": "Levander", "given": "Fredrik", "initials": "F"}, {"family": "Andreasson", "given": "Erik", "initials": "E"}], "type": "journal article", "published": "2024-10-00", "journal": {"title": "Plant Physiol Biochem", "issn": "1873-2690", "volume": "215", "pages": "109032", "issn-l": null}, "abstract": "There are limited molecular data and few biomarkers available for studies of field-grown plants, especially for plants grown during extremely long days. In this study we present quantitative proteomics data from 3 years of field trials on potato, conducted in northern and southern Sweden and analyze over 3000 proteins per year of the study and complement the proteomic analysis with metabolomic and transcriptomic analyses. Small but consistent differences linked to the longer days (an average of four more hours of light per day) in northern Sweden (20 h light/day) compared to southern Sweden can be observed, with a high correlation between the mRNA determined by RNA-seq and protein abundances. The majority of the proteins with differential abundances between northern and southern Sweden could be divided into three groups: metabolic enzymes (especially GABA metabolism), proteins involved in redox metabolism, and hydrolytic enzymes. The observed differences in metabolic enzyme abundances corresponded well with untargeted metabolite data determined by GC and LC mass-spectrometry. We also analyzed differences in protein abundance between potato varieties that performed relatively well in northern Sweden in terms of yield with those that performed relatively less well. This comparison indicates that the proteins with higher abundance in the high-yield quotient group are more anabolic in their character, whereas the proteins with lower abundance are more catabolic. Our results create a base of information about potato \"field-omics\" for improved understanding of physiological and molecular processes in field-grown plants, and our data indicate that the potato plant is not generally stressed by extremely long days.", "doi": "10.1016/j.plaphy.2024.109032", "pmid": "39181085", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Short read": "Service", "National Genomics Infrastructure": "Service", "Swedish Metabolomics Centre": "Service"}, "xrefs": [{"db": "pii", "key": "S0981-9428(24)00700-9"}], "notes": [], "created": "2024-10-21T11:17:16.284Z", "modified": "2025-10-17T13:03:13.007Z"}, {"entity": "publication", "iuid": "39a3713a7f8e4699b510aad93490c0b4", "links": {"self": {"href": "https://publications.scilifelab.se/publication/39a3713a7f8e4699b510aad93490c0b4.json"}, "display": {"href": "https://publications.scilifelab.se/publication/39a3713a7f8e4699b510aad93490c0b4"}}, "title": "Associations between epigenetic aging and diabetes mellitus in a Swedish longitudinal study.", "authors": [{"family": "Wikstr\u00f6m Shemer", "given": "Daniel", "initials": "D"}, {"family": "Mostafaei", "given": "Shayan", "initials": "S"}, {"family": "Tang", "given": "Bowen", "initials": "B"}, {"family": "Pedersen", "given": "Nancy L", "initials": "NL"}, {"family": "Karlsson", "given": "Ida K", "initials": "IK"}, {"family": "Fall", "given": "Tove", "initials": "T"}, {"family": "H\u00e4gg", "given": "Sara", "initials": "S", "orcid": "0000-0002-2452-1500", "researcher": {"href": "https://publications.scilifelab.se/researcher/e1d010dfe5d84a33b6a6c7ec815ca3dc.json"}}], "type": "journal article", "published": "2024-10-00", "journal": {"title": "Geroscience", "issn": "2509-2723", "volume": "46", "issue": "5", "pages": "5003-5014", "issn-l": null}, "abstract": "Diabetes mellitus type 2 (T2D) is associated with accelerated biological aging and the increased risk of onset of other age-related diseases. Epigenetic changes in DNA methylation levels have been found to serve as reliable biomarkers for biological aging. This study explores the relationship between various epigenetic biomarkers of aging and diabetes risk using longitudinal data. Data from the Swedish Adoption/Twin Study of Aging (SATSA) was collected from 1984 to 2014 and included 536 individuals with at least one epigenetic measurement. The following epigenetic biomarkers of aging were employed: DNAm PAI-1, DNAmTL, DunedinPACE, PCHorvath1, PCHorvath2, PCHannum, PCPhenoAge, and PCGrimAge. Firstly, longitudinal analysis of biomarker trajectories was done. Secondly, linear correlations between the biomarkers and time to diabetes were studied within individuals developing diabetes. Thirdly, Cox proportional hazards (PH) models were used to assess the associations between these biomarkers and time of diabetes diagnosis, with adjustments for chronological age, sex, education, smoking, blood glucose, and BMI. The longitudinal trajectories of the biomarkers revealed differences between individuals with and without diabetes. Smoothened average curves for DunedinPACE and DNAm PAI-1 were higher for individuals with diabetes around the age 60-70, compared to controls. Likewise, DunedinPACE and DNAm PAI-1 were higher closer to diabetes onset. However, no significant associations were found between the epigenetic biomarkers of aging and risk of diabetes in Cox PH models. Our findings suggest the potential value of developing epigenetic biomarkers specifically tailored to T2D, should we wish to model and explore the potential for predicting the disease.", "doi": "10.1007/s11357-024-01252-7", "pmid": "38937415", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI SNP genotyping": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11335983"}, {"db": "pii", "key": "10.1007/s11357-024-01252-7"}], "notes": [], "created": "2024-10-21T11:23:00.308Z", "modified": "2024-10-21T11:23:00.355Z"}, {"entity": "publication", "iuid": "46bc0cd9439d4cffbec0472e91aa975b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/46bc0cd9439d4cffbec0472e91aa975b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/46bc0cd9439d4cffbec0472e91aa975b"}}, "title": "\"Metagenomics reveal the potential for geosmin and 2-methylisoborneol production across multiple bacterial phyla in recirculating aquaculture systems\".", "authors": [{"family": "Zheng", "given": "Dan", "initials": "D", "orcid": "0000-0002-8680-432X", "researcher": {"href": "https://publications.scilifelab.se/researcher/a36d31143d764232898009845c059013.json"}}, {"family": "Wil\u00e9n", "given": "Britt-Marie", "initials": "BM"}, {"family": "\u00d6berg", "given": "Ola", "initials": "O"}, {"family": "Wik", "given": "Torsten", "initials": "T"}, {"family": "Modin", "given": "Oskar", "initials": "O"}], "type": "journal article", "published": "2024-10-00", "journal": {"title": "Environ. Microbiol.", "issn": "1462-2920", "volume": "26", "issue": "10", "pages": "e16696", "issn-l": "1462-2912"}, "abstract": "Geosmin and 2-methylisoborneol (MIB) are known to cause taste-and-odour problems in recirculating aquaculture systems (RAS). Both geosmin and MIB are microbial metabolites belonging to terpenoids. Precursors for terpenoids are biosynthesized via the methylerythritol phosphate (MEP) and the mevalonate (MVA) pathways. We carried out a metagenomic analysis of 50 samples from five RAS to investigate terpenoid biosynthesis and metabolic potential for geosmin and MIB production in RAS microbiomes. A total of 1008 metagenome-assembled genomes (MAGs) representing 26 bacterial and three archaeal phyla were recovered. Although most archaea are thought to use the MVA pathway for terpenoid precursor biosynthesis, an Iainarchaeota archaeal MAG is shown to harbour a complete set of genes encoding the MEP pathway but lacking genes associated with the MVA pathway. In this study, a total of 16 MAGs affiliated with five bacterial phyla (Acidobacteriota, Actinobacteriota, Bacteroidota, Chloroflexota, and Myxococcota) were identified as possessing potential geosmin or MIB synthases. These putative taste and odour producers were diverse, many were taxonomically unidentified at the genus or species level, and their relative abundance differed between the investigated RAS farms. The metagenomic study of the RAS microbiomes revealed a previously unknown phylogenetic diversity of the potential to produce geosmin and MIB.", "doi": "10.1111/1462-2920.16696", "pmid": "39379175", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2024-11-12T10:39:04.883Z", "modified": "2025-02-28T14:19:59.973Z"}, {"entity": "publication", "iuid": "e17d4a0e0e434723a36f929e80935cd5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e17d4a0e0e434723a36f929e80935cd5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e17d4a0e0e434723a36f929e80935cd5"}}, "title": "The European Reference Genome Atlas: piloting a decentralised approach to equitable biodiversity genomics.", "authors": [{"family": "Mc Cartney", "given": "Ann M", "initials": "AM"}, {"family": "Formenti", "given": "Giulio", "initials": "G"}, {"family": "Mouton", "given": "Alice", "initials": "A"}, {"family": "De Panis", "given": "Diego", "initials": "D"}, {"family": "Marins", "given": "Lu\u00edsa S", "initials": "LS"}, {"family": "Leit\u00e3o", "given": "Henrique G", "initials": "HG"}, {"family": "Diedericks", "given": "Genevieve", "initials": "G"}, {"family": "Kirangwa", "given": "Joseph", "initials": "J"}, {"family": "Morselli", "given": "Marco", "initials": "M"}, {"family": "Salces-Ortiz", "given": "Judit", "initials": "J"}, {"family": "Escudero", "given": "Nuria", "initials": "N"}, {"family": "Iannucci", "given": "Alessio", "initials": "A"}, {"family": "Natali", "given": "Chiara", "initials": "C"}, {"family": "Svardal", "given": "Hannes", "initials": "H"}, {"family": "Fern\u00e1ndez", "given": "Rosa", "initials": "R"}, {"family": "De Pooter", "given": "Tim", "initials": "T"}, {"family": "Joris", "given": "Geert", "initials": "G"}, {"family": "Strazisar", "given": "Mojca", "initials": "M"}, {"family": "Wood", "given": "Jonathan M D", "initials": "JMD"}, {"family": "Herron", "given": "Katie E", "initials": "KE"}, {"family": "Seehausen", "given": "Ole", "initials": "O"}, {"family": "Watts", "given": "Phillip C", "initials": "PC"}, {"family": "Shaw", "given": "Felix", "initials": "F"}, {"family": "Davey", "given": "Robert P", "initials": "RP"}, {"family": "Minotto", "given": "Alice", "initials": "A"}, {"family": "Fern\u00e1ndez", "given": "Jos\u00e9 M", "initials": "JM"}, {"family": "B\u00f6hne", "given": "Astrid", "initials": "A"}, {"family": "Alegria", "given": "Carla", "initials": "C"}, {"family": "Alioto", "given": "Tyler", "initials": "T"}, {"family": "Alves", "given": "Paulo C", "initials": "PC"}, {"family": "Amorim", "given": "Isabel R", "initials": "IR"}, {"family": "Aury", "given": "Jean-Marc", "initials": "J"}, {"family": "Backstrom", "given": "Niclas", "initials": "N"}, {"family": "Baldrian", "given": "Petr", "initials": "P"}, {"family": "Baltrunaite", "given": "Laima", "initials": "L"}, {"family": "Barta", "given": "Endre", "initials": "E"}, {"family": "BedHom", "given": "Bertrand", "initials": "B"}, {"family": "Belser", "given": "Caroline", "initials": "C"}, {"family": "Bergsten", "given": "Johannes", "initials": "J"}, {"family": "Bertrand", "given": "Laurie", "initials": "L"}, {"family": "Bilandija", "given": "Helena", "initials": "H"}, {"family": "Binzer-Panchal", "given": "Mahesh", "initials": "M"}, {"family": "Bista", "given": "Iliana", "initials": "I"}, {"family": "Blaxter", "given": "Mark", "initials": "M"}, {"family": "Borges", "given": "Paulo A V", "initials": "PAV"}, {"family": "Dias", "given": "Guilherme Borges", "initials": "GB"}, {"family": "Bosse", "given": "Mirte", "initials": "M"}, {"family": "Brown", "given": "Tom", "initials": "T"}, {"family": "Bruggmann", "given": "R\u00e9my", "initials": "R"}, {"family": "Buena-Atienza", "given": "Elena", "initials": "E"}, {"family": "Burgin", "given": "Josephine", "initials": "J"}, {"family": "Buzan", "given": "Elena", "initials": "E"}, {"family": "Cariani", "given": "Alessia", "initials": "A"}, {"family": "Casadei", "given": "Nicolas", "initials": "N"}, {"family": "Chiara", "given": "Matteo", "initials": "M"}, {"family": "Chozas", "given": "Sergio", "initials": "S"}, {"family": "\u010ciampor", "given": "Fedor", "initials": "F"}, {"family": "Crottini", "given": "Angelica", "initials": "A"}, {"family": "Cruaud", "given": "Corinne", "initials": "C"}, {"family": "Cruz", "given": "Fernando", "initials": "F"}, {"family": "Dalen", "given": "Love", "initials": "L"}, {"family": "De Biase", "given": "Alessio", "initials": "A"}, {"family": "Del Campo", "given": "Javier", "initials": "J"}, {"family": "Delic", "given": "Teo", "initials": "T"}, {"family": "Dennis", "given": "Alice B", "initials": "AB"}, {"family": "Derks", "given": "Martijn F L", "initials": "MFL"}, {"family": "Diroma", "given": "Maria Angela", "initials": "MA"}, {"family": "Djan", "given": "Mihajla", "initials": "M"}, {"family": "Duprat", "given": "Simone", "initials": "S"}, {"family": "Eleftheriadi", "given": "Klara", "initials": "K"}, {"family": "Feulner", "given": "Philine G D", "initials": "PGD"}, {"family": "Flot", "given": "Jean-Fran\u00e7ois", "initials": "J"}, {"family": "Forni", "given": "Giobbe", "initials": "G"}, {"family": "Fosso", "given": "Bruno", "initials": "B"}, {"family": "Fournier", "given": "Pascal", "initials": "P"}, {"family": "Fournier-Chambrillon", "given": "Christine", "initials": "C"}, {"family": "Gabaldon", "given": "Toni", "initials": "T"}, {"family": "Garg", "given": "Shilpa", "initials": "S"}, {"family": "Gissi", "given": "Carmela", "initials": "C"}, {"family": "Giupponi", "given": "Luca", "initials": "L"}, {"family": "Gomez-Garrido", "given": "Jessica", "initials": "J"}, {"family": "Gonz\u00e1lez", "given": "Josefa", "initials": "J"}, {"family": "Grilo", "given": "Miguel L", "initials": "ML"}, {"family": "Gr\u00fcning", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Guerin", "given": "Thomas", "initials": "T"}, {"family": "Guiglielmoni", "given": "Nadege", "initials": "N"}, {"family": "Gut", "given": "Marta", "initials": "M"}, {"family": "Haesler", "given": "Marcel P", "initials": "MP"}, {"family": "Hahn", "given": "Christoph", "initials": "C"}, {"family": "Halpern", "given": "Balint", "initials": "B"}, {"family": "Harrison", "given": "Peter W", "initials": "PW"}, {"family": "Heintz", "given": "Julia", "initials": "J"}, {"family": "Hindrikson", "given": "Maris", "initials": "M"}, {"family": "H\u00f6glund", "given": "Jacob", "initials": "J"}, {"family": "Howe", "given": "Kerstin", "initials": "K"}, {"family": "Hughes", "given": "Graham M", "initials": "GM"}, {"family": "Istace", "given": "Benjamin", "initials": "B"}, {"family": "Cock", "given": "Mark J", "initials": "MJ"}, {"family": "Jan\u017eekovi\u010d", "given": "Franc", "initials": "F"}, {"family": "Jonsson", "given": "Zophonias O", "initials": "ZO"}, {"family": "Joye-Dind", "given": "Sagane", "initials": "S"}, {"family": "Koskim\u00e4ki", "given": "Janne J", "initials": "JJ"}, {"family": "Krystufek", "given": "Boris", "initials": "B"}, {"family": "Kubacka", "given": "Justyna", "initials": "J"}, {"family": "Kuhl", "given": "Heiner", "initials": "H"}, {"family": "Kusza", "given": "Szilvia", "initials": "S"}, {"family": "Labadie", "given": "Karine", "initials": "K"}, {"family": "L\u00e4hteenaro", "given": "Meri", "initials": "M"}, {"family": "Lantz", "given": "Henrik", "initials": "H"}, {"family": "Lavrinienko", "given": "Anton", "initials": "A"}, {"family": "Lecl\u00e8re", "given": "Lucas", "initials": "L"}, {"family": "Lopes", "given": "Ricardo Jorge", "initials": "RJ"}, {"family": "Madsen", "given": "Ole", "initials": "O"}, {"family": "Magdelenat", "given": "Ghislaine", "initials": "G"}, {"family": "Magoga", "given": "Giulia", "initials": "G"}, {"family": "Manousaki", "given": "Tereza", "initials": "T"}, {"family": "Mappes", "given": "Tapio", "initials": "T"}, {"family": "Marques", "given": "Joao Pedro", "initials": "JP"}, {"family": "Redondo", "given": "Gemma I Martinez", "initials": "GIM"}, {"family": "Maumus", "given": "Florian", "initials": "F"}, {"family": "McCarthy", "given": "Shane A", "initials": "SA"}, {"family": "Megens", "given": "Hendrik-Jan", "initials": "H"}, {"family": "Melo-Ferreira", "given": "Jose", "initials": "J"}, {"family": "Mendes", "given": "Sofia L", "initials": "SL"}, {"family": "Montagna", "given": "Matteo", "initials": "M"}, {"family": "Moreno", "given": "Joao", "initials": "J"}, {"family": "Mosbech", "given": "Mai-Britt", "initials": "M"}, {"family": "Moura", "given": "M\u00f3nica", "initials": "M"}, {"family": "Musilova", "given": "Zuzana", "initials": "Z"}, {"family": "Myers", "given": "Eugene", "initials": "E"}, {"family": "Nash", "given": "Will J", "initials": "WJ"}, {"family": "Nater", "given": "Alexander", "initials": "A"}, {"family": "Nicholson", "given": "Pamela", "initials": "P"}, {"family": "Niell", "given": "Manuel", "initials": "M"}, {"family": "Nijland", "given": "Reindert", "initials": "R"}, {"family": "Noel", "given": "Benjamin", "initials": "B"}, {"family": "Noren", "given": "Karin", "initials": "K"}, {"family": "Oliveira", "given": "Pedro H", "initials": "PH"}, {"family": "Olsen", "given": "Remi-Andre", "initials": "R"}, {"family": "Ometto", "given": "Lino", "initials": "L"}, {"family": "Oomen", "given": "Rebekah A", "initials": "RA"}, {"family": "Ossowski", "given": "Stephan", "initials": "S"}, {"family": "Palinauskas", "given": "Vaidas", "initials": "V"}, {"family": "Palsson", "given": "Snaebjorn", "initials": "S"}, {"family": "Panibe", "given": "Jerome P", "initials": "JP"}, {"family": "Pauperio", "given": "Joana", "initials": "J"}, {"family": "Pavlek", "given": "Martina", "initials": "M"}, {"family": "Payen", "given": "Emilie", "initials": "E"}, {"family": "Pawlowska", "given": "Julia", "initials": "J"}, {"family": "Pellicer", "given": "Jaume", "initials": "J"}, {"family": "Pesole", "given": "Graziano", "initials": "G"}, {"family": "Pimenta", "given": "Joao", "initials": "J"}, {"family": "Pippel", "given": "Martin", "initials": "M"}, {"family": "Pirttil\u00e4", "given": "Anna Maria", "initials": "AM"}, {"family": "Poulakakis", "given": "Nikos", "initials": "N"}, {"family": "Rajan", "given": "Jeena", "initials": "J"}, {"family": "M C Rego", "given": "R\u00faben", "initials": "R"}, {"family": "Resendes", "given": "Roberto", "initials": "R"}, {"family": "Resl", "given": "Philipp", "initials": "P"}, {"family": "Riesgo", "given": "Ana", "initials": "A"}, {"family": "Rodin-Morch", "given": "Patrik", "initials": "P"}, {"family": "Soares", "given": "Andre E R", "initials": "AER"}, {"family": "Fernandes", "given": "Carlos Rodriguez", "initials": "CR"}, {"family": "Romeiras", "given": "Maria M", "initials": "MM"}, {"family": "Roxo", "given": "Guilherme", "initials": "G"}, {"family": "R\u00fcber", "given": "Lukas", "initials": "L"}, {"family": "Ruiz-Lopez", "given": "Maria Jose", "initials": "MJ"}, {"family": "Saarma", "given": "Urmas", "initials": "U"}, {"family": "da Silva", "given": "Luis P", "initials": "LP"}, {"family": "Sim-Sim", "given": "Manuela", "initials": "M"}, {"family": "Soler", "given": "Lucile", "initials": "L"}, {"family": "Sousa", "given": "Vitor C", "initials": "VC"}, {"family": "Santos", "given": "Carla Sousa", "initials": "CS"}, {"family": "Spada", "given": "Alberto", "initials": "A"}, {"family": "Stefanovic", "given": "Milomir", "initials": "M"}, {"family": "Steger", "given": "Viktor", "initials": "V"}, {"family": "Stiller", "given": "Josefin", "initials": "J"}, {"family": "St\u00f6ck", "given": "Matthias", "initials": "M"}, {"family": "Struck", "given": "Torsten H", "initials": "TH"}, {"family": "Sudasinghe", "given": "Hiranya", "initials": "H"}, {"family": "Tapanainen", "given": "Riikka", "initials": "R"}, {"family": "Tellgren-Roth", "given": "Christian", "initials": "C"}, {"family": "Trindade", "given": "Helena", "initials": "H"}, {"family": "Tukalenko", "given": "Yevhen", "initials": "Y"}, {"family": "Urso", "given": "Ilenia", "initials": "I"}, {"family": "Vacherie", "given": "Benoit", "initials": "B"}, {"family": "Van Belleghem", "given": "Steven M", "initials": "SM"}, {"family": "Van Oers", "given": "Kees", "initials": "K"}, {"family": "Vargas-Chavez", "given": "Carlos", "initials": "C"}, {"family": "Velickovic", "given": "Nevena", "initials": "N"}, {"family": "Vella", "given": "Noel", "initials": "N"}, {"family": "Vella", "given": "Adriana", "initials": "A"}, {"family": "Vernesi", "given": "Cristiano", "initials": "C"}, {"family": "Vicente", "given": "Sara", "initials": "S"}, {"family": "Villa", "given": "Sara", "initials": "S"}, {"family": "Pettersson", "given": "Olga Vinnere", "initials": "OV"}, {"family": "Volckaert", "given": "Filip A M", "initials": "FAM"}, {"family": "Voros", "given": "Judit", "initials": "J"}, {"family": "Wincker", "given": "Patrick", "initials": "P"}, {"family": "Winkler", "given": "Sylke", "initials": "S"}, {"family": "Ciofi", "given": "Claudio", "initials": "C"}, {"family": "Waterhouse", "given": "Robert M", "initials": "RM"}, {"family": "Mazzoni", "given": "Camila J", "initials": "CJ"}], "type": "journal article", "published": "2024-09-17", "journal": {"title": "NPJ Biodivers", "issn": "2731-4243", "issn-l": null, "volume": "3", "issue": "1", "pages": "28"}, "abstract": "A genomic database of all Earth's eukaryotic species could contribute to many scientific discoveries; however, only a tiny fraction of species have genomic information available. In 2018, scientists across the world united under the Earth BioGenome Project (EBP), aiming to produce a database of high-quality reference genomes containing all ~1.5 million recognized eukaryotic species. As the European node of the EBP, the European Reference Genome Atlas (ERGA) sought to implement a new decentralised, equitable and inclusive model for producing reference genomes. For this, ERGA launched a Pilot Project establishing the first distributed reference genome production infrastructure and testing it on 98 eukaryotic species from 33 European countries. Here we outline the infrastructure and explore its effectiveness for scaling high-quality reference genome production, whilst considering equity and inclusion. The outcomes and lessons learned provide a solid foundation for ERGA while offering key learnings to other transnational, national genomic resource projects and the EBP.", "doi": "10.1038/s44185-024-00054-6", "pmid": "39289538", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "NGI Uppsala (Uppsala Genome Center)": "Service", "NGI Long read": "Service", "National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Short read": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC11408602"}, {"db": "pii", "key": "10.1038/s44185-024-00054-6"}], "notes": [], "created": "2024-10-28T09:59:00.105Z", "modified": "2024-11-12T11:36:01.896Z"}, {"entity": "publication", "iuid": "ce86c408ca0b4ec2817b2742ac8f7e03", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ce86c408ca0b4ec2817b2742ac8f7e03.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ce86c408ca0b4ec2817b2742ac8f7e03"}}, "title": "Genetic differentiation and diversity do not explain variation in heterosis or inbreeding depression: empirical evidence from a long-lived iteroparous plant", "authors": [{"family": "S\u00f6derquist", "given": "Linus", "initials": "L", "orcid": "0000-0002-9894-4119", "researcher": {"href": "https://publications.scilifelab.se/researcher/6a0c370d6402423284ea40a2f51179ae.json"}}, {"family": "Karrenberg", "given": "Sophie", "initials": "S", "orcid": "0000-0002-7146-588X", "researcher": {"href": "https://publications.scilifelab.se/researcher/3a982636b44f4b93b7ec0bd64e5d6bfb.json"}}, {"family": "Sletvold", "given": "Nina", "initials": "N", "orcid": "0000-0002-9868-3449", "researcher": {"href": "https://publications.scilifelab.se/researcher/e342483c6e3f44c29453f9bc5ce5bb05.json"}}], "type": "journal-article", "published": "2024-09-17", "journal": {"title": "Conserv Genet", "issn": "1566-0621", "issn-l": null}, "abstract": null, "doi": "10.1007/s10592-024-01641-7", "pmid": null, "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI SNP genotyping": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [], "notes": [], "created": "2024-10-21T11:15:02.010Z", "modified": "2024-10-21T11:15:02.042Z"}, {"entity": "publication", "iuid": "398f1d2bf6b74444b97bca0bd97f93a0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/398f1d2bf6b74444b97bca0bd97f93a0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/398f1d2bf6b74444b97bca0bd97f93a0"}}, "title": "Mosaic loss of Y chromosome and the association to mortality in Danish men aged 56-100 years.", "authors": [{"family": "Hozakowska-Roszkowska", "given": "Dominika Marzena", "initials": "DM"}, {"family": "Mengel-From", "given": "Jonas", "initials": "J"}, {"family": "Hristozova", "given": "Teodora K", "initials": "TK"}, {"family": "Pedersen", "given": "Jacob Krabbe", "initials": "JK"}, {"family": "Jeune", "given": "Bernard", "initials": "B"}, {"family": "Andersen-Ranberg", "given": "Karen", "initials": "K"}, {"family": "Hjelmborg", "given": "Jacob V B", "initials": "JVB"}, {"family": "Christensen", "given": "Kaare", "initials": "K"}, {"family": "R\u00f6ttger", "given": "Richard", "initials": "R"}, {"family": "Nygaard", "given": "Marianne", "initials": "M"}], "type": "journal article", "published": "2024-09-16", "journal": {"title": "Mech Ageing Dev", "issn": "1872-6216", "volume": "222", "pages": "111979", "issn-l": null}, "abstract": "Mosaic loss of the Y chromosome (mLOY) is a common somatic mutation in the blood of elderly men and several studies have found mLOY in blood cells to be associated with an increased risk of various diseases and mortality. However, most of these studies have focused on middle-aged and older adults, meaning that mLOY in extremely old individuals like centenarians is understudied. To explore mLOY across a wider age range compared to earlier studies and to specifically focus on centenarians, mLOY was estimated in 917 Danish men aged 56-100 years. We found that the percentage of men with LOY increased with age until age 85, after which it plateaued at around 40 %. Consistently, a longitudinal comparison of mLOY revealed that mLOY predominantly increased with age, although inter-individual variation was seen. Using a twin sub-sample, the broad-sense heritability of mLOY was estimated at 72 %, indicating a substantial genetic influence. Supporting previous findings, mLOY was found to associate with increased mortality across all study participants and in men younger than 80 years. In centenarians, however, a higher level of mLOY associated with better survival, most likely due to selection, although confirmation of our findings in larger studies is needed.", "doi": "10.1016/j.mad.2024.111979", "pmid": "39265710", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI SNP genotyping": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pii", "key": "S0047-6374(24)00079-4"}], "notes": [], "created": "2024-10-21T11:22:57.751Z", "modified": "2024-10-21T11:22:57.809Z"}, {"entity": "publication", "iuid": "da70971f10de48a2a607c9b51dc45c38", "links": {"self": {"href": "https://publications.scilifelab.se/publication/da70971f10de48a2a607c9b51dc45c38.json"}, "display": {"href": "https://publications.scilifelab.se/publication/da70971f10de48a2a607c9b51dc45c38"}}, "title": "Enrichment of Cis-Acting Regulatory Elements in Differentially Methylated Regions Following Lipopolysaccharide Treatment of Bovine Endometrial Epithelial Cells.", "authors": [{"family": "Jhamat", "given": "Naveed", "initials": "N", "orcid": "0009-0002-9876-4262", "researcher": {"href": "https://publications.scilifelab.se/researcher/e95627ce396b48f3828f038706cad7ac.json"}}, {"family": "Guo", "given": "Yongzhi", "initials": "Y", "orcid": "0000-0002-5057-9095", "researcher": {"href": "https://publications.scilifelab.se/researcher/8040d6c76eb6467585d054d55a1965fe.json"}}, {"family": "Han", "given": "Jilong", "initials": "J", "orcid": "0000-0001-9747-8163", "researcher": {"href": "https://publications.scilifelab.se/researcher/6849bbc1472c447a82af373ca5a44e21.json"}}, {"family": "Humblot", "given": "Patrice", "initials": "P", "orcid": "0000-0002-5292-1798", "researcher": {"href": "https://publications.scilifelab.se/researcher/7d74c76f33864331ab7c72614ae855f0.json"}}, {"family": "Bongcam-Rudloff", "given": "Erik", "initials": "E", "orcid": "0000-0002-1947-8288", "researcher": {"href": "https://publications.scilifelab.se/researcher/6970ca57259d498588ecf9e1ad28a9b0.json"}}, {"family": "Andersson", "given": "G\u00f6ran", "initials": "G", "orcid": "0000-0001-5131-3144", "researcher": {"href": "https://publications.scilifelab.se/researcher/39ce81c314db47c8ad63c3ed38dffcb3.json"}}, {"family": "Niazi", "given": "Adnan", "initials": "A", "orcid": "0000-0003-0311-5279", "researcher": {"href": "https://publications.scilifelab.se/researcher/c9e07c9891804a60980eb07956a7cd0d.json"}}], "type": "journal article", "published": "2024-09-11", "journal": {"title": "Int J Mol Sci", "issn": "1422-0067", "volume": "25", "issue": "18", "issn-l": null}, "abstract": "Endometritis is an inflammatory disease that negatively influences fertility and is common in milk-producing cows. An in vitro model for bovine endometrial inflammation was used to identify enrichment of cis-acting regulatory elements in differentially methylated regions (DMRs) in the genome of in vitro-cultured primary bovine endometrial epithelial cells (bEECs) before and after treatment with lipopolysaccharide (LPS) from E. coli, a key player in the development of endometritis. The enriched regulatory elements contain binding sites for transcription factors with established roles in inflammation and hypoxia including NFKB and Hif-1\u03b1. We further showed co-localization of certain enriched cis-acting regulatory motifs including ARNT, Hif-1\u03b1, and NRF1. Our results show an intriguing interplay between increased mRNA levels in LPS-treated bEECs of the mRNAs encoding the key transcription factors such as AHR, EGR2, and STAT1, whose binding sites were enriched in the DMRs. Our results demonstrate an extraordinary cis-regulatory complexity in these DMRs having binding sites for both inflammatory and hypoxia-dependent transcription factors. Obtained data using this in vitro model for bacterial-induced endometrial inflammation have provided valuable information regarding key transcription factors relevant for clinical endometritis in both cattle and humans.", "doi": "10.3390/ijms25189832", "pmid": "39337320", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pii", "key": "ijms25189832"}, {"db": "pmc", "key": "PMC11432661"}], "notes": [], "created": "2024-09-30T06:07:03.182Z", "modified": "2024-09-30T06:07:04.535Z"}, {"entity": "publication", "iuid": "73cad3816af2484e851c50eb262486d1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/73cad3816af2484e851c50eb262486d1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/73cad3816af2484e851c50eb262486d1"}}, "title": "Loss of Lamin A leads to the nuclear translocation of AGO2 and compromised RNA interference.", "authors": [{"family": "Lobo", "given": "Vivian", "initials": "V"}, {"family": "Nowak", "given": "Iwona", "initials": "I"}, {"family": "Fernandez", "given": "Carola", "initials": "C"}, {"family": "Correa Muler", "given": "Ana Iris", "initials": "AI"}, {"family": "Westholm", "given": "Jakub O", "initials": "JO"}, {"family": "Huang", "given": "Hsiang-Chi", "initials": "HC"}, {"family": "Fabrik", "given": "Ivo", "initials": "I"}, {"family": "Huynh", "given": "Hang T", "initials": "HT"}, {"family": "Shcherbinina", "given": "Evgeniia", "initials": "E"}, {"family": "Poyraz", "given": "Melis", "initials": "M"}, {"family": "H\u00e4rtlova", "given": "Anetta", "initials": "A"}, {"family": "Benhalevy", "given": "Daniel", "initials": "D"}, {"family": "Angeletti", "given": "Davide", "initials": "D", "orcid": "0000-0002-5256-1972", "researcher": {"href": "https://publications.scilifelab.se/researcher/ae59c12bf82b4ad9a8d9ad8603d03d9c.json"}}, {"family": "Sarshad", "given": "Aishe A", "initials": "AA", "orcid": "0000-0001-7153-5959", "researcher": {"href": "https://publications.scilifelab.se/researcher/42c62bd8dbe34b5da39de17d6a2a06ab.json"}}], "type": "journal article", "published": "2024-09-09", "journal": {"title": "Nucleic Acids Res.", "issn": "1362-4962", "issn-l": "0305-1048", "volume": "52", "issue": "16", "pages": "9917-9935"}, "abstract": "In mammals, RNA interference (RNAi) was historically studied as a cytoplasmic event; however, in the last decade, a growing number of reports convincingly show the nuclear localization of the Argonaute (AGO) proteins. Nevertheless, the extent of nuclear RNAi and its implication in biological mechanisms remain to be elucidated. We found that reduced Lamin A levels significantly induce nuclear influx of AGO2 in SHSY5Y neuroblastoma and A375 melanoma cancer cell lines, which normally have no nuclear AGO2. Lamin A KO manifested a more pronounced effect in SHSY5Y cells compared to A375 cells, evident by changes in cell morphology, increased cell proliferation, and oncogenic miRNA expression. Moreover, AGO fPAR-CLIP in Lamin A KO SHSY5Y cells revealed significantly reduced RNAi activity. Further exploration of the nuclear AGO interactome by mass spectrometry identified FAM120A, an RNA-binding protein and known interactor of AGO2. Subsequent FAM120A fPAR-CLIP, revealed that FAM120A co-binds AGO targets and that this competition reduces the RNAi activity. Therefore, loss of Lamin A triggers nuclear AGO2 translocation, FAM120A mediated RNAi impairment, and upregulation of oncogenic miRNAs, facilitating cancer cell proliferation.", "doi": "10.1093/nar/gkae589", "pmid": "38994560", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Short read": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC11381323"}, {"db": "pii", "key": "7712617"}], "notes": [], "created": "2024-10-21T11:21:54.725Z", "modified": "2025-02-28T14:19:11.123Z"}, {"entity": "publication", "iuid": "411c02d828c14370a99a8a2b57b28e22", "links": {"self": {"href": "https://publications.scilifelab.se/publication/411c02d828c14370a99a8a2b57b28e22.json"}, "display": {"href": "https://publications.scilifelab.se/publication/411c02d828c14370a99a8a2b57b28e22"}}, "title": "Male-biased recombination at chromosome ends in a songbird revealed by precisely mapping crossover positions.", "authors": [{"family": "Zhang", "given": "Hongkai", "initials": "H", "orcid": "0000-0001-7371-9612", "researcher": {"href": "https://publications.scilifelab.se/researcher/33b4db2c681b400c9106f8d27b6fb714.json"}}, {"family": "Lundberg", "given": "Max", "initials": "M", "orcid": "0000-0002-1895-3622", "researcher": {"href": "https://publications.scilifelab.se/researcher/5b6a6dafa8fe4371ab26ed02ca5a550c.json"}}, {"family": "Ponnikas", "given": "Suvi", "initials": "S", "orcid": "0000-0003-3526-2118", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ddd324bbfbb4833b25ba6dfe4c7dcb4.json"}}, {"family": "Hasselquist", "given": "Dennis", "initials": "D", "orcid": "0000-0002-0056-6616", "researcher": {"href": "https://publications.scilifelab.se/researcher/73a24d358af64f22b81735f577c33bbb.json"}}, {"family": "Hansson", "given": "Bengt", "initials": "B", "orcid": "0000-0001-6694-8169", "researcher": {"href": "https://publications.scilifelab.se/researcher/01f0144e207c41dcbc4d5aec68690e4b.json"}}], "type": "journal article", "published": "2024-09-04", "journal": {"title": "G3 (Bethesda)", "issn": "2160-1836", "volume": "14", "issue": "9", "issn-l": "2160-1836"}, "abstract": "Recombination plays a crucial role in evolution by generating novel haplotypes and disrupting linkage between genes, thereby enhancing the efficiency of selection. Here, we analyze the genomes of 12 great reed warblers (Acrocephalus arundinaceus) in a 3-generation pedigree to identify precise crossover positions along the chromosomes. We located more than 200 crossovers and found that these were highly concentrated toward the telomeric ends of the chromosomes. Apart from this major pattern in the recombination landscape, we found significantly higher frequencies of crossovers in genic compared with intergenic regions, and in exons compared with introns. Moreover, while the number of recombination events was similar between the sexes, the crossovers were located significantly closer to the ends of paternal compared with maternal chromosomes. In conclusion, our study of the great reed warbler revealed substantial variation in crossover frequencies within chromosomes, with a distinct bias toward the sub-telomeric regions, particularly on the paternal side. These findings emphasize the importance of thoroughly screening the entire length of chromosomes to characterize the recombination landscape and uncover potential sex-biases in recombination.", "doi": "10.1093/g3journal/jkae150", "pmid": "38985659", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Short read": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11373659"}, {"db": "pii", "key": "7710635"}], "notes": [], "created": "2024-10-21T11:19:13.917Z", "modified": "2024-11-25T10:23:45.131Z"}, {"entity": "publication", "iuid": "74e6bcf9f810455aafeb36c2253b4848", "links": {"self": {"href": "https://publications.scilifelab.se/publication/74e6bcf9f810455aafeb36c2253b4848.json"}, "display": {"href": "https://publications.scilifelab.se/publication/74e6bcf9f810455aafeb36c2253b4848"}}, "title": "Gene-based association analysis of a large patient cohort provides insights into genetics of atypical femur fractures.", "authors": [{"family": "Zhou", "given": "Wei", "initials": "W", "orcid": "0000-0002-6748-6303", "researcher": {"href": "https://publications.scilifelab.se/researcher/6f7e9b3a6ffa45dba854cb6acf59739b.json"}}, {"family": "\u00c5s", "given": "Joel", "initials": "J"}, {"family": "Shore-Lorenti", "given": "Catherine", "initials": "C"}, {"family": "Nguyen", "given": "Hanh H", "initials": "HH", "orcid": "0000-0002-8846-6168", "researcher": {"href": "https://publications.scilifelab.se/researcher/6a4cb30d23e54b8c8b328859ead81ba7.json"}}, {"family": "van de Laarschot", "given": "Denise M", "initials": "DM"}, {"family": "Sztal-Mazer", "given": "Shoshana", "initials": "S"}, {"family": "Grill", "given": "Vivian", "initials": "V"}, {"family": "Girgis", "given": "Christian M", "initials": "CM"}, {"family": "Stricker", "given": "Bruno H Ch", "initials": "BHC"}, {"family": "van der Eerden", "given": "Bram C J", "initials": "BCJ"}, {"family": "Thakker", "given": "Rajesh V", "initials": "RV"}, {"family": "Appelman-Dijkstra", "given": "Natasha M", "initials": "NM", "orcid": "0000-0001-5035-127X", "researcher": {"href": "https://publications.scilifelab.se/researcher/5f26fbf2e8d14f8ebf65acd9e22d7b41.json"}}, {"family": "Wadelius", "given": "Mia", "initials": "M"}, {"family": "Clifton-Bligh", "given": "Roderick J", "initials": "RJ"}, {"family": "Hallberg", "given": "P\u00e4r", "initials": "P"}, {"family": "Verkerk", "given": "Annemieke J M H", "initials": "AJMH"}, {"family": "van Rooij", "given": "Jeroen G J", "initials": "JGJ"}, {"family": "Ebeling", "given": "Peter R", "initials": "PR"}, {"family": "Zillikens", "given": "M Carola", "initials": "MC", "orcid": "0000-0001-9186-3423", "researcher": {"href": "https://publications.scilifelab.se/researcher/8c71c257a4de4ac7b59381237a0fa500.json"}}], "type": "journal article", "published": "2024-09-02", "journal": {"title": "J. Bone Miner. Res.", "issn": "1523-4681", "volume": "39", "issue": "9", "pages": "1315-1326", "issn-l": "0884-0431"}, "abstract": "Several small genetic association studies have been conducted for atypical femur fracture (AFF) without replication of results. We assessed previously implicated and novel genes associated with AFFs in a larger set of unrelated AFF cases using whole exome sequencing (WES). We performed gene-based association analysis on 139 European AFF cases and 196 controls matched for bisphosphonate use. We tested all rare, protein-altering variants using both candidate gene and hypothesis-free approaches. In the latter, genes suggestively associated with AFFs (uncorrected p-values <.01) were investigated in a Swedish whole-genome sequencing replication study and assessed in 46 non-European cases. In the candidate gene analysis, PLOD2 showed a suggestive signal. The hypothesis-free approach revealed 10 tentative associations, with XRN2, SORD, and PLOD2 being the most likely candidates for AFF. XRN2 and PLOD2 showed consistent direction of effect estimates in the replication analysis, albeit not statistically significant. Three SNPs associated with SORD expression according to the GTEx portal were in linkage disequilibrium (R2 \u2265 0.2) with an SNP previously reported in a genome-wide association study of AFF. The prevalence of carriers of variants for both PLOD2 and SORD was higher in Asian versus European cases. While we did not identify genes enriched for damaging variants, we found suggestive evidence of a role for XRN2, PLOD2, and SORD, which requires further investigation. Our findings indicate that genetic factors responsible for AFFs are not widely shared among AFF cases. The study provides a stepping-stone for future larger genetic studies of AFF.", "doi": "10.1093/jbmr/zjae122", "pmid": "39126371", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Short read": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11371903"}, {"db": "pii", "key": "7731319"}], "notes": [], "created": "2024-10-21T11:12:51.933Z", "modified": "2024-10-21T11:13:04.359Z"}, {"entity": "publication", "iuid": "04e23b32f608475991bc284705d024a8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/04e23b32f608475991bc284705d024a8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/04e23b32f608475991bc284705d024a8"}}, "title": "Transcriptomic and functional analyses on a Botrytis cinerea multidrug-resistant (MDR) strain provides new insights into the potential molecular mechanisms of MDR and fitness.", "authors": [{"family": "Sofianos", "given": "Georgios", "initials": "G", "orcid": "0009-0002-2678-7158", "researcher": {"href": "https://publications.scilifelab.se/researcher/6caa00e6738e4dfaa70832c456ddc6e6.json"}}, {"family": "Piombo", "given": "Edoardo", "initials": "E", "orcid": "0000-0003-2830-1967", "researcher": {"href": "https://publications.scilifelab.se/researcher/4ff26b84d14643f3ae4e45a23cd2107b.json"}}, {"family": "Dubey", "given": "Mukesh", "initials": "M", "orcid": "0000-0001-7393-366X", "researcher": {"href": "https://publications.scilifelab.se/researcher/da047e9540e344cc93b54a96d5c82b72.json"}}, {"family": "Karlsson", "given": "Magnus", "initials": "M", "orcid": "0000-0001-6098-138X", "researcher": {"href": "https://publications.scilifelab.se/researcher/34e4b8bad4e34912b011f2ead759b422.json"}}, {"family": "Karaoglanidis", "given": "George", "initials": "G", "orcid": "0000-0002-7413-2052", "researcher": {"href": "https://publications.scilifelab.se/researcher/477fa9557e904366aabb7d7b6b53e4d6.json"}}, {"family": "Tzelepis", "given": "Georgios", "initials": "G", "orcid": "0000-0001-6144-2185", "researcher": {"href": "https://publications.scilifelab.se/researcher/60b2114dba0640d3aeecba0c4e729ce0.json"}}], "type": "journal article", "published": "2024-09-00", "journal": {"title": "Mol. Plant Pathol.", "issn": "1364-3703", "volume": "25", "issue": "9", "pages": "e70004", "issn-l": null}, "abstract": "Botrytis cinerea is a notorious pathogen causing pre- and post-harvest spoilage in many economically important crops. Excessive application of site-specific fungicides to control the pathogen has led to the selection of strains possessing target site alterations associated with resistance to these fungicides and/or strains overexpressing efflux transporters associated with multidrug resistance (MDR). MDR in B. cinerea has been correlated with the overexpression of atrB and mfsM2, encoding an ATP-binding cassette (ABC) and a major facilitator superfamily (MFS) transporter, respectively. However, it remains unknown whether other transporters may also contribute to the MDR phenotype. In the current study, the transcriptome of a B. cinerea multidrug-resistant (MDR) field strain was analysed upon exposure to the fungicide fludioxonil, and compared to the B05.10 reference strain. The transcriptome of this field strain displayed significant differences as compared to B05.10, including genes involved in sugar membrane transport, toxin production and virulence. Among the induced genes in the field strain, even before exposure to fludioxonil, were several putatively encoding ABC and MFS transmembrane transporters. Overexpression of a highly induced MFS transporter gene in the B05.10 strain led to an increased tolerance to the fungicides fluopyram and boscalid, indicating an involvement in efflux transport of these compounds. Overall, the data from this study give insights towards better understanding the molecular mechanisms involved in MDR and fitness cost, contributing to the development of more efficient control strategies against this pathogen.", "doi": "10.1111/mpp.70004", "pmid": "39244735", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Short read": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11380696"}], "notes": [], "created": "2024-10-21T11:12:58.472Z", "modified": "2024-10-21T11:13:08.829Z"}, {"entity": "publication", "iuid": "41ddca0947d04600adb7ac6263f21f5c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/41ddca0947d04600adb7ac6263f21f5c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/41ddca0947d04600adb7ac6263f21f5c"}}, "title": "Species-genetic diversity correlation in a metacommunity of urban pond invertebrates", "authors": [{"family": "Johansson", "given": "Frank", "initials": "F"}, {"family": "Yildirim", "given": "Yeserin", "initials": "Y"}, {"family": "Hyseni", "given": "Chaz", "initials": "C", "orcid": "0000-0003-2567-8013", "researcher": {"href": "https://publications.scilifelab.se/researcher/7327304d59cb41a7a97cdcba953f9cdc.json"}}, {"family": "Heino", "given": "Jani", "initials": "J"}, {"family": "H\u00f6glund", "given": "Jacob", "initials": "J"}, {"family": "Bini", "given": "Luis Mauricio", "initials": "LM", "orcid": "0000-0003-3398-9399", "researcher": {"href": "https://publications.scilifelab.se/researcher/490cfde8f1824571a07f21bf11ea61f0.json"}}], "type": "journal-article", "published": "2024-09-00", "journal": {"title": "Basic and Applied Ecology", "issn": "1439-1791", "volume": "79", "pages": "114-122", "issn-l": null}, "abstract": null, "doi": "10.1016/j.baae.2024.07.002", "pmid": null, "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Short read": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [], "notes": [], "created": "2024-10-21T11:15:57.869Z", "modified": "2024-10-21T11:15:58.840Z"}, {"entity": "publication", "iuid": "a3c5e0204138422aa03a305231f99f89", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a3c5e0204138422aa03a305231f99f89.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a3c5e0204138422aa03a305231f99f89"}}, "title": "An intronic copy number variation in Syntaxin 17 determines speed of greying and melanoma incidence in Grey horses.", "authors": [{"family": "Rubin", "given": "Carl-Johan", "initials": "CJ", "orcid": "0000-0001-8238-5052", "researcher": {"href": "https://publications.scilifelab.se/researcher/0bd98ada4083444e8336ef3ec53df488.json"}}, {"family": "Hodge", "given": "McKaela", "initials": "M"}, {"family": "Naboulsi", "given": "Rakan", "initials": "R"}, {"family": "Beckman", "given": "Madeleine", "initials": "M"}, {"family": "Bellone", "given": "Rebecca R", "initials": "RR", "orcid": "0000-0001-8838-7227", "researcher": {"href": "https://publications.scilifelab.se/researcher/8c3235fb9bc24da59f4b2685ab0924a4.json"}}, {"family": "Kallenberg", "given": "Angelica", "initials": "A", "orcid": "0000-0001-7993-6597", "researcher": {"href": "https://publications.scilifelab.se/researcher/b86eca5b3e87464ca2e00fc0f1ad44e0.json"}}, {"family": "J'Usrey", "given": "Stephanie", "initials": "S"}, {"family": "Ohmura", "given": "Hajime", "initials": "H"}, {"family": "Seki", "given": "Kazuhiro", "initials": "K"}, {"family": "Furukawa", "given": "Risako", "initials": "R", "orcid": "0009-0002-4673-0845", "researcher": {"href": "https://publications.scilifelab.se/researcher/b5000c3c34a44dcebe85e6c8418b065e.json"}}, {"family": "Ohnuma", "given": "Aoi", "initials": "A"}, {"family": "Davis", "given": "Brian W", "initials": "BW", "orcid": "0000-0002-6121-135X", "researcher": {"href": "https://publications.scilifelab.se/researcher/63981f53ab2e4dc09a4a2a62ae0b7a84.json"}}, {"family": "Tozaki", "given": "Teruaki", "initials": "T", "orcid": "0000-0001-8797-6644", "researcher": {"href": "https://publications.scilifelab.se/researcher/8246b65d8481438885db4d4be0691aaa.json"}}, {"family": "Lindgren", "given": "Gabriella", "initials": "G", "orcid": "0000-0001-6046-9669", "researcher": {"href": "https://publications.scilifelab.se/researcher/a050dea8e99c47fabac28c14fe4daabb.json"}}, {"family": "Andersson", "given": "Leif", "initials": "L", "orcid": "0000-0002-4085-6968", "researcher": {"href": "https://publications.scilifelab.se/researcher/bd3343c12f994b1fabcae23027d3a76d.json"}}], "type": "journal article", "published": "2024-08-29", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "15", "issue": "1", "pages": "7510", "issn-l": "2041-1723"}, "abstract": "The Greying with age phenotype in horses involves loss of hair pigmentation whereas skin pigmentation is not reduced, and a predisposition to melanoma. The causal mutation was initially reported as a duplication of a 4.6 kb intronic sequence in Syntaxin 17. The speed of greying varies considerably among Grey horses. Here we demonstrate the presence of two different Grey alleles, G2 carrying two tandem copies of the duplicated sequence and G3 carrying three. The latter is by far the most common allele, probably due to strong selection for the striking white phenotype. Our results reveal a remarkable dosage effect where the G3 allele is associated with fast greying and high incidence of melanoma whereas G2 is associated with slow greying and low incidence of melanoma. The copy number expansion transforms a weak enhancer to a strong melanocyte-specific enhancer that underlies hair greying (G2 and G3) and a drastically elevated risk of melanoma (G3 only). Our direct pedigree-based observation of the origin of a G2 allele from a G3 allele by copy number contraction demonstrates the dynamic evolution of this locus and provides the ultimate evidence for causality of the copy number variation of the 4.6 kb intronic sequence.", "doi": "10.1038/s41467-024-51898-2", "pmid": "39209879", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Short read": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11362437"}, {"db": "pii", "key": "10.1038/s41467-024-51898-2"}], "notes": [], "created": "2024-10-21T11:17:13.688Z", "modified": "2024-11-25T10:17:52.816Z"}, {"entity": "publication", "iuid": "80a12b9f6cde4b0f81b779dbcdbf29ad", "links": {"self": {"href": "https://publications.scilifelab.se/publication/80a12b9f6cde4b0f81b779dbcdbf29ad.json"}, "display": {"href": "https://publications.scilifelab.se/publication/80a12b9f6cde4b0f81b779dbcdbf29ad"}}, "title": "Polygenic Risk Scores and Twin Concordance for Schizophrenia and Bipolar Disorder.", "authors": [{"family": "Song", "given": "Jie", "initials": "J"}, {"family": "Pasman", "given": "Jo\u00eblle A", "initials": "JA"}, {"family": "Johansson", "given": "Viktoria", "initials": "V"}, {"family": "Kuja-Halkola", "given": "Ralf", "initials": "R"}, {"family": "Harder", "given": "Arvid", "initials": "A"}, {"family": "Karlsson", "given": "Robert", "initials": "R"}, {"family": "Lu", "given": "Yi", "initials": "Y"}, {"family": "Kowalec", "given": "Kaarina", "initials": "K"}, {"family": "Pedersen", "given": "Nancy L", "initials": "NL"}, {"family": "Cannon", "given": "Tyrone D", "initials": "TD"}, {"family": "Hultman", "given": "Christina M", "initials": "CM"}, {"family": "Sullivan", "given": "Patrick F", "initials": "PF"}], "type": "journal article", "published": "2024-08-28", "journal": {"title": "JAMA Psychiatry", "issn": "2168-6238", "issn-l": "2168-622X"}, "abstract": "Schizophrenia and bipolar disorder are highly heritable psychiatric disorders with strong genetic and phenotypic overlap. Twin and molecular methods can be leveraged to predict the shared genetic liability to these disorders.\n\nTo investigate whether twin concordance for psychosis depends on the level of polygenic risk score (PRS) for psychosis and zygosity and compare PRS from cases and controls from several large samples and estimate the twin heritability of psychosis.\n\nIn this case-control study, psychosis PRS were generated from a genome-wide association study (GWAS) combining schizophrenia and bipolar disorder into a single psychosis phenotype and compared between cases and controls from the Schizophrenia and Bipolar Twin Study in Sweden (STAR) project. Further tests were conducted to ascertain if twin concordance for psychosis depended on the mean PRS for psychosis. Structural equation modeling was used to estimate heritability. This study constituted an analysis of existing clinical and population datasets with genotype and/or twin data. Included were twins from the STAR cohort and from the Swedish Twin Registry. Data were collected during the 2006 to 2013 period and analyzed from March 2023 to June 2024.\n\nPRS for psychosis based on the most recent GWAS of combined schizophrenia/bipolar disorder.\n\nPsychosis case status was assessed by clinical interviews and/or Swedish National Register data.\n\nThe final cohort comprised 87 pairs of twins with 1 or both affected and 59 unaffected pairs from the STAR project (for a total of 292 twins) as well as 443 pairs with 1 or both affected and 20 913 unaffected pairs from the Swedish Twin Registry. Among the 292 twins (mean [SD] birth year, 1960 [10.8] years; 158 female [54.1%]; 134 male [45.9%]), 134 were monozygotic twins, and 158 were dyzygotic twins. PRS for psychosis was higher in cases than in controls and associated with twin concordance for psychosis (1-SD increase in PRS, odds ratio [OR], 2.12; 95% CI, 1.23-3.87 on case status in monozygotic twins and OR, 2.74; 95% CI, 1.56-5.30 in dizygotic twins). The association between PRS for psychosis and concordance was not modified by zygosity. The twin heritability was estimated at 0.73 (95% CI, 0.30-1.00), which overlapped with the estimate in the full Swedish Twin Registry (0.69; 95% CI, 0.43-0.85).\n\nIn this case-control study, using the natural experiment of twins, results suggest that twins with greater inherited liability for psychosis were more likely to have an affected co-twin. Results from twin and molecular designs largely aligned. Even as illness vulnerability is not solely genetic, PRS carried predictive power for psychosis even in a modest sample size.", "doi": "10.1001/jamapsychiatry.2024.2406", "pmid": "39196586", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI SNP genotyping": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11359115"}, {"db": "pii", "key": "2822688"}], "notes": [], "created": "2024-10-21T11:14:59.762Z", "modified": "2024-10-21T11:14:59.771Z"}, {"entity": "publication", "iuid": "e25c443cc2a84c89b1642a768afa88b0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e25c443cc2a84c89b1642a768afa88b0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e25c443cc2a84c89b1642a768afa88b0"}}, "title": "BaTwa populations from Zambia retain ancestry of past hunter-gatherer groups.", "authors": [{"family": "Breton", "given": "Gwenna", "initials": "G", "orcid": "0000-0002-4100-9963", "researcher": {"href": "https://publications.scilifelab.se/researcher/757353d5314b4c20ac2ef4833dd207d9.json"}}, {"family": "Barham", "given": "Lawrence", "initials": "L"}, {"family": "Mudenda", "given": "George", "initials": "G"}, {"family": "Soodyall", "given": "Himla", "initials": "H"}, {"family": "Schlebusch", "given": "Carina M", "initials": "CM", "orcid": "0000-0002-8160-9621", "researcher": {"href": "https://publications.scilifelab.se/researcher/682f10853c1145649b8c76680605dd9b.json"}}, {"family": "Jakobsson", "given": "Mattias", "initials": "M", "orcid": "0000-0001-7840-7853", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a4abe0fcb20492d9ec849c9fbf58a71.json"}}], "type": "journal article", "published": "2024-08-24", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "15", "issue": "1", "pages": "7307", "issn-l": "2041-1723"}, "abstract": "Sub-equatorial Africa is today inhabited predominantly by Bantu-speaking groups of Western African descent who brought agriculture to the Luangwa valley in eastern Zambia ~2000 years ago. Before their arrival the area was inhabited by hunter-gatherers, who in many cases were subsequently replaced, displaced or assimilated. In Zambia, we know little about the genetic affinities of these hunter-gatherers. We examine ancestry of two isolated communities in Zambia, known as BaTwa and possible descendants of recent hunter-gatherers. We genotype over two million genome-wide SNPs from two BaTwa populations (total of 80 individuals) and from three comparative farming populations to: (i) determine if the BaTwa carry genetic links to past hunter-gatherer-groups, and (ii) characterise the genetic affinities of past Zambian hunter-gatherer-groups. The BaTwa populations do harbour a hunter-gatherer-like genetic ancestry and Western African ancestry. The hunter-gatherer component is a unique local signature, intermediate between current-day Khoe-San ancestry from southern Africa and central African rainforest hunter-gatherer ancestry.", "doi": "10.1038/s41467-024-50733-y", "pmid": "39181874", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI SNP genotyping": "Service", "National Genomics Infrastructure": "Service", "Clinical Genomics Gothenburg": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Clinical Genomics": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC11344834"}, {"db": "pii", "key": "10.1038/s41467-024-50733-y"}], "notes": [], "created": "2024-10-21T11:15:04.878Z", "modified": "2024-11-25T10:17:25.391Z"}, {"entity": "publication", "iuid": "47741b433ff341d898259372903d7f89", "links": {"self": {"href": "https://publications.scilifelab.se/publication/47741b433ff341d898259372903d7f89.json"}, "display": {"href": "https://publications.scilifelab.se/publication/47741b433ff341d898259372903d7f89"}}, "title": "Massively parallel analysis of single-molecule dynamics on next-generation sequencing chips.", "authors": [{"family": "Aguirre Rivera", "given": "J", "initials": "J", "orcid": "0000-0002-5263-3577", "researcher": {"href": "https://publications.scilifelab.se/researcher/f164778943f24897a1fa31ac3c6fd2ce.json"}}, {"family": "Mao", "given": "G", "initials": "G", "orcid": "0000-0001-5841-0991", "researcher": {"href": "https://publications.scilifelab.se/researcher/827d755ddbd24c2ca839364c9e139965.json"}}, {"family": "Sabantsev", "given": "A", "initials": "A", "orcid": "0000-0002-8559-8894", "researcher": {"href": "https://publications.scilifelab.se/researcher/ae73150df15e4730be688fc5137a1389.json"}}, {"family": "Panfilov", "given": "M", "initials": "M", "orcid": "0000-0003-2875-7315", "researcher": {"href": "https://publications.scilifelab.se/researcher/58d227ea91aa4b90915a7e2afeb9283e.json"}}, {"family": "Hou", "given": "Q", "initials": "Q", "orcid": "0009-0007-9296-4788", "researcher": {"href": "https://publications.scilifelab.se/researcher/e1048338ae024e9fbc9d82d79f61ffee.json"}}, {"family": "Lindell", "given": "M", "initials": "M"}, {"family": "Chanez", "given": "C", "initials": "C", "orcid": "0000-0002-3432-4375", "researcher": {"href": "https://publications.scilifelab.se/researcher/0ce66636fd1344819df3518ffa6406ce.json"}}, {"family": "Ritort", "given": "F", "initials": "F", "orcid": "0000-0002-4869-5003", "researcher": {"href": "https://publications.scilifelab.se/researcher/f7a34940c8ae42f1a2381b0b48fe06be.json"}}, {"family": "Jinek", "given": "M", "initials": "M", "orcid": "0000-0002-7601-210X", "researcher": {"href": "https://publications.scilifelab.se/researcher/5b86b5f94bbf4b87849dd4d8cebf80f8.json"}}, {"family": "Deindl", "given": "S", "initials": "S", "orcid": "0000-0001-6807-8654", "researcher": {"href": "https://publications.scilifelab.se/researcher/2e45e8288a3445e2b346f29b73141738.json"}}], "type": "journal article", "published": "2024-08-23", "journal": {"title": "Science", "issn": "1095-9203", "issn-l": "0036-8075", "volume": "385", "issue": "6711", "pages": "892-898"}, "abstract": "Single-molecule techniques are ideally poised to characterize complex dynamics but are typically limited to investigating a small number of different samples. However, a large sequence or chemical space often needs to be explored to derive a comprehensive understanding of complex biological processes. Here we describe multiplexed single-molecule characterization at the library scale (MUSCLE), a method that combines single-molecule fluorescence microscopy with next-generation sequencing to enable highly multiplexed observations of complex dynamics. We comprehensively profiled the sequence dependence of DNA hairpin properties and Cas9-induced target DNA unwinding-rewinding dynamics. The ability to explore a large sequence space for Cas9 allowed us to identify a number of target sequences with unexpected behaviors. We envision that MUSCLE will enable the mechanistic exploration of many fundamental biological processes.", "doi": "10.1126/science.adn5371", "pmid": "39172826", "labels": {"NGI Short read": "Technology development", "NGI Uppsala (SNP&SEQ Technology Platform)": "Technology development", "National Genomics Infrastructure": "Technology development"}, "xrefs": [], "notes": [], "created": "2024-08-23T12:11:46.194Z", "modified": "2024-11-05T18:25:16.868Z"}, {"entity": "publication", "iuid": "5b55070b76c24485b9ebf1088919dd92", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5b55070b76c24485b9ebf1088919dd92.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5b55070b76c24485b9ebf1088919dd92"}}, "title": "CDK8 of the mediator kinase module connects leaf development to the establishment of correct stomata patterning by regulating the levels of the transcription factor SPEECHLESS (SPCH).", "authors": [{"family": "Hermida-Carrera", "given": "Carmen", "initials": "C", "orcid": "0000-0003-3272-3054", "researcher": {"href": "https://publications.scilifelab.se/researcher/2623d07dbfa54495aa50ddb18c8fd77a.json"}}, {"family": "Vergara", "given": "Alexander", "initials": "A"}, {"family": "Cervela-Cardona", "given": "Luis", "initials": "L", "orcid": "0000-0002-7293-4473", "researcher": {"href": "https://publications.scilifelab.se/researcher/3afcbfea5e0d4fc0bb91e2954105a29e.json"}}, {"family": "Jin", "given": "Xu", "initials": "X"}, {"family": "Bj\u00f6rklund", "given": "Stefan", "initials": "S"}, {"family": "Strand", "given": "\u00c5sa", "initials": "\u00c5", "orcid": "0000-0001-6664-0471", "researcher": {"href": "https://publications.scilifelab.se/researcher/a6cf82047f9d47bd863874878c1d0b2a.json"}}], "type": "journal article", "published": "2024-08-23", "journal": {"title": "Plant Cell Environ.", "issn": "1365-3040", "issn-l": "0140-7791"}, "abstract": "The components of the mediator kinase module are highly conserved across all eukaryotic lineages, and cyclin-dependent kinase 8 (CDK8) is essential for correct cell proliferation and differentiation in diverse eukaryotic systems. We show that CDK8 couples leaf development with the establishment of correct stomata patterning for prevailing CO2 conditions. In Arabidopsis, the basic helix-loop-helix (bHLH) transcription factor SPEECHLESS (SPCH) controls cellular entry into the stomatal cell lineage, and CDK8 interacts with and phosphorylates SPCH, controlling SPCH protein levels and thereby also expression of the SPCH target genes encoding key regulators of cell fate and asymmetric cell divisions. The lack of the CDK8-mediated control of SPCH results in an increased number of meristemoid and guard mother cells, and increased stomata index in the cdk8 mutants. Increasing atmospheric CO2 concentrations trigger a developmental programme controlling cell entry into stomatal lineage by limiting the asymmetric divisions. In cdk8, the number of meristemoids and guard mother cells remains the same under ambient and high CO2 concentrations, as the accumulated levels of SPCH caused by the lack of CDK8 appear to override the negative regulation of increased CO2. Thus, our work provides novel mechanistic understanding of how plants alter critical leaf properties in response to increasing atmospheric CO2.", "doi": "10.1111/pce.15102", "pmid": "39177450", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Short read": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [], "notes": [], "created": "2024-10-21T11:25:58.331Z", "modified": "2024-10-21T11:25:58.481Z"}, {"entity": "publication", "iuid": "fcbd7b36b40943fc8cdd7edffb61ddc6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/fcbd7b36b40943fc8cdd7edffb61ddc6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/fcbd7b36b40943fc8cdd7edffb61ddc6"}}, "title": "FOXO-regulated OSER1 reduces oxidative stress and extends lifespan in multiple species.", "authors": [{"family": "Song", "given": "Jiangbo", "initials": "J", "orcid": "0000-0002-1349-632X", "researcher": {"href": "https://publications.scilifelab.se/researcher/456a6f81be6a405f9d611180a3a2ab11.json"}}, {"family": "Li", "given": "Zhiquan", "initials": "Z", "orcid": "0000-0003-3253-7606", "researcher": {"href": "https://publications.scilifelab.se/researcher/3b4fd9aa55244f45bb6fb5aa065491b0.json"}}, {"family": "Zhou", "given": "Lei", "initials": "L", "orcid": "0000-0002-6101-6669", "researcher": {"href": "https://publications.scilifelab.se/researcher/3f17a6beaee1412d8944e6a3866147da.json"}}, {"family": "Chen", "given": "Xin", "initials": "X", "orcid": "0000-0001-8968-2711", "researcher": {"href": "https://publications.scilifelab.se/researcher/e11213ffc2174216aa1d9aad2d4c182c.json"}}, {"family": "Sew", "given": "Wei Qi Guinevere", "initials": "WQG"}, {"family": "Herranz", "given": "H\u00e9ctor", "initials": "H"}, {"family": "Ye", "given": "Zilu", "initials": "Z", "orcid": "0000-0001-8829-6579", "researcher": {"href": "https://publications.scilifelab.se/researcher/9dafd75832df4a1ba72f6e8df4fbedc1.json"}}, {"family": "Olsen", "given": "Jesper Velgaard", "initials": "JV", "orcid": "0000-0002-4747-4938", "researcher": {"href": "https://publications.scilifelab.se/researcher/c537b77eb960461f8d087aa5aeaa1f71.json"}}, {"family": "Li", "given": "Yuan", "initials": "Y", "orcid": "0000-0001-8275-2916", "researcher": {"href": "https://publications.scilifelab.se/researcher/1fc11bfbd9b243dcb13459b2ebc006a1.json"}}, {"family": "Nygaard", "given": "Marianne", "initials": "M", "orcid": "0000-0003-0703-2665", "researcher": {"href": "https://publications.scilifelab.se/researcher/1d68eda16735460d81993dc39006d5a5.json"}}, {"family": "Christensen", "given": "Kaare", "initials": "K", "orcid": "0000-0002-5429-5292", "researcher": {"href": "https://publications.scilifelab.se/researcher/e79ea43d09544efc95351b52ac682910.json"}}, {"family": "Tong", "given": "Xiaoling", "initials": "X", "orcid": "0000-0002-2649-899X", "researcher": {"href": "https://publications.scilifelab.se/researcher/f5f43ec02e48493ba6898d502abf972e.json"}}, {"family": "Bohr", "given": "Vilhelm A", "initials": "VA", "orcid": "0000-0003-4823-6429", "researcher": {"href": "https://publications.scilifelab.se/researcher/2623c8d5da76485198b91ac4b43cfd10.json"}}, {"family": "Rasmussen", "given": "Lene Juel", "initials": "LJ", "orcid": "0000-0001-6864-963X", "researcher": {"href": "https://publications.scilifelab.se/researcher/989eb06874c845979459f2f09068f4c8.json"}}, {"family": "Dai", "given": "Fangyin", "initials": "F", "orcid": "0000-0002-0215-2177", "researcher": {"href": "https://publications.scilifelab.se/researcher/aaa81aaa281d4970bfe587d012478d03.json"}}], "type": "journal article", "published": "2024-08-21", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "15", "issue": "1", "pages": "7144", "issn-l": "2041-1723"}, "abstract": "FOXO transcription factors modulate aging-related pathways and influence longevity in multiple species, but the transcriptional targets that mediate these effects remain largely unknown. Here, we identify an evolutionarily conserved FOXO target gene, Oxidative stress-responsive serine-rich protein 1 (OSER1), whose overexpression extends lifespan in silkworms, nematodes, and flies, while its depletion correspondingly shortens lifespan. In flies, overexpression of OSER1 increases resistance to oxidative stress, starvation, and heat shock, while OSER1-depleted flies are more vulnerable to these stressors. In silkworms, hydrogen peroxide both induces and is scavenged by OSER1 in vitro and in vivo. Knockdown of OSER1 in Caenorhabditis elegans leads to increased ROS production and shorter lifespan, mitochondrial fragmentation, decreased ATP production, and altered transcription of mitochondrial genes. Human proteomic analysis suggests that OSER1 plays roles in oxidative stress response, cellular senescence, and reproduction, which is consistent with the data and suggests that OSER1 could play a role in fertility in silkworms and nematodes. Human studies demonstrate that polymorphic variants in OSER1 are associated with human longevity. In summary, OSER1 is an evolutionarily conserved FOXO-regulated protein that improves resistance to oxidative stress, maintains mitochondrial functional integrity, and increases lifespan in multiple species. Additional studies will clarify the role of OSER1 as a critical effector of healthy aging.", "doi": "10.1038/s41467-024-51542-z", "pmid": "39164296", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI SNP genotyping": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11336091"}, {"db": "pii", "key": "10.1038/s41467-024-51542-z"}], "notes": [], "created": "2024-10-21T11:23:02.650Z", "modified": "2024-10-21T11:23:03.401Z"}, {"entity": "publication", "iuid": "69d3c968e92644688b9b1341bc588cc9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/69d3c968e92644688b9b1341bc588cc9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/69d3c968e92644688b9b1341bc588cc9"}}, "title": "Decrease due to pollution in the rhizosphere microbial diversity can be amended by supplementation from adapted plants of another species.", "authors": [{"family": "Fetsiukh", "given": "Anastasiia", "initials": "A"}, {"family": "Pall", "given": "Taavi", "initials": "T"}, {"family": "Timmusk", "given": "Salme", "initials": "S"}], "type": "journal article", "published": "2024-08-13", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "14", "issue": "1", "pages": "18806", "issn-l": "2045-2322"}, "abstract": "Manipulating the rhizosphere microbiome to enhance plant stress tolerance is an environmentally friendly technology and a renewable resource to restore degraded environments. Here we suggest a sustainable bioremediation strategy on the example of Stebnyk mine tailings storage. We consider Salicornia europaea rhizosphere community, and the ability of the phytoremediation plant Salix viminalis to recruit its beneficial microbiome to mediate the pollution stress at the Stebnyk mine tailings storage. The tailings contain large amounts of brine salts and heavy metals that contaminate the ground water and surrounding areas, changing soil biogeochemistry and causing increased erosion. The species richness of the endophytic bacterial community of S. viminalis roots was assessed based on observed OTUs, Shannon-InvSimpson, and evenness index. Our results obtained using the plant-based enrichment strategy show that biodiversity was decreased across the contamination zones and that S. europaea supplementation significantly increased the species richness. Our results also indicate that the number of dominating bacteria was not changed across zones in both S. europaea-treated and untreated bacterial populations, and that the decrease in richness was mainly caused by the low abundant bacterial OTUs. The importance of selecting the bioremediation strains that are likely to harbor a reservoir of genetic traits that aid in bioremediation function from the target environment is discussed.", "doi": "10.1038/s41598-024-68123-1", "pmid": "39138231", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Short read": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11322436"}, {"db": "pii", "key": "10.1038/s41598-024-68123-1"}], "notes": [], "created": "2024-10-21T11:17:11.546Z", "modified": "2024-10-21T11:17:11.551Z"}, {"entity": "publication", "iuid": "b9c616c6a3f44619b2d580f86240faab", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b9c616c6a3f44619b2d580f86240faab.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b9c616c6a3f44619b2d580f86240faab"}}, "title": "The genetic architecture of dog ownership: large-scale genome-wide association study in 97,552 European-ancestry individuals.", "authors": [{"family": "Gong", "given": "Tong", "initials": "T", "orcid": "0000-0002-6887-9432", "researcher": {"href": "https://publications.scilifelab.se/researcher/33d5234e26c34fbbbe299a4a9af3b16d.json"}}, {"family": "Karlsson", "given": "Robert", "initials": "R", "orcid": "0000-0002-8949-2587", "researcher": {"href": "https://publications.scilifelab.se/researcher/9df14bf33f3342408d624caa70d45b7c.json"}}, {"family": "Yao", "given": "Shuyang", "initials": "S"}, {"family": "Magnusson", "given": "Patrik K E", "initials": "PKE"}, {"family": "Ajnakina", "given": "Olesya", "initials": "O", "orcid": "0000-0003-3987-1236", "researcher": {"href": "https://publications.scilifelab.se/researcher/fdf03781a7ad467299c57c202bb6ed3e.json"}}, {"family": "Steptoe", "given": "Andrew", "initials": "A", "orcid": "0000-0001-7808-4943", "researcher": {"href": "https://publications.scilifelab.se/researcher/3b9a9b27d525428a86117f449268b779.json"}}, {"family": "Bhatta", "given": "Laxmi", "initials": "L"}, {"family": "Brumpton", "given": "Ben", "initials": "B"}, {"family": "Kumar", "given": "Ashish", "initials": "A"}, {"family": "M\u00e9len", "given": "Erik", "initials": "E"}, {"family": "23andMe research team\n", "given": "", "initials": ""}, {"family": "Lin", "given": "Keng-Han", "initials": "KH"}, {"family": "Tian", "given": "Chao", "initials": "C"}, {"family": "Fall", "given": "Tove", "initials": "T"}, {"family": "Almqvist", "given": "Catarina", "initials": "C", "orcid": "0000-0002-1045-1898", "researcher": {"href": "https://publications.scilifelab.se/researcher/c7b0899897f046499272a916fd0c6ba5.json"}}], "type": "journal article", "published": "2024-08-07", "journal": {"title": "G3 (Bethesda)", "issn": "2160-1836", "volume": "14", "issue": "8", "issn-l": "2160-1836"}, "abstract": "Dog ownership has been associated with several complex traits, and there is evidence of genetic influence. We performed a genome-wide association study of dog ownership through a meta-analysis of 31,566 Swedish twins in 5 discovery cohorts and an additional 65,986 European-ancestry individuals in 3 replication cohorts from Sweden, Norway, and the United Kingdom. Association tests with >7.4 million single-nucleotide polymorphisms were meta-analyzed using a fixed effect model after controlling for population structure and relatedness. We identified 2 suggestive loci using discovery cohorts, which did not reach genome-wide significance after meta-analysis with replication cohorts. Single-nucleotide polymorphism-based heritability of dog ownership using linkage disequilibrium score regression was estimated at 0.123 (CI 0.038-0.207) using the discovery cohorts and 0.018 (CI -0.002 to 0.039) when adding in replication cohorts. Negative genetic correlation with complex traits including type 2 diabetes, depression, neuroticism, and asthma was only found using discovery summary data. Furthermore, we did not identify any genes/gene-sets reaching even a suggestive level of significance. This genome-wide association study does not, by itself, provide clear evidence on common genetic variants that influence dog ownership among European-ancestry individuals.", "doi": "10.1093/g3journal/jkae116", "pmid": "38820132", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI SNP genotyping": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11304603"}, {"db": "pii", "key": "7686067"}], "notes": [], "created": "2024-10-21T11:18:16.973Z", "modified": "2024-10-21T11:18:17.203Z"}, {"entity": "publication", "iuid": "629725b0fd4d4f85bd4cbe31d33f7570", "links": {"self": {"href": "https://publications.scilifelab.se/publication/629725b0fd4d4f85bd4cbe31d33f7570.json"}, "display": {"href": "https://publications.scilifelab.se/publication/629725b0fd4d4f85bd4cbe31d33f7570"}}, "title": "Why we thrive beneath a northern sky - genomic signals of selection in apple for adaptation to northern Sweden.", "authors": [{"family": "Skytte Af S\u00e4tra", "given": "J", "initials": "J", "orcid": "0000-0002-2827-4842", "researcher": {"href": "https://publications.scilifelab.se/researcher/00b323220517477eb3c4acda1bb64c81.json"}}, {"family": "Garkava-Gustavsson", "given": "L", "initials": "L"}, {"family": "Ingvarsson", "given": "P K", "initials": "PK", "orcid": "0000-0001-9225-7521", "researcher": {"href": "https://publications.scilifelab.se/researcher/52a2c210ff754465a69f839b40fe8312.json"}}], "type": "journal article", "published": "2024-08-00", "journal": {"title": "Heredity (Edinb)", "issn": "1365-2540", "volume": "133", "issue": "2", "pages": "67-77", "issn-l": "0018-067X"}, "abstract": "Good understanding of the genomic regions underlying adaptation of apple to boreal climates is needed to facilitate efficient breeding of locally adapted apple cultivars. Proper infrastructure for phenotyping and evaluation is essential for identification of traits responsible for adaptation, and dissection of their genetic composition. However, such infrastructure is costly and currently not available for the boreal zone of northern Sweden. Therefore, we used historical pomological data on climate adaptation of 59 apple cultivars and whole genome sequencing to identify genomic regions that have undergone historical selection among apple cultivars recommended for cultivation in northern Sweden. We found the apple collection to be composed of two ancestral groups that are largely concordant with the grouping into 'hardy' and 'not hardy' cultivars based on the pomological literature. Using a number of genome-wide scans for signals of selection, we obtained strong evidence of positive selection at a genomic region around 29 MbHFTH1 of chromosome 1 among apple cultivars in the 'hardy' group. Using phased genotypic data from the 20 K apple Infinium\u00ae SNP array, we identified haplotypes associated with the two cultivar groups and traced transmission of these haplotypes through the pedigrees of some apple cultivars. This demonstrates that historical data from pomological literature can be analyzed by population genomic approaches as a step towards revealing the genomic control of a key property for a horticultural niche market. Such knowledge is needed to facilitate efficient breeding strategies for development of locally adapted apple cultivars in the future. The current study illustrates the response to a very strong selective pressure imposed on tree crops by climatic factors, and the importance of genetic research on this topic and feasibility of breeding efforts in the light of the ongoing climate change.", "doi": "10.1038/s41437-024-00693-2", "pmid": "38834867", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Short read": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11286948"}, {"db": "pii", "key": "10.1038/s41437-024-00693-2"}], "notes": [], "created": "2024-10-21T11:08:23.983Z", "modified": "2024-11-25T10:15:45.034Z"}, {"entity": "publication", "iuid": "7cdd71fc9b3a4e96bbece5625ab29d9e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7cdd71fc9b3a4e96bbece5625ab29d9e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7cdd71fc9b3a4e96bbece5625ab29d9e"}}, "title": "Selection against domestication alleles in introduced rabbit populations.", "authors": [{"family": "Andrade", "given": "Pedro", "initials": "P", "orcid": "0000-0003-2540-2471", "researcher": {"href": "https://publications.scilifelab.se/researcher/beb2336f18d94c57bbf9089dd6d06ccf.json"}}, {"family": "Alves", "given": "Joel M", "initials": "JM", "orcid": "0000-0001-6138-9134", "researcher": {"href": "https://publications.scilifelab.se/researcher/118178b7f76e4b5ba3ec39914aee7b57.json"}}, {"family": "Pereira", "given": "Paulo", "initials": "P", "orcid": "0000-0001-9519-7691", "researcher": {"href": "https://publications.scilifelab.se/researcher/c8913fec8d89466480fa55e47e47e2ce.json"}}, {"family": "Rubin", "given": "Carl-Johan", "initials": "CJ", "orcid": "0000-0001-8238-5052", "researcher": {"href": "https://publications.scilifelab.se/researcher/0bd98ada4083444e8336ef3ec53df488.json"}}, {"family": "Silva", "given": "Eug\u00e9nio", "initials": "E", "orcid": "0000-0002-9680-3494", "researcher": {"href": "https://publications.scilifelab.se/researcher/099c8fd4d8324c5f8e39f8798d680e29.json"}}, {"family": "Sprehn", "given": "C Grace", "initials": "CG", "orcid": "0000-0002-4164-4246", "researcher": {"href": "https://publications.scilifelab.se/researcher/b51f6d45361e4aa187fc74870a38ac3f.json"}}, {"family": "Enbody", "given": "Erik", "initials": "E", "orcid": "0000-0003-1349-628X", "researcher": {"href": "https://publications.scilifelab.se/researcher/7a4df51b279746539cae2fa83c37456d.json"}}, {"family": "Afonso", "given": "Sandra", "initials": "S", "orcid": "0000-0001-7212-991X", "researcher": {"href": "https://publications.scilifelab.se/researcher/ced62caf88e446c796ad9b022517442c.json"}}, {"family": "Faria", "given": "Rui", "initials": "R"}, {"family": "Zhang", "given": "Yexin", "initials": "Y", "orcid": "0000-0001-8253-4951", "researcher": {"href": "https://publications.scilifelab.se/researcher/b5f20139428b4ebf93a8c478dd969264.json"}}, {"family": "Bonino", "given": "Never", "initials": "N"}, {"family": "Duckworth", "given": "Janine A", "initials": "JA"}, {"family": "Garreau", "given": "Herv\u00e9", "initials": "H", "orcid": "0000-0001-6195-1457", "researcher": {"href": "https://publications.scilifelab.se/researcher/e9687c1ad7c04774aadaeb3f22abb034.json"}}, {"family": "Letnic", "given": "Mike", "initials": "M"}, {"family": "Strive", "given": "Tanja", "initials": "T", "orcid": "0000-0003-2971-8406", "researcher": {"href": "https://publications.scilifelab.se/researcher/f0155b46301d490d974c8045f43ba4f6.json"}}, {"family": "Thulin", "given": "Carl-Gustaf", "initials": "CG", "orcid": "0000-0001-6543-748X", "researcher": {"href": "https://publications.scilifelab.se/researcher/b71a9794d2f94bdea1793abe41790d69.json"}}, {"family": "Queney", "given": "Guillaume", "initials": "G"}, {"family": "Villafuerte", "given": "Rafael", "initials": "R"}, {"family": "Jiggins", "given": "Francis M", "initials": "FM", "orcid": "0000-0001-7470-8157", "researcher": {"href": "https://publications.scilifelab.se/researcher/f3992869d5e249968d550b75307fdc4a.json"}}, {"family": "Ferrand", "given": "Nuno", "initials": "N"}, {"family": "Andersson", "given": "Leif", "initials": "L", "orcid": "0000-0002-4085-6968", "researcher": {"href": "https://publications.scilifelab.se/researcher/bd3343c12f994b1fabcae23027d3a76d.json"}}, {"family": "Carneiro", "given": "Miguel", "initials": "M", "orcid": "0000-0001-9882-7775", "researcher": {"href": "https://publications.scilifelab.se/researcher/b1d62d41fce4469b878ea399d2d0abbf.json"}}], "type": "journal article", "published": "2024-08-00", "journal": {"title": "Nat Ecol Evol", "issn": "2397-334X", "volume": "8", "issue": "8", "pages": "1543-1555", "issn-l": "2397-334X"}, "abstract": "Humans have moved domestic animals around the globe for thousands of years. These have occasionally established feral populations in nature, often with devastating ecological consequences. To understand how natural selection shapes re-adaptation into the wild, we investigated one of the most successful colonizers in history, the European rabbit. By sequencing the genomes of 297 rabbits across three continents, we show that introduced populations exhibit a mixed wild-domestic ancestry. We show that alleles that increased in frequency during domestication were preferentially selected against in novel natural environments. Interestingly, causative mutations for common domestication traits sometimes segregate at considerable frequencies if associated with less drastic phenotypes (for example, coat colour dilution), whereas mutations that are probably strongly maladaptive in nature are absent. Whereas natural selection largely targeted different genomic regions in each introduced population, some of the strongest signals of parallelism overlap genes associated with neuronal or brain function. This limited parallelism is probably explained by extensive standing genetic variation resulting from domestication together with the complex mixed ancestry of introduced populations. Our findings shed light on the selective and molecular mechanisms that enable domestic animals to re-adapt to the wild and provide important insights for the mitigation and management of invasive populations.", "doi": "10.1038/s41559-024-02443-3", "pmid": "38907020", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41559-024-02443-3"}], "notes": [], "created": "2024-11-12T10:54:12.925Z", "modified": "2024-11-25T10:19:02.495Z"}, {"entity": "publication", "iuid": "8b0ca8d9347d4e589bbd155951bd924a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8b0ca8d9347d4e589bbd155951bd924a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8b0ca8d9347d4e589bbd155951bd924a"}}, "title": "Dominance between self-incompatibility alleles determines the mating system of Capsella allopolyploids.", "authors": [{"family": "Duan", "given": "Tianlin", "initials": "T"}, {"family": "Zhang", "given": "Zebin", "initials": "Z"}, {"family": "Genete", "given": "Mathieu", "initials": "M"}, {"family": "Poux", "given": "C\u00e9line", "initials": "C"}, {"family": "Sicard", "given": "Adrien", "initials": "A", "orcid": "0000-0002-4104-6844", "researcher": {"href": "https://publications.scilifelab.se/researcher/559469d6cd9a4435beffc526f2655c5c.json"}}, {"family": "Lascoux", "given": "Martin", "initials": "M", "orcid": "0000-0003-1699-9042", "researcher": {"href": "https://publications.scilifelab.se/researcher/4ad3fadfb69448f397ad3bf55b2d2cb3.json"}}, {"family": "Castric", "given": "Vincent", "initials": "V"}, {"family": "Vekemans", "given": "Xavier", "initials": "X"}], "type": "journal article", "published": "2024-08-00", "journal": {"issn": "2056-3744", "title": "Evolution Letters", "volume": "8", "issue": "4", "pages": "550-560", "issn-l": "2056-3744"}, "abstract": "The shift from outcrossing to self-fertilization is one of the main evolutionary transitions in plants and has broad effects on evolutionary trajectories. In Brassicaceae, the ability to inhibit self-fertilization is controlled by 2 genes, SCR and SRK, tightly linked within the S-locus. A series of small non-coding RNAs also encoded within the S-locus regulates the transcriptional activity of SCR alleles, resulting in a linear dominance hierarchy between them. In Brassicaceae, natural allopolyploid species are often self-compatible (SC) even when one of the progenitor species is self-incompatible, but the reason why polyploid lineages tend to lose self-incompatibility (SI) and the timing of the loss of SI (immediately after ancestral hybridization between the progenitor species, or at a later stage after the formation of allopolyploid lineages) have generally remained elusive. We used a series of synthetic diploid and tetraploid hybrids obtained between self-fertilizing Capsella orientalis and outcrossing Capsella grandiflora to test whether the breakdown of SI could be observed immediately after hybridization, and whether the occurrence of SC phenotypes could be explained by the dominance interactions between S-haplotypes inherited from the parental lineages. We used RNA-sequencing data from young inflorescences to measure allele-specific expression of the SCR gene and infer dominance interactions in the synthetic hybrids. We then evaluated the seed set from autonomous self-pollination in the synthetic hybrids. Our results demonstrate that self-compatibility of the hybrids depends on the relative dominance between S-alleles inherited from the parental species, confirming that SI can be lost instantaneously upon formation of the ancestral allopolyploid lineage. They also confirm that the epigenetic regulation that controls dominance interactions between S-alleles can function between subgenomes in allopolyploids. Together, our results illustrate how a detailed knowledge of the mechanisms controlling SI can illuminate our understanding of the patterns of co-variation between the mating system and changes in ploidy.", "doi": "10.1093/evlett/qrae011", "pmid": "39100231", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11291619"}, {"db": "pii", "key": "qrae011"}, {"db": "figshare", "key": "10.6084/m9.figshare.22567558.v2"}], "notes": [], "created": "2024-05-16T06:32:00.828Z", "modified": "2025-02-28T14:17:25.871Z"}, {"entity": "publication", "iuid": "92996e534bd244ad802a06aba40392a9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/92996e534bd244ad802a06aba40392a9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/92996e534bd244ad802a06aba40392a9"}}, "title": "A multiomic characterization of the leukemia cell line REH using short- and long-read sequencing.", "authors": [{"family": "Lysenkova Wiklander", "given": "Mariya", "initials": "M", "orcid": "0000-0002-0012-2310", "researcher": {"href": "https://publications.scilifelab.se/researcher/48850e5606b9470caa6b130286055388.json"}}, {"family": "Arvidsson", "given": "Gustav", "initials": "G", "orcid": "0000-0001-7396-1820", "researcher": {"href": "https://publications.scilifelab.se/researcher/29beb4f9dd8b460382eab4f916fc1072.json"}}, {"family": "Bunikis", "given": "Ignas", "initials": "I", "orcid": "0009-0008-8375-0451", "researcher": {"href": "https://publications.scilifelab.se/researcher/d2a9c139b7d64681a5712250d3cf63ff.json"}}, {"family": "Lundmark", "given": "Anders", "initials": "A"}, {"family": "Raine", "given": "Amanda", "initials": "A", "orcid": "0000-0002-2775-6516", "researcher": {"href": "https://publications.scilifelab.se/researcher/a97b7df8379f42f0a412fb7c234a6c70.json"}}, {"family": "Marincevic-Zuniga", "given": "Yanara", "initials": "Y", "orcid": "0000-0001-5576-2115", "researcher": {"href": "https://publications.scilifelab.se/researcher/eb045b70f16140b6b6e69476d701012c.json"}}, {"family": "Gezelius", "given": "Henrik", "initials": "H", "orcid": "0000-0002-6242-6344", "researcher": {"href": "https://publications.scilifelab.se/researcher/7ad329767af94f9f9ad2c96771ff01d9.json"}}, {"family": "Bremer", "given": "Anna", "initials": "A"}, {"family": "Feuk", "given": "Lars", "initials": "L", "orcid": "0000-0003-2355-2919", "researcher": {"href": "https://publications.scilifelab.se/researcher/3eb2f826b3554d4b9971bf0766b275c4.json"}}, {"family": "Ameur", "given": "Adam", "initials": "A", "orcid": "0000-0001-6085-6749", "researcher": {"href": "https://publications.scilifelab.se/researcher/e960811513664a78b2804a00ee70f7c3.json"}}, {"family": "Nordlund", "given": "Jessica", "initials": "J", "orcid": "0000-0001-8699-9959", "researcher": {"href": "https://publications.scilifelab.se/researcher/ddf48c9262134821bcc6ce1180049753.json"}}], "type": "journal article", "published": "2024-08-00", "journal": {"title": "Life Sci. Alliance", "issn": "2575-1077", "issn-l": "2575-1077", "volume": "7", "issue": "8", "pages": null}, "abstract": "The B-cell acute lymphoblastic leukemia (ALL) cell line REH, with the t(12;21) ETV6::RUNX1 translocation, is known to have a complex karyotype defined by a series of large-scale chromosomal rearrangements. Taken from a 15-yr-old at relapse, the cell line offers a practical model for the study of pediatric B-ALL. In recent years, short- and long-read DNA and RNA sequencing have emerged as a complement to karyotyping techniques in the resolution of structural variants in an oncological context. Here, we explore the integration of long-read PacBio and Oxford Nanopore whole-genome sequencing, IsoSeq RNA sequencing, and short-read Illumina sequencing to create a detailed genomic and transcriptomic characterization of the REH cell line. Whole-genome sequencing clarified the molecular traits of disrupted ALL-associated genes including CDKN2A, PAX5, BTG1, VPREB1, and TBL1XR1, as well as the glucocorticoid receptor NR3C1 Meanwhile, transcriptome sequencing identified seven fusion genes within the genomic breakpoints. Together, our extensive whole-genome investigation makes high-quality open-source data available to the leukemia genomics community.", "doi": "10.26508/lsa.202302481", "pmid": "38777370", "labels": {"NGI Uppsala (Uppsala Genome Center)": "Collaborative", "NGI Long read": "Collaborative", "National Genomics Infrastructure": "Collaborative", "NGI Uppsala (SNP&SEQ Technology Platform)": "Collaborative", "NGI Short read": "Collaborative", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11111970"}, {"db": "pii", "key": "7/8/e202302481"}], "notes": [], "created": "2024-08-02T11:59:07.510Z", "modified": "2025-02-28T14:23:51.125Z"}, {"entity": "publication", "iuid": "4a894ab59574495e857e2b2155acc78b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4a894ab59574495e857e2b2155acc78b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4a894ab59574495e857e2b2155acc78b"}}, "title": "A pipeline for identification of causal mutations in barley identifies Xantha-j as the chlorophyll synthase gene.", "authors": [{"family": "Stuart", "given": "David", "initials": "D", "orcid": "0000-0001-5624-3608", "researcher": {"href": "https://publications.scilifelab.se/researcher/a18828bd03f04188b454b5ffc62ad106.json"}}, {"family": "Zakhrabekova", "given": "Shakhira", "initials": "S", "orcid": "0000-0002-5309-5459", "researcher": {"href": "https://publications.scilifelab.se/researcher/4ebd0fe7ba0a48d1bb1d7e34a13b6c36.json"}}, {"family": "J\u00f8rgensen", "given": "Morten Egevang", "initials": "ME", "orcid": "0000-0001-6503-0495", "researcher": {"href": "https://publications.scilifelab.se/researcher/569eabce9b404d04adc3d85120140adc.json"}}, {"family": "Dockter", "given": "Christoph", "initials": "C", "orcid": "0000-0001-5923-3667", "researcher": {"href": "https://publications.scilifelab.se/researcher/a7c36daf65a3443aace9f0803a4b1a62.json"}}, {"family": "Hansson", "given": "Mats", "initials": "M", "orcid": "0000-0002-0168-9968", "researcher": {"href": "https://publications.scilifelab.se/researcher/63440c24a3874af18614b26ac550e5cc.json"}}], "type": "journal article", "published": "2024-07-31", "journal": {"title": "Plant Physiol.", "issn": "1532-2548", "volume": "195", "issue": "4", "pages": "2877-2890", "issn-l": "0032-0889"}, "abstract": "Thousands of barley (Hordeum vulgare L.) mutants have been isolated over the last century, and many are stored in gene banks across various countries. In the present work, we developed a pipeline to efficiently identify causal mutations in barley. The pipeline is also efficient for mutations located in centromeric regions. Through bulked segregant analyses using whole genome sequencing of pooled F2 seedlings, we mapped 2 mutations and identified a limited number of candidate genes. We applied the pipeline on F2 mapping populations made from xan-j.59 (unknown mutation) and xan-l.82 (previously known). The Xantha-j (xan-j) gene was identified as encoding chlorophyll synthase, which catalyzes the last step in the chlorophyll biosynthetic pathway: the addition of a phytol moiety to the propionate side chain of chlorophyllide. Key amino acid residues in the active site, including the binding sites of the isoprenoid and chlorophyllide substrates, were analyzed in an AlphaFold2-generated structural model of the barley chlorophyll synthase. Three allelic mutants, xan-j.19, xan-j.59, and xan-j.64, were characterized. While xan-j.19 is a 1 base pair deletion and xan-j.59 is a nonsense mutation, xan-j.64 causes an S212F substitution in chlorophyll synthase. Our analyses of xan-j.64 and treatment of growing barley with clomazone, an inhibitor of chloroplastic isoprenoid biosynthesis, suggest that binding of the isoprenoid substrate is a prerequisite for the stable maintenance of chlorophyll synthase in the plastid. We further suggest that chlorophyll synthase is a sensor for coordinating chlorophyll and isoprenoid biosynthesis.", "doi": "10.1093/plphys/kiae218", "pmid": "38630859", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11288739"}, {"db": "pii", "key": "7649211"}], "notes": [], "created": "2024-11-12T10:48:23.148Z", "modified": "2024-11-25T10:25:51.770Z"}, {"entity": "publication", "iuid": "cb40d036f76546bcaf773bb135db83a3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/cb40d036f76546bcaf773bb135db83a3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/cb40d036f76546bcaf773bb135db83a3"}}, "title": "The rate of W chromosome degeneration across multiple avian neo-sex chromosomes.", "authors": [{"family": "Sigeman", "given": "Hanna", "initials": "H", "orcid": "0000-0002-1457-4174", "researcher": {"href": "https://publications.scilifelab.se/researcher/f75fea472d1d495a92228c50bd63891e.json"}}, {"family": "Downing", "given": "Philip A", "initials": "PA", "orcid": "0000-0002-5286-3153", "researcher": {"href": "https://publications.scilifelab.se/researcher/e004ff0660ee411cb310ab108f29c171.json"}}, {"family": "Zhang", "given": "Hongkai", "initials": "H", "orcid": "0000-0001-7371-9612", "researcher": {"href": "https://publications.scilifelab.se/researcher/33b4db2c681b400c9106f8d27b6fb714.json"}}, {"family": "Hansson", "given": "Bengt", "initials": "B", "orcid": "0000-0001-6694-8169", "researcher": {"href": "https://publications.scilifelab.se/researcher/01f0144e207c41dcbc4d5aec68690e4b.json"}}], "type": "journal article", "published": "2024-07-17", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "14", "issue": "1", "pages": "16548", "issn-l": "2045-2322"}, "abstract": "When sex chromosomes evolve recombination suppression, the sex-limited chromosome (Y/W) commonly degenerate by losing functional genes. The rate of Y/W degeneration is believed to slow down over time as the most essential genes are maintained by purifying selection, but supporting data are scarce especially for ZW systems. Here, we study W degeneration in Sylvioidea songbirds where multiple autosomal translocations to the sex chromosomes, and multiple recombination suppression events causing separate evolutionary strata, have occurred during the last ~ 28.1-4.5 million years (Myr). We show that the translocated regions have maintained 68.3-97.7% of their original gene content, compared to only 4.2% on the much older ancestral W chromosome. By mapping W gene losses onto a dated phylogeny, we estimate an average gene loss rate of 1.0% per Myr, with only moderate variation between four independent lineages. Consistent with previous studies, evolutionarily constrained and haploinsufficient genes were preferentially maintained on W. However, the gene loss rate did not show any consistent association with strata age or with the number of W genes at strata formation. Our study provides a unique account on the pace of W gene loss and reinforces the significance of purifying selection in maintaining essential genes on sex chromosomes.", "doi": "10.1038/s41598-024-66470-7", "pmid": "39020011", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Short read": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11255319"}, {"db": "pii", "key": "10.1038/s41598-024-66470-7"}], "notes": [], "created": "2024-10-21T11:21:49.931Z", "modified": "2024-11-25T10:21:24.059Z"}, {"entity": "publication", "iuid": "95e57751a0274736bc6b15540a8e4885", "links": {"self": {"href": "https://publications.scilifelab.se/publication/95e57751a0274736bc6b15540a8e4885.json"}, "display": {"href": "https://publications.scilifelab.se/publication/95e57751a0274736bc6b15540a8e4885"}}, "title": "DNA methylation of exercise-responsive genes differs between trained and untrained men.", "authors": [{"family": "Geiger", "given": "Carla", "initials": "C"}, {"family": "Needhamsen", "given": "Maria", "initials": "M"}, {"family": "Emanuelsson", "given": "Eric B", "initials": "EB"}, {"family": "Norrbom", "given": "Jessica", "initials": "J"}, {"family": "Steindorf", "given": "Karen", "initials": "K"}, {"family": "Sundberg", "given": "Carl Johan", "initials": "CJ"}, {"family": "Reitzner", "given": "Stefan M", "initials": "SM"}, {"family": "Lindholm", "given": "Malene E", "initials": "ME", "orcid": "0000-0002-5763-7833", "researcher": {"href": "https://publications.scilifelab.se/researcher/f06626001b0e4fc5a81e0801720d6aaf.json"}}], "type": "journal article", "published": "2024-07-04", "journal": {"title": "BMC Biol.", "issn": "1741-7007", "volume": "22", "issue": "1", "pages": "147", "issn-l": "1741-7007"}, "abstract": "Physical activity is well known for its multiple health benefits and although the knowledge of the underlying molecular mechanisms is increasing, our understanding of the role of epigenetics in long-term training adaptation remains incomplete. In this intervention study, we included individuals with a history of > 15 years of regular endurance or resistance training compared to age-matched untrained controls performing endurance or resistance exercise. We examined skeletal muscle DNA methylation of genes involved in key adaptation processes, including myogenesis, gene regulation, angiogenesis and metabolism.\n\nA greater number of differentially methylated regions and differentially expressed genes were identified when comparing the endurance group with the control group than in the comparison between the strength group and the control group at baseline. Although the cellular composition of skeletal muscle samples was generally consistent across groups, variations were observed in the distribution of muscle fiber types. Slow-twitch fiber type genes MYH7 and MYL3 exhibited lower promoter methylation and elevated expression in endurance-trained athletes, while the same group showed higher methylation in transcription factors such as FOXO3, CREB5, and PGC-1\u03b1. The baseline DNA methylation state of those genes was associated with the transcriptional response to an acute bout of exercise. Acute exercise altered very few of the investigated CpG sites.\n\nEndurance- compared to resistance-trained athletes and untrained individuals demonstrated a different DNA methylation signature of selected skeletal muscle genes, which may influence transcriptional dynamics following a bout of acute exercise. Skeletal muscle fiber type distribution is associated with methylation of fiber type specific genes. Our results suggest that the baseline DNA methylation landscape in skeletal muscle influences the transcription of regulatory genes in response to an acute exercise bout.", "doi": "10.1186/s12915-024-01938-6", "pmid": "38965555", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11225400"}, {"db": "pii", "key": "10.1186/s12915-024-01938-6"}], "notes": [], "created": "2024-11-12T10:39:08.137Z", "modified": "2024-11-12T10:39:08.230Z"}, {"entity": "publication", "iuid": "0477d212635a4177b3e68b39e3fa2f20", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0477d212635a4177b3e68b39e3fa2f20.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0477d212635a4177b3e68b39e3fa2f20"}}, "title": "Limited Parallelism in Genetic Adaptation to Brackish Water Bodies in European Sprat and Atlantic Herring.", "authors": [{"family": "Pettersson", "given": "Mats E", "initials": "ME", "orcid": "0000-0002-7372-9076", "researcher": {"href": "https://publications.scilifelab.se/researcher/27011c7fbb8a44dda536a4fc876675b0.json"}}, {"family": "Quintela", "given": "Mar\u00eda", "initials": "M"}, {"family": "Besnier", "given": "Fran\u00e7ois", "initials": "F"}, {"family": "Deng", "given": "Qiaoling", "initials": "Q"}, {"family": "Berg", "given": "Florian", "initials": "F", "orcid": "0000-0003-1543-8112", "researcher": {"href": "https://publications.scilifelab.se/researcher/902b6c39c4f5463ea25888c17732fc3e.json"}}, {"family": "Kvamme", "given": "Cecilie", "initials": "C"}, {"family": "Bekkevold", "given": "Dorte", "initials": "D", "orcid": "0000-0002-5297-032X", "researcher": {"href": "https://publications.scilifelab.se/researcher/38c62afa02e94554ba1c3afcfc622555.json"}}, {"family": "Mosbech", "given": "Mai-Britt", "initials": "MB"}, {"family": "Bunikis", "given": "Ignas", "initials": "I"}, {"family": "Lille-Lang\u00f8y", "given": "Roger", "initials": "R"}, {"family": "Leonori", "given": "Iole", "initials": "I", "orcid": "0000-0001-7673-1684", "researcher": {"href": "https://publications.scilifelab.se/researcher/abf52b64cdde43838c36347af47ea670.json"}}, {"family": "Wallberg", "given": "Andreas", "initials": "A", "orcid": "0000-0002-9081-9663", "researcher": {"href": "https://publications.scilifelab.se/researcher/b67a52aca631482d8b8f58e525a82d14.json"}}, {"family": "Glover", "given": "Kevin A", "initials": "KA"}, {"family": "Andersson", "given": "Leif", "initials": "L", "orcid": "0000-0002-4085-6968", "researcher": {"href": "https://publications.scilifelab.se/researcher/bd3343c12f994b1fabcae23027d3a76d.json"}}], "type": "journal article", "published": "2024-07-03", "journal": {"title": "Genome Biol Evol", "issn": "1759-6653", "issn-l": "1759-6653", "volume": "16", "issue": "7", "pages": null}, "abstract": "The European sprat is a small plankton-feeding clupeid present in the northeastern Atlantic Ocean, in the Mediterranean Sea, and in the brackish Baltic Sea and Black Sea. This species is the target of a major fishery and, therefore, an accurate characterization of its genetic population structure is crucial to delineate proper stock assessments that aid ensuring the fishery's sustainability. Here, we present (i) a draft genome assembly, (ii) pooled whole genome sequencing of 19 population samples covering most of the species' distribution range, and (iii) the design and test of a single nucleotide polymorphism (SNP)-chip resource and use this to validate the population structure inferred from pooled sequencing. These approaches revealed, using the populations sampled here, three major groups of European sprat: Oceanic, Coastal, and Brackish with limited differentiation within groups even over wide geographical stretches. Genetic structure is largely driven by six large putative inversions that differentiate Oceanic and Brackish sprats, while Coastal populations display intermediate frequencies of haplotypes at each locus. Interestingly, populations from the Baltic and the Black Seas share similar frequencies of haplotypes at these putative inversions despite their distant geographic location. The closely related clupeids European sprat and Atlantic herring both show genetic adaptation to the brackish Baltic Sea, providing an opportunity to explore the extent of genetic parallelism. This analysis revealed limited parallelism because out of 125 independent loci detected in the Atlantic herring, three showed sharp signals of selection that overlapped between the two species and contained single genes such as PRLRA, which encodes the receptor for prolactin, a freshwater-adapting hormone in euryhaline species, and THRB, a receptor for thyroid hormones, important both for metabolic regulation and the development of red cone photoreceptors.", "doi": "10.1093/gbe/evae133", "pmid": "38918882", "labels": {"NGI Uppsala (Uppsala Genome Center)": "Collaborative", "NGI Long read": "Collaborative", "National Genomics Infrastructure": "Collaborative", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Short read": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11226789"}, {"db": "pii", "key": "7699122"}], "notes": [], "created": "2024-11-04T20:50:27.197Z", "modified": "2024-11-25T10:24:21.553Z"}, {"entity": "publication", "iuid": "c8247c4a542e4c94ae4a3ee22db83900", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c8247c4a542e4c94ae4a3ee22db83900.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c8247c4a542e4c94ae4a3ee22db83900"}}, "title": "Comparative Genomic Analysis of the Pattern of Evolution of Male and Female Reproductive Proteins in Seed Beetles.", "authors": [{"family": "Papachristos", "given": "Konstantinos", "initials": "K", "orcid": "0000-0002-4777-9088", "researcher": {"href": "https://publications.scilifelab.se/researcher/2bf7a545a218455fa134b3dd8bb1b895.json"}}, {"family": "Sayadi", "given": "Ahmed", "initials": "A", "orcid": "0000-0002-5662-9145", "researcher": {"href": "https://publications.scilifelab.se/researcher/0f74f301499b4f888e0ac7c5161ae161.json"}}, {"family": "Arnqvist", "given": "G\u00f6ran", "initials": "G", "orcid": "0000-0002-3501-3376", "researcher": {"href": "https://publications.scilifelab.se/researcher/a2e926bfdd22419eb57d2c375041150f.json"}}], "type": "journal article", "published": "2024-07-03", "journal": {"title": "Genome Biol Evol", "issn": "1759-6653", "issn-l": "1759-6653", "volume": "16", "issue": "7", "pages": null}, "abstract": "Male seminal fluid proteins often show signs of positive selection and divergent evolution, believed to reflect male-female coevolution. Yet, our understanding of the predicted concerted evolution of seminal fluid proteins and female reproductive proteins is limited. We sequenced, assembled, and annotated the genome of two species of seed beetles allowing a comparative analysis of four closely related species of these herbivorous insects. We compare the general pattern of evolution in genes encoding seminal fluid proteins and female reproductive proteins with those in digestive protein genes and well-conserved reference genes. We found that female reproductive proteins showed an overall ratio of nonsynonymous to synonymous substitutions (\u03c9) similar to that of conserved genes, while seminal fluid proteins and digestive proteins exhibited higher overall \u03c9 values. Further, seminal fluid proteins and digestive proteins showed a higher proportion of sites putatively under positive selection, and explicit tests showed no difference in relaxed selection between protein types. Evolutionary rate covariation analyses showed that evolutionary rates among seminal fluid proteins were on average more closely correlated with those in female reproductive proteins than with either digestive or conserved genes. Gene expression showed the expected negative covariation with \u03c9 values, except for male-biased genes where this negative relationship was reversed. In conclusion, seminal fluid proteins showed relatively rapid evolution and signs of positive selection. In contrast, female reproductive proteins evolved at a lower rate under selective constraints, on par with genes known to be well conserved. Although our findings provide support for concerted evolution of seminal fluid proteins and female reproductive proteins, they also suggest that these two classes of proteins evolve under partly distinct selective regimes.", "doi": "10.1093/gbe/evae143", "pmid": "38941482", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Long-term Support WABI": "Service", "Bioinformatics Support and Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11251426"}, {"db": "pii", "key": "7701342"}], "notes": [], "created": "2024-11-12T10:52:28.961Z", "modified": "2024-11-25T10:24:28.390Z"}, {"entity": "publication", "iuid": "71bc285bc319470d9958c5404641f2a3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/71bc285bc319470d9958c5404641f2a3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/71bc285bc319470d9958c5404641f2a3"}}, "title": "Predicting type 2 diabetes via machine learning integration of multiple omics from human pancreatic islets.", "authors": [{"family": "R\u00f6nn", "given": "Tina", "initials": "T"}, {"family": "Perfilyev", "given": "Alexander", "initials": "A"}, {"family": "Oskolkov", "given": "Nikolay", "initials": "N"}, {"family": "Ling", "given": "Charlotte", "initials": "C"}], "type": "journal article", "published": "2024-06-25", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "14", "issue": "1", "pages": "14637", "issn-l": "2045-2322"}, "abstract": "Type 2 diabetes (T2D) is the fastest growing non-infectious disease worldwide. Impaired insulin secretion from pancreatic beta-cells is a hallmark of T2D, but the mechanisms behind this defect are insufficiently characterized. Integrating multiple layers of biomedical information, such as different Omics, may allow more accurate understanding of complex diseases such as T2D. Our aim was to explore and use Machine Learning to integrate multiple sources of biological/molecular information (multiOmics), in our case RNA-sequening, DNA methylation, SNP and phenotypic data from islet donors with T2D and non-diabetic controls. We exploited Machine Learning to perform multiOmics integration of DNA methylation, expression, SNPs, and phenotypes from pancreatic islets of 110 individuals, with ~ 30% being T2D cases. DNA methylation was analyzed using Infinium MethylationEPIC array, expression was analyzed using RNA-sequencing, and SNPs were analyzed using HumanOmniExpress arrays. Supervised linear multiOmics integration via DIABLO based on Partial Least Squares (PLS) achieved an accuracy of 91 \u00b1 15% of T2D prediction with an area under the curve of 0.96 \u00b1 0.08 on the test dataset after cross-validation. Biomarkers identified by this multiOmics integration, including SACS and TXNIP DNA methylation, OPRD1 and RHOT1 expression and a SNP annotated to ANO1, provide novel insights into the interplay between different biological mechanisms contributing to T2D. This Machine Learning approach of multiOmics cross-sectional data from human pancreatic islets achieved a promising accuracy of T2D prediction, which may potentially find broad applications in clinical diagnostics. In addition, it delivered novel candidate biomarkers for T2D and links between them across the different Omics.", "doi": "10.1038/s41598-024-64846-3", "pmid": "38918439", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI SNP genotyping": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC11199577"}, {"db": "pii", "key": "10.1038/s41598-024-64846-3"}], "notes": [], "created": "2024-10-21T11:11:23.000Z", "modified": "2024-11-08T13:48:34.777Z"}, {"entity": "publication", "iuid": "c119e76b14514e52b934f2411b16aff8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c119e76b14514e52b934f2411b16aff8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c119e76b14514e52b934f2411b16aff8"}}, "title": "Chromosome-level genome assembly and annotation of the social amoeba Dictyostelium firmibasis.", "authors": [{"family": "Edelbroek", "given": "Bart", "initials": "B", "orcid": "0000-0002-5184-0873", "researcher": {"href": "https://publications.scilifelab.se/researcher/164d0bef1b3e48668e136dbe0d2e8736.json"}}, {"family": "Kjellin", "given": "Jonas", "initials": "J", "orcid": "0000-0002-3830-7046", "researcher": {"href": "https://publications.scilifelab.se/researcher/daf9964b08fa498e9c0eb3540a0aa1fa.json"}}, {"family": "Jerlstr\u00f6m-Hultqvist", "given": "Jon", "initials": "J"}, {"family": "Koskiniemi", "given": "Sanna", "initials": "S"}, {"family": "S\u00f6derbom", "given": "Fredrik", "initials": "F", "orcid": "0000-0003-3616-3509", "researcher": {"href": "https://publications.scilifelab.se/researcher/4952b493871a4970a089074117bb303f.json"}}], "type": "dataset", "published": "2024-06-22", "journal": {"title": "Sci Data", "issn": "2052-4463", "volume": "11", "issue": "1", "pages": "678", "issn-l": "2052-4463"}, "abstract": "Dicytostelium firmibasis is a member of Dictyostelia, a group of social amoebae that upon starvation display aggregative multicellularity where the amoebae transition from uni- to multicellular life. The D. firmibasis genome assembly that is currently available is of limited use due to its low contiguity, large number of undetermined bases, and lack of annotations. Here we used Nanopore long read sequencing, complemented with Illumina sequencing, and developmental transcriptomics as well as small RNA-sequencing, to present a new, fully annotated, chromosome-level D. firmibasis genome assembly. The new assembly contains no undetermined bases, and consists mainly of six large contigs representing the chromosomes, as well as a complete mitochondrial genome. This new genome assembly will be a valuable tool, allowing comprehensive comparison to Dictyostelium discoideum, the dictyostelid genetically tractable model. Further, the new genome will be important for studies of evolutionary processes governing the transition from unicellular to multicellular organisms and will aid in the sequencing and annotation of other dictyostelids genomes, many of which are currently of poor quality.", "doi": "10.1038/s41597-024-03513-8", "pmid": "38909042", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11193728"}, {"db": "pii", "key": "10.1038/s41597-024-03513-8"}], "notes": [], "created": "2024-06-28T06:39:46.481Z", "modified": "2024-11-25T10:20:11.383Z"}, {"entity": "publication", "iuid": "c9468bade168413f9365ee51ab1da260", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c9468bade168413f9365ee51ab1da260.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c9468bade168413f9365ee51ab1da260"}}, "title": "Completed genome and emergence scenario of the multidrug-resistant nosocomial pathogen Staphylococcus epidermidis ST215.", "authors": [{"family": "Kellgren", "given": "Therese", "initials": "T", "orcid": "0000-0002-4911-7037", "researcher": {"href": "https://publications.scilifelab.se/researcher/52c7a5a8c5024d5186f1a4d7385778e2.json"}}, {"family": "Dwibedi", "given": "Chinmay", "initials": "C", "orcid": "0000-0001-6416-4440", "researcher": {"href": "https://publications.scilifelab.se/researcher/a0b0dbf807be449da1856c0c018f13a3.json"}}, {"family": "Widerstr\u00f6m", "given": "Micael", "initials": "M", "orcid": "0000-0002-1483-4255", "researcher": {"href": "https://publications.scilifelab.se/researcher/563f129fdb4e468395de5df2a7e80ee4.json"}}, {"family": "Sundell", "given": "David", "initials": "D", "orcid": "0000-0002-6269-0217", "researcher": {"href": "https://publications.scilifelab.se/researcher/084bd7876637499b929007562d5ac03a.json"}}, {"family": "\u00d6hrman", "given": "Caroline", "initials": "C", "orcid": "0000-0003-0516-7523", "researcher": {"href": "https://publications.scilifelab.se/researcher/a347bde191ef42a98a8aaba829adb553.json"}}, {"family": "Sj\u00f6din", "given": "Andreas", "initials": "A", "orcid": "0000-0001-5350-4219", "researcher": {"href": "https://publications.scilifelab.se/researcher/6398d7c06a414ea6bcaf2579a8587452.json"}}, {"family": "Monsen", "given": "Tor", "initials": "T", "orcid": "0000-0001-8489-757X", "researcher": {"href": "https://publications.scilifelab.se/researcher/804b654aa0be4d7a9ecdf113487fe443.json"}}, {"family": "Ryd\u00e9n", "given": "Patrik", "initials": "P", "orcid": "0000-0002-0577-123X", "researcher": {"href": "https://publications.scilifelab.se/researcher/65e733a3351940749605f054834eebef.json"}}, {"family": "Johansson", "given": "Anders", "initials": "A", "orcid": "0000-0003-0548-5943", "researcher": {"href": "https://publications.scilifelab.se/researcher/e4cd5b852fab4d5da3231939f060e3f5.json"}}], "type": "journal article", "published": "2024-06-19", "journal": {"title": "BMC Microbiol.", "issn": "1471-2180", "volume": "24", "issue": "1", "pages": "215", "issn-l": "1471-2180"}, "abstract": "A multidrug-resistant lineage of Staphylococcus epidermidis named ST215 is a common cause of prosthetic joint infections and other deep surgical site infections in Northern Europe, but is not present elsewhere. The increasing resistance among S. epidermidis strains is a global concern. We used whole-genome sequencing to characterize ST215 from healthcare settings.\n\nWe completed the genome of a ST215 isolate from a Swedish hospital using short and long reads, resulting in a circular 2,676,787 bp chromosome and a 2,326 bp plasmid. The new ST215 genome was placed in phylogenetic context using 1,361 finished public S. epidermidis reference genomes. We generated 10 additional short-read ST215 genomes and 11 short-read genomes of ST2, which is another common multidrug-resistant lineage at the same hospital. We studied recombination's role in the evolution of ST2 and ST215, and found multiple recombination events averaging 30-50 kb. By comparing the results of antimicrobial susceptibility testing for 31 antimicrobial drugs with the genome content encoding antimicrobial resistance in the ST215 and ST2 isolates, we found highly similar resistance traits between the isolates, with 22 resistance genes being shared between all the ST215 and ST2 genomes. The ST215 genome contained 29 genes that were historically identified as virulence genes of S. epidermidis ST2. We established that in the nucleotide sequence stretches identified as recombination events, virulence genes were overrepresented in ST215, while antibiotic resistance genes were overrepresented in ST2.\n\nThis study features the extensive antibiotic resistance and virulence gene content in ST215 genomes. ST215 and ST2 lineages have similarly evolved, acquiring resistance and virulence through genomic recombination. The results highlight the threat of new multidrug-resistant S. epidermidis lineages emerging in healthcare settings.", "doi": "10.1186/s12866-024-03367-5", "pmid": "38890594", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11186124"}, {"db": "pii", "key": "10.1186/s12866-024-03367-5"}], "notes": [], "created": "2024-06-28T06:39:22.789Z", "modified": "2024-11-25T10:30:17.631Z"}, {"entity": "publication", "iuid": "0c956dac242b42c78baa9303c9d96fc0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0c956dac242b42c78baa9303c9d96fc0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0c956dac242b42c78baa9303c9d96fc0"}}, "title": "Intra-Individual Variations in How Insulin Sensitivity Responds to Long-Term Exercise: Predictions by Machine Learning Based on Large-Scale Serum Proteomics.", "authors": [{"family": "Viken", "given": "Jonas Krag", "initials": "JK", "orcid": "0009-0003-6889-9171", "researcher": {"href": "https://publications.scilifelab.se/researcher/9baf893dd1e84c349669f9fbd293f852.json"}}, {"family": "Olsen", "given": "Thomas", "initials": "T", "orcid": "0000-0003-1805-5221", "researcher": {"href": "https://publications.scilifelab.se/researcher/f4c18ceb78204c028e01fdf9dea51866.json"}}, {"family": "Drevon", "given": "Christian Andr\u00e9", "initials": "CA"}, {"family": "Hjorth", "given": "Marit", "initials": "M", "orcid": "0000-0001-8067-714X", "researcher": {"href": "https://publications.scilifelab.se/researcher/696d72b5590649dfa4281e84ad4da5fe.json"}}, {"family": "Birkeland", "given": "K\u00e5re Inge", "initials": "KI", "orcid": "0000-0003-3002-6933", "researcher": {"href": "https://publications.scilifelab.se/researcher/7ee1d9c1d7074e35b19941ee194cdf02.json"}}, {"family": "Norheim", "given": "Frode", "initials": "F"}, {"family": "Lee-\u00d8deg\u00e5rd", "given": "Sindre", "initials": "S", "orcid": "0000-0002-0670-7555", "researcher": {"href": "https://publications.scilifelab.se/researcher/7cd4f35ea21f4df1abafcbfcb14f51f2.json"}}], "type": "journal article", "published": "2024-06-15", "journal": {"title": "Metabolites", "issn": "2218-1989", "issn-l": null, "volume": "14", "issue": "6", "pages": null}, "abstract": "Physical activity is effective for preventing and treating type 2 diabetes, but some individuals do not achieve metabolic benefits from exercise (\"non-responders\"). We investigated non-responders in terms of insulin sensitivity changes following a 12-week supervised strength and endurance exercise program. We used a hyperinsulinaemic euglycaemic clamp to measure insulin sensitivity among 26 men aged 40-65, categorizing them into non-responders or responders based on their insulin sensitivity change scores. The exercise regimen included VO2max, muscle strength, whole-body MRI scans, muscle and fat biopsies, and serum samples. mRNA sequencing was performed on biopsies and Olink proteomics on serum samples. Non-responders showed more visceral and intramuscular fat and signs of dyslipidaemia and low-grade inflammation at baseline and did not improve in insulin sensitivity following exercise, although they showed gains in VO2max and muscle strength. Impaired IL6-JAK-STAT3 signalling in non-responders was suggested by serum proteomics analysis, and a baseline serum proteomic machine learning (ML) algorithm predicted insulin sensitivity responses with high accuracy, validated across two independent exercise cohorts. The ML model identified 30 serum proteins that could forecast exercise-induced insulin sensitivity changes.", "doi": "10.3390/metabo14060335", "pmid": "38921470", "labels": {"Affinity Proteomics Uppsala": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Proteomics": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11206077"}, {"db": "pii", "key": "metabo14060335"}], "notes": [], "created": "2024-11-27T16:05:02.319Z", "modified": "2024-11-27T19:29:25.964Z"}, {"entity": "publication", "iuid": "caa37fd92a5c432fbea7349ddc016e59", "links": {"self": {"href": "https://publications.scilifelab.se/publication/caa37fd92a5c432fbea7349ddc016e59.json"}, "display": {"href": "https://publications.scilifelab.se/publication/caa37fd92a5c432fbea7349ddc016e59"}}, "title": "Integrative transcriptomic and proteomic profiling of the effects of cell confluency on gene expression.", "authors": [{"family": "Lobo", "given": "Vivian", "initials": "V"}, {"family": "Shcherbinina", "given": "Evgeniia", "initials": "E"}, {"family": "Westholm", "given": "Jakub O", "initials": "JO"}, {"family": "Nowak", "given": "Iwona", "initials": "I"}, {"family": "Huang", "given": "Hsiang-Chi", "initials": "HC"}, {"family": "Angeletti", "given": "Davide", "initials": "D", "orcid": "0000-0002-5256-1972", "researcher": {"href": "https://publications.scilifelab.se/researcher/ae59c12bf82b4ad9a8d9ad8603d03d9c.json"}}, {"family": "Anastasakis", "given": "Dimitrios G", "initials": "DG"}, {"family": "Sarshad", "given": "Aishe A", "initials": "AA", "orcid": "0000-0001-7153-5959", "researcher": {"href": "https://publications.scilifelab.se/researcher/42c62bd8dbe34b5da39de17d6a2a06ab.json"}}], "type": "dataset", "published": "2024-06-12", "journal": {"title": "Sci Data", "issn": "2052-4463", "issn-l": "2052-4463", "volume": "11", "issue": "1", "pages": "617"}, "abstract": "In this study we examine the impact of cell confluency on gene expression. We focused on Argonaute (AGO) protein dynamics and associated gene and protein expression in HEK293, A375, and SHSY5Y cell lines. As a consequence of cell confluency, AGO2 protein translocates into the nucleus. Therefore, we generated transcriptomic data using RNA sequencing to compare gene expression in subconfluent versus confluent cells, which highlighted significant alterations in gene regulation patterns directly corresponding to changes in cell density. Our study also encompasses miRNA profiling data obtained through small RNA sequencing, revealing miRNA expressional changes dependent on cellular confluency, as well as cellular localization. Finally, we derived proteomic data from mass spectrometry analyses following AGO1-4 immunoprecipitation, providing a comprehensive view of AGO interactome in both nuclear and cytoplasmic compartments under varying confluency. These datasets offer a detailed exploration of the cellular and molecular dynamics, influenced by cell confluency, presenting a valuable resource for further research in cellular biology, particularly in understanding the basic mechanisms of cell density in cancer cells.", "doi": "10.1038/s41597-024-03465-z", "pmid": "38866801", "labels": {"Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Short read": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service", "Glycoproteomics and MS Proteomics": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC11169490"}, {"db": "pii", "key": "10.1038/s41597-024-03465-z"}], "notes": [], "created": "2024-06-14T17:35:54.427Z", "modified": "2024-11-27T15:37:51.552Z"}, {"entity": "publication", "iuid": "0f7252933b2540c4a11ca7fcc3c1e960", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0f7252933b2540c4a11ca7fcc3c1e960.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0f7252933b2540c4a11ca7fcc3c1e960"}}, "title": "Detection of rare variants among nuclei populating the arbuscular mycorrhizal fungal model species Rhizophagus irregularis DAOM197198.", "authors": [{"family": "Manyara", "given": "David", "initials": "D", "orcid": "0000-0002-8370-2651", "researcher": {"href": "https://publications.scilifelab.se/researcher/2132548af20445b2b0561fa38b8f8b89.json"}}, {"family": "S\u00e1nchez-Garc\u00eda", "given": "Marisol", "initials": "M"}, {"family": "Montoliu-Nerin", "given": "Merce", "initials": "M"}, {"family": "Rosling", "given": "Anna", "initials": "A"}], "type": "journal article", "published": "2024-06-05", "journal": {"title": "G3 (Bethesda)", "issn": "2160-1836", "volume": "14", "issue": "6", "issn-l": "2160-1836"}, "abstract": "Identifying genuine polymorphic variants is a significant challenge in sequence data analysis, although detecting low-frequency variants in sequence data is essential for estimating demographic parameters and investigating genetic processes, such as selection, within populations. Arbuscular mycorrhizal (AM) fungi are multinucleate organisms, in which individual nuclei collectively operate as a population, and the extent of genetic variation across nuclei has long been an area of scientific interest. In this study, we investigated the patterns of polymorphism discovery and the alternate allele frequency distribution by comparing polymorphism discovery in 2 distinct genomic sequence datasets of the AM fungus model species, Rhizophagus irregularis strain DAOM197198. The 2 datasets used in this study are publicly available and were generated either from pooled spores and hyphae or amplified single nuclei from a single spore. We also estimated the intraorganismal variation within the DAOM197198 strain. Our results showed that the 2 datasets exhibited different frequency patterns for discovered variants. The whole-organism dataset showed a distribution spanning low-, intermediate-, and high-frequency variants, whereas the single-nucleus dataset predominantly featured low-frequency variants with smaller proportions in intermediate and high frequencies. Furthermore, single nucleotide polymorphism density estimates within both the whole organism and individual nuclei confirmed the low intraorganismal variation of the DAOM197198 strain and that most variants are rare. Our study highlights the methodological challenges associated with detecting low-frequency variants in AM fungal whole-genome sequence data and demonstrates that alternate alleles can be reliably identified in single nuclei of AM fungi.", "doi": "10.1093/g3journal/jkae074", "pmid": "38656424", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11152072"}, {"db": "pii", "key": "7657467"}], "notes": [], "created": "2024-06-28T06:37:32.605Z", "modified": "2025-02-28T14:17:52.446Z"}, {"entity": "publication", "iuid": "85509550f8a04133b34f785895ed87e7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/85509550f8a04133b34f785895ed87e7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/85509550f8a04133b34f785895ed87e7"}}, "title": "Ancient Sheep Genomes Reveal Four Millennia of North European Short-Tailed Sheep in the Baltic Sea Region.", "authors": [{"family": "Larsson", "given": "Martin N A", "initials": "MNA"}, {"family": "Morell Miranda", "given": "Pedro", "initials": "P"}, {"family": "Pan", "given": "Li", "initials": "L"}, {"family": "Ba\u015fak Vural", "given": "K\u0131v\u0131lc\u0131m", "initials": "K"}, {"family": "Kaptan", "given": "Damla", "initials": "D"}, {"family": "Rodrigues Soares", "given": "Andr\u00e9 Elias", "initials": "AE"}, {"family": "Kivikero", "given": "Hanna", "initials": "H"}, {"family": "Kantanen", "given": "Juha", "initials": "J", "orcid": "0000-0001-6350-6373", "researcher": {"href": "https://publications.scilifelab.se/researcher/bd2d0b84728048f39df9c1153300252a.json"}}, {"family": "Somel", "given": "Mehmet", "initials": "M"}, {"family": "\u00d6zer", "given": "F\u00fcsun", "initials": "F"}, {"family": "Johansson", "given": "Anna M", "initials": "AM", "orcid": "0000-0002-9762-0497", "researcher": {"href": "https://publications.scilifelab.se/researcher/dbd1ea80ec964bc3ab675e84b27d17e6.json"}}, {"family": "Stor\u00e5", "given": "Jan", "initials": "J", "orcid": "0000-0001-6319-7857", "researcher": {"href": "https://publications.scilifelab.se/researcher/57e9174cbd2a4c39be948b88b9ab2d3a.json"}}, {"family": "G\u00fcnther", "given": "Torsten", "initials": "T", "orcid": "0000-0001-9460-390X", "researcher": {"href": "https://publications.scilifelab.se/researcher/84159bff82a64a938bcff107f550c901.json"}}], "type": "journal article", "published": "2024-06-04", "journal": {"title": "Genome Biol Evol", "issn": "1759-6653", "volume": "16", "issue": "6", "issn-l": "1759-6653"}, "abstract": "Sheep are among the earliest domesticated livestock species, with a wide variety of breeds present today. However, it remains unclear how far back this diversity goes, with formal documentation only dating back a few centuries. North European short-tailed (NEST) breeds are often assumed to be among the oldest domestic sheep populations, even thought to represent relicts of the earliest sheep expansions during the Neolithic period reaching Scandinavia <6,000 years ago. This study sequenced the genomes (up to 11.6X) of five sheep remains from the Baltic islands of Gotland and \u00c5land, dating from the Late Neolithic (\u223c4,100 cal BP) to historical times (\u223c1,600 CE). Our findings indicate that these ancient sheep largely possessed the genetic characteristics of modern NEST breeds, suggesting a substantial degree of long-term continuity of this sheep type in the Baltic Sea region. Despite the wide temporal spread, population genetic analyses show high levels of affinity between the ancient genomes and they also exhibit relatively high genetic diversity when compared to modern NEST breeds, implying a loss of diversity in most breeds during the last centuries associated with breed formation and recent bottlenecks. Our results shed light on the development of breeds in Northern Europe specifically as well as the development of genetic diversity in sheep breeds, and their expansion from the domestication center in general.", "doi": "10.1093/gbe/evae114", "pmid": "38795367", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Ancient DNA": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11162877"}, {"db": "pii", "key": "7682331"}], "notes": [], "created": "2024-07-01T06:11:08.407Z", "modified": "2025-02-28T14:18:19.091Z"}, {"entity": "publication", "iuid": "be8e2e67fa824f9da9b80e1a8d9e15c2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/be8e2e67fa824f9da9b80e1a8d9e15c2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/be8e2e67fa824f9da9b80e1a8d9e15c2"}}, "title": "Expedient Bayesian prediction of subfossil bone protein content using portable ATR-FTIR data", "authors": [{"family": "Hixon", "given": "Sean", "initials": "S", "orcid": "0000-0001-6147-7118", "researcher": {"href": "https://publications.scilifelab.se/researcher/9b38fdd8b3424dcca122a3faf0f9d4b7.json"}}, {"family": "Roberts", "given": "Patrick", "initials": "P"}, {"family": "Rodr\u00edguez-Varela", "given": "Ricardo", "initials": "R"}, {"family": "G\u00f6therstr\u00f6m", "given": "Anders", "initials": "A", "orcid": "0000-0001-8579-1304", "researcher": {"href": "https://publications.scilifelab.se/researcher/1088a8b6a9af4cc396c610383576690f.json"}}, {"family": "Rossoni-Notter", "given": "Elena", "initials": "E", "orcid": "0000-0002-3437-9923", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a6f9285c47c4d919bb9333735d87f42.json"}}, {"family": "Notter", "given": "Olivier", "initials": "O", "orcid": "0000-0002-1068-7649", "researcher": {"href": "https://publications.scilifelab.se/researcher/688e704c28184e2d9ac2cf94a9e11ef9.json"}}, {"family": "Raimondeau", "given": "Pauline", "initials": "P"}, {"family": "Besnard", "given": "Guillaume", "initials": "G", "orcid": "0000-0003-2275-6012", "researcher": {"href": "https://publications.scilifelab.se/researcher/ca6f10e15f5a40f8b64bc6b2ba3e4ab8.json"}}, {"family": "Paust", "given": "Enrico", "initials": "E", "orcid": "0000-0001-6150-7196", "researcher": {"href": "https://publications.scilifelab.se/researcher/e5741617fbe34163a3eff32797795886.json"}}, {"family": "Lucas", "given": "Mary", "initials": "M"}, {"family": "Lagia", "given": "Anna", "initials": "A", "orcid": "0000-0003-4158-8296", "researcher": {"href": "https://publications.scilifelab.se/researcher/b1105178630f4a3ea6378e995e449044.json"}}, {"family": "Fernandes", "given": "Ricardo", "initials": "R"}], "type": "journal-article", "published": "2024-06-00", "journal": {"title": "Quaternary International", "issn": "1040-6182", "volume": "694", "pages": "1-12", "issn-l": null}, "abstract": null, "doi": "10.1016/j.quaint.2024.05.002", "pmid": null, "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Short read": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [], "notes": [], "created": "2024-10-21T11:19:03.673Z", "modified": "2024-10-21T11:19:18.929Z"}, {"entity": "publication", "iuid": "33f838f6e3d2497fa4b6fd9a71cd282a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/33f838f6e3d2497fa4b6fd9a71cd282a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/33f838f6e3d2497fa4b6fd9a71cd282a"}}, "title": "An endothelial regulatory module links blood pressure regulation with elite athletic performance.", "authors": [{"family": "Fegraeus", "given": "Kim", "initials": "K", "orcid": "0000-0002-6428-3420", "researcher": {"href": "https://publications.scilifelab.se/researcher/f232e1deee984344a57c88f550020e61.json"}}, {"family": "Rosengren", "given": "Maria K", "initials": "MK", "orcid": "0000-0003-0144-7034", "researcher": {"href": "https://publications.scilifelab.se/researcher/2b771ed57d3e4c409c2a208173945786.json"}}, {"family": "Naboulsi", "given": "Rakan", "initials": "R", "orcid": "0000-0002-3610-4341", "researcher": {"href": "https://publications.scilifelab.se/researcher/ae740ff060a5499fa477891138e95117.json"}}, {"family": "Orlando", "given": "Ludovic", "initials": "L"}, {"family": "\u00c5brink", "given": "Magnus", "initials": "M", "orcid": "0000-0002-1335-3927", "researcher": {"href": "https://publications.scilifelab.se/researcher/50a91636c1064a0c944f7d794ba6ec72.json"}}, {"family": "Jouni", "given": "Ahmad", "initials": "A"}, {"family": "Velie", "given": "Brandon D", "initials": "BD"}, {"family": "Raine", "given": "Amanda", "initials": "A"}, {"family": "Egner", "given": "Beate", "initials": "B"}, {"family": "Mattsson", "given": "C Mikael", "initials": "CM", "orcid": "0000-0002-0642-4838", "researcher": {"href": "https://publications.scilifelab.se/researcher/2ca360922eb047129f945ec3ca5f59e3.json"}}, {"family": "L\u00e5ng", "given": "Karin", "initials": "K"}, {"family": "Zhigulev", "given": "Artemy", "initials": "A", "orcid": "0000-0001-9251-1059", "researcher": {"href": "https://publications.scilifelab.se/researcher/81a7e8bb937744b5a18ed42d4f2dea5e.json"}}, {"family": "Bj\u00f6rck", "given": "Hanna M", "initials": "HM", "orcid": "0000-0002-9155-3609", "researcher": {"href": "https://publications.scilifelab.se/researcher/3d162f3de0f941e0a91387357892d656.json"}}, {"family": "Franco-Cereceda", "given": "Anders", "initials": "A"}, {"family": "Eriksson", "given": "Per", "initials": "P"}, {"family": "Andersson", "given": "G\u00f6ran", "initials": "G", "orcid": "0000-0001-5131-3144", "researcher": {"href": "https://publications.scilifelab.se/researcher/39ce81c314db47c8ad63c3ed38dffcb3.json"}}, {"family": "Sahl\u00e9n", "given": "Pelin", "initials": "P", "orcid": "0000-0001-6943-9618", "researcher": {"href": "https://publications.scilifelab.se/researcher/d032e807335049b2ac8a5e2398dd48e7.json"}}, {"family": "Meadows", "given": "Jennifer R S", "initials": "JRS", "orcid": "0000-0002-0850-230X", "researcher": {"href": "https://publications.scilifelab.se/researcher/86acdca0104c4552880d5a7cb5ac6565.json"}}, {"family": "Lindgren", "given": "Gabriella", "initials": "G", "orcid": "0000-0001-6046-9669", "researcher": {"href": "https://publications.scilifelab.se/researcher/a050dea8e99c47fabac28c14fe4daabb.json"}}], "type": "journal article", "published": "2024-06-00", "journal": {"title": "PLoS Genet.", "issn": "1553-7404", "volume": "20", "issue": "6", "pages": "e1011285", "issn-l": "1553-7390"}, "abstract": "The control of transcription is crucial for homeostasis in mammals. A previous selective sweep analysis of horse racing performance revealed a 19.6 kb candidate regulatory region 50 kb downstream of the Endothelin3 (EDN3) gene. Here, the region was narrowed to a 5.5 kb span of 14 SNVs, with elite and sub-elite haplotypes analyzed for association to racing performance, blood pressure and plasma levels of EDN3 in Coldblooded trotters and Standardbreds. Comparative analysis of human HiCap data identified the span as an enhancer cluster active in endothelial cells, interacting with genes relevant to blood pressure regulation. Coldblooded trotters with the sub-elite haplotype had significantly higher blood pressure compared to horses with the elite performing haplotype during exercise. Alleles within the elite haplotype were part of the standing variation in pre-domestication horses, and have risen in frequency during the era of breed development and selection. These results advance our understanding of the molecular genetics of athletic performance and vascular traits in both horses and humans.", "doi": "10.1371/journal.pgen.1011285", "pmid": "38885195", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Short read": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11182536"}, {"db": "pii", "key": "PGENETICS-D-23-00898"}], "notes": [], "created": "2024-10-21T11:19:11.160Z", "modified": "2024-11-25T10:31:46.138Z"}, {"entity": "publication", "iuid": "2f35c9b1f5d04d34b625afe231498b38", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2f35c9b1f5d04d34b625afe231498b38.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2f35c9b1f5d04d34b625afe231498b38"}}, "title": "Regulatory and evolutionary impact of DNA methylation in two songbird species and their naturally occurring F1 hybrids.", "authors": [{"family": "Boman", "given": "Jesper", "initials": "J", "orcid": "0000-0002-0537-8219", "researcher": {"href": "https://publications.scilifelab.se/researcher/669c974e6e284e94bfb6009f49ffc06d.json"}}, {"family": "Qvarnstr\u00f6m", "given": "Anna", "initials": "A"}, {"family": "Mugal", "given": "Carina F", "initials": "CF"}], "type": "journal article", "published": "2024-05-29", "journal": {"title": "BMC Biol.", "issn": "1741-7007", "volume": "22", "issue": "1", "pages": "124", "issn-l": "1741-7007"}, "abstract": "Regulation of transcription by DNA methylation in 5'-CpG-3' context is a widespread mechanism allowing differential expression of genetically identical cells to persist throughout development. Consequently, differences in DNA methylation can reinforce variation in gene expression among cells, tissues, populations, and species. Despite a surge in studies on DNA methylation, we know little about the importance of DNA methylation in population differentiation and speciation. Here we investigate the regulatory and evolutionary impact of DNA methylation in five tissues of two Ficedula flycatcher species and their naturally occurring F1 hybrids.\n\nWe show that the density of CpG in the promoters of genes determines the strength of the association between DNA methylation and gene expression. The impact of DNA methylation on gene expression varies among tissues with the brain showing unique patterns. Differentially expressed genes between parental species are predicted by genetic and methylation differentiation in CpG-rich promoters. However, both these factors fail to predict hybrid misexpression suggesting that promoter mismethylation is not a main determinant of hybrid misexpression in Ficedula flycatchers. Using allele-specific methylation estimates in hybrids, we also determine the genome-wide contribution of cis- and trans effects in DNA methylation differentiation. These distinct mechanisms are roughly balanced in all tissues except the brain, where trans differences predominate.\n\nOverall, this study provides insight on the regulatory and evolutionary impact of DNA methylation in songbirds.", "doi": "10.1186/s12915-024-01920-2", "pmid": "38807214", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Short read": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11134931"}, {"db": "pii", "key": "10.1186/s12915-024-01920-2"}], "notes": [], "created": "2024-10-21T11:21:52.507Z", "modified": "2024-11-25T10:30:43.234Z"}, {"entity": "publication", "iuid": "0b47a1ccf6df45f189be4688ab57ff66", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0b47a1ccf6df45f189be4688ab57ff66.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0b47a1ccf6df45f189be4688ab57ff66"}}, "title": "Saccharomyces cerevisiae strains performing similarly during fermentation of lignocellulosic hydrolysates show pronounced differences in transcriptional stress responses.", "authors": [{"family": "C\u00e1mara", "given": "Elena", "initials": "E", "orcid": "0000-0003-4271-7555", "researcher": {"href": "https://publications.scilifelab.se/researcher/7b95845cfd0040449c13682905f082d4.json"}}, {"family": "Mormino", "given": "Maurizio", "initials": "M", "orcid": "0000-0003-2055-5081", "researcher": {"href": "https://publications.scilifelab.se/researcher/6bfdb794959c4feeb11d6e12d68efc06.json"}}, {"family": "Siewers", "given": "Verena", "initials": "V", "orcid": "0000-0002-9502-9804", "researcher": {"href": "https://publications.scilifelab.se/researcher/d4d2f2bc4e6a4ce29372afbc86cefda0.json"}}, {"family": "Nyg\u00e5rd", "given": "Yvonne", "initials": "Y", "orcid": "0000-0001-6117-0343", "researcher": {"href": "https://publications.scilifelab.se/researcher/a136743764bc4dc4aa4d363c5a930592.json"}}], "type": "journal article", "published": "2024-05-21", "journal": {"title": "Appl. Environ. Microbiol.", "issn": "1098-5336", "issn-l": "0099-2240", "volume": "90", "issue": "5", "pages": "e0233023"}, "abstract": "Improving our understanding of the transcriptional changes of Saccharomyces cerevisiae during fermentation of lignocellulosic hydrolysates is crucial for the creation of more efficient strains to be used in biorefineries. We performed RNA sequencing of a CEN.PK laboratory strain, two industrial strains (KE6-12 and Ethanol Red), and two wild-type isolates of the LBCM collection when cultivated anaerobically in wheat straw hydrolysate. Many of the differently expressed genes identified among the strains have previously been reported to be important for tolerance to lignocellulosic hydrolysates or inhibitors therein. Our study demonstrates that stress responses typically identified during aerobic conditions such as glutathione metabolism, osmotolerance, and detoxification processes also are important for anaerobic processes. Overall, the transcriptomic responses were largely strain dependent, and we focused our study on similarities and differences in the transcriptomes of the LBCM strains. The expression of sugar transporter-encoding genes was higher in LBCM31 compared with LBCM109 that showed high expression of genes involved in iron metabolism and genes promoting the accumulation of sphingolipids, phospholipids, and ergosterol. These results highlight different evolutionary adaptations enabling S. cerevisiae to strive in lignocellulosic hydrolysates and suggest novel gene targets for improving fermentation performance and robustness.\r\n\r\nThe need for sustainable alternatives to oil-based production of biochemicals and biofuels is undisputable. Saccharomyces cerevisiae is the most commonly used industrial fermentation workhorse. The fermentation of lignocellulosic hydrolysates, second-generation biomass unsuited for food and feed, is still hampered by lowered productivities as the raw material is inhibitory for the cells. In order to map the genetic responses of different S. cerevisiae strains, we performed RNA sequencing of a CEN.PK laboratory strain, two industrial strains (KE6-12 and Ethanol Red), and two wild-type isolates of the LBCM collection when cultivated anaerobically in wheat straw hydrolysate. While the response to inhibitors of S. cerevisiae has been studied earlier, this has in previous studies been done in aerobic conditions. The transcriptomic analysis highlights different evolutionary adaptations among the different S. cerevisiae strains and suggests novel gene targets for improving fermentation performance and robustness.", "doi": "10.1128/aem.02330-23", "pmid": "38587374", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Short read": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11107148"}], "notes": [], "created": "2024-11-12T10:46:30.209Z", "modified": "2024-11-12T10:49:33.922Z"}, {"entity": "publication", "iuid": "1edd0b0187124503928edd662f1beb87", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1edd0b0187124503928edd662f1beb87.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1edd0b0187124503928edd662f1beb87"}}, "title": "Prediction models of persistent taxane-induced peripheral neuropathy among breast cancer survivors using whole-exome sequencing.", "authors": [{"family": "Engvall", "given": "Kristina", "initials": "K", "orcid": "0000-0002-7291-7227", "researcher": {"href": "https://publications.scilifelab.se/researcher/9d42004025f8455e9ea979abff4bd7c3.json"}}, {"family": "Uvdal", "given": "Hanna", "initials": "H", "orcid": "0009-0009-3191-495X", "researcher": {"href": "https://publications.scilifelab.se/researcher/76a13b46df5040da93bf5f1e9c8f31bb.json"}}, {"family": "Bj\u00f6rn", "given": "Niclas", "initials": "N", "orcid": "0000-0001-6806-4527", "researcher": {"href": "https://publications.scilifelab.se/researcher/a39cecc1714f4331b08a47f1f1bbe7ac.json"}}, {"family": "\u00c5vall-Lundqvist", "given": "Elisabeth", "initials": "E", "orcid": "0000-0001-7274-1770", "researcher": {"href": "https://publications.scilifelab.se/researcher/088f2c4f20ca4b3cb20490abeec77700.json"}}, {"family": "Gr\u00e9en", "given": "Henrik", "initials": "H", "orcid": "0000-0002-8015-5728", "researcher": {"href": "https://publications.scilifelab.se/researcher/0d92037931f64b70b8d4bf78dab628b4.json"}}], "type": "journal article", "published": "2024-05-16", "journal": {"title": "NPJ Precis Oncol", "issn": "2397-768X", "volume": "8", "issue": "1", "pages": "102", "issn-l": null}, "abstract": "Persistent taxane-induced peripheral neuropathy (TIPN) is highly prevalent among early-stage breast cancer survivors (ESBCS) and has detrimental effect on quality of life. We leveraged logistic regression models to develop and validate polygenic prediction models to estimate the risk of persistent PN symptoms in a training cohort and validation cohort taking clinical risk factors into account. Based on 337 whole-exome sequenced ESBCS two of five prediction models for individual PN symptoms obtained AUC results above 60% when validated. Using the model for numbness in feet (35 SNVs) in the test cohort, 73% survivors were correctly predicted. For tingling in feet (55 SNVs) 70% were correctly predicted. Both models included SNVs from the ADAMTS20, APT6V0A2, CCDC88C, CYP2C8, EPHA5, NR1H3, PSKH2/APTV0D2, and SCN10A genes. For cramps in feet, difficulty climbing stairs and difficulty opening a jar the validation was unsuccessful. Polygenic prediction models including clinical risk factors can estimate the risk of persistent taxane-induced numbness in feet and tingling in feet in ESBCS.", "doi": "10.1038/s41698-024-00594-x", "pmid": "38755266", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Short read": "Service", "National Genomics Infrastructure": "Service", "Clinical Genomics Gothenburg": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Service", "Clinical Genomics": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11099113"}, {"db": "pii", "key": "10.1038/s41698-024-00594-x"}], "notes": [], "created": "2024-10-21T11:10:16.668Z", "modified": "2025-02-28T14:16:00.044Z"}, {"entity": "publication", "iuid": "be905f5215af4f5daa928c5e4dd48155", "links": {"self": {"href": "https://publications.scilifelab.se/publication/be905f5215af4f5daa928c5e4dd48155.json"}, "display": {"href": "https://publications.scilifelab.se/publication/be905f5215af4f5daa928c5e4dd48155"}}, "title": "Complex genetic architecture of the chicken Growth1 QTL region.", "authors": [{"family": "Ou", "given": "Jen-Hsiang", "initials": "JH", "orcid": "0000-0001-9305-2931", "researcher": {"href": "https://publications.scilifelab.se/researcher/ccf5baf37c03451e95d76c42731f1490.json"}}, {"family": "R\u00f6nneburg", "given": "Tilman", "initials": "T"}, {"family": "Carlborg", "given": "\u00d6rjan", "initials": "\u00d6"}, {"family": "Honaker", "given": "Christa Ferst", "initials": "CF"}, {"family": "Siegel", "given": "Paul B", "initials": "PB"}, {"family": "Rubin", "given": "Carl-Johan", "initials": "CJ", "orcid": "0000-0001-8238-5052", "researcher": {"href": "https://publications.scilifelab.se/researcher/0bd98ada4083444e8336ef3ec53df488.json"}}], "type": "journal article", "published": "2024-05-13", "journal": {"title": "PLoS ONE", "issn": "1932-6203", "volume": "19", "issue": "5", "pages": "e0295109", "issn-l": "1932-6203"}, "abstract": "The genetic complexity of polygenic traits represents a captivating and intricate facet of biological inheritance. Unlike Mendelian traits controlled by a single gene, polygenic traits are influenced by multiple genetic loci, each exerting a modest effect on the trait. This cumulative impact of numerous genes, interactions among them, environmental factors, and epigenetic modifications results in a multifaceted architecture of genetic contributions to complex traits. Given the well-characterized genome, diverse traits, and range of genetic resources, chicken (Gallus gallus) was employed as a model organism to dissect the intricate genetic makeup of a previously identified major Quantitative Trait Loci (QTL) for body weight on chromosome 1. A multigenerational advanced intercross line (AIL) of 3215 chickens whose genomes had been sequenced to an average of 0.4x was analyzed using genome-wide association study (GWAS) and variance-heterogeneity GWAS (vGWAS) to identify markers associated with 8-week body weight. Additionally, epistatic interactions were studied using the natural and orthogonal interaction (NOIA) model. Six genetic modules, two from GWAS and four from vGWAS, were strongly associated with the studied trait. We found evidence of both additive- and non-additive interactions between these modules and constructed a putative local epistasis network for the region. Our screens for functional alleles revealed a missense variant in the gene ribonuclease H2 subunit B (RNASEH2B), which has previously been associated with growth-related traits in chickens and Darwin's finches. In addition, one of the most strongly associated SNPs identified is located in a non-coding region upstream of the long non-coding RNA, ENSGALG00000053256, previously suggested as a candidate gene for regulating chicken body weight. By studying large numbers of individuals from a family material using approaches to capture both additive and non-additive effects, this study advances our understanding of genetic complexities in a highly polygenic trait and has practical implications for poultry breeding and agriculture.", "doi": "10.1371/journal.pone.0295109", "pmid": "38739572", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11090294"}, {"db": "pii", "key": "PONE-D-23-37785"}], "notes": [], "created": "2024-06-28T06:38:07.479Z", "modified": "2024-11-25T10:32:02.110Z"}, {"entity": "publication", "iuid": "8115a4dd80094d05a57d1e654e0122b2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8115a4dd80094d05a57d1e654e0122b2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8115a4dd80094d05a57d1e654e0122b2"}}, "title": "Growth and mortality rates of picophytoplankton in the Baltic Sea Proper", "authors": [{"family": "Alegria Zufia", "given": "J", "initials": "J"}, {"family": "Laber", "given": "CP", "initials": "C"}, {"family": "Legrand", "given": "C", "initials": "C"}, {"family": "Lindehoff", "given": "E", "initials": "E"}, {"family": "Farnelid", "given": "H", "initials": "H"}], "type": "journal-article", "published": "2024-05-02", "journal": {"title": "Mar. Ecol. Prog. Ser.", "issn": "0171-8630", "volume": "735", "pages": "63-76", "issn-l": null}, "abstract": null, "doi": "10.3354/meps14572", "pmid": null, "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2024-05-16T06:30:12.035Z", "modified": "2024-11-25T10:32:58.447Z"}, {"entity": "publication", "iuid": "859f1ea1d197479ebdf6b48216eba94c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/859f1ea1d197479ebdf6b48216eba94c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/859f1ea1d197479ebdf6b48216eba94c"}}, "title": "Sex-biased gene expression during neural differentiation of human embryonic stem cells.", "authors": [{"family": "Pottmeier", "given": "Philipp", "initials": "P"}, {"family": "Nikolantonaki", "given": "Danai", "initials": "D"}, {"family": "Lanner", "given": "Fredrik", "initials": "F"}, {"family": "Peuckert", "given": "Christiane", "initials": "C"}, {"family": "Jazin", "given": "Elena", "initials": "E"}], "type": "journal article", "published": "2024-05-01", "journal": {"title": "Front Cell Dev Biol", "issn": "2296-634X", "volume": "12", "pages": "1341373", "issn-l": null}, "abstract": "Sex differences in the developing human brain are primarily attributed to hormonal influence. Recently however, genetic differences and their impact on the developing nervous system have attracted increased attention. To understand genetically driven sexual dimorphisms in neurodevelopment, we investigated genome-wide gene expression in an in vitro differentiation model of male and female human embryonic stem cell lines (hESC), independent of the effects of human sex hormones. Four male and four female-derived hESC lines were differentiated into a population of mixed neurons over 37 days. Differential gene expression and gene set enrichment analyses were conducted on bulk RNA sequencing data. While similar differentiation tendencies in all cell lines demonstrated the robustness and reproducibility of our differentiation protocol, we found sex-biased gene expression already in undifferentiated ESCs at day 0, but most profoundly after 37 days of differentiation. Male and female cell lines exhibited sex-biased expression of genes involved in neurodevelopment, suggesting that sex influences the differentiation trajectory. Interestingly, the highest contribution to sex differences was found to arise from the male transcriptome, involving both Y chromosome and autosomal genes. We propose 13 sex-biased candidate genes (10 upregulated in male cell lines and 3 in female lines) that are likely to affect neuronal development. Additionally, we confirmed gene dosage compensation of X/Y homologs escaping X chromosome inactivation through their Y homologs and identified a significant overexpression of the Y-linked demethylase UTY and KDM5D in male hESC during neuron development, confirming previous results in neural stem cells. Our results suggest that genetic sex differences affect neuronal differentiation trajectories, which could ultimately contribute to sex biases during human brain development.", "doi": "10.3389/fcell.2024.1341373", "pmid": "38764741", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11101176"}, {"db": "pii", "key": "1341373"}], "notes": [], "created": "2024-05-16T06:33:09.053Z", "modified": "2025-12-04T17:14:46.303Z"}, {"entity": "publication", "iuid": "9b508c1fd9064736b2a6e61b2a90718a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9b508c1fd9064736b2a6e61b2a90718a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9b508c1fd9064736b2a6e61b2a90718a"}}, "title": "Unlocking the secret life of blue mussels: Exploring connectivity in the Skagerrak through biophysical modeling and population genomics.", "authors": [{"family": "Gustafsson", "given": "Malin", "initials": "M"}, {"family": "Strand", "given": "\u00c5sa", "initials": "\u00c5", "orcid": "0000-0002-9029-4123", "researcher": {"href": "https://publications.scilifelab.se/researcher/9702edaf28fe4a56b9d345f0045d6165.json"}}, {"family": "Laugen", "given": "Ane T", "initials": "AT", "orcid": "0000-0001-6196-8304", "researcher": {"href": "https://publications.scilifelab.se/researcher/ed598dee082844f8b057abe7c4902ab3.json"}}, {"family": "Albretsen", "given": "Jon", "initials": "J", "orcid": "0000-0001-5863-2439", "researcher": {"href": "https://publications.scilifelab.se/researcher/fc5786b0b2f64052a1288038dc5a6310.json"}}, {"family": "Andr\u00e9", "given": "Carl", "initials": "C", "orcid": "0000-0003-4404-7292", "researcher": {"href": "https://publications.scilifelab.se/researcher/66e1d059567644a7b7080eb10d209723.json"}}, {"family": "Brostr\u00f6m", "given": "G\u00f6ran", "initials": "G"}, {"family": "Jorde", "given": "Per Erik", "initials": "PE", "orcid": "0000-0001-5515-7257", "researcher": {"href": "https://publications.scilifelab.se/researcher/0466e9d7fdff40718e81e9bd530510f9.json"}}, {"family": "Knutsen", "given": "Halvor", "initials": "H", "orcid": "0000-0002-7627-7634", "researcher": {"href": "https://publications.scilifelab.se/researcher/a822f994fed046018a713105bc5e03a0.json"}}, {"family": "Ortega-Martinez", "given": "Olga", "initials": "O", "orcid": "0000-0003-2734-6434", "researcher": {"href": "https://publications.scilifelab.se/researcher/bc84f54ca2cc49bc869cd23adeffc7ac.json"}}, {"family": "Sodeland", "given": "Marte", "initials": "M", "orcid": "0000-0001-6703-3972", "researcher": {"href": "https://publications.scilifelab.se/researcher/577d007c219b48f3919ca2d62c3303d3.json"}}, {"family": "Waern", "given": "Malin", "initials": "M", "orcid": "0000-0002-2459-040X", "researcher": {"href": "https://publications.scilifelab.se/researcher/15f48c8e09ab4b0880b4ed44feacbd87.json"}}, {"family": "Wrange", "given": "Anna-Lisa", "initials": "AL", "orcid": "0000-0002-3574-1779", "researcher": {"href": "https://publications.scilifelab.se/researcher/359e203f84144c26878b1dcbf1657dda.json"}}, {"family": "De Wit", "given": "Pierre", "initials": "P", "orcid": "0000-0003-4709-3438", "researcher": {"href": "https://publications.scilifelab.se/researcher/95b69d4724ce4b69819c0a1578cd56eb.json"}}], "type": "journal article", "published": "2024-05-00", "journal": {"title": "Evol Appl", "issn": "1752-4571", "volume": "17", "issue": "5", "pages": "e13704", "issn-l": "1752-4571"}, "abstract": "Knowledge of functional dispersal barriers in the marine environment can be used to inform a wide variety of management actions, such as marine spatial planning, restoration efforts, fisheries regulations, and invasive species management. Locations and causes of dispersal barriers can be studied through various methods, including movement tracking, biophysical modeling, demographic models, and genetics. Combining methods illustrating potential dispersal, such as biophysical modeling, with realized dispersal through, e.g., genetic connectivity estimates, provides particularly useful information for teasing apart potential causes of observed barriers. In this study, we focus on blue mussels (Mytilus edulis) in the Skagerrak-a marginal sea connected to the North Sea in Northern Europe-and combine biophysical models of larval dispersal with genomic data to infer locations and causes of dispersal barriers in the area. Results from both methods agree; patterns of ocean currents are a major structuring factor in the area. We find a complex pattern of source-sink dynamics with several dispersal barriers and show that some areas can be isolated despite an overall high dispersal capability. Finally, we translate our finding into management advice that can be used to sustainably manage this ecologically and economically important species in the future.", "doi": "10.1111/eva.13704", "pmid": "38770102", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Short read": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11104481"}, {"db": "pii", "key": "EVA13704"}], "notes": [], "created": "2024-10-21T11:15:54.793Z", "modified": "2024-11-25T10:26:53.880Z"}, {"entity": "publication", "iuid": "1d87703f951040d3ba20c90a98d45a20", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1d87703f951040d3ba20c90a98d45a20.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1d87703f951040d3ba20c90a98d45a20"}}, "title": "Fluorescently labeled prey surrogates in combination with fluorescence\u2010activated cell sorting successfully discriminate actively feeding mixotrophs in a lake water sample", "authors": [{"family": "Florenza", "given": "Javier", "initials": "J", "orcid": "0000-0002-3284-3702", "researcher": {"href": "https://publications.scilifelab.se/researcher/45ee0fc9406f4a9ea7c6b0d3b7740183.json"}}, {"family": "Divne", "given": "Anna\u2010Maria", "initials": "A"}, {"family": "Bertilsson", "given": "Stefan", "initials": "S", "orcid": "0000-0002-4265-1835", "researcher": {"href": "https://publications.scilifelab.se/researcher/2c17765c2a9f4383b5383138d11ae93f.json"}}], "type": "journal-article", "published": "2024-05-00", "journal": {"title": "Limnol Oceanogr", "issn": "0024-3590", "volume": "69", "issue": "5", "pages": "1030-1044", "issn-l": null}, "abstract": null, "doi": "10.1002/lno.12545", "pmid": null, "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Short read": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [], "notes": [], "created": "2024-10-21T11:25:54.028Z", "modified": "2024-10-21T11:25:54.050Z"}, {"entity": "publication", "iuid": "036d938b353a4b6084fc027f2a6fc9d6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/036d938b353a4b6084fc027f2a6fc9d6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/036d938b353a4b6084fc027f2a6fc9d6"}}, "title": "Growth-regulated co-occupancy of Mediator and Lsm3 at intronic ribosomal protein genes.", "authors": [{"family": "Abdel-Fattah", "given": "Wael R", "initials": "WR"}, {"family": "Carlsson", "given": "Mattias", "initials": "M"}, {"family": "Hu", "given": "Guo-Zhen", "initials": "G"}, {"family": "Singh", "given": "Ajeet", "initials": "A"}, {"family": "Vergara", "given": "Alexander", "initials": "A", "orcid": "0000-0001-6535-9282", "researcher": {"href": "https://publications.scilifelab.se/researcher/8003432c3c264e78a754fe595297453b.json"}}, {"family": "Aslam", "given": "Rameen", "initials": "R"}, {"family": "Ronne", "given": "Hans", "initials": "H", "orcid": "0000-0002-1645-6091", "researcher": {"href": "https://publications.scilifelab.se/researcher/d700b0be9ea04b588f539186fb92df5d.json"}}, {"family": "Bj\u00f6rklund", "given": "Stefan", "initials": "S", "orcid": "0000-0003-1181-0415", "researcher": {"href": "https://publications.scilifelab.se/researcher/dae5cb7a54364e74b4f0261ab8d8e0ce.json"}}], "type": "journal article", "published": "2024-04-13", "journal": {"title": "Nucleic Acids Res.", "issn": "1362-4962", "issn-l": "0305-1048", "volume": null, "issue": null, "pages": null}, "abstract": "Mediator is a well-known transcriptional co-regulator and serves as an adaptor between gene-specific regulatory proteins and RNA polymerase II. Studies on the chromatin-bound form of Mediator revealed interactions with additional protein complexes involved in various transcription-related processes, such as the Lsm2-8 complex that is part of the spliceosomal U6 small nuclear ribonucleoprotein complex. Here, we employ Chromatin Immunoprecipitation sequencing (ChIP-seq) of chromatin associated with the Lsm3 protein and the Med1 or Med15 Mediator subunits. We identify 86 genes co-occupied by both Lsm3 and Mediator, of which 73 were intron-containing ribosomal protein genes. In logarithmically growing cells, Mediator primarily binds to their promoter regions but also shows a second, less pronounced occupancy at their 3'-exons. During the late exponential phase, we observe a near-complete transition of Mediator from these promoters to a position in their 3'-ends, overlapping the Lsm3 binding sites \u223c250 bp downstream of their last intron-exon boundaries. Using an unbiased RNA sequencing approach, we show that transition of Mediator from promoters to the last exon of these genes correlates to reduction of both their messenger RNA levels and splicing ratios, indicating that the Mediator and Lsm complexes cooperate to control growth-regulated expression of intron-containing ribosomal protein genes at the levels of transcription and splicing.", "doi": "10.1093/nar/gkae266", "pmid": "38613396", "labels": {"NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "7645241"}], "notes": [], "created": "2024-04-26T08:51:21.044Z", "modified": "2024-06-28T06:31:12.260Z"}, {"entity": "publication", "iuid": "7a0719a5a1cc4cef963a4832ec073fd7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7a0719a5a1cc4cef963a4832ec073fd7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7a0719a5a1cc4cef963a4832ec073fd7"}}, "title": "Evolution of microRNAs in Amoebozoa and implications for the origin of multicellularity.", "authors": [{"family": "Edelbroek", "given": "Bart", "initials": "B", "orcid": "0000-0002-5184-0873", "researcher": {"href": "https://publications.scilifelab.se/researcher/164d0bef1b3e48668e136dbe0d2e8736.json"}}, {"family": "Kjellin", "given": "Jonas", "initials": "J", "orcid": "0000-0002-3830-7046", "researcher": {"href": "https://publications.scilifelab.se/researcher/daf9964b08fa498e9c0eb3540a0aa1fa.json"}}, {"family": "Biryukova", "given": "Inna", "initials": "I", "orcid": "0000-0003-0701-2808", "researcher": {"href": "https://publications.scilifelab.se/researcher/47d787e9d8e14b8fa598d8c3e82e4058.json"}}, {"family": "Liao", "given": "Zhen", "initials": "Z"}, {"family": "Lundberg", "given": "Torgny", "initials": "T"}, {"family": "Noegel", "given": "Angelika A", "initials": "AA"}, {"family": "Eichinger", "given": "Ludwig", "initials": "L", "orcid": "0000-0003-1594-6117", "researcher": {"href": "https://publications.scilifelab.se/researcher/a2b977ccf8604c2a9a048b21878fc828.json"}}, {"family": "Friedl\u00e4nder", "given": "Marc R", "initials": "MR", "orcid": "0000-0001-6577-4363", "researcher": {"href": "https://publications.scilifelab.se/researcher/744f7c6d0a884d9daa2e7303ed1779b8.json"}}, {"family": "S\u00f6derbom", "given": "Fredrik", "initials": "F", "orcid": "0000-0003-3616-3509", "researcher": {"href": "https://publications.scilifelab.se/researcher/4952b493871a4970a089074117bb303f.json"}}], "type": "journal article", "published": "2024-04-12", "journal": {"title": "Nucleic Acids Res.", "issn": "1362-4962", "volume": "52", "issue": "6", "pages": "3121-3136", "issn-l": "0305-1048"}, "abstract": "MicroRNAs (miRNAs) are important and ubiquitous regulators of gene expression in both plants and animals. They are thought to have evolved convergently in these lineages and hypothesized to have played a role in the evolution of multicellularity. In line with this hypothesis, miRNAs have so far only been described in few unicellular eukaryotes. Here, we investigate the presence and evolution of miRNAs in Amoebozoa, focusing on species belonging to Acanthamoeba, Physarum and dictyostelid taxonomic groups, representing a range of unicellular and multicellular lifestyles. miRNAs that adhere to both the stringent plant and animal miRNA criteria were identified in all examined amoebae, expanding the total number of protists harbouring miRNAs from 7 to 15. We found conserved miRNAs between closely related species, but the majority of species feature only unique miRNAs. This shows rapid gain and/or loss of miRNAs in Amoebozoa, further illustrated by a detailed comparison between two evolutionary closely related dictyostelids. Additionally, loss of miRNAs in the Dictyostelium discoideum drnB mutant did not seem to affect multicellular development and, hence, demonstrates that the presence of miRNAs does not appear to be a strict requirement for the transition from uni- to multicellular life.", "doi": "10.1093/nar/gkae109", "pmid": "38375870", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11014262"}, {"db": "pii", "key": "7611030"}], "notes": [], "created": "2024-10-22T07:38:55.161Z", "modified": "2024-11-25T10:25:30.684Z"}, {"entity": "publication", "iuid": "577c244ab9fc4be88fafc3a8861cee93", "links": {"self": {"href": "https://publications.scilifelab.se/publication/577c244ab9fc4be88fafc3a8861cee93.json"}, "display": {"href": "https://publications.scilifelab.se/publication/577c244ab9fc4be88fafc3a8861cee93"}}, "title": "Exploring the short linear motif-mediated protein-protein interactions of CrkL through ProP-PD.", "authors": [{"family": "Pagano", "given": "L", "initials": "L"}, {"family": "Simonetti", "given": "L", "initials": "L"}, {"family": "Pennacchietti", "given": "V", "initials": "V"}, {"family": "Toto", "given": "A", "initials": "A"}, {"family": "Malagrin\u00f2", "given": "F", "initials": "F"}, {"family": "Ivarsson", "given": "Y", "initials": "Y"}, {"family": "Gianni", "given": "S", "initials": "S"}], "type": "journal article", "published": "2024-04-09", "journal": {"title": "Biochem. Biophys. Res. Commun.", "issn": "1090-2104", "volume": "703", "pages": "149658", "issn-l": "0006-291X"}, "abstract": "Adaptor proteins play a pivotal role in cellular signaling mediating a multitude of protein-protein interaction critical for cellular homeostasis. Dysregulation of these interactions has been linked to the onset of various cancer pathologies and exploited by viral pathogens during host cell takeover. CrkL is an adaptor protein composed of an N-terminal SH2 domain followed by two SH3 domains that mediate interactions with diverse partners through the recognition of specific binding motifs. In this study, we employed proteomic peptide-phage display (ProP-PD) to comprehensively explore the short linear motif (SLiM)-based interactions of CrkL. Furthermore, we scrutinized how the binding affinity for selected peptides was influenced in the context of the full-length CrkL versus the isolated N-SH3 domain. Importantly, our results provided insights into SLiM-binding sites within previously reported interactors, as well as revealing novel human and viral ligands, expanding our understanding of the interactions mediated by CrkL and highlighting the significance of SLiM-based interactions in mediating adaptor protein function, with implications for cancer and viral pathologies.", "doi": "10.1016/j.bbrc.2024.149658", "pmid": "38387229", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pii", "key": "S0006-291X(24)00194-3"}], "notes": [], "created": "2024-03-21T09:26:15.858Z", "modified": "2024-03-21T09:26:15.862Z"}, {"entity": "publication", "iuid": "a82091c31c4d4910869e7a8476a5f298", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a82091c31c4d4910869e7a8476a5f298.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a82091c31c4d4910869e7a8476a5f298"}}, "title": "Treatment Monitoring of a Patient with Synchronous Metastatic Angiosarcoma and Breast Cancer Using ctDNA.", "authors": [{"family": "Vannas", "given": "Christoffer", "initials": "C", "orcid": "0000-0002-1029-0393", "researcher": {"href": "https://publications.scilifelab.se/researcher/d0e2981f2d6d4da586bf9f02abdfa539.json"}}, {"family": "Escobar", "given": "Mandy", "initials": "M", "orcid": "0000-0002-9095-1429", "researcher": {"href": "https://publications.scilifelab.se/researcher/84cd7b6436cf4b5585c0c53370d88728.json"}}, {"family": "\u00d6sterlund", "given": "Tobias", "initials": "T", "orcid": "0000-0002-7870-8645", "researcher": {"href": "https://publications.scilifelab.se/researcher/dd452c3f815846eba9a0da736ed6b252.json"}}, {"family": "Andersson", "given": "Daniel", "initials": "D", "orcid": "0000-0002-4564-6652", "researcher": {"href": "https://publications.scilifelab.se/researcher/655089dbe08b4b2283c3bf81a3db3abc.json"}}, {"family": "Mouhanna", "given": "Pia", "initials": "P", "orcid": "0009-0000-2722-2963", "researcher": {"href": "https://publications.scilifelab.se/researcher/17cb3367a55f432ba11e67badc6178b8.json"}}, {"family": "Soom\u00e4gi", "given": "Amanda", "initials": "A"}, {"family": "Molin", "given": "Claes", "initials": "C"}, {"family": "Wennergren", "given": "David", "initials": "D"}, {"family": "Fagman", "given": "Henrik", "initials": "H"}, {"family": "St\u00e5hlberg", "given": "Anders", "initials": "A", "orcid": "0000-0003-4243-0191", "researcher": {"href": "https://publications.scilifelab.se/researcher/05306b130d6543eea88a4f518085981e.json"}}], "type": "case reports", "published": "2024-04-04", "journal": {"title": "Int J Mol Sci", "issn": "1422-0067", "volume": "25", "issue": "7", "issn-l": null}, "abstract": "Angiosarcoma is a rare and aggressive type of soft-tissue sarcoma with high propensity to metastasize. For patients with metastatic angiosarcoma, prognosis is dismal and treatment options are limited. To improve the outcomes, identifying patients with poor treatment response at an earlier stage is imperative, enabling alternative therapy. Consequently, there is a need for improved methods and biomarkers for treatment monitoring. Quantification of circulating tumor-DNA (ctDNA) is a promising approach for patient-specific monitoring of treatment response. In this case report, we demonstrate that quantification of ctDNA using SiMSen-Seq was successfully utilized to monitor a patient with metastatic angiosarcoma. By quantifying ctDNA levels using 25 patient-specific mutations in blood plasma throughout surgery and palliative chemotherapy, we predicted the outcome and monitored the clinical response to treatment. This was accomplished despite the additional complexity of the patient having a synchronous breast cancer. The levels of ctDNA showed a superior correlation to the clinical outcome compared with the radiological evaluations. Our data propose a promising approach for personalized biomarker analysis to monitor treatment in angiosarcomas, with potential applicability to other cancers and for patients with synchronous malignancies.", "doi": "10.3390/ijms25074023", "pmid": "38612833", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11012383"}, {"db": "pii", "key": "ijms25074023"}], "notes": [], "created": "2024-05-16T06:28:56.803Z", "modified": "2024-05-16T06:28:57.902Z"}, {"entity": "publication", "iuid": "63e7b29f92a149148163f3d5af923fbd", "links": {"self": {"href": "https://publications.scilifelab.se/publication/63e7b29f92a149148163f3d5af923fbd.json"}, "display": {"href": "https://publications.scilifelab.se/publication/63e7b29f92a149148163f3d5af923fbd"}}, "title": "The HLA region in ANCA-associated vasculitis: characterisation of genetic associations in a Scandinavian patient population.", "authors": [{"family": "Lundtoft", "given": "Christian", "initials": "C"}, {"family": "Knight", "given": "Ann", "initials": "A"}, {"family": "Meadows", "given": "Jennifer R S", "initials": "JRS"}, {"family": "Karlsson", "given": "\u00c5sa", "initials": "\u00c5"}, {"family": "Rantap\u00e4\u00e4-Dahlqvist", "given": "Solbritt", "initials": "S", "orcid": "0000-0001-8259-3863", "researcher": {"href": "https://publications.scilifelab.se/researcher/dfca4bfdcf3946fda64397d3b7debc59.json"}}, {"family": "Berglin", "given": "Ewa", "initials": "E"}, {"family": "Palm", "given": "\u00d8yvind", "initials": "\u00d8"}, {"family": "Haukeland", "given": "Hilde", "initials": "H"}, {"family": "Gunnarsson", "given": "Iva", "initials": "I"}, {"family": "Bruchfeld", "given": "Annette", "initials": "A"}, {"family": "Segelmark", "given": "M\u00e5rten", "initials": "M"}, {"family": "Ohlsson", "given": "Sophie", "initials": "S"}, {"family": "Mohammad", "given": "Aladdin J", "initials": "AJ", "orcid": "0000-0002-7169-6936", "researcher": {"href": "https://publications.scilifelab.se/researcher/d7010c3f5b91415dbc26c87d6a923f68.json"}}, {"family": "Eriksson", "given": "Per", "initials": "P"}, {"family": "S\u00f6derkvist", "given": "Peter", "initials": "P"}, {"family": "Ronnblom", "given": "Lars", "initials": "L"}, {"family": "Omdal", "given": "Roald", "initials": "R"}, {"family": "Jonsson", "given": "Roland", "initials": "R", "orcid": "0000-0002-9588-0260", "researcher": {"href": "https://publications.scilifelab.se/researcher/f6edb43a7da34bf9af85c876b1b8974a.json"}}, {"family": "Lindblad-Toh", "given": "Kerstin", "initials": "K"}, {"family": "Dahlqvist", "given": "Johanna", "initials": "J", "orcid": "0000-0002-6283-644X", "researcher": {"href": "https://publications.scilifelab.se/researcher/8fb2ab2d83b6437f9918f330e5fb81b2.json"}}], "type": "journal article", "published": "2024-04-04", "journal": {"title": "RMD Open", "issn": "2056-5933", "volume": "10", "issue": "2", "issn-l": "2056-5933"}, "abstract": "The antineutrophil cytoplasmic antibody (ANCA)-associated vasculitides (AAV) are inflammatory disorders with ANCA autoantibodies recognising either proteinase 3 (PR3-AAV) or myeloperoxidase (MPO-AAV). PR3-AAV and MPO-AAV have been associated with distinct loci in the human leucocyte antigen (HLA) region. While the association between MPO-AAV and HLA has been well characterised in East Asian populations where MPO-AAV is more common, studies in populations of European descent are limited. The aim of this study was to thoroughly characterise associations to the HLA region in Scandinavian patients with PR3-AAV as well as MPO-AAV.\n\nGenotypes of single-nucleotide polymorphisms (SNPs) located in the HLA region were extracted from a targeted exome-sequencing dataset comprising Scandinavian AAV cases and controls. Classical HLA alleles were called using xHLA. After quality control, association analyses were performed of a joint SNP/classical HLA allele dataset for cases with PR3-AAV (n=411) and MPO-AAV (n=162) versus controls (n=1595). Disease-associated genetic variants were analysed for association with organ involvement, age at diagnosis and relapse, respectively.\n\nPR3-AAV was significantly associated with both HLA-DPB1*04:01 and rs1042335 at the HLA-DPB1 locus, also after stepwise conditional analysis. MPO-AAV was significantly associated with HLA-DRB1*04:04. Neither carriage of HLA-DPB1*04:01 alleles in PR3-AAV nor of HLA-DRB1*04:04 alleles in MPO-AAV were associated with organ involvement, age at diagnosis or relapse.\n\nThe association to the HLA region was distinct in Scandinavian cases with MPO-AAV compared with cases of East Asian descent. In PR3-AAV, the two separate signals of association to the HLD-DPB1 region mediate potentially different functional effects.", "doi": "10.1136/rmdopen-2023-004039", "pmid": "38580345", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support and Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11002376"}, {"db": "pii", "key": "rmdopen-2023-004039"}], "notes": [], "created": "2024-04-15T06:10:27.649Z", "modified": "2024-11-25T10:28:43.870Z"}, {"entity": "publication", "iuid": "433fbcdbe4af4353acf3eda9ea1ddc67", "links": {"self": {"href": "https://publications.scilifelab.se/publication/433fbcdbe4af4353acf3eda9ea1ddc67.json"}, "display": {"href": "https://publications.scilifelab.se/publication/433fbcdbe4af4353acf3eda9ea1ddc67"}}, "title": "Microbial succession and denitrifying woodchip bioreactor performance at low water temperatures.", "authors": [{"family": "Hellman", "given": "Maria", "initials": "M"}, {"family": "Juhanson", "given": "Jaanis", "initials": "J"}, {"family": "Walln\u00e4s", "given": "Felicia", "initials": "F"}, {"family": "Herbert", "given": "Roger B", "initials": "RB"}, {"family": "Hallin", "given": "Sara", "initials": "S"}], "type": "journal article", "published": "2024-04-00", "journal": {"title": "J Environ Manage", "issn": "1095-8630", "volume": "356", "pages": "120607", "issn-l": null}, "abstract": "Mining activities are increasingly recognized for contributing to nitrogen (N) pollution and possibly also to emissions of the greenhouse gas nitrous oxide (N2O) due to undetonated, N-based explosives. A woodchip denitrifying bioreactor, installed to treat nitrate-rich leachate from waste rock dumps in northern Sweden, was monitored for two years to determine the spatial and temporal distribution of microbial communities, including the genetic potential for different N transformation processes, in pore water and woodchips and how this related to reactor N removal capacity. About 80 and 65 % of the nitrate was removed during the first and second operational year, respectively. There was a succession in the microbial community over time and in space along the reactor length in both pore water and woodchips, which was reflected in reactor performance. Nitrate ammonification likely had minimal impact on N removal efficiency due to the low production of ammonium and low abundance of the key gene nrfA in ammonifiers. Nitrite and N2O were formed in the bioreactor and released in the effluent water, although direct N2O emissions from the surface was low. That these unwanted reactive N species were produced at different times and locations in the reactor indicate that the denitrification pathway was temporally as well as spatially separated along the reactor length. We conclude that the succession of microbial communities in woodchip denitrifying bioreactors treating mining water develops slowly at low temperature, which impacts reactor performance.", "doi": "10.1016/j.jenvman.2024.120607", "pmid": "38537471", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pii", "key": "S0301-4797(24)00593-0"}], "notes": [], "created": "2024-05-16T06:31:09.458Z", "modified": "2024-05-16T06:31:09.461Z"}, {"entity": "publication", "iuid": "4d3993643a224b9b98910f1921767b5f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4d3993643a224b9b98910f1921767b5f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4d3993643a224b9b98910f1921767b5f"}}, "title": "Meta-analysis of ACE inhibitor-induced angioedema identifies novel risk locus.", "authors": [{"family": "Mathey", "given": "Carina M", "initials": "CM"}, {"family": "Maj", "given": "Carlo", "initials": "C"}, {"family": "Eriksson", "given": "Niclas", "initials": "N"}, {"family": "Krebs", "given": "Kristi", "initials": "K"}, {"family": "Westmeier", "given": "Julia", "initials": "J"}, {"family": "David", "given": "Friederike S", "initials": "FS"}, {"family": "Koromina", "given": "Maria", "initials": "M"}, {"family": "Scheer", "given": "Annika B", "initials": "AB"}, {"family": "Szabo", "given": "Nora", "initials": "N"}, {"family": "Wedi", "given": "Bettina", "initials": "B"}, {"family": "Wieczorek", "given": "Dorothea", "initials": "D"}, {"family": "Amann", "given": "Philipp M", "initials": "PM"}, {"family": "L\u00f6ffler", "given": "Harald", "initials": "H"}, {"family": "Koch", "given": "Lukas", "initials": "L"}, {"family": "Sch\u00f6ffl", "given": "Clemens", "initials": "C"}, {"family": "Dickel", "given": "Heinrich", "initials": "H"}, {"family": "Ganjuur", "given": "Nomun", "initials": "N"}, {"family": "Hornung", "given": "Thorsten", "initials": "T"}, {"family": "Buhl", "given": "Timo", "initials": "T"}, {"family": "Greve", "given": "Jens", "initials": "J"}, {"family": "Wurpts", "given": "Gerda", "initials": "G"}, {"family": "Ayg\u00f6ren-P\u00fcrs\u00fcn", "given": "Emel", "initials": "E"}, {"family": "Steffens", "given": "Michael", "initials": "M"}, {"family": "Herms", "given": "Stefan", "initials": "S"}, {"family": "Heilmann-Heimbach", "given": "Stefanie", "initials": "S"}, {"family": "Hoffmann", "given": "Per", "initials": "P"}, {"family": "Schmidt", "given": "B\u00f6rge", "initials": "B"}, {"family": "Mavarani", "given": "Laven", "initials": "L"}, {"family": "Andresen", "given": "Trine", "initials": "T"}, {"family": "S\u00f8rensen", "given": "Signe Bek", "initials": "SB"}, {"family": "Andersen", "given": "Vibeke", "initials": "V"}, {"family": "Vogel", "given": "Ulla", "initials": "U"}, {"family": "Land\u00e9n", "given": "Mikael", "initials": "M"}, {"family": "Bulik", "given": "Cynthia M", "initials": "CM"}, {"family": "Estonian Biobank Research Team", "given": "", "initials": ""}, {"family": "DBDS Genomic Consortium", "given": "", "initials": ""}, {"family": "Bygum", "given": "Anette", "initials": "A"}, {"family": "Magnusson", "given": "Patrik K E", "initials": "PKE"}, {"family": "von Buchwald", "given": "Christian", "initials": "C"}, {"family": "Hallberg", "given": "P\u00e4r", "initials": "P"}, {"family": "Rye Ostrowski", "given": "Sisse", "initials": "S"}, {"family": "S\u00f8rensen", "given": "Erik", "initials": "E"}, {"family": "Pedersen", "given": "Ole B", "initials": "OB"}, {"family": "Ullum", "given": "Henrik", "initials": "H"}, {"family": "Erikstrup", "given": "Christian", "initials": "C"}, {"family": "Bundgaard", "given": "Henning", "initials": "H"}, {"family": "Milani", "given": "Lili", "initials": "L"}, {"family": "Rasmussen", "given": "Eva Rye", "initials": "ER"}, {"family": "Wadelius", "given": "Mia", "initials": "M"}, {"family": "Ghouse", "given": "Jonas", "initials": "J"}, {"family": "Sachs", "given": "Bernhardt", "initials": "B"}, {"family": "N\u00f6then", "given": "Markus M", "initials": "MM"}, {"family": "Forstner", "given": "Andreas J", "initials": "AJ"}], "type": "meta-analysis", "published": "2024-04-00", "journal": {"title": "J. Allergy Clin. Immunol.", "issn": "1097-6825", "volume": "153", "issue": "4", "pages": "1073-1082", "issn-l": "0091-6749"}, "abstract": "Angioedema is a rare but potentially life-threatening adverse drug reaction in patients receiving angiotensin-converting enzyme inhibitors (ACEis). Research suggests that susceptibility to ACEi-induced angioedema (ACEi-AE) involves both genetic and nongenetic risk factors. Genome- and exome-wide studies of ACEi-AE have identified the first genetic risk loci. However, understanding of the underlying pathophysiology remains limited.\n\nWe sought to identify further genetic factors of ACEi-AE to eventually gain a deeper understanding of its pathophysiology.\n\nBy combining data from 8 cohorts, a genome-wide association study meta-analysis was performed in more than 1000 European patients with ACEi-AE. Secondary bioinformatic analyses were conducted to fine-map associated loci, identify relevant genes and pathways, and assess the genetic overlap between ACEi-AE and other traits. Finally, an exploratory cross-ancestry analysis was performed to assess shared genetic factors in European and African-American patients with ACEi-AE.\n\nThree genome-wide significant risk loci were identified. One of these, located on chromosome 20q11.22, has not been implicated previously in ACEi-AE. Integrative secondary analyses highlighted previously reported genes (BDKRB2 [bradykinin receptor B2] and F5 [coagulation factor 5]) as well as biologically plausible novel candidate genes (PROCR [protein C receptor] and EDEM2 [endoplasmic reticulum degradation enhancing alpha-mannosidase like protein 2]). Lead variants at the risk loci were found with similar effect sizes and directions in an African-American cohort.\n\nThe present results contributed to a deeper understanding of the pathophysiology of ACEi-AE by (1) providing further evidence for the involvement of bradykinin signaling and coagulation pathways and (2) suggesting, for the first time, the involvement of the fibrinolysis pathway in this adverse drug reaction. An exploratory cross-ancestry comparison implicated the relevance of the associated risk loci across diverse ancestries.", "doi": "10.1016/j.jaci.2023.11.921", "pmid": "38300190", "labels": {"NGI SNP genotyping": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pii", "key": "S0091-6749(23)02457-0"}], "notes": [], "created": "2024-03-21T12:08:52.535Z", "modified": "2024-10-21T11:21:07.009Z"}, {"entity": "publication", "iuid": "e6cc001910f440a9a2b1eb0ef4ee7edc", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e6cc001910f440a9a2b1eb0ef4ee7edc.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e6cc001910f440a9a2b1eb0ef4ee7edc"}}, "title": "Refining risk prediction in pediatric acute lymphoblastic leukemia through DNA methylation profiling.", "authors": [{"family": "Mosquera Orgueira", "given": "Adri\u00e1n", "initials": "A"}, {"family": "Krali", "given": "Olga", "initials": "O"}, {"family": "P\u00e9rez M\u00edguez", "given": "Carlos", "initials": "C"}, {"family": "Peleteiro Ra\u00edndo", "given": "Andr\u00e9s", "initials": "A"}, {"family": "D\u00edaz Arias", "given": "Jos\u00e9 \u00c1ngel", "initials": "J\u00c1"}, {"family": "Gonz\u00e1lez P\u00e9rez", "given": "Marta Sonia", "initials": "MS"}, {"family": "P\u00e9rez Encinas", "given": "Manuel Mateo", "initials": "MM"}, {"family": "Fern\u00e1ndez Sanmart\u00edn", "given": "Manuel", "initials": "M"}, {"family": "Sinnet", "given": "Daniel", "initials": "D"}, {"family": "Heyman", "given": "Mats", "initials": "M"}, {"family": "L\u00f6nnerholm", "given": "Gudmar", "initials": "G"}, {"family": "Nor\u00e9n-Nystr\u00f6m", "given": "Ulrika", "initials": "U"}, {"family": "Schmiegelow", "given": "Kjeld", "initials": "K"}, {"family": "Nordlund", "given": "Jessica", "initials": "J"}], "type": "journal article", "published": "2024-03-28", "journal": {"title": "Clin Epigenetics", "issn": "1868-7083", "issn-l": "1868-7075", "volume": "16", "issue": "1", "pages": "49"}, "abstract": "Acute lymphoblastic leukemia (ALL) is the most prevalent cancer in children, and despite considerable progress in treatment outcomes, relapses still pose significant risks of mortality and long-term complications. To address this challenge, we employed a supervised machine learning technique, specifically random survival forests, to predict the risk of relapse and mortality using array-based DNA methylation data from a cohort of 763 pediatric ALL patients treated in Nordic countries. The relapse risk predictor (RRP) was constructed based on 16 CpG sites, demonstrating c-indexes of 0.667 and 0.677 in the training and test sets, respectively. The mortality risk predictor (MRP), comprising 53 CpG sites, exhibited c-indexes of 0.751 and 0.754 in the training and test sets, respectively. To validate the prognostic value of the predictors, we further analyzed two independent cohorts of Canadian (n = 42) and Nordic (n = 384) ALL patients. The external validation confirmed our findings, with the RRP achieving a c-index of 0.667 in the Canadian cohort, and the RRP and MRP achieving c-indexes of 0.529 and 0.621, respectively, in an independent Nordic cohort. The precision of the RRP and MRP models improved when incorporating traditional risk group data, underscoring the potential for synergistic integration of clinical prognostic factors. The MRP model also enabled the definition of a risk group with high rates of relapse and mortality. Our results demonstrate the potential of DNA methylation as a prognostic factor and a tool to refine risk stratification in pediatric ALL. This may lead to personalized treatment strategies based on epigenetic profiling.", "doi": "10.1186/s13148-024-01662-6", "pmid": "38549146", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "NGI SNP genotyping": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10976833"}, {"db": "pii", "key": "10.1186/s13148-024-01662-6"}], "notes": [], "created": "2024-11-05T18:15:40.697Z", "modified": "2024-11-25T10:31:14.110Z"}, {"entity": "publication", "iuid": "d95f4f6b8ceb4ca7b80714ec7fcb18f4", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d95f4f6b8ceb4ca7b80714ec7fcb18f4.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d95f4f6b8ceb4ca7b80714ec7fcb18f4"}}, "title": "Identification and surveillance of rare relapse-initiating stem cells during complete remission after transplantation.", "authors": [{"family": "Dimitriou", "given": "Marios", "initials": "M", "orcid": "0000-0001-8362-2099", "researcher": {"href": "https://publications.scilifelab.se/researcher/531c153359bb400fb48c7324a3bd69ad.json"}}, {"family": "Mortera-Blanco", "given": "Teresa", "initials": "T"}, {"family": "Tobiasson", "given": "Magnus", "initials": "M", "orcid": "0000-0002-3633-5852", "researcher": {"href": "https://publications.scilifelab.se/researcher/37b88e8e02af4145b95cc379c68ebee9.json"}}, {"family": "Mazzi", "given": "Stefania", "initials": "S"}, {"family": "Lehander", "given": "Madeleine", "initials": "M", "orcid": "0009-0005-0114-4502", "researcher": {"href": "https://publications.scilifelab.se/researcher/ad724c37fc354c209b21b9b60431bf8e.json"}}, {"family": "H\u00f6gstrand", "given": "Kari", "initials": "K"}, {"family": "Karimi", "given": "Mohsen", "initials": "M"}, {"family": "Walldin", "given": "Gunilla", "initials": "G", "orcid": "0009-0005-6663-6540", "researcher": {"href": "https://publications.scilifelab.se/researcher/24fb888d0212421eaa2353ed6cc31ac7.json"}}, {"family": "Jansson", "given": "Monika", "initials": "M"}, {"family": "Vonlanthen", "given": "Sofie", "initials": "S", "orcid": "0000-0002-6215-7631", "researcher": {"href": "https://publications.scilifelab.se/researcher/376695e4d6f54d1caf6e776bf537864b.json"}}, {"family": "Ljungman", "given": "Per", "initials": "P", "orcid": "0000-0002-8281-3245", "researcher": {"href": "https://publications.scilifelab.se/researcher/0e5e4220ae354a2e99cd69797638a529.json"}}, {"family": "Langemeijer", "given": "Saskia", "initials": "S"}, {"family": "Yoshizato", "given": "Tetsuichi", "initials": "T", "orcid": "0000-0003-4283-2983", "researcher": {"href": "https://publications.scilifelab.se/researcher/d6f499e339d2444b817a81ab2712b9e5.json"}}, {"family": "Hellstr\u00f6m-Lindberg", "given": "Eva", "initials": "E"}, {"family": "Woll", "given": "Petter S", "initials": "PS", "orcid": "0000-0002-2340-2526", "researcher": {"href": "https://publications.scilifelab.se/researcher/77ae0c1d2cf5461894c6d0d80ed42f68.json"}}, {"family": "Jacobsen", "given": "Sten Eirik W", "initials": "SEW", "orcid": "0000-0002-1362-3659", "researcher": {"href": "https://publications.scilifelab.se/researcher/648fc5e4f49e4330b095c26cd965cc98.json"}}], "type": "journal article", "published": "2024-03-14", "journal": {"title": "Blood", "issn": "1528-0020", "volume": "143", "issue": "11", "pages": "953-966", "issn-l": "0006-4971"}, "abstract": "Relapse after complete remission (CR) remains the main cause of mortality after allogeneic stem cell transplantation for hematological malignancies and, therefore, improved biomarkers for early prediction of relapse remains a critical goal toward development and assessment of preemptive relapse treatment. Because the significance of cancer stem cells as a source of relapses remains unclear, we investigated whether mutational screening for persistence of rare cancer stem cells would enhance measurable residual disease (MRD) and early relapse prediction after transplantation. In a retrospective study of patients who relapsed and patients who achieved continuous-CR with myelodysplastic syndromes and related myeloid malignancies, combined flow cytometric cell sorting and mutational screening for persistence of rare relapse-initiating stem cells was performed in the bone marrow at multiple CR time points after transplantation. In 25 CR samples from 15 patients that later relapsed, only 9 samples were MRD-positive in mononuclear cells (MNCs) whereas flowcytometric-sorted hematopoietic stem and progenitor cells (HSPCs) were MRD-positive in all samples, and always with a higher variant allele frequency than in MNCs (mean, 97-fold). MRD-positivity in HSPCs preceded MNCs in multiple sequential samples, in some cases preceding relapse by >2 years. In contrast, in 13 patients in long-term continuous-CR, HSPCs remained MRD-negative. Enhanced MRD sensitivity was also observed in total CD34+ cells, but HSPCs were always more clonally involved (mean, 8-fold). In conclusion, identification of relapse-initiating cancer stem cells and mutational MRD screening for their persistence consistently enhances MRD sensitivity and earlier prediction of relapse after allogeneic stem cell transplantation.", "doi": "10.1182/blood.2023022851", "pmid": "38096358", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Short read": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10950475"}, {"db": "pii", "key": "S0006-4971(23)14644-1"}], "notes": [], "created": "2024-10-21T11:19:06.816Z", "modified": "2024-10-21T11:19:21.211Z"}, {"entity": "publication", "iuid": "3450b7c1f75249119cccdb958020c5dc", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3450b7c1f75249119cccdb958020c5dc.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3450b7c1f75249119cccdb958020c5dc"}}, "title": "Identification of microbial pathogens in Neolithic Scandinavian humans.", "authors": [{"family": "Bergfeldt", "given": "Nora", "initials": "N"}, {"family": "K\u0131rd\u00f6k", "given": "Emrah", "initials": "E"}, {"family": "Oskolkov", "given": "Nikolay", "initials": "N"}, {"family": "Mirabello", "given": "Claudio", "initials": "C"}, {"family": "Unneberg", "given": "Per", "initials": "P"}, {"family": "Malmstr\u00f6m", "given": "Helena", "initials": "H"}, {"family": "Fraser", "given": "Magdalena", "initials": "M"}, {"family": "Sanchez-Quinto", "given": "Federico", "initials": "F"}, {"family": "Jorgensen", "given": "Roger", "initials": "R"}, {"family": "Skar", "given": "Birgitte", "initials": "B"}, {"family": "Lid\u00e9n", "given": "Kerstin", "initials": "K"}, {"family": "Jakobsson", "given": "Mattias", "initials": "M"}, {"family": "Stor\u00e5", "given": "Jan", "initials": "J"}, {"family": "G\u00f6therstr\u00f6m", "given": "Anders", "initials": "A"}], "type": "journal article", "published": "2024-03-07", "journal": {"title": "Sci Rep", "issn": "2045-2322", "issn-l": "2045-2322", "volume": "14", "issue": "1", "pages": "5630"}, "abstract": "With the Neolithic transition, human lifestyle shifted from hunting and gathering to farming. This change altered subsistence patterns, cultural expression, and population structures as shown by the archaeological/zooarchaeological record, as well as by stable isotope and ancient DNA data. Here, we used metagenomic data to analyse if the transitions also impacted the microbiome composition in 25 Mesolithic and Neolithic hunter-gatherers and 13 Neolithic farmers from several Scandinavian Stone Age cultural contexts. Salmonella enterica, a bacterium that may have been the cause of death for the infected individuals, was found in two Neolithic samples from Battle Axe culture contexts. Several species of the bacterial genus Yersinia were found in Neolithic individuals from Funnel Beaker culture contexts as well as from later Neolithic context. Transmission of e.g. Y. enterocolitica may have been facilitated by the denser populations in agricultural contexts.", "doi": "10.1038/s41598-024-56096-0", "pmid": "38453993", "labels": {"NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC10920878"}, {"db": "pii", "key": "10.1038/s41598-024-56096-0"}], "notes": [], "created": "2024-03-14T11:09:30.525Z", "modified": "2024-11-25T10:21:03.650Z"}, {"entity": "publication", "iuid": "1fe7298fac0643f4aad58a25d24aa7d0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1fe7298fac0643f4aad58a25d24aa7d0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1fe7298fac0643f4aad58a25d24aa7d0"}}, "title": "Loss of chromosome Y in regulatory T cells.", "authors": [{"family": "Mattisson", "given": "Jonas", "initials": "J"}, {"family": "Halvardson", "given": "Jonatan", "initials": "J"}, {"family": "Davies", "given": "Hanna", "initials": "H"}, {"family": "Bruhn-Olszewska", "given": "Bo\u017cena", "initials": "B"}, {"family": "Olszewski", "given": "Pawe\u0142", "initials": "P"}, {"family": "Danielsson", "given": "Marcus", "initials": "M"}, {"family": "Bjurling", "given": "Josefin", "initials": "J"}, {"family": "Lindberg", "given": "Amanda", "initials": "A"}, {"family": "Zaghlool", "given": "Ammar", "initials": "A"}, {"family": "Rychlicka-Buniowska", "given": "Edyta", "initials": "E"}, {"family": "Dumanski", "given": "Jan P", "initials": "JP"}, {"family": "Forsberg", "given": "Lars A", "initials": "LA"}], "type": "journal article", "published": "2024-03-05", "journal": {"title": "BMC Genomics", "issn": "1471-2164", "volume": "25", "issue": "1", "pages": "243", "issn-l": "1471-2164"}, "abstract": "Mosaic loss of chromosome Y (LOY) in leukocytes is the most prevalent somatic aneuploidy in aging humans. Men with LOY have increased risks of all-cause mortality and the major causes of death, including many forms of cancer. It has been suggested that the association between LOY and disease risk depends on what type of leukocyte is affected with Y loss, with prostate cancer patients showing higher levels of LOY in CD4 + T lymphocytes. In previous studies, Y loss has however been observed at relatively low levels in this cell type. This motivated us to investigate whether specific subsets of CD4 + T lymphocytes are particularly affected by LOY. Publicly available, T lymphocyte enriched, single-cell RNA sequencing datasets from patients with liver, lung or colorectal cancer were used to study how LOY affects different subtypes of T lymphocyte. To validate the observations from the public data, we also generated a single-cell RNA sequencing dataset comprised of 23 PBMC samples and 32 CD4 + T lymphocytes enriched samples.\n\nRegulatory T cells had significantly more LOY than any other studied T lymphocytes subtype. Furthermore, LOY in regulatory T cells increased the ratio of regulatory T cells compared with other T lymphocyte subtypes, indicating an effect of Y loss on lymphocyte differentiation. This was supported by developmental trajectory analysis of CD4 + T lymphocytes culminating in the regulatory T cells cluster most heavily affected by LOY. Finally, we identify dysregulation of 465 genes in regulatory T cells with Y loss, many involved in the immunosuppressive functions and development of regulatory T cells.\n\nHere, we show that regulatory T cells are particularly affected by Y loss, resulting in an increased fraction of regulatory T cells and dysregulated immune functions. Considering that regulatory T cells plays a critical role in the process of immunosuppression; this enrichment for regulatory T cells with LOY might contribute to the increased risk for cancer observed among men with Y loss in leukocytes.", "doi": "10.1186/s12864-024-10168-7", "pmid": "38443832", "labels": {"NGI Single cell": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10913415"}, {"db": "pii", "key": "10.1186/s12864-024-10168-7"}], "notes": [], "created": "2024-03-06T13:04:09.255Z", "modified": "2025-02-28T14:21:55.540Z"}, {"entity": "publication", "iuid": "c033e6d550b3493f91cfc42d9b9ebccd", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c033e6d550b3493f91cfc42d9b9ebccd.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c033e6d550b3493f91cfc42d9b9ebccd"}}, "title": "Genomic ancestry and social dynamics of the last hunter-gatherers of Atlantic France.", "authors": [{"family": "Sim\u00f5es", "given": "Luciana G", "initials": "LG", "orcid": "0000-0002-6119-9776", "researcher": {"href": "https://publications.scilifelab.se/researcher/eea5b7ccd8f84d44b2e0be03f5c4e762.json"}}, {"family": "Peyroteo-Stjerna", "given": "Rita", "initials": "R", "orcid": "0000-0002-3309-474X", "researcher": {"href": "https://publications.scilifelab.se/researcher/e6a9ae2a39e94beba21b461ef827ce17.json"}}, {"family": "Marchand", "given": "Gr\u00e9gor", "initials": "G"}, {"family": "Bernhardsson", "given": "Carolina", "initials": "C", "orcid": "0000-0002-3258-275X", "researcher": {"href": "https://publications.scilifelab.se/researcher/b8fce67de4e14fa68c0edadfec0de085.json"}}, {"family": "Vialet", "given": "Am\u00e9lie", "initials": "A"}, {"family": "Chetty", "given": "Darshan", "initials": "D", "orcid": "0000-0003-4668-1182", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a9c8096ccbc4b4e943373d9a3acd5b1.json"}}, {"family": "Ala\u00e7aml\u0131", "given": "Erkin", "initials": "E", "orcid": "0009-0009-0702-3313", "researcher": {"href": "https://publications.scilifelab.se/researcher/9fb8084ce6634c9c8e33cc29e98f8252.json"}}, {"family": "Edlund", "given": "Hanna", "initials": "H"}, {"family": "Bouquin", "given": "Denis", "initials": "D"}, {"family": "Dina", "given": "Christian", "initials": "C"}, {"family": "Garmond", "given": "Nicolas", "initials": "N"}, {"family": "G\u00fcnther", "given": "Torsten", "initials": "T", "orcid": "0000-0001-9460-390X", "researcher": {"href": "https://publications.scilifelab.se/researcher/84159bff82a64a938bcff107f550c901.json"}}, {"family": "Jakobsson", "given": "Mattias", "initials": "M", "orcid": "0000-0001-7840-7853", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a4abe0fcb20492d9ec849c9fbf58a71.json"}}], "type": "journal article", "published": "2024-03-05", "journal": {"title": "Proc. Natl. Acad. Sci. U.S.A.", "issn": "1091-6490", "volume": "121", "issue": "10", "pages": "e2310545121", "issn-l": "0027-8424"}, "abstract": "Since the early Holocene, western and central Europe was inhabited by a genetically distinct group of Western Hunter-Gatherers (WHGs). This group was eventually replaced and assimilated by the incoming Neolithic farmers. The western Atlantic fa\u00e7ade was home to some of the last Mesolithic sites of mainland Europe, represented by the iconic open-air sites at Hoedic and T\u00e9viec in southern Brittany, France. These sites are known for the unusually well-preserved and rich burials. Genomic studies of Mesolithic European hunter-gatherers have been limited to single or a few individuals per site and our understanding of the social dynamics of the last Mesolithic hunter-gatherers of Europe and their interactions with incoming farmers is limited. We sequenced and analyzed the complete genomes of 10 individuals from the Late Mesolithic sites of Hoedic, T\u00e9viec, and Champigny, in France, four of which sequenced to between 23- and 8-times genome coverage. The analysis of genomic, chronological and dietary data revealed that the Late Mesolithic populations in Brittany maintained distinct social units within a network of exchanging mates. This resulted in low intra-group biological relatedness that prevented consanguineous mating, despite the small population size of the Late Mesolithic groups. We found no genetic ancestry from Neolithic farmers in the analyzed hunter-gatherers, even though some of them may have coexisted with the first farming groups in neighboring regions. Hence, contrary to previous conclusions based on stable isotope data from the same sites, the Late Mesolithic forager community was limited in mate-exchange to neighboring hunter-gatherer groups, to the exclusion of Neolithic farmers.", "doi": "10.1073/pnas.2310545121", "pmid": "38408241", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10927518"}], "notes": [], "created": "2024-02-27T13:17:58.460Z", "modified": "2024-11-25T10:22:31.622Z"}, {"entity": "publication", "iuid": "6dad922586f84341baf632ac55a61367", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6dad922586f84341baf632ac55a61367.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6dad922586f84341baf632ac55a61367"}}, "title": "High-Quality Genome Assemblies of 4 Members of the Podospora anserina Species Complex.", "authors": [{"family": "Ament-Vel\u00e1squez", "given": "S Lorena", "initials": "SL", "orcid": "0000-0003-3371-9292", "researcher": {"href": "https://publications.scilifelab.se/researcher/9d54ef94f91c4c1c85d5dc3a846023e5.json"}}, {"family": "Vogan", "given": "Aaron A", "initials": "AA", "orcid": "0000-0003-2013-7445", "researcher": {"href": "https://publications.scilifelab.se/researcher/71c6d460e3b44712a1a9dc19066211a4.json"}}, {"family": "Wallerman", "given": "Ola", "initials": "O"}, {"family": "Hartmann", "given": "Fanny E", "initials": "FE", "orcid": "0000-0002-9365-4008", "researcher": {"href": "https://publications.scilifelab.se/researcher/ac8e717031aa4621925ab90684adecdc.json"}}, {"family": "Gautier", "given": "Val\u00e9rie", "initials": "V"}, {"family": "Silar", "given": "Philippe", "initials": "P", "orcid": "0000-0003-0104-987X", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a40756e83bc493ebc1d98d8c5c374da.json"}}, {"family": "Giraud", "given": "Tatiana", "initials": "T"}, {"family": "Johannesson", "given": "Hanna", "initials": "H", "orcid": "0000-0001-6359-9856", "researcher": {"href": "https://publications.scilifelab.se/researcher/36e8fe278e01470e8cddaaccc5dad596.json"}}], "type": "journal article", "published": "2024-03-02", "journal": {"title": "Genome Biol Evol", "issn": "1759-6653", "volume": "16", "issue": "3", "issn-l": "1759-6653"}, "abstract": "The filamentous fungus Podospora anserina is a model organism used extensively in the study of molecular biology, senescence, prion biology, meiotic drive, mating-type chromosome evolution, and plant biomass degradation. It has recently been established that P. anserina is a member of a complex of 7 closely related species. In addition to P. anserina, high-quality genomic resources are available for 2 of these taxa. Here, we provide chromosome-level annotated assemblies of the 4 remaining species of the complex, as well as a comprehensive data set of annotated assemblies from a total of 28 Podospora genomes. We find that all 7 species have genomes of around 35 Mb arranged in 7 chromosomes that are mostly collinear and less than 2% divergent from each other at genic regions. We further attempt to resolve their phylogenetic relationships, finding significant levels of phylogenetic conflict as expected from a rapid and recent diversification.", "doi": "10.1093/gbe/evae034", "pmid": "38386982", "labels": {"NGI Uppsala (Uppsala Genome Center)": "Service", "National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Short read": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10936905"}, {"db": "pii", "key": "7612620"}], "notes": [], "created": "2024-08-02T12:17:18.611Z", "modified": "2025-02-28T14:18:08.086Z"}, {"entity": "publication", "iuid": "0d08036c5f154cf0b2c0036250a0fa7e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0d08036c5f154cf0b2c0036250a0fa7e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0d08036c5f154cf0b2c0036250a0fa7e"}}, "title": "The regulation of methylation on the Z chromosome and the identification of multiple novel Male Hyper-Methylated regions in the chicken.", "authors": [{"family": "H\u00f6glund", "given": "Andrey", "initials": "A", "orcid": "0000-0002-1130-374X", "researcher": {"href": "https://publications.scilifelab.se/researcher/70a484451caf40f2a1a196b36bb9c423.json"}}, {"family": "Henriksen", "given": "Rie", "initials": "R"}, {"family": "Churcher", "given": "Allison M", "initials": "AM", "orcid": "0000-0003-1902-3002", "researcher": {"href": "https://publications.scilifelab.se/researcher/d97e6fb500a043f08d4f882e802cd91b.json"}}, {"family": "Guerrero-Bosagna", "given": "Carlos M", "initials": "CM"}, {"family": "Martinez-Barrio", "given": "Alvaro", "initials": "A", "orcid": "0000-0001-5064-2093", "researcher": {"href": "https://publications.scilifelab.se/researcher/d6ff319fe64340f2bb2350121848ecff.json"}}, {"family": "Johnsson", "given": "Martin", "initials": "M", "orcid": "0000-0003-1262-4585", "researcher": {"href": "https://publications.scilifelab.se/researcher/02b768197c08422aaad526f35c526eaf.json"}}, {"family": "Jensen", "given": "Per", "initials": "P"}, {"family": "Wright", "given": "Dominic", "initials": "D", "orcid": "0000-0003-2329-2635", "researcher": {"href": "https://publications.scilifelab.se/researcher/6447b896ea3b453ab10136b5f44ae241.json"}}], "type": "journal article", "published": "2024-03-00", "journal": {"title": "PLoS Genet.", "issn": "1553-7404", "volume": "20", "issue": "3", "pages": "e1010719", "issn-l": "1553-7390"}, "abstract": "DNA methylation is a key regulator of eukaryote genomes, and is of particular relevance in the regulation of gene expression on the sex chromosomes, with a key role in dosage compensation in mammalian XY systems. In the case of birds, dosage compensation is largely absent, with it being restricted to two small Male Hyper-Methylated (MHM) regions on the Z chromosome. To investigate how variation in DNA methylation is regulated on the Z chromosome we utilised a wild x domestic advanced intercross in the chicken, with both hypothalamic methylomes and transcriptomes assayed in 124 individuals. The relatively large numbers of individuals allowed us to identify additional genomic MHM regions on the Z chromosome that were significantly differentially methylated between the sexes. These regions appear to down-regulate local gene expression in males, but not remove it entirely (unlike the lncRNAs identified in the initial MHM regions). These MHM regions were further tested and the most balanced genes appear to show decreased expression in males, whilst methylation appeared to be far more correlated with gene expression in the less balanced, as compared to the most balanced genes. In addition, quantitative trait loci (QTL) that regulate variation in methylation on the Z chromosome, and those loci that regulate methylation on the autosomes that derive from the Z chromosome were mapped. Trans-effect hotspots were also identified that were based on the autosomes but affected the Z, and also one that was based on the Z chromosome but that affected both autosomal and sex chromosome DNA methylation regulation. We show that both cis and trans loci that originate from the Z chromosome never exhibit an interaction with sex, whereas trans loci originating from the autosomes but affecting the Z chromosome always display such an interaction. Our results highlight how additional MHM regions are actually present on the Z chromosome, and they appear to have smaller-scale effects on gene expression in males. Quantitative variation in methylation is also regulated both from the autosomes to the Z chromosome, and from the Z chromosome to the autosomes.", "doi": "10.1371/journal.pgen.1010719", "pmid": "38457441", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "Service", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC10954189"}, {"db": "pii", "key": "PGENETICS-D-23-00328"}], "notes": [], "created": "2024-11-12T10:39:26.077Z", "modified": "2024-11-25T10:31:41.001Z"}, {"entity": "publication", "iuid": "8d17e70e0b5b4f70bad804ace9812eb2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8d17e70e0b5b4f70bad804ace9812eb2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8d17e70e0b5b4f70bad804ace9812eb2"}}, "title": "Sorption of pharmaceuticals to foam and aerobic granular sludge with different morphologies", "authors": [{"family": "Burzio", "given": "Cecilia", "initials": "C", "orcid": "0000-0003-3887-2720", "researcher": {"href": "https://publications.scilifelab.se/researcher/6ce542ce47d54ef88fb4306b282aacf8.json"}}, {"family": "Mohammadi", "given": "Amir Saeid", "initials": "AS", "orcid": "0000-0002-4600-773X", "researcher": {"href": "https://publications.scilifelab.se/researcher/6ed821235675423489a4cefa067f4800.json"}}, {"family": "Smith", "given": "Sanne", "initials": "S"}, {"family": "Abadikhah", "given": "Marie", "initials": "M", "orcid": "0000-0002-4270-3340", "researcher": {"href": "https://publications.scilifelab.se/researcher/94d7106a506f42b7bffcce6ffe6b455a.json"}}, {"family": "Svahn", "given": "Ola", "initials": "O"}, {"family": "Modin", "given": "Oskar", "initials": "O", "orcid": "0000-0002-9232-6096", "researcher": {"href": "https://publications.scilifelab.se/researcher/e1cfa2dd97cc472c9307498a65b5a8c6.json"}}, {"family": "Persson", "given": "Frank", "initials": "F", "orcid": "0000-0002-0269-9375", "researcher": {"href": "https://publications.scilifelab.se/researcher/40290cae1a7e44c1939801323653b31c.json"}}, {"family": "Wil\u00e9n", "given": "Britt Marie", "initials": "BM"}], "type": "journal-article", "published": "2024-03-00", "journal": {"title": "Resources, Environment and Sustainability", "issn": "2666-9161", "volume": "15", "pages": "100149", "issn-l": null}, "abstract": null, "doi": "10.1016/j.resenv.2024.100149", "pmid": null, "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2024-03-21T09:00:42.585Z", "modified": "2025-12-04T19:40:39.711Z"}, {"entity": "publication", "iuid": "3338a6f2c5b143219504dff0b95a9424", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3338a6f2c5b143219504dff0b95a9424.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3338a6f2c5b143219504dff0b95a9424"}}, "title": "Rare coding variants in NOX4 link high ROS levels to psoriatic arthritis mutilans.", "authors": [{"family": "Wang", "given": "Sailan", "initials": "S", "orcid": "0000-0002-1269-0649", "researcher": {"href": "https://publications.scilifelab.se/researcher/c0dc9eda6e3a4cc2a68abf0e6d47f9f9.json"}}, {"family": "Nikamo", "given": "Pernilla", "initials": "P"}, {"family": "Laasonen", "given": "Leena", "initials": "L"}, {"family": "Gudbjornsson", "given": "Bjorn", "initials": "B", "orcid": "0000-0003-4631-6505", "researcher": {"href": "https://publications.scilifelab.se/researcher/0fb0b2ab4bd24099966d487f6f299303.json"}}, {"family": "Ejstrup", "given": "Leif", "initials": "L"}, {"family": "Iversen", "given": "Lars", "initials": "L", "orcid": "0000-0003-1816-4508", "researcher": {"href": "https://publications.scilifelab.se/researcher/ed66867f11dd4dffb67e3f32e37d1ec8.json"}}, {"family": "Lindqvist", "given": "Ulla", "initials": "U"}, {"family": "Alm", "given": "Jessica J", "initials": "JJ", "orcid": "0000-0002-2066-9073", "researcher": {"href": "https://publications.scilifelab.se/researcher/9800995eec454011a4ec3b682789eca0.json"}}, {"family": "Eisfeldt", "given": "Jesper", "initials": "J"}, {"family": "Zheng", "given": "Xiaowei", "initials": "X"}, {"family": "Catrina", "given": "Sergiu-Bogdan", "initials": "SB", "orcid": "0000-0002-6914-3902", "researcher": {"href": "https://publications.scilifelab.se/researcher/efbe5c0830144b63a644c0dcc6864e02.json"}}, {"family": "Taylan", "given": "Fulya", "initials": "F", "orcid": "0000-0002-2907-0235", "researcher": {"href": "https://publications.scilifelab.se/researcher/c250909cc40f42ff9d6e2f640d12451b.json"}}, {"family": "Vaz", "given": "Raquel", "initials": "R"}, {"family": "St\u00e5hle", "given": "Mona", "initials": "M", "orcid": "0000-0002-3916-9343", "researcher": {"href": "https://publications.scilifelab.se/researcher/4efdec4c51bb4cfa8186086179a73254.json"}}, {"family": "Tapia-Paez", "given": "Isabel", "initials": "I", "orcid": "0000-0002-0535-4233", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ed50bc3a5034bafbff8ee63e129fb10.json"}}], "type": "journal article", "published": "2024-03-00", "journal": {"title": "EMBO Mol Med", "issn": "1757-4684", "issn-l": "1757-4676", "volume": "16", "issue": "3", "pages": "596-615"}, "abstract": "Psoriatic arthritis mutilans (PAM) is the rarest and most severe form of psoriatic arthritis, characterized by erosions of the small joints and osteolysis leading to joint disruption. Despite its severity, the underlying mechanisms are unknown, and no susceptibility genes have hitherto been identified. We aimed to investigate the genetic basis of PAM by performing massive parallel sequencing in sixty-one patients from the PAM Nordic cohort. We found rare variants in the NADPH oxidase 4 (NOX4) in four patients. In silico predictions show that the identified variants are potentially damaging. NOXs are the only enzymes producing reactive oxygen species (ROS). NOX4 is specifically involved in the differentiation of osteoclasts, the cells implicated in bone resorption. Functional follow-up studies using cell culture, zebrafish models, and measurement of ROS in patients uncovered that these NOX4 variants increase ROS levels both in vitro and in vivo. We propose NOX4 as the first candidate susceptibility gene for PAM. Our study links high levels of ROS caused by NOX4 variants to the development of PAM, offering a potential therapeutic target.", "doi": "10.1038/s44321-024-00035-z", "pmid": "38379095", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service", "Clinical Genomics Stockholm": "Service", "Clinical Genomics": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10940640"}, {"db": "pii", "key": "10.1038/s44321-024-00035-z"}], "notes": [], "created": "2024-03-21T12:09:34.802Z", "modified": "2025-02-28T14:16:43.516Z"}, {"entity": "publication", "iuid": "70f7e504674e40c3866005700c623f0a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/70f7e504674e40c3866005700c623f0a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/70f7e504674e40c3866005700c623f0a"}}, "title": "Human PRH1, PRH2 susceptibility and resistance and Streptococcus mutans virulence phenotypes specify different microbial profiles in caries.", "authors": [{"family": "Sheng", "given": "Nongfei", "initials": "N"}, {"family": "M\u00e5rell", "given": "Lena", "initials": "L"}, {"family": "Sitaram", "given": "Raviprakash Tumkur", "initials": "RT"}, {"family": "Svens\u00e4ter", "given": "Gunnel", "initials": "G"}, {"family": "Westerlund", "given": "Anna", "initials": "A"}, {"family": "Str\u00f6mberg", "given": "Nicklas", "initials": "N"}], "type": "journal article", "published": "2024-03-00", "journal": {"title": "EBioMedicine", "issn": "2352-3964", "volume": "101", "pages": "105001", "issn-l": "2352-3964"}, "abstract": "Lifestyle- and sucrose-dependent polymicrobial ecological shifts are a primary cause of caries in populations with high caries prevalence. In populations with low prevalence, PRH1, PRH2 susceptibility and resistance phenotypes may interact with the Streptococcus mutans adhesin cariogenicity phenotype to affect caries progression, but studies are lacking on how these factors affect the microbial profile of caries.\n\nWe analysed how the residency and infection profiles of S. mutans adhesin (SpaP A/B/C and Cnm/Cbm) phenotypes and commensal streptococci and lactobacilli influenced caries progression in a prospective case-referent sample of 452 Swedish adolescents with high (P4a), moderate (P6), and low (P1) caries PRH1, PRH2 phenotypes. Isolates of S. mutans from participants were analysed for adhesin expression and glycosylation and in vitro and in situ mechanisms related to caries activity.\n\nAmong adolescents with the resistant (P1) phenotype, infection with S. mutans high-virulence phenotypes was required for caries progression. In contrast, with highly (P4a) or moderately (P6) susceptible phenotypes, caries developed from a broader polymicrobial flora that included moderately cariogenic oral commensal streptococci and lactobacilli and S. mutans phenotypes. High virulence involved unstable residency and fluctuating SpaP ABC, B-1, or Cnm expression/glycosylation phenotypes, whereas low/moderate virulence involved SpaP A phenotypes with stable residency. Adhesin phenotypes did not display changes in individual host residency but were paired within individuals and geographic regions.\n\nThese results suggest that receptor PRH1, PRH2 susceptibility and resistance and S. mutans adhesin virulence phenotypes specify different microbial profiles in caries.\n\nSwedish Research Council and funding bodies listed in the acknowledgement section.", "doi": "10.1016/j.ebiom.2024.105001", "pmid": "38364699", "labels": {"NGI SNP genotyping": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10878843"}, {"db": "pii", "key": "S2352-3964(24)00036-7"}], "notes": [], "created": "2024-03-21T09:25:34.490Z", "modified": "2024-03-21T09:25:34.494Z"}, {"entity": "publication", "iuid": "c301b4d4c3a547c0b128bb82f1379493", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c301b4d4c3a547c0b128bb82f1379493.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c301b4d4c3a547c0b128bb82f1379493"}}, "title": "Gustavson syndrome is caused by an in-frame deletion in RBMX associated with potentially disturbed SH3 domain interactions.", "authors": [{"family": "Johansson", "given": "Josefin", "initials": "J", "orcid": "0000-0002-5152-4096", "researcher": {"href": "https://publications.scilifelab.se/researcher/e568827124304b769a3f336d76b6954e.json"}}, {"family": "Lid\u00e9us", "given": "Sarah", "initials": "S"}, {"family": "Frykholm", "given": "Carina", "initials": "C"}, {"family": "Gunnarsson", "given": "Cecilia", "initials": "C", "orcid": "0000-0001-9474-6820", "researcher": {"href": "https://publications.scilifelab.se/researcher/ed1a42fede5f4f6d87c20d6bb9f694de.json"}}, {"family": "Mihalic", "given": "Filip", "initials": "F", "orcid": "0000-0002-6840-2319", "researcher": {"href": "https://publications.scilifelab.se/researcher/5f57a961e98e4e15b1b96ec8efc95d4f.json"}}, {"family": "Gudmundsson", "given": "Sanna", "initials": "S", "orcid": "0000-0002-2332-074X", "researcher": {"href": "https://publications.scilifelab.se/researcher/adb097c987504b2ca309e5f4e1cea5d2.json"}}, {"family": "Ekvall", "given": "Sara", "initials": "S"}, {"family": "Molin", "given": "Anna-Maja", "initials": "AM"}, {"family": "Pham", "given": "Mai", "initials": "M"}, {"family": "Vihinen", "given": "Mauno", "initials": "M", "orcid": "0000-0002-9614-7976", "researcher": {"href": "https://publications.scilifelab.se/researcher/250999f129ad4b4cb6e7e14c96988db9.json"}}, {"family": "Lagerstedt-Robinson", "given": "Kristina", "initials": "K"}, {"family": "Nordgren", "given": "Ann", "initials": "A"}, {"family": "Jemth", "given": "Per", "initials": "P"}, {"family": "Ameur", "given": "Adam", "initials": "A", "orcid": "0000-0001-6085-6749", "researcher": {"href": "https://publications.scilifelab.se/researcher/e960811513664a78b2804a00ee70f7c3.json"}}, {"family": "Anner\u00e9n", "given": "G\u00f6ran", "initials": "G"}, {"family": "Wilbe", "given": "Maria", "initials": "M"}, {"family": "Bondeson", "given": "Marie-Louise", "initials": "ML", "orcid": "0000-0002-3391-5341", "researcher": {"href": "https://publications.scilifelab.se/researcher/9bcb92e271664d9a83e618d5f3e43200.json"}}], "type": "journal article", "published": "2024-03-00", "journal": {"title": "Eur. J. Hum. Genet.", "issn": "1476-5438", "issn-l": "1018-4813", "volume": "32", "issue": "3", "pages": "333-341"}, "abstract": "RNA binding motif protein X-linked (RBMX) encodes the heterogeneous nuclear ribonucleoprotein G (hnRNP G) that regulates splicing, sister chromatid cohesion and genome stability. RBMX knock down experiments in various model organisms highlight the gene's importance for brain development. Deletion of the RGG/RG motif in hnRNP G has previously been associated with Shashi syndrome, however involvement of other hnRNP G domains in intellectual disability remain unknown. In the current study, we present the underlying genetic and molecular cause of Gustavson syndrome. Gustavson syndrome was first reported in 1993 in a large Swedish five-generation family presented with profound X-linked intellectual disability and an early death. Extensive genomic analyses of the family revealed hemizygosity for a novel in-frame deletion in RBMX in affected individuals (NM_002139.4; c.484_486del, p.(Pro162del)). Carrier females were asymptomatic and presented with skewed X-chromosome inactivation, indicating silencing of the pathogenic allele. Affected individuals presented minor phenotypic overlap with Shashi syndrome, indicating a different disease-causing mechanism. Investigation of the variant effect in a neuronal cell line (SH-SY5Y) revealed differentially expressed genes enriched for transcription factors involved in RNA polymerase II transcription. Prediction tools and a fluorescence polarization assay imply a novel SH3-binding motif of hnRNP G, and potentially a reduced affinity to SH3 domains caused by the deletion. In conclusion, we present a novel in-frame deletion in RBMX segregating with Gustavson syndrome, leading to disturbed RNA polymerase II transcription, and potentially reduced SH3 binding. The results indicate that disruption of different protein domains affects the severity of RBMX-associated intellectual disabilities.", "doi": "10.1038/s41431-023-01392-y", "pmid": "37277488", "labels": {"NGI Uppsala (Uppsala Genome Center)": "Collaborative", "National Genomics Infrastructure": "Service", "Clinical Genomics Stockholm": "Service", "NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service", "Clinical Genomics": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10923852"}, {"db": "pii", "key": "10.1038/s41431-023-01392-y"}], "notes": [], "created": "2023-08-15T07:12:40.774Z", "modified": "2024-11-25T10:15:29.202Z"}, {"entity": "publication", "iuid": "48838c48da18481db8283614f606bee7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/48838c48da18481db8283614f606bee7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/48838c48da18481db8283614f606bee7"}}, "title": "Comparison of high-throughput single-cell RNA-seq methods for ex vivo drug screening.", "authors": [{"family": "Gezelius", "given": "Henrik", "initials": "H", "orcid": "0000-0002-6242-6344", "researcher": {"href": "https://publications.scilifelab.se/researcher/7ad329767af94f9f9ad2c96771ff01d9.json"}}, {"family": "Enblad", "given": "Anna Pia", "initials": "AP", "orcid": "0000-0001-6505-4198", "researcher": {"href": "https://publications.scilifelab.se/researcher/b51093d7e7b14d5d859502c535117aad.json"}}, {"family": "Lundmark", "given": "Anders", "initials": "A", "orcid": "0000-0003-2611-1772", "researcher": {"href": "https://publications.scilifelab.se/researcher/52d2e64456104adcba388414d4197a35.json"}}, {"family": "\u00c5berg", "given": "Martin", "initials": "M"}, {"family": "Blom", "given": "Kristin", "initials": "K"}, {"family": "Rudfeldt", "given": "Jakob", "initials": "J"}, {"family": "Raine", "given": "Amanda", "initials": "A", "orcid": "0000-0002-2775-6516", "researcher": {"href": "https://publications.scilifelab.se/researcher/a97b7df8379f42f0a412fb7c234a6c70.json"}}, {"family": "Harila", "given": "Arja", "initials": "A", "orcid": "0000-0003-2767-5828", "researcher": {"href": "https://publications.scilifelab.se/researcher/440e4d697787402283eded5995b706b7.json"}}, {"family": "Rendo", "given": "Ver\u00f3nica", "initials": "V", "orcid": "0000-0002-2983-4020", "researcher": {"href": "https://publications.scilifelab.se/researcher/7f3fe17dd4464af585b16916a88c34b7.json"}}, {"family": "Hein\u00e4niemi", "given": "Merja", "initials": "M", "orcid": "0000-0003-0071-6802", "researcher": {"href": "https://publications.scilifelab.se/researcher/f47bcb3a6ec94202afc945a9f02984da.json"}}, {"family": "Andersson", "given": "Claes", "initials": "C"}, {"family": "Nordlund", "given": "Jessica", "initials": "J", "orcid": "0000-0001-8699-9959", "researcher": {"href": "https://publications.scilifelab.se/researcher/ddf48c9262134821bcc6ce1180049753.json"}}], "type": "journal article", "published": "2024-03-00", "journal": {"title": "NAR Genom Bioinform", "issn": "2631-9268", "issn-l": null, "volume": "6", "issue": "1", "pages": "lqae001"}, "abstract": "Functional precision medicine (FPM) aims to optimize patient-specific drug selection based on the unique characteristics of their cancer cells. Recent advancements in high throughput ex vivo drug profiling have accelerated interest in FPM. Here, we present a proof-of-concept study for an integrated experimental system that incorporates ex vivo treatment response with a single-cell gene expression output enabling barcoding of several drug conditions in one single-cell sequencing experiment. We demonstrate this through a proof-of-concept investigation focusing on the glucocorticoid-resistant acute lymphoblastic leukemia (ALL) E/R+ Reh cell line. Three different single-cell transcriptome sequencing (scRNA-seq) approaches were evaluated, each exhibiting high cell recovery and accurate tagging of distinct drug conditions. Notably, our comprehensive analysis revealed variations in library complexity, sensitivity (gene detection), and differential gene expression detection across the methods. Despite these differences, we identified a substantial transcriptional response to fludarabine, a highly relevant drug for treating high-risk ALL, which was consistently recapitulated by all three methods. These findings highlight the potential of our integrated approach for studying drug responses at the single-cell level and emphasize the importance of method selection in scRNA-seq studies. Finally, our data encompassing 27 327 cells are freely available to extend to future scRNA-seq methodological comparisons.", "doi": "10.1093/nargab/lqae001", "pmid": "38288374", "labels": {"NGI Short read": "Technology development", "NGI Single cell": "Technology development", "NGI Uppsala (SNP&SEQ Technology Platform)": "Technology development", "National Genomics Infrastructure": "Technology development", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10823582"}, {"db": "pii", "key": "lqae001"}], "notes": [], "created": "2024-02-27T08:22:26.710Z", "modified": "2024-11-25T10:25:20.383Z"}, {"entity": "publication", "iuid": "7d88f50cb8d04a5fbc77dec9965b97fd", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7d88f50cb8d04a5fbc77dec9965b97fd.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7d88f50cb8d04a5fbc77dec9965b97fd"}}, "title": "Whole genome case-control study of central nervous system toxicity due to antimicrobial drugs.", "authors": [{"family": "\u00c5s", "given": "Joel", "initials": "J", "orcid": "0000-0001-8687-0629", "researcher": {"href": "https://publications.scilifelab.se/researcher/21836f99416d438c90f2fabd9620c38f.json"}}, {"family": "Bertulyte", "given": "Ilma", "initials": "I"}, {"family": "Norgren", "given": "Nina", "initials": "N"}, {"family": "Johansson", "given": "Anna", "initials": "A"}, {"family": "Eriksson", "given": "Niclas", "initials": "N"}, {"family": "Green", "given": "Henrik", "initials": "H"}, {"family": "Wadelius", "given": "Mia", "initials": "M", "orcid": "0000-0002-6368-2622", "researcher": {"href": "https://publications.scilifelab.se/researcher/ec07b9869a1f4b77b734c5dc567dc630.json"}}, {"family": "Hallberg", "given": "P\u00e4r", "initials": "P"}], "type": "journal article", "published": "2024-02-29", "journal": {"title": "PLoS ONE", "issn": "1932-6203", "issn-l": "1932-6203", "volume": "19", "issue": "2", "pages": "e0299075"}, "abstract": "A genetic predisposition to central nervous system (CNS) toxicity induced by antimicrobial drugs (antibiotics, antivirals, antifungals, and antiparasitic drugs) has been suspected. Whole genome sequencing of 66 cases and 833 controls was performed to investigate whether antimicrobial drug-induced CNS toxicity was associated with genetic variation. The primary objective was to test whether antimicrobial-induced CNS toxicity was associated with seventeen efflux transporters at the blood-brain barrier. In this study, variants or structural elements in efflux transporters were not significantly associated with CNS toxicity. Secondary objectives were to test whether antimicrobial-induced CNS toxicity was associated with genes over the whole genome, with HLA, or with structural genetic variation. Uncommon variants in and close to three genes were significantly associated with CNS toxicity according to a sequence kernel association test combined with an optimal unified test (SKAT-O). These genes were LCP1 (q = 0.013), RETSAT (q = 0.013) and SFMBT2 (q = 0.035). Two variants were driving the LCP1 association: rs6561297 (p = 1.15x10-6, OR: 4.60 [95% CI: 2.51-8.46]) and the regulatory variant rs10492451 (p = 1.15x10-6, OR: 4.60 [95% CI: 2.51-8.46]). No common genetic variant, HLA-type or structural variation was associated with CNS toxicity. In conclusion, CNS toxicity due to antimicrobial drugs was associated with uncommon variants in LCP1, RETSAT and SFMBT2.", "doi": "10.1371/journal.pone.0299075", "pmid": "38422004", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC10903854"}, {"db": "pii", "key": "PONE-D-23-09336"}], "notes": [], "created": "2024-03-21T08:23:52.159Z", "modified": "2024-11-25T10:32:17.378Z"}, {"entity": "publication", "iuid": "c00414cd923a4f9e9a0751b4edc7a150", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c00414cd923a4f9e9a0751b4edc7a150.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c00414cd923a4f9e9a0751b4edc7a150"}}, "title": "Population genomic analyses reveal that salinity and geographic isolation drive diversification in a free-living protist.", "authors": [{"family": "Rengefors", "given": "Karin", "initials": "K"}, {"family": "Annenkova", "given": "Nataliia", "initials": "N"}, {"family": "Wallenius", "given": "Joel", "initials": "J"}, {"family": "Svensson", "given": "Marie", "initials": "M"}, {"family": "Kremp", "given": "Anke", "initials": "A"}, {"family": "Ahr\u00e9n", "given": "Dag", "initials": "D"}], "type": "journal article", "published": "2024-02-29", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "14", "issue": "1", "pages": "4986", "issn-l": "2045-2322"}, "abstract": "Protists make up the vast diversity of eukaryotic life and play a critical role in biogeochemical cycling and in food webs. Because of their small size, cryptic life cycles, and large population sizes, our understanding of speciation in these organisms is very limited. We performed population genomic analyses on 153 strains isolated from eight populations of the recently radiated dinoflagellate genus Apocalathium, to explore the drivers and mechanisms of speciation processes. Species of this genus inhabit both freshwater and saline habitats, lakes and seas, and are found in cold temperate environments across the world. RAD sequencing analyses revealed that the populations were overall highly differentiated, but morphological similarity was not congruent with genetic similarity. While geographic isolation was to some extent coupled to genetic distance, this pattern was not consistent. Instead, we found evidence that the environment, specifically salinity, is a major factor in driving ecological speciation in Apocalathium. While saline populations were unique in loci coupled to genes involved in osmoregulation, freshwater populations appear to lack these. Our study highlights that adaptation to freshwater through loss of osmoregulatory genes may be an important speciation mechanism in free-living aquatic protists.", "doi": "10.1038/s41598-024-55362-5", "pmid": "38424140", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10904836"}, {"db": "pii", "key": "10.1038/s41598-024-55362-5"}], "notes": [], "created": "2024-03-06T13:04:42.545Z", "modified": "2024-11-25T10:20:53.163Z"}, {"entity": "publication", "iuid": "a67f3e238b3e4111bd9611513342ec90", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a67f3e238b3e4111bd9611513342ec90.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a67f3e238b3e4111bd9611513342ec90"}}, "title": "Transcriptomic analysis identifies candidate genes for Aphanomyces root rot disease resistance in pea.", "authors": [{"family": "K\u00e4lin", "given": "Carol", "initials": "C"}, {"family": "Piombo", "given": "Edoardo", "initials": "E"}, {"family": "Bourras", "given": "Salim", "initials": "S"}, {"family": "Brantestam", "given": "Agnese Kolodinska", "initials": "AK"}, {"family": "Dubey", "given": "Mukesh", "initials": "M"}, {"family": "Elfstrand", "given": "Malin", "initials": "M"}, {"family": "Karlsson", "given": "Magnus", "initials": "M"}], "type": "journal article", "published": "2024-02-28", "journal": {"title": "BMC Plant Biol.", "issn": "1471-2229", "volume": "24", "issue": "1", "pages": "144", "issn-l": "1471-2229"}, "abstract": "Aphanomyces euteiches is a soil-borne oomycete that causes root rot in pea and other legume species. Symptoms of Aphanomyces root rot (ARR) include root discoloration and wilting, leading to significant yield losses in pea production. Resistance to ARR is known to be polygenic but the roles of single genes in the pea immune response are still poorly understood. This study uses transcriptomics to elucidate the immune response of two pea genotypes varying in their levels of resistance to A. euteiches.\n\nIn this study, we inoculated roots of the pea (P. sativum L.) genotypes 'Linnea' (susceptible) and 'PI180693' (resistant) with two different A. euteiches strains varying in levels of virulence. The roots were harvested at 6 h post-inoculation (hpi), 20 hpi and 48 hpi, followed by differential gene expression analysis. Our results showed a time- and genotype-dependent immune response towards A. euteiches infection, involving several WRKY and MYB-like transcription factors, along with genes associated with jasmonic acid (JA) and abscisic acid (ABA) signaling. By cross-referencing with genes segregating with partial resistance to ARR, we identified 39 candidate disease resistance genes at the later stage of infection. Among the genes solely upregulated in the resistant genotype 'PI180693', Psat7g091800.1 was polymorphic between the pea genotypes and encoded a Leucine-rich repeat receptor-like kinase reminiscent of the Arabidopsis thaliana FLAGELLIN-SENSITIVE 2 receptor.\n\nThis study provides new insights into the gene expression dynamics controlling the immune response of resistant and susceptible pea genotypes to A. euteiches infection. We present a set of 39 candidate disease resistance genes for ARR in pea, including the putative immune receptor Psat7g091800.1, for future functional validation.", "doi": "10.1186/s12870-024-04817-y", "pmid": "38413860", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10900555"}, {"db": "pii", "key": "10.1186/s12870-024-04817-y"}], "notes": [], "created": "2024-03-21T08:59:08.449Z", "modified": "2025-02-28T14:22:21.812Z"}, {"entity": "publication", "iuid": "d7727b44644f4a45bf2e7b3843b07b3d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d7727b44644f4a45bf2e7b3843b07b3d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d7727b44644f4a45bf2e7b3843b07b3d"}}, "title": "Tumor Predisposing Post-Zygotic Chromosomal Alterations in Bladder Cancer-Insights from Histologically Normal Urothelium.", "authors": [{"family": "Sta\u0144kowska", "given": "Wiktoria", "initials": "W"}, {"family": "Sarkisyan", "given": "Daniil", "initials": "D"}, {"family": "Bruhn-Olszewska", "given": "Bo\u017cena", "initials": "B"}, {"family": "Duzowska", "given": "Katarzyna", "initials": "K"}, {"family": "Bie\u0144kowski", "given": "Micha\u0142", "initials": "M", "orcid": "0000-0002-9291-3928", "researcher": {"href": "https://publications.scilifelab.se/researcher/8227f94ec50e481fa45e9bec035b6708.json"}}, {"family": "J\u0105kalski", "given": "Marcin", "initials": "M", "orcid": "0000-0002-5481-9148", "researcher": {"href": "https://publications.scilifelab.se/researcher/e4411ec776b94c89b0444bd8d49672ca.json"}}, {"family": "W\u00f3jcik-Zalewska", "given": "Magdalena", "initials": "M"}, {"family": "Davies", "given": "Hanna", "initials": "H"}, {"family": "Dr\u0119\u017cek-Chy\u0142a", "given": "Kinga", "initials": "K", "orcid": "0009-0007-1008-7145", "researcher": {"href": "https://publications.scilifelab.se/researcher/5dbc662c14754a468de99e24a60cedf2.json"}}, {"family": "P\u0119ksa", "given": "Rafa\u0142", "initials": "R", "orcid": "0000-0002-4904-7059", "researcher": {"href": "https://publications.scilifelab.se/researcher/3dd33f6e4a9a49d6af2265bc91b77d4e.json"}}, {"family": "Harazin-Lechowska", "given": "Agnieszka", "initials": "A"}, {"family": "Ambicka", "given": "Aleksandra", "initials": "A"}, {"family": "Przewo\u017anik", "given": "Marcin", "initials": "M"}, {"family": "Adamczyk", "given": "Agnieszka", "initials": "A"}, {"family": "Sasim", "given": "Karol", "initials": "K"}, {"family": "Makarewicz", "given": "Wojciech", "initials": "W"}, {"family": "Matuszewski", "given": "Marcin", "initials": "M"}, {"family": "Biernat", "given": "Wojciech", "initials": "W"}, {"family": "J\u00e4rhult", "given": "Josef D", "initials": "JD", "orcid": "0000-0002-7075-1059", "researcher": {"href": "https://publications.scilifelab.se/researcher/2598129f86ee47ebafc696148f9da01f.json"}}, {"family": "Lipcsey", "given": "Mikl\u00f3s", "initials": "M", "orcid": "0000-0002-1976-4129", "researcher": {"href": "https://publications.scilifelab.se/researcher/81805f2324634628abefcf0ab6ce6a15.json"}}, {"family": "Hultstr\u00f6m", "given": "Michael", "initials": "M", "orcid": "0000-0003-4675-1099", "researcher": {"href": "https://publications.scilifelab.se/researcher/c9a74d3380a24c31930e6e671e685b5b.json"}}, {"family": "Frithiof", "given": "Robert", "initials": "R", "orcid": "0000-0003-2278-7951", "researcher": {"href": "https://publications.scilifelab.se/researcher/8fec11dd18f941b7842610ad14237a35.json"}}, {"family": "Jaszczy\u0144ski", "given": "Janusz", "initials": "J"}, {"family": "Ry\u015b", "given": "Janusz", "initials": "J"}, {"family": "Genovese", "given": "Giulio", "initials": "G"}, {"family": "Piotrowski", "given": "Arkadiusz", "initials": "A"}, {"family": "Filipowicz", "given": "Natalia", "initials": "N", "orcid": "0000-0002-9673-2649", "researcher": {"href": "https://publications.scilifelab.se/researcher/153a4d73f8cb4ec68cedfd85556e383e.json"}}, {"family": "Dumanski", "given": "Jan P", "initials": "JP"}], "type": "journal article", "published": "2024-02-27", "journal": {"title": "Cancers (Basel)", "issn": "2072-6694", "volume": "16", "issue": "5", "issn-l": "2072-6694"}, "abstract": "Bladder urothelial carcinoma (BLCA) is the 10th most common cancer with a low survival rate and strong male bias. We studied the field cancerization in BLCA using multi-sample- and multi-tissue-per-patient protocol for sensitive detection of autosomal post-zygotic chromosomal alterations and loss of chromosome Y (LOY). We analysed 277 samples of histologically normal urothelium, 145 tumors and 63 blood samples from 52 males and 15 females, using the in-house adapted Mosaic Chromosomal Alterations (MoChA) pipeline. This approach allows identification of the early aberrations in urothelium from BLCA patients. Overall, 45% of patients exhibited at least one alteration in at least one normal urothelium sample. Recurrence analysis resulted in 16 hotspots composed of either gains and copy number neutral loss of heterozygosity (CN-LOH) or deletions and CN-LOH, encompassing well-known and new BLCA cancer driver genes. Conservative assessment of LOY showed 29%, 27% and 18% of LOY-cells in tumors, blood and normal urothelium, respectively. We provide a proof of principle that our approach can characterize the earliest alterations preconditioning normal urothelium to BLCA development. Frequent LOY in blood and urothelium-derived tissues suggest its involvement in BLCA.", "doi": "10.3390/cancers16050961", "pmid": "38473323", "labels": {"NGI SNP genotyping": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10930680"}, {"db": "pii", "key": "cancers16050961"}], "notes": [], "created": "2024-03-21T08:55:56.265Z", "modified": "2024-03-21T08:55:57.016Z"}, {"entity": "publication", "iuid": "d53efd169d754ccca5fd70684c689438", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d53efd169d754ccca5fd70684c689438.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d53efd169d754ccca5fd70684c689438"}}, "title": "Ancient reindeer mitogenomes reveal island-hopping colonisation of the Arctic archipelagos.", "authors": [{"family": "Hold", "given": "Katharina", "initials": "K"}, {"family": "Lord", "given": "Edana", "initials": "E"}, {"family": "Brealey", "given": "Jaelle C", "initials": "JC"}, {"family": "Le Moullec", "given": "Mathilde", "initials": "M"}, {"family": "Bieker", "given": "Vanessa C", "initials": "VC"}, {"family": "Ellegaard", "given": "Martin R", "initials": "MR"}, {"family": "Rasmussen", "given": "Jacob A", "initials": "JA"}, {"family": "Kellner", "given": "Fabian L", "initials": "FL"}, {"family": "Guschanski", "given": "Katerina", "initials": "K"}, {"family": "Yannic", "given": "Glenn", "initials": "G"}, {"family": "R\u00f8ed", "given": "Knut H", "initials": "KH"}, {"family": "Hansen", "given": "Brage B", "initials": "BB"}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L"}, {"family": "Martin", "given": "Michael D", "initials": "MD"}, {"family": "Dussex", "given": "Nicolas", "initials": "N"}], "type": "journal article", "published": "2024-02-20", "journal": {"title": "Sci Rep", "issn": "2045-2322", "issn-l": "2045-2322", "volume": "14", "issue": "1", "pages": "4143"}, "abstract": "Climate warming at the end of the last glacial period had profound effects on the distribution of cold-adapted species. As their range shifted towards northern latitudes, they were able to colonise previously glaciated areas, including remote Arctic islands. However, there is still uncertainty about the routes and timing of colonisation. At the end of the last ice age, reindeer/caribou (Rangifer tarandus) expanded to the Holarctic region and colonised the archipelagos of Svalbard and Franz Josef Land. Earlier studies have proposed two possible colonisation routes, either from the Eurasian mainland or from Canada via Greenland. Here, we used 174 ancient, historical and modern mitogenomes to reconstruct the phylogeny of reindeer across its whole range and to infer the colonisation route of the Arctic islands. Our data shows a close affinity among Svalbard, Franz Josef Land and Novaya Zemlya reindeer. We also found tentative evidence for positive selection in the mitochondrial gene ND4, which is possibly associated with increased heat production. Our results thus support a colonisation of the Eurasian Arctic archipelagos from the Eurasian mainland and provide some insights into the evolutionary history and adaptation of the species to its High Arctic habitat.", "doi": "10.1038/s41598-024-54296-2", "pmid": "38374421", "labels": {"NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10876933"}, {"db": "pii", "key": "10.1038/s41598-024-54296-2"}], "notes": [], "created": "2024-03-14T11:11:17.523Z", "modified": "2024-11-25T10:20:42.576Z"}, {"entity": "publication", "iuid": "367948cbf0ae47cf812c5b5b3726fccf", "links": {"self": {"href": "https://publications.scilifelab.se/publication/367948cbf0ae47cf812c5b5b3726fccf.json"}, "display": {"href": "https://publications.scilifelab.se/publication/367948cbf0ae47cf812c5b5b3726fccf"}}, "title": "Long noncoding RNA plasmacytoma variant translocation 1 is overexpressed in cutaneous squamous cell carcinoma and exon 2 is critical for its oncogenicity.", "authors": [{"family": "Li", "given": "Chen", "initials": "C"}, {"family": "Sun", "given": "Chengxi", "initials": "C"}, {"family": "Mahapatra", "given": "Kunal Das", "initials": "KD"}, {"family": "Riihil\u00e4", "given": "Pilvi", "initials": "P"}, {"family": "Knuutila", "given": "Jaakko", "initials": "J"}, {"family": "Nissinen", "given": "Liisa", "initials": "L"}, {"family": "Lapins", "given": "Jan", "initials": "J"}, {"family": "K\u00e4h\u00e4ri", "given": "Veli-Matti", "initials": "VM"}, {"family": "Homey", "given": "Bernhard", "initials": "B"}, {"family": "Sonkoly", "given": "Enik\u00f6", "initials": "E"}, {"family": "Pivarcsi", "given": "Andor", "initials": "A", "orcid": "0000-0003-2196-1102", "researcher": {"href": "https://publications.scilifelab.se/researcher/77ca870317234573a3da5dffb24bb268.json"}}], "type": "journal article", "published": "2024-02-16", "journal": {"title": "Br J Dermatol", "issn": "1365-2133", "volume": "190", "issue": "3", "pages": "415-426", "issn-l": null}, "abstract": "Cutaneous squamous cell carcinoma (cSCC) is one of the most common and fastest increasing forms of cancer worldwide with metastatic potential. Long noncoding RNAs (lncRNAs) are a group of RNA molecules with essential regulatory functions in both physiological and pathological processes.\n\nTo investigate the function and mode of action of lncRNA plasmacytoma variant translocation 1 (PVT1) in cSCC.\n\nQuantitative reverse transcriptase polymerase chain reaction and single-molecule in situ hybridization were used to quantify the expression level of PVT1 in normal skin, premalignant skin lesions, actinic keratosis (AK) and primary and metastatic cSCCs. The function of PVT1 in cSCC was investigated both in vivo (tumour xenografts) and in vitro (competitive cell growth assay, 5-ethynyl-2'-deoxyuridine incorporation assay, colony formation assay and tumour spheroid formation assay) upon CRISPR-Cas9-mediated knockout of the entire PVT1 locus, the knockout of exon 2 of PVT1, and locked nucleic acid (LNA) gapmer-mediated PVT1 knockdown. RNA sequencing analysis was conducted to identify genes and processes regulated by PVT1.\n\nWe identified PVT1 as a lncRNA upregulated in cSCC in situ and cSCC, associated with the malignant phenotype of cSCC. We showed that the expression of PVT1 in cSCC was regulated by MYC. Both CRISPR-Cas9 deletion of the entire PVT1 locus and LNA gapmer-mediated knockdown of PVT1 transcript impaired the malignant behaviour of cSCC cells, suggesting that PVT1 is an oncogenic transcript in cSCC. Furthermore, knockout of PVT1 exon 2 inhibited cSCC tumour growth both in vivo and in vitro, demonstrating that exon 2 is a critical element for the oncogenic role of PVT1. Mechanistically, we showed that PVT1 was localized in the cell nucleus and its deletion resulted in cellular senescence, increased cyclin-dependent kinase inhibitor 1 (p21/CDKN1A) expression and cell cycle arrest.\n\nOur study revealed a previously unrecognized role for exon 2 of PVT1 in its oncogenic role and that PVT1 suppresses cellular senescence in cSCC. PVT1 may be a potential biomarker and therapeutic target in cSCC.", "doi": "10.1093/bjd/ljad419", "pmid": "37930852", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "7335666"}], "notes": [], "created": "2024-03-21T09:00:02.277Z", "modified": "2024-11-25T10:22:57.516Z"}, {"entity": "publication", "iuid": "3abf486719004525bfa8c5400692a689", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3abf486719004525bfa8c5400692a689.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3abf486719004525bfa8c5400692a689"}}, "title": "Sustained looking at faces at 5 months of age is associated with socio-communicative skills in the second year of life.", "authors": [{"family": "Viktorsson", "given": "Charlotte", "initials": "C", "orcid": "0000-0003-2727-2957", "researcher": {"href": "https://publications.scilifelab.se/researcher/465e2969410c4109aaa466735d26002b.json"}}, {"family": "Portugal", "given": "Ana Maria", "initials": "AM"}, {"family": "Taylor", "given": "Mark J", "initials": "MJ"}, {"family": "Ronald", "given": "Angelica", "initials": "A"}, {"family": "Falck-Ytter", "given": "Terje", "initials": "T"}], "type": "journal article", "published": "2024-02-15", "journal": {"title": "Infancy", "issn": "1532-7078", "volume": "29", "issue": "3", "pages": "459-478", "issn-l": null}, "abstract": "Efficiently processing information from faces in infancy is foundational for nonverbal communication. We studied individual differences in 5-month-old infants' (N = 517) sustained attention to faces and preference for emotional faces. We assessed the contribution of genetic and environmental influences to individual differences in these gaze behaviors, and the association between these traits and other concurrent and later phenotypes. We found an association between the mean duration of looking at a face (before looking away from it) at 5 months and socio-communicative abilities at 14 months (\u03b2 = 0.17, 95% CI: 0.08; 0.26, p < 0.001). Sustained attention to faces predicted socio-communicative abilities over and above variance captured by mean fixation duration. We also found a statistically significant but weak tendency to prefer looking at smiling faces (relative to neutral faces), but no indication that variability in this behavior was explained by genetic effects. Moderate heritability was found for sustained attention to faces (A = 0.23, CI: 0.06; 0.38), while shared environmental influences were non-significant for both phenotypes. These findings suggest that sustained looking at individual faces before looking away is a developmentally significant 'social attention' phenotype in infancy, characterized by moderate heritability and a specific relation to later socio-communicative abilities.", "doi": "10.1111/infa.12586", "pmid": "38358338", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "NGI SNP genotyping": "Service"}, "xrefs": [], "notes": [], "created": "2024-10-22T07:41:10.088Z", "modified": "2024-10-22T07:41:10.096Z"}, {"entity": "publication", "iuid": "32a17c9018c043279b6599771e1991ba", "links": {"self": {"href": "https://publications.scilifelab.se/publication/32a17c9018c043279b6599771e1991ba.json"}, "display": {"href": "https://publications.scilifelab.se/publication/32a17c9018c043279b6599771e1991ba"}}, "title": "Gene co-expression network analysis reveal core responsive genes in Parascaris univalens tissues following ivermectin exposure.", "authors": [{"family": "Dube", "given": "Faruk", "initials": "F", "orcid": "0000-0003-1340-9123", "researcher": {"href": "https://publications.scilifelab.se/researcher/efd709b6ebf04946bf70f1ab4c8c5cbf.json"}}, {"family": "Delhomme", "given": "Nicolas", "initials": "N", "orcid": "0000-0002-3053-0796", "researcher": {"href": "https://publications.scilifelab.se/researcher/107fbbd40f1444fb838ad4c0365738fa.json"}}, {"family": "Martin", "given": "Frida", "initials": "F"}, {"family": "Hinas", "given": "Andrea", "initials": "A", "orcid": "0000-0002-9353-0742", "researcher": {"href": "https://publications.scilifelab.se/researcher/1d94108597af4151876bcb67a3ce857e.json"}}, {"family": "\u00c5brink", "given": "Magnus", "initials": "M"}, {"family": "Sv\u00e4rd", "given": "Staffan", "initials": "S"}, {"family": "Tyd\u00e9n", "given": "Eva", "initials": "E"}], "type": "journal article", "published": "2024-02-15", "journal": {"title": "PLoS ONE", "issn": "1932-6203", "volume": "19", "issue": "2", "pages": "e0298039", "issn-l": "1932-6203"}, "abstract": "Anthelmintic resistance in equine parasite Parascaris univalens, compromises ivermectin (IVM) effectiveness and necessitates an in-depth understanding of its resistance mechanisms. Most research, primarily focused on holistic gene expression analyses, may overlook vital tissue-specific responses and often limit the scope of novel genes. This study leveraged gene co-expression network analysis to elucidate tissue-specific transcriptional responses and to identify core genes implicated in the IVM response in P. univalens. Adult worms (n = 28) were exposed to 10-11 M and 10-9 M IVM in vitro for 24 hours. RNA-sequencing examined transcriptional changes in the anterior end and intestine. Differential expression analysis revealed pronounced tissue differences, with the intestine exhibiting substantially more IVM-induced transcriptional activity. Gene co-expression network analysis identified seven modules significantly associated with the response to IVM. Within these, 219 core genes were detected, largely expressed in the intestinal tissue and spanning diverse biological processes with unspecific patterns. After 10-11 M IVM, intestinal tissue core genes showed transcriptional suppression, cell cycle inhibition, and ribosomal alterations. Interestingly, genes PgR028_g047 (sorb-1), PgB01_g200 (gmap-1) and PgR046_g017 (col-37 & col-102) switched from downregulation at 10-11 M to upregulation at 10-9 M IVM. The 10-9 M concentration induced expression of cuticle and membrane integrity core genes in the intestinal tissue. No clear core gene patterns were visible in the anterior end after 10-11 M IVM. However, after 10-9 M IVM, the anterior end mostly displayed downregulation, indicating disrupted transcriptional regulation. One interesting finding was the non-modular calcium-signaling gene, PgR047_g066 (gegf-1), which uniquely connected 71 genes across four modules. These genes were enriched for transmembrane signaling activity, suggesting that PgR047_g066 (gegf-1) could have a key signaling role. By unveiling tissue-specific expression patterns and highlighting biological processes through unbiased core gene detection, this study reveals intricate IVM responses in P. univalens. These findings suggest alternative drug uptake of IVM and can guide functional validations to further IVM resistance mechanism understanding.", "doi": "10.1371/journal.pone.0298039", "pmid": "38359071", "labels": {"NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10868809"}, {"db": "pii", "key": "PONE-D-23-41473"}], "notes": [], "created": "2024-03-14T11:08:49.813Z", "modified": "2024-11-25T10:32:12.300Z"}, {"entity": "publication", "iuid": "7fbb4159eeef44e6ae1681e36879d476", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7fbb4159eeef44e6ae1681e36879d476.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7fbb4159eeef44e6ae1681e36879d476"}}, "title": "Genetic and environmental contributions to gaze lateralization across social and non-social stimuli in human infants.", "authors": [{"family": "Viktorsson", "given": "Charlotte", "initials": "C"}, {"family": "Portugal", "given": "Ana Maria", "initials": "AM"}, {"family": "Falck-Ytter", "given": "Terje", "initials": "T"}], "type": "journal article", "published": "2024-02-14", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "14", "issue": "1", "pages": "3668", "issn-l": "2045-2322"}, "abstract": "A tendency to look at the left side of faces from the observer's point of view has been found in older children and adults, but it is not known when this face-specific left gaze bias develops and what factors may influence individual differences in gaze lateralization. Therefore, the aims of this study were to estimate gaze lateralization during face observation and to more broadly estimate lateralization tendencies across a wider set of social and non-social stimuli, in early infancy. In addition, we aimed to estimate the influence of genetic and environmental factors on lateralization of gaze. We studied gaze lateralization in 592 5-month-old twins (282 females, 330 monozygotic twins) by recording their gaze while viewing faces and two other types of stimuli that consisted of either collections of dots (non-social stimuli) or faces interspersed with objects (mixed stimuli). A right gaze bias was found when viewing faces, and this measure was moderately heritable (A = 0.38, 95% CI 0.24; 0.50). A left gaze bias was observed in the non-social condition, while a right gaze bias was found in the mixed condition, suggesting that there is no general left gaze bias at this age. Genetic influence on individual differences in gaze lateralization was only found for the tendency to look at the right versus left side of faces, suggesting genetic specificity of lateralized gaze when viewing faces.", "doi": "10.1038/s41598-024-54373-6", "pmid": "38351309", "labels": {"NGI SNP genotyping": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10864339"}, {"db": "pii", "key": "10.1038/s41598-024-54373-6"}], "notes": [], "created": "2024-03-21T12:10:13.155Z", "modified": "2024-03-21T12:10:13.169Z"}, {"entity": "publication", "iuid": "c050833f0c82481bb5fca4a4262261f2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c050833f0c82481bb5fca4a4262261f2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c050833f0c82481bb5fca4a4262261f2"}}, "title": "Phylogeography and phenotypic wing shape variation in a damselfly across populations in Europe.", "authors": [{"family": "Yildirim", "given": "Y", "initials": "Y"}, {"family": "Kristensson", "given": "D", "initials": "D"}, {"family": "Outomuro", "given": "D", "initials": "D"}, {"family": "Mikolajewski", "given": "D", "initials": "D"}, {"family": "R\u00f6din M\u00f6rch", "given": "P", "initials": "P"}, {"family": "Sniegula", "given": "S", "initials": "S"}, {"family": "Johansson", "given": "F", "initials": "F"}], "type": "journal article", "published": "2024-02-03", "journal": {"title": "BMC Ecol Evol", "issn": "2730-7182", "volume": "24", "issue": "1", "pages": "19", "issn-l": null}, "abstract": "Describing geographical variation in morphology of organisms in combination with data on genetic differentiation and biogeography can provide important information on how natural selection shapes such variation. Here we study genetic structure using ddRAD seq and wing shape variation using geometric morphometrics in 14 populations of the damselfly Lestes sponsa along its latitudinal range in Europe.\n\nThe genetic analysis showed a significant, yet relatively weak population structure with high genetic heterozygosity and low inbreeding coefficients, indicating that neutral processes contributed very little to the observed wing shape differences. The genetic analysis also showed that some regions of the genome (about 10%) are putatively shaped by selection. The phylogenetic analysis showed that the Spanish and French populations were the ancestral ones with northern Swedish and Finnish populations being the most derived ones. We found that wing shape differed significantly among populations and showed a significant quadratic (but weak) relationship with latitude. This latitudinal relationship was largely attributed to allometric effects of wing size, but non-allometric variation also explained a portion of this relationship. However, wing shape showed no phylogenetic signal suggesting that lineage-specific variation did not contribute to the variation along the latitudinal gradient. In contrast, wing size, which is correlated with body size in L. sponsa, had a strong negative correlation with latitude.\n\nOur results suggest a relatively weak population structure among the sampled populations across Europe, but a clear differentiation between south and north populations. The observed geographic phenotypic variation in wing shape may have been affected by different local selection pressures or environmental effects.", "doi": "10.1186/s12862-024-02207-4", "pmid": "38308224", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10838002"}, {"db": "pii", "key": "10.1186/s12862-024-02207-4"}], "notes": [], "created": "2024-03-21T09:24:09.188Z", "modified": "2024-11-25T10:29:31.490Z"}, {"entity": "publication", "iuid": "f9d5f8d15fc7400e9233f987f8a71a33", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f9d5f8d15fc7400e9233f987f8a71a33.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f9d5f8d15fc7400e9233f987f8a71a33"}}, "title": "Multimodal Single-Cell Sequencing of B Cells in Primary Sj\u00f6gren's Syndrome.", "authors": [{"family": "Arvidsson", "given": "Gustav", "initials": "G", "orcid": "0000-0001-7396-1820", "researcher": {"href": "https://publications.scilifelab.se/researcher/29beb4f9dd8b460382eab4f916fc1072.json"}}, {"family": "Czarnewski", "given": "Paulo", "initials": "P", "orcid": "0000-0001-8150-4021", "researcher": {"href": "https://publications.scilifelab.se/researcher/b84309de4e3946159c374ffa6d977560.json"}}, {"family": "Johansson", "given": "Alina", "initials": "A"}, {"family": "Raine", "given": "Amanda", "initials": "A"}, {"family": "Imgenberg-Kreuz", "given": "Juliana", "initials": "J", "orcid": "0000-0002-7230-8990", "researcher": {"href": "https://publications.scilifelab.se/researcher/5d4c2f630d484ee780c2c12aaabdb939.json"}}, {"family": "Nordlund", "given": "Jessica", "initials": "J", "orcid": "0000-0001-8699-9959", "researcher": {"href": "https://publications.scilifelab.se/researcher/ddf48c9262134821bcc6ce1180049753.json"}}, {"family": "Nordmark", "given": "Gunnel", "initials": "G", "orcid": "0000-0002-3829-7431", "researcher": {"href": "https://publications.scilifelab.se/researcher/188fda53498740dbb007441cc94bb1ad.json"}}, {"family": "Syv\u00e4nen", "given": "Ann-Christine", "initials": "A"}], "type": "journal article", "published": "2024-02-00", "journal": {"title": "Arthritis & rheumatology (Hoboken, N.J.)", "issn": "2326-5205", "issn-l": "2326-5191", "volume": "76", "issue": "2", "pages": "255-267"}, "abstract": "B cells are important in the pathogenesis of primary Sj\u00f6gren's syndrome (pSS). Patients positive for Sj\u00f6gren's syndrome antigen A/Sj\u00f6gren syndrome antigen B (SSA/SSB) autoantibodies are more prone to systemic disease manifestations and adverse outcomes. We aimed to determine the role of B cell composition, gene expression, and B cell receptor usage in pSS subgroups stratified for SSA/SSB antibodies.\r\n\r\nOver 230,000 B cells were isolated from peripheral blood of patients with pSS (n = 6 SSA-, n = 8 SSA+ single positive and n = 10 SSA/SSB+ double positive) and four healthy controls and processed for single-cell RNA sequencing (scRNA-seq) and single-cell variable, diversity, and joining (VDJ) gene sequencing (scVDJ-seq).\r\n\r\nWe show that SSA/SSB+ patients present the highest and lowest proportion of na\u00efve and memory B cells, respectively, and the highest up-regulation of interferon-induced genes across all B cell subtypes. Differential usage of IGHV showed that IGHV1-69 and IGHV4-30-4 were more often used in all pSS subgroups compared with controls. Memory B cells from SSA/SSB+ patients displayed a higher proportion of cells with unmutated VDJ transcripts compared with other pSS patient groups and controls, indicating altered somatic hypermutation processes. Comparison with previous studies revealed heterogeneous clonotype pools, with little overlap in CDR3 sequences. Joint analysis using scRNA-seq and scVDJ-seq data allowed unsupervised stratification of patients with pSS and identified novel parameters that correlated to disease manifestations and antibody status.\r\n\r\nWe describe heterogeneity and molecular characteristics in B cells from patients with pSS, providing clues to intrinsic differences in B cells that affect the phenotype and outcome and allowing stratification of patients with pSS at improved resolution.", "doi": "10.1002/art.42683", "pmid": "37610265", "labels": {"Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "NGI Single cell": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [], "notes": [], "created": "2023-09-20T16:42:27.105Z", "modified": "2024-11-05T18:21:35.829Z"}, {"entity": "publication", "iuid": "b6c8b4628a8b4d1e9ad4c1345f3d8d26", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b6c8b4628a8b4d1e9ad4c1345f3d8d26.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b6c8b4628a8b4d1e9ad4c1345f3d8d26"}}, "title": "Genetic diversity patterns in farmed rainbow trout (Oncorhynchus mykiss) populations using genome-wide SNP and haplotype data.", "authors": [{"family": "Longo", "given": "Alessio", "initials": "A"}, {"family": "Kurta", "given": "Khrystyna", "initials": "K"}, {"family": "Vanhala", "given": "Tytti", "initials": "T"}, {"family": "Jeuthe", "given": "Henrik", "initials": "H"}, {"family": "de Koning", "given": "Dirk-Jan", "initials": "DJ"}, {"family": "Palaiokostas", "given": "Christos", "initials": "C", "orcid": "0000-0002-4480-4612", "researcher": {"href": "https://publications.scilifelab.se/researcher/a1d6c65f53a8434cb1d5dd4c7bf5d444.json"}}], "type": "journal article", "published": "2024-02-00", "journal": {"title": "Anim Genet", "issn": "1365-2052", "volume": "55", "issue": "1", "pages": "87-98", "issn-l": "0268-9146"}, "abstract": "Rainbow trout is one of the most popular aquaculture species worldwide, with a long history of domestication. However, limited information exists about the genetic diversity of farmed rainbow trout populations globally, with most available reports relying on low-throughput genotyping technologies. Notably, no information exists about the genetic diversity status of farmed rainbow trout in Sweden. Double-digest restriction-site-associated DNA sequencing was performed on more than 500 broodfish from two leading producers in Sweden and from the country's national breeding program. Following the detection of single nucleotide polymorphisms (SNPs), genetic diversity was studied by using either individual SNPs (n = 8680; one SNP retained per 300 bp sequence reads) or through SNP haplotypes (n = 20 558; all SNPs retained in 300 bp sequence reads). Similar amounts of genetic diversity were found amongst the three populations when individual SNPs were used. Furthermore, principal component analysis and discriminant analysis of principal components suggested two genetic clusters with the two industry populations grouped together. Genetic differentiation based on the FST fixation index was ~0.01 between the industry populations and ~0.05 when those were compared with the breeding program. Preliminary estimates of effective population size (Ne ) and inbreeding (based on runs of homozygosity; FROH ) were similar amongst the three populations (Ne \u2248 50-80; median FROH \u2248 0.11). Finally, the haplotype-based analysis suggested that animals from the breeding program had higher shared coancestry levels than those from the other two populations. Overall, our study provides novel insights into the genetic diversity and structure of Sweden's three main farmed rainbow trout populations, which could guide their future management.", "doi": "10.1111/age.13378", "pmid": "37994156", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "RefSeq", "key": "GCA_013265735.3"}], "notes": [], "created": "2024-03-21T08:48:47.551Z", "modified": "2024-03-21T08:48:47.647Z"}, {"entity": "publication", "iuid": "40e39f732bdc4aefac9c02eb82c634fe", "links": {"self": {"href": "https://publications.scilifelab.se/publication/40e39f732bdc4aefac9c02eb82c634fe.json"}, "display": {"href": "https://publications.scilifelab.se/publication/40e39f732bdc4aefac9c02eb82c634fe"}}, "title": "Fine-scale genetic structure in the orchid Gymnadenia conopsea is not associated with local density of flowering plants.", "authors": [{"family": "Sletvold", "given": "Nina", "initials": "N", "orcid": "0000-0002-9868-3449", "researcher": {"href": "https://publications.scilifelab.se/researcher/e342483c6e3f44c29453f9bc5ce5bb05.json"}}, {"family": "Joffard", "given": "Nina", "initials": "N", "orcid": "0000-0003-3712-6080", "researcher": {"href": "https://publications.scilifelab.se/researcher/fae9d351d1d14a129908a73c37ff5728.json"}}, {"family": "S\u00f6derquist", "given": "Linus", "initials": "L", "orcid": "0000-0002-9894-4119", "researcher": {"href": "https://publications.scilifelab.se/researcher/6a0c370d6402423284ea40a2f51179ae.json"}}], "type": "journal article", "published": "2024-02-00", "journal": {"title": "Am. J. Bot.", "issn": "1537-2197", "volume": "111", "issue": "2", "pages": "e16273", "issn-l": "0002-9122"}, "abstract": "Density-dependent pollinator visitation can lead to density-dependent mating patterns and within-population genetic structure. In Gymnadenia conopsea, individuals in low-density patches receive more self pollen than individuals in high-density patches, suggesting higher relatedness at low density. Ongoing fragmentation is also expected to cause more local matings, potentially leading to biparental inbreeding depression.\n\nTo evaluate whether relatedness decreases with local density, we analyzed 1315 SNP loci in 113 individuals within two large populations. We quantified within-population genetic structure in one of the populations, recorded potential habitat barriers, and visualized gene flow using estimated effective migration surfaces (EEMS). We further estimated the magnitude of biparental inbreeding depression that would result from matings restricted to within 5 m.\n\nThere was no significant relationship between local density and relatedness in any population. We detected significant fine-scale genetic structure consistent with isolation by distance, with positive kinship coefficients at distances below 10 m. Kinship coefficients were low, and predicted biparental inbreeding depression resulting from matings within the closest 5 m was a modest 1-3%. The EEMS suggested that rocks and bushes may act as barriers to gene flow within a population.\n\nThe results suggest that increased self-pollen deposition in sparse patches does not necessarily cause higher selfing rates or that inbreeding depression results in low establishment success of inbred individuals. The modest relatedness suggests that biparental inbreeding depression is unlikely to be an immediate problem following fragmentation of large populations. The results further indicate that habitat structure may contribute to governing fine-scale genetic structure in G. conopsea.", "doi": "10.1002/ajb2.16273", "pmid": "38290971", "labels": {"NGI SNP genotyping": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2024-03-21T08:50:48.512Z", "modified": "2025-02-28T14:09:33.905Z"}, {"entity": "publication", "iuid": "c6ee9d682b4440b98f597b4ff57d6037", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c6ee9d682b4440b98f597b4ff57d6037.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c6ee9d682b4440b98f597b4ff57d6037"}}, "title": "A survey of ficolin-3 activity in Systemic Lupus Erythematosus reveals a link to hematological disease manifestations and autoantibody profile.", "authors": [{"family": "Lindel\u00f6f", "given": "Linnea", "initials": "L"}, {"family": "Rantap\u00e4\u00e4-Dahlqvist", "given": "Solbritt", "initials": "S"}, {"family": "Lundtoft", "given": "Christian", "initials": "C"}, {"family": "Sandling", "given": "Johanna K", "initials": "JK"}, {"family": "Leonard", "given": "Dag", "initials": "D"}, {"family": "Sayadi", "given": "Ahmed", "initials": "A"}, {"family": "R\u00f6nnblom", "given": "Lars", "initials": "L"}, {"family": "Enocsson", "given": "Helena", "initials": "H"}, {"family": "Sj\u00f6wall", "given": "Christopher", "initials": "C"}, {"family": "J\u00f6nsen", "given": "Andreas", "initials": "A"}, {"family": "Bengtsson", "given": "Anders A", "initials": "AA"}, {"family": "Hong", "given": "Mun-Gwan", "initials": "MG"}, {"family": "Diaz-Gallo", "given": "Lina-Marcela", "initials": "LM"}, {"family": "Bianchi", "given": "Matteo", "initials": "M"}, {"family": "Kozyrev", "given": "Sergey V", "initials": "SV"}, {"family": "Lindblad-Toh", "given": "Kerstin", "initials": "K"}, {"family": "DISSECT consortium", "given": "", "initials": ""}, {"family": "ImmunoArray consortium", "given": "", "initials": ""}, {"family": "Nilsson Ekdahl", "given": "Kristina", "initials": "K"}, {"family": "Nilsson", "given": "Bo", "initials": "B"}, {"family": "Gunnarsson", "given": "Iva", "initials": "I"}, {"family": "Svenungsson", "given": "Elisabet", "initials": "E"}, {"family": "Eriksson", "given": "Oskar", "initials": "O"}], "type": "multicenter study", "published": "2024-02-00", "journal": {"title": "J. Autoimmun.", "issn": "1095-9157", "issn-l": "0896-8411", "volume": "143", "issue": null, "pages": "103166"}, "abstract": "The complement system plays a central role in the pathogenesis of Systemic Lupus Erythematosus (SLE), but most studies have focused on the classical pathway. Ficolin-3 is the main initiator of the lectin pathway of complement in humans, but its role in systemic autoimmune disease has not been conclusively determined. Here, we combined biochemical and genetic approaches to assess the contribution of ficolin-3 to SLE risk and disease manifestations. Ficolin-3 activity was measured by a functional assay in serum or plasma samples from Swedish SLE patients (n = 786) and controls matched for age and sex (n = 566). Genetic variants in an extended 300 kb genomic region spanning the FCN3 locus were analyzed for their association with ficolin-3 activity and SLE manifestations in a Swedish multicenter cohort (n = 985). Patients with ficolin-3 activity in the highest tertile showed a strong enrichment in an SLE cluster defined by anti-Sm/DNA/nucleosome antibodies (OR 3.0, p < 0.001) and had increased rates of hematological disease (OR 1.4, p = 0.078) and lymphopenia (OR = 1.6, p = 0.039). Genetic variants associated with low ficolin-3 activity mapped to an extended haplotype in high linkage disequilibrium upstream of the FCN3 gene. Patients carrying the lead genetic variant associated with low ficolin-3 activity had a lower frequency of hematological disease (OR 0.67, p = 0.018) and lymphopenia (OR 0.63, p = 0.031) and fewer autoantibodies (p = 0.0019). Loss-of-function variants in the FCN3 gene were not associated with SLE, but four (0.5 %) SLE patients developed acquired ficolin-3 deficiency where ficolin-3 activity in serum was depleted following diagnosis of SLE. Taken together, our results provide genetic and biochemical evidence that implicate the lectin pathway in hematological SLE manifestations. We also identify lectin pathway activation through ficolin-3 as a factor that contributes to the autoantibody response in SLE.", "doi": "10.1016/j.jaut.2023.103166", "pmid": "38219652", "labels": {"Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "S0896-8411(23)00175-0"}], "notes": [], "created": "2024-01-16T08:53:44.077Z", "modified": "2025-02-28T14:12:16.457Z"}, {"entity": "publication", "iuid": "652ef4bf70e84b36b7d9aa8a86e01efa", "links": {"self": {"href": "https://publications.scilifelab.se/publication/652ef4bf70e84b36b7d9aa8a86e01efa.json"}, "display": {"href": "https://publications.scilifelab.se/publication/652ef4bf70e84b36b7d9aa8a86e01efa"}}, "title": "Batrachochytrium dendrobatidis strain affects transcriptomic response in liver but not skin in latitudinal populations of the common toad (Bufo bufo).", "authors": [{"family": "Chondrelli", "given": "Niki", "initials": "N"}, {"family": "Kuehn", "given": "Emily", "initials": "E"}, {"family": "Meurling", "given": "Sara", "initials": "S"}, {"family": "Cort\u00e1zar-Chinarro", "given": "Maria", "initials": "M"}, {"family": "Laurila", "given": "Anssi", "initials": "A"}, {"family": "H\u00f6glund", "given": "Jacob", "initials": "J"}], "type": "journal article", "published": "2024-01-30", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "14", "issue": "1", "pages": "2495", "issn-l": "2045-2322"}, "abstract": "Batrachochytrium dendrobatidis (Bd) is a fungal pathogen that has decimated amphibian populations worldwide for several decades. We examined the changes in gene expression in response to Bd infection in two populations of the common toad, Bufo bufo, in a laboratory experiment. We collected B. bufo eggs in southern and northern Sweden, and infected the laboratory-raised metamorphs with two strains of the global panzoonotic lineage Bd-GPL. Differential expression analysis showed significant differences between infected and control individuals in both liver and skin. The skin samples showed no discernible differences in gene expression between the two strains used, while liver samples were differentiated by strain, with one of the strains eliciting no immune response from infected toads. Immune system genes were overexpressed in skin samples from surviving infected individuals, while in liver samples the pattern was more diffuse. Splitting samples by population revealed a stronger immune response in northern individuals. Differences in transcriptional regulation between populations are particularly relevant to study in Swedish amphibians, which may have experienced varying exposure to Bd. Earlier exposure to this pathogen and subsequent adaptation or selection pressure may contribute to the survival of some populations over others, while standing genetic diversity in different populations may also affect the infection outcome.", "doi": "10.1038/s41598-024-52975-8", "pmid": "38291226", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10828426"}, {"db": "pii", "key": "10.1038/s41598-024-52975-8"}], "notes": [], "created": "2024-03-21T09:01:24.203Z", "modified": "2025-01-02T10:35:06.385Z"}, {"entity": "publication", "iuid": "bd2469b856a34c23bf93587d768559f2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/bd2469b856a34c23bf93587d768559f2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/bd2469b856a34c23bf93587d768559f2"}}, "title": "A two-step activation mechanism enables mast cells to differentiate their response between extracellular and invasive enterobacterial infection.", "authors": [{"family": "von Beek", "given": "Christopher", "initials": "C", "orcid": "0000-0001-6310-7583", "researcher": {"href": "https://publications.scilifelab.se/researcher/a3ea7730832f4f45ae6583076d90418a.json"}}, {"family": "Fahlgren", "given": "Anna", "initials": "A"}, {"family": "Geiser", "given": "Petra", "initials": "P", "orcid": "0000-0003-2785-4201", "researcher": {"href": "https://publications.scilifelab.se/researcher/ae0bf10f41dc4698b19288809bae2dd6.json"}}, {"family": "Di Martino", "given": "Maria Letizia", "initials": "ML", "orcid": "0000-0002-9491-4000", "researcher": {"href": "https://publications.scilifelab.se/researcher/708eae058cb3494f8407574a666a16f0.json"}}, {"family": "Lindahl", "given": "Otto", "initials": "O", "orcid": "0000-0001-7518-9483", "researcher": {"href": "https://publications.scilifelab.se/researcher/78053dd357c3435ba53aff83f06f28a4.json"}}, {"family": "Prensa", "given": "Grisna I", "initials": "GI", "orcid": "0009-0002-7101-7224", "researcher": {"href": "https://publications.scilifelab.se/researcher/3d030d78925948d993999b66e1959acc.json"}}, {"family": "Mendez-Enriquez", "given": "Erika", "initials": "E", "orcid": "0000-0002-2114-2812", "researcher": {"href": "https://publications.scilifelab.se/researcher/dae73474be904a638ec13a8f704a9154.json"}}, {"family": "Eriksson", "given": "Jens", "initials": "J", "orcid": "0000-0002-8945-2665", "researcher": {"href": "https://publications.scilifelab.se/researcher/b94e7f542841474d86d53aa48958f870.json"}}, {"family": "Hallgren", "given": "Jenny", "initials": "J", "orcid": "0000-0002-3685-5364", "researcher": {"href": "https://publications.scilifelab.se/researcher/fe8b929dbe60446f96db17a5eb2ba6f3.json"}}, {"family": "F\u00e4llman", "given": "Maria", "initials": "M", "orcid": "0000-0001-6874-6384", "researcher": {"href": "https://publications.scilifelab.se/researcher/cadcd4e3e63742e7b9cbbb74907bf9fc.json"}}, {"family": "Pejler", "given": "Gunnar", "initials": "G"}, {"family": "Sellin", "given": "Mikael E", "initials": "ME", "orcid": "0000-0002-8355-0803", "researcher": {"href": "https://publications.scilifelab.se/researcher/f797357bcd3d4447bff96c20873dd500.json"}}], "type": "journal article", "published": "2024-01-30", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "15", "issue": "1", "pages": "904", "issn-l": "2041-1723"}, "abstract": "Mast cells localize to mucosal tissues and contribute to innate immune defense against infection. How mast cells sense, differentiate between, and respond to bacterial pathogens remains a topic of ongoing debate. Using the prototype enteropathogen Salmonella Typhimurium (S.Tm) and other related enterobacteria, here we show that mast cells can regulate their cytokine secretion response to distinguish between extracellular and invasive bacterial infection. Tissue-invasive S.Tm and mast cells colocalize in the mouse gut during acute Salmonella infection. Toll-like Receptor 4 (TLR4) sensing of extracellular S.Tm, or pure lipopolysaccharide, causes a modest induction of cytokine transcripts and proteins, including IL-6, IL-13, and TNF. By contrast, type-III-secretion-system-1 (TTSS-1)-dependent S.Tm invasion of both mouse and human mast cells triggers rapid and potent inflammatory gene expression and >100-fold elevated cytokine secretion. The S.Tm TTSS-1 effectors SopB, SopE, and SopE2 here elicit a second activation signal, including Akt phosphorylation downstream of effector translocation, which combines with TLR activation to drive the full-blown mast cell response. Supernatants from S.Tm-infected mast cells boost macrophage survival and maturation from bone-marrow progenitors. Taken together, this study shows that mast cells can differentiate between extracellular and host-cell invasive enterobacteria via a two-step activation mechanism and tune their inflammatory output accordingly.", "doi": "10.1038/s41467-024-45057-w", "pmid": "38291037", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10828507"}, {"db": "pii", "key": "10.1038/s41467-024-45057-w"}], "notes": [], "created": "2024-03-21T12:10:55.423Z", "modified": "2024-03-21T12:10:55.804Z"}, {"entity": "publication", "iuid": "999556e1041547b49d0a807a80249103", "links": {"self": {"href": "https://publications.scilifelab.se/publication/999556e1041547b49d0a807a80249103.json"}, "display": {"href": "https://publications.scilifelab.se/publication/999556e1041547b49d0a807a80249103"}}, "title": "Single-cell RNA-seq mapping of chicken peripheral blood leukocytes.", "authors": [{"family": "Maxwell", "given": "Matilda", "initials": "M"}, {"family": "S\u00f6derlund", "given": "Robert", "initials": "R"}, {"family": "H\u00e4rtle", "given": "Sonja", "initials": "S"}, {"family": "Wattrang", "given": "Eva", "initials": "E"}], "type": "journal article", "published": "2024-01-29", "journal": {"title": "BMC Genomics", "issn": "1471-2164", "volume": "25", "issue": "1", "pages": "124", "issn-l": "1471-2164"}, "abstract": "Single-cell transcriptomics provides means to study cell populations at the level of individual cells. In leukocyte biology this approach could potentially aid the identification of subpopulations and functions without the need to develop species-specific reagents. The present study aimed to evaluate single-cell RNA-seq as a tool for identification of chicken peripheral blood leukocytes. For this purpose, purified and thrombocyte depleted leukocytes from 4 clinically healthy hens were subjected to single-cell 3' RNA-seq. Bioinformatic analysis of data comprised unsupervised clustering of the cells, and annotation of clusters based on expression profiles. Immunofluorescence phenotyping of the cell preparations used was also performed.\n\nComputational analysis identified 31 initial cell clusters and based on expression of defined marker genes 28 cluster were identified as comprising mainly B-cells, T-cells, monocytes, thrombocytes and red blood cells. Of the remaining clusters, two were putatively identified as basophils and eosinophils, and one as proliferating cells of mixed origin. In depth analysis on gene expression profiles within and between the initial cell clusters allowed further identification of cell identity and possible functions for some of them. For example, analysis of the group of monocyte clusters revealed subclusters comprising heterophils, as well as putative monocyte subtypes. Also, novel aspects of TCR\u03b3/\u03b4 + T-cell subpopulations could be inferred such as evidence of at least two subtypes based on e.g., different expression of transcription factors MAF, SOX13 and GATA3. Moreover, a novel subpopulation of chicken peripheral B-cells with high SOX5 expression was identified. An overall good correlation between mRNA and cell surface phenotypic cell identification was shown.\n\nTaken together, we were able to identify and infer functional aspects of both previously well known as well as novel chicken leukocyte populations although some cell types. e.g., T-cell subtypes, proved more challenging to decipher. Although this methodology to some extent is limited by incomplete annotation of the chicken genome, it definitively has benefits in chicken immunology by expanding the options to distinguish identity and functions of immune cells also without access to species specific reagents.", "doi": "10.1186/s12864-024-10044-4", "pmid": "38287279", "labels": {"NGI Single cell": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10826067"}, {"db": "pii", "key": "10.1186/s12864-024-10044-4"}], "notes": [], "created": "2024-01-31T13:03:41.480Z", "modified": "2024-11-25T10:29:46.749Z"}, {"entity": "publication", "iuid": "0533fbff25544d368a04f51d1e5e1a3b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0533fbff25544d368a04f51d1e5e1a3b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0533fbff25544d368a04f51d1e5e1a3b"}}, "title": "Genetic diversity and recent ancestry based on whole-genome sequencing of endangered Swedish cattle breeds.", "authors": [{"family": "Harish", "given": "Ajith", "initials": "A"}, {"family": "Lopes Pinto", "given": "Fernando A", "initials": "FA"}, {"family": "Eriksson", "given": "Susanne", "initials": "S"}, {"family": "Johansson", "given": "Anna M", "initials": "AM"}], "type": "journal article", "published": "2024-01-22", "journal": {"title": "BMC Genomics", "issn": "1471-2164", "volume": "25", "issue": "1", "pages": "89", "issn-l": "1471-2164"}, "abstract": "Several indigenous cattle breeds in Sweden are endangered. Conservation of their genetic diversity and genomic characterization is a priority.Whole-genome sequences (WGS) with a mean coverage of 25X, ranging from 14 to 41X were obtained for 30 individuals of the breeds Fj\u00e4llko, Fj\u00e4lln\u00e4ra, Bohuskulla, R\u00f6dkulla, Ringam\u00e5la, and V\u00e4neko. WGS-based genotyping revealed 22,548,028 variants in total, comprising 18,876,115 single nucleotide polymorphisms (SNPs) and 3,671,913 indels. Out of these, 1,154,779 SNPs and 304,467 indels were novel. Population stratification based on roughly 19 million SNPs showed two major groups of the breeds that correspond to northern and southern breeds. Overall, a higher genetic diversity was observed in the southern breeds compared to the northern breeds. While the population stratification was consistent with previous genome-wide SNP array-based analyses, the genealogy of the individuals inferred from WGS based estimates turned out to be more complex than expected from previous SNP-array based estimates. Polymorphisms and their predicted phenotypic consequences were associated with differences in the coat color phenotypes between the northern and southern breeds. Notably, these high-consequence polymorphisms were not represented in SNP arrays, which are used routinely for genotyping of cattle breeds.This study is the first WGS-based population genetic analysis of Swedish native cattle breeds. The genetic diversity of native breeds was found to be high. High-consequence polymorphisms were linked with desirable phenotypes using whole-genome genotyping, which highlights the pressing need for intensifying WGS-based characterization of the native breeds.", "doi": "10.1186/s12864-024-09959-9", "pmid": "38254050", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10802049"}, {"db": "pii", "key": "10.1186/s12864-024-09959-9"}], "notes": [], "created": "2024-03-21T08:57:34.995Z", "modified": "2024-03-21T08:57:34.998Z"}, {"entity": "publication", "iuid": "50f17519fbe44f2eb49fdc91933ee0ee", "links": {"self": {"href": "https://publications.scilifelab.se/publication/50f17519fbe44f2eb49fdc91933ee0ee.json"}, "display": {"href": "https://publications.scilifelab.se/publication/50f17519fbe44f2eb49fdc91933ee0ee"}}, "title": "Metagenomic analysis of Mesolithic chewed pitch reveals poor oral health among stone age individuals.", "authors": [{"family": "K\u0131rd\u00f6k", "given": "Emrah", "initials": "E"}, {"family": "Kashuba", "given": "Natalija", "initials": "N"}, {"family": "Damlien", "given": "Hege", "initials": "H"}, {"family": "Manninen", "given": "Mikael A", "initials": "MA"}, {"family": "Nordqvist", "given": "Bengt", "initials": "B"}, {"family": "Kjellstr\u00f6m", "given": "Anna", "initials": "A"}, {"family": "Jakobsson", "given": "Mattias", "initials": "M"}, {"family": "Lindberg", "given": "A Michael", "initials": "AM"}, {"family": "Stor\u00e5", "given": "Jan", "initials": "J"}, {"family": "Persson", "given": "Per", "initials": "P"}, {"family": "Andersson", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Aravena", "given": "Andr\u00e9s", "initials": "A"}, {"family": "G\u00f6therstr\u00f6m", "given": "Anders", "initials": "A"}], "type": "case reports", "published": "2024-01-18", "journal": {"title": "Sci Rep", "issn": "2045-2322", "issn-l": "2045-2322", "volume": "13", "issue": "1", "pages": "22125"}, "abstract": "Prehistoric chewed pitch has proven to be a useful source of ancient DNA, both from humans and their microbiomes. Here we present the metagenomic analysis of three pieces of chewed pitch from Huseby Klev, Sweden, that were dated to 9,890-9,540 before present. The metagenomic profile exposes a Mesolithic oral microbiome that includes opportunistic oral pathogens. We compared the data with healthy and dysbiotic microbiome datasets and we identified increased abundance of periodontitis-associated microbes. In addition, trained machine learning models predicted dysbiosis with 70-80% probability. Moreover, we identified DNA sequences from eukaryotic species such as red fox, hazelnut, red deer and apple. Our results indicate a case of poor oral health during the Scandinavian Mesolithic, and show that pitch pieces have the potential to provide information on material use, diet and oral health.", "doi": "10.1038/s41598-023-48762-6", "pmid": "38238372", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10796427"}, {"db": "pii", "key": "10.1038/s41598-023-48762-6"}], "notes": [], "created": "2024-01-19T06:32:34.876Z", "modified": "2024-11-25T10:20:27.063Z"}, {"entity": "publication", "iuid": "b4caed4485bd40efab57b71f77ec67ce", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b4caed4485bd40efab57b71f77ec67ce.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b4caed4485bd40efab57b71f77ec67ce"}}, "title": "Ciliate Grazing on the Bloom-Forming Microalga Gonyostomum semen.", "authors": [{"family": "Bergman", "given": "Ingrid", "initials": "I"}, {"family": "Lindstr\u00f6m", "given": "Eva S", "initials": "ES"}, {"family": "Sassenhagen", "given": "Ingrid", "initials": "I"}], "type": "journal article", "published": "2024-01-18", "journal": {"title": "Microb. Ecol.", "issn": "1432-184X", "volume": "87", "issue": "1", "pages": "33", "issn-l": "0095-3628"}, "abstract": "The freshwater raphidophyte Gonyostomum semen forms extensive summer blooms in northern European humic lakes. The development of these blooms might be facilitated by a lack of natural top-down control, as few zooplankton species are able to prey on these large algal cells (up to 100 \u03bcm) that expel trichocysts upon physical stress. In this study, we describe a small ciliate species (< 17 \u03bcm) that preys on G. semen by damaging the cell membrane until cytoplasm and organelles spill out. Sequencing of clonal cultures of the ciliate tentatively identified it as the prostomatid species Urotricha pseudofurcata. Grazing experiments illustrated that feeding by U. cf. pseudofurcata can significantly reduce cell concentrations of the microalga. However, differences in cell size and growth rate between two investigated ciliate strains resulted in noticeably different grazing pressure. Environmental sequencing data from five different lakes supported potential interactions between the two species. Urotricha cf. pseudofurcata might, thus, play an important role in aquatic ecosystems that are regularly dominated by G. semen, reducing the abundance of this bloom-forming microalga and enabling transfer of organic carbon to higher trophic levels.", "doi": "10.1007/s00248-024-02344-9", "pmid": "38236289", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10796478"}, {"db": "pii", "key": "10.1007/s00248-024-02344-9"}], "notes": [], "created": "2024-03-21T09:24:50.987Z", "modified": "2024-03-21T09:24:50.990Z"}, {"entity": "publication", "iuid": "20c1a1e54fca4f0cb892dc1d755b69c0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/20c1a1e54fca4f0cb892dc1d755b69c0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/20c1a1e54fca4f0cb892dc1d755b69c0"}}, "title": "Differential expression and alternative splicing analyses of multiple tissues reveal albinism-associated genes in the Wels catfish (Silurus glanis).", "authors": [{"family": "Ozerov", "given": "M Y", "initials": "MY"}, {"family": "Noreikiene", "given": "K", "initials": "K"}, {"family": "Kahar", "given": "S", "initials": "S"}, {"family": "Flaj\u0161hans", "given": "M", "initials": "M"}, {"family": "Gross", "given": "R", "initials": "R"}, {"family": "Vasem\u00e4gi", "given": "A", "initials": "A"}], "type": "journal article", "published": "2024-01-11", "journal": {"title": "Comp Biochem Physiol B Biochem Mol Biol", "issn": "1879-1107", "volume": "271", "pages": "110941", "issn-l": null}, "abstract": "Albinism is a widespread departure from a typical body colouration due to altered melanin production. The Wels catfish (Silurus glanis) is among the largest freshwater fish species in the world, and albino individuals occur both in the wild and in aquaculture. Here, we performed transcriptome-wide analysis of albino and normally pigmented S. glanis using four tissues (skin, dorsal fin, whole eye and liver) to identify genes associated with albinism by exploring patterns of differential expression (DE) and differential alternative splicing (DAS). Multi-tissue analyses revealed a large number of genes in skin (n = 1355) and fin (n = 614) tissue associated with the albino phenotype in S. glanis, while the number of DE genes in eye and liver tissues was lower (n = 188, n = 189, respectively). Several DE genes across multiple tissues were detected as the most promising candidates (e.g., hsp4, hsp90b1, raph1, uqcrfs1, adcy-family and wnt-family) potentially causally linked to the albino phenotype in Wels catfish. Moreover, our findings supported earlier observations of physiological differences between albino and normally pigmented individuals, particularly in energy metabolism and immune response. In contrast, there were only a few pigmentation-related genes observed among DAS genes (4 in skin, 2 in fin), the overlap between DAS and DE genes was low (n = 25) and did not include known pigmentation-related genes. This suggests that DAS and DE in Wels catfish are, to a large extent, independent processes, and the observed alternative splicing cases are probably not causally linked with albinism in S. glanis. This work provides the first transcriptome-wide multi-tissue insights into the albinism of Wels catfish and serves as a valuable resource for further understanding the genetic mechanisms of pigmentation in fish.", "doi": "10.1016/j.cbpb.2024.110941", "pmid": "38218377", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "S1096-4959(24)00008-3"}], "notes": [], "created": "2024-03-21T08:56:46.467Z", "modified": "2025-02-28T14:11:45.742Z"}, {"entity": "publication", "iuid": "f0568a2c147043eeb312c4016dbb907f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f0568a2c147043eeb312c4016dbb907f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f0568a2c147043eeb312c4016dbb907f"}}, "title": "Single-cell genomics of a bloom-forming phytoplankton species reveals population genetic structure across continents.", "authors": [{"family": "Gollnisch", "given": "Raphael", "initials": "R"}, {"family": "Ahr\u00e9n", "given": "Dag", "initials": "D"}, {"family": "Rengefors", "given": "Karin", "initials": "K"}], "type": "journal article", "published": "2024-01-08", "journal": {"title": "ISME J", "issn": "1751-7370", "volume": "18", "issue": "1", "issn-l": "1751-7362"}, "abstract": "The study of microbial diversity over time and space is fundamental to the understanding of their ecology and evolution. The underlying processes driving these patterns are not fully resolved but can be studied using population genetic approaches. Here we investigated the population genetic structure of Gonyostomum semen, a bloom-forming phytoplankton species, across two continents. The species appears to be expanding in Europe, whereas similar trends are not observed in the USA. Our aim was to investigate if populations of Gonyostomum semen in Europe and in the USA are genetically differentiated, if there is population genetic structure within the continents, and what the potential drivers of differentiation are. To this end, we used a novel method based on single-amplified genomes combined with Restriction-site Associated DNA sequencing that allows de novo genotyping of natural single-cell isolates without the need for culturing. We amplified over 900 single-cell genomes from 25 lake populations across Europe and the USA and identified two distinct population clusters, one in Europe and another in the USA. Low genetic diversity in European populations supports the hypothesized recent expansion of Gonyostomum semen on this continent. Geographic population structure within each continent was associated with differences in environmental variables that may have led to ecological divergence of population clusters. Overall, our results show that single-amplified genomes combined with Restriction-site Associated DNA sequencing can be used to analyze microalgal population structure and differentiation based on single-cell isolates from natural, uncultured samples.", "doi": "10.1093/ismejo/wrae045", "pmid": "38489771", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11065318"}, {"db": "pii", "key": "7630124"}], "notes": [], "created": "2024-05-16T06:27:02.910Z", "modified": "2025-02-28T14:18:49.908Z"}, {"entity": "publication", "iuid": "98e4505a97e8498295f664d0b66ace12", "links": {"self": {"href": "https://publications.scilifelab.se/publication/98e4505a97e8498295f664d0b66ace12.json"}, "display": {"href": "https://publications.scilifelab.se/publication/98e4505a97e8498295f664d0b66ace12"}}, "title": "Separating phases of allopolyploid evolution with resynthesized and natural Capsella bursa-pastoris.", "authors": [{"family": "Duan", "given": "Tianlin", "initials": "T", "orcid": "0000-0002-8719-7998", "researcher": {"href": "https://publications.scilifelab.se/researcher/78c1a5d458814388bbcbbe6a020944d6.json"}}, {"family": "Sicard", "given": "Adrien", "initials": "A"}, {"family": "Gl\u00e9min", "given": "Sylvain", "initials": "S", "orcid": "0000-0001-7260-4573", "researcher": {"href": "https://publications.scilifelab.se/researcher/0ce5a8d7ac9a490eb2e261aeb75088d4.json"}}, {"family": "Lascoux", "given": "Martin", "initials": "M", "orcid": "0000-0003-1699-9042", "researcher": {"href": "https://publications.scilifelab.se/researcher/4ad3fadfb69448f397ad3bf55b2d2cb3.json"}}], "type": "journal article", "published": "2024-01-08", "journal": {"title": "Elife", "issn": "2050-084X", "volume": "12", "issn-l": "2050-084X"}, "abstract": "Allopolyploidization is a frequent evolutionary transition in plants that combines whole-genome duplication (WGD) and interspecific hybridization. The genome of an allopolyploid species results from initial interactions between parental genomes and long-term evolution. Distinguishing the contributions of these two phases is essential to understanding the evolutionary trajectory of allopolyploid species. Here, we compared phenotypic and transcriptomic changes in natural and resynthesized Capsella allotetraploids with their diploid parental species. We focused on phenotypic traits associated with the selfing syndrome and on transcription-level phenomena such as expression-level dominance (ELD), transgressive expression (TRE), and homoeolog expression bias (HEB). We found that selfing syndrome, high pollen, and seed quality in natural allotetraploids likely resulted from long-term evolution. Similarly, TRE and most down-regulated ELD were only found in natural allopolyploids. Natural allotetraploids also had more ELD toward the self-fertilizing parental species than resynthesized allotetraploids, mirroring the establishment of the selfing syndrome. However, short-term changes mattered, and 40% of the cases of ELD in natural allotetraploids were already observed in resynthesized allotetraploids. Resynthesized allotetraploids showed striking variation of HEB among chromosomes and individuals. Homoeologous synapsis was its primary source and may still be a source of genetic variation in natural allotetraploids. In conclusion, both short- and long-term mechanisms contributed to transcriptomic and phenotypic changes in natural allotetraploids. However, the initial gene expression changes were largely reshaped during long-term evolution leading to further morphological changes.", "doi": "10.7554/eLife.88398", "pmid": "38189348", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10945474"}, {"db": "pii", "key": "88398"}], "notes": [], "created": "2024-03-21T13:55:14.769Z", "modified": "2024-11-25T10:34:07.268Z"}, {"entity": "publication", "iuid": "56fbf8aaced9497f957befcc3c5c0dbb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/56fbf8aaced9497f957befcc3c5c0dbb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/56fbf8aaced9497f957befcc3c5c0dbb"}}, "title": "A pan-genomic approach reveals novel Sulfurimonas clade in the ferruginous meromictic Lake Pavin.", "authors": [{"family": "Biderre-Petit", "given": "Corinne", "initials": "C", "orcid": "0000-0001-7962-4171", "researcher": {"href": "https://publications.scilifelab.se/researcher/8199e3021db54bb9b2f9124a682ac305.json"}}, {"family": "Courtine", "given": "Damien", "initials": "D"}, {"family": "Hennequin", "given": "Claire", "initials": "C"}, {"family": "Galand", "given": "Pierre E", "initials": "PE", "orcid": "0000-0002-2238-3247", "researcher": {"href": "https://publications.scilifelab.se/researcher/a36433c063bf4305afd6ac1ba7a67ddf.json"}}, {"family": "Bertilsson", "given": "Stefan", "initials": "S", "orcid": "0000-0002-4265-1835", "researcher": {"href": "https://publications.scilifelab.se/researcher/2c17765c2a9f4383b5383138d11ae93f.json"}}, {"family": "Debroas", "given": "Didier", "initials": "D", "orcid": "0000-0002-9915-1268", "researcher": {"href": "https://publications.scilifelab.se/researcher/6146106a7ee449e5bda7d6e8773b60dc.json"}}, {"family": "Monjot", "given": "Arthur", "initials": "A", "orcid": "0000-0002-6978-4785", "researcher": {"href": "https://publications.scilifelab.se/researcher/46d5728dbea84c50bf7f2b183558f7c2.json"}}, {"family": "Lep\u00e8re", "given": "C\u00e9cile", "initials": "C", "orcid": "0000-0003-4767-0477", "researcher": {"href": "https://publications.scilifelab.se/researcher/796cc43ff3074c069d822502ad0e3449.json"}}, {"family": "Divne", "given": "Anna-Maria", "initials": "A"}, {"family": "Hochart", "given": "Corentin", "initials": "C"}], "type": "journal article", "published": "2024-01-08", "journal": {"title": "Mol Ecol Resour", "issn": "1755-0998", "issn-l": "1755-098X", "volume": null, "issue": null, "pages": "e13923"}, "abstract": "The permanently anoxic waters in meromictic lakes create suitable niches for the growth of bacteria using sulphur metabolisms like sulphur oxidation. In Lake Pavin, the anoxic water mass hosts an active cryptic sulphur cycle that interacts narrowly with iron cycling, however the metabolisms of the microorganisms involved are poorly known. Here we combined metagenomics, single-cell genomics, and pan-genomics to further expand our understanding of the bacteria and the corresponding metabolisms involved in sulphur oxidation in this ferruginous sulphide- and sulphate-poor meromictic lake. We highlighted two new species within the genus Sulfurimonas that belong to a novel clade of chemotrophic sulphur oxidisers exclusive to freshwaters. We moreover conclude that this genus holds a key-role not only in limiting sulphide accumulation in the upper part of the anoxic layer but also constraining carbon, phosphate and iron cycling.", "doi": "10.1111/1755-0998.13923", "pmid": "38189173", "labels": {"Microbial Single Cell Genomics": "Collaborative", "NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [], "notes": [], "created": "2024-01-15T10:09:02.759Z", "modified": "2024-02-27T08:39:51.267Z"}, {"entity": "publication", "iuid": "edb9aa23ac704f2384a042691edc79e2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/edb9aa23ac704f2384a042691edc79e2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/edb9aa23ac704f2384a042691edc79e2"}}, "title": "Sex-limited experimental evolution drives transcriptomic divergence in a hermaphrodite.", "authors": [{"family": "C\u012brulis", "given": "Aivars", "initials": "A", "orcid": "0000-0003-3472-865X", "researcher": {"href": "https://publications.scilifelab.se/researcher/ed7cd12abf3e450288217a8acaa2190d.json"}}, {"family": "Nord\u00e9n", "given": "Anna K", "initials": "AK"}, {"family": "Churcher", "given": "Allison M", "initials": "AM"}, {"family": "Ramm", "given": "Steven A", "initials": "SA"}, {"family": "Zadesenets", "given": "Kira S", "initials": "KS"}, {"family": "Abbott", "given": "Jessica K", "initials": "JK", "orcid": "0000-0002-8743-2089", "researcher": {"href": "https://publications.scilifelab.se/researcher/7be37bf315f34e18b7ad8714da1381b8.json"}}], "type": "journal article", "published": "2024-01-05", "journal": {"title": "Genome Biol Evol", "issn": "1759-6653", "issn-l": "1759-6653", "volume": "16", "issue": "1", "pages": null}, "abstract": "The evolution of gonochorism from hermaphroditism is linked with the formation of sex chromosomes, as well as the evolution of sex-biased and sex-specific gene expression to allow both sexes to reach their fitness optimum. There is evidence that sexual selection drives the evolution of male-biased gene expression in particular. However, previous research in this area in animals comes from either theoretical models or comparative studies of already old sex chromosomes. We therefore investigated changes in gene expression under 3 different selection regimes for the simultaneous hermaphrodite Macrostomum lignano subjected to sex-limited experimental evolution (i.e. selection for fitness via eggs, sperm, or a control regime allowing both). After 21 and 22 generations of selection for male-specific or female-specific fitness, we characterized changes in whole-organism gene expression. We found that female-selected lines had changed the most in their gene expression. Although annotation for this species is limited, gene ontology term and Kyoto Encyclopedia of Genes and Genomes pathway analyses suggest that metabolic changes (e.g. biosynthesis of amino acids and carbon metabolism) are an important adaptive component. As predicted, we found that the expression of genes previously identified as testis-biased candidates tended to be downregulated in the female-selected lines. We did not find any significant expression differences for previously identified candidates of other sex-specific organs, but this may simply reflect that few transcripts have been characterized in this way. In conclusion, our experiment suggests that changes in testis-biased gene expression are important in the early evolution of sex chromosomes and gonochorism.", "doi": "10.1093/gbe/evad235", "pmid": "38155579", "labels": {"Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC10786194"}, {"db": "pii", "key": "7503504"}], "notes": [], "created": "2024-01-09T14:09:35.198Z", "modified": "2025-02-28T14:17:57.633Z"}, {"entity": "publication", "iuid": "5c597fc7742544a6b34a0e5fd1b7a1bb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5c597fc7742544a6b34a0e5fd1b7a1bb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5c597fc7742544a6b34a0e5fd1b7a1bb"}}, "title": "Whole-genome selective sweep analyses identifies the region and candidate gene associated with white earlobe color in Mediterranean chickens.", "authors": [{"family": "Guo", "given": "Ying", "initials": "Y"}, {"family": "Rubin", "given": "Carl-Johan", "initials": "CJ"}, {"family": "R\u00f6nneburg", "given": "Tilman", "initials": "T"}, {"family": "Wang", "given": "Shouzhi", "initials": "S"}, {"family": "Li", "given": "Hui", "initials": "H"}, {"family": "Hu", "given": "Xiaoxiang", "initials": "X"}, {"family": "Carlborg", "given": "\u00d6rjan", "initials": "\u00d6"}], "type": "journal article", "published": "2024-01-00", "journal": {"title": "Poult. Sci.", "issn": "1525-3171", "volume": "103", "issue": "1", "pages": "103232", "issn-l": "0032-5791"}, "abstract": "We compared the genomes of multiple domestic chicken breeds with red and white earlobes to identify the differentiated regions between groups of breeds differing in earlobe color. This was done using a selective sweep mapping approach based on whole-genome sequence data. The most significant selective sweep was identified on chromosome 11, where the white earlobe chicken breeds originated from Mediterranean share a common haplotype, and where multiple candidate genes are located. The most plausible functional candidate gene is the Melanocortin 1 Receptor (MC1R), a receptor known to regulate pigmentation in the skin and hair, and it is also the gene with the strongest positional support from the haplotype-based analyses. It, however, still needs to be explored experimentally to identify effects also on chicken earlobe color variation. Our study is the first exploration of the genetic basis of white earlobe color in Mediterranean chickens using a selective sweep mapping method based on whole-genome sequencing data and shows its value for identifying likely functional genes mediating the pigmentation in earlobe. It also indicates a potential novel role of MC1R in birds and exemplifies how selection on fancy traits has influenced the genome during formation of the modern chicken breeds.", "doi": "10.1016/j.psj.2023.103232", "pmid": "37980749", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10692716"}, {"db": "pii", "key": "S0032-5791(23)00751-4"}], "notes": [], "created": "2024-01-08T15:29:48.324Z", "modified": "2024-01-08T15:29:48.327Z"}, {"entity": "publication", "iuid": "bfae70dd68a54db286b9e8e040803c9f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/bfae70dd68a54db286b9e8e040803c9f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/bfae70dd68a54db286b9e8e040803c9f"}}, "title": "The genetic legacy of the expansion of Bantu-speaking peoples in Africa.", "authors": [{"family": "Fortes-Lima", "given": "Cesar A", "initials": "CA", "orcid": "0000-0002-9310-5009", "researcher": {"href": "https://publications.scilifelab.se/researcher/0a1afb9addfa42b4aa92a74ed8a8586b.json"}}, {"family": "Burgarella", "given": "Concetta", "initials": "C"}, {"family": "Hammar\u00e9n", "given": "Rickard", "initials": "R", "orcid": "0000-0001-9017-591X", "researcher": {"href": "https://publications.scilifelab.se/researcher/01a7b62a04c14b99bd73fb436006e4ff.json"}}, {"family": "Eriksson", "given": "Anders", "initials": "A", "orcid": "0000-0003-3436-3726", "researcher": {"href": "https://publications.scilifelab.se/researcher/85d31ca9cd2d4c658ff92d9726311d75.json"}}, {"family": "Vicente", "given": "M\u00e1rio", "initials": "M"}, {"family": "Jolly", "given": "Cecile", "initials": "C"}, {"family": "Semo", "given": "Armando", "initials": "A"}, {"family": "Gunnink", "given": "Hilde", "initials": "H", "orcid": "0000-0002-5508-8156", "researcher": {"href": "https://publications.scilifelab.se/researcher/153efdc0d8f54dc1bd754526479a3b42.json"}}, {"family": "Pacchiarotti", "given": "Sara", "initials": "S", "orcid": "0000-0003-1360-5060", "researcher": {"href": "https://publications.scilifelab.se/researcher/e8565dac645f45aaaf34ea46fac71703.json"}}, {"family": "Mundeke", "given": "Leon", "initials": "L"}, {"family": "Matonda", "given": "Igor", "initials": "I"}, {"family": "Muluwa", "given": "Joseph Koni", "initials": "JK"}, {"family": "Coutros", "given": "Peter", "initials": "P", "orcid": "0000-0002-4861-6432", "researcher": {"href": "https://publications.scilifelab.se/researcher/2c95e69649fb40d3944d65a07c7e76b8.json"}}, {"family": "Nyambe", "given": "Terry S", "initials": "TS"}, {"family": "Cikomola", "given": "Justin Cirhuza", "initials": "JC", "orcid": "0000-0002-0856-5992", "researcher": {"href": "https://publications.scilifelab.se/researcher/4058aac2a3bf4fe4a6d8724d002ea864.json"}}, {"family": "Coetzee", "given": "Vinet", "initials": "V"}, {"family": "de Castro", "given": "Minique", "initials": "M"}, {"family": "Ebbesen", "given": "Peter", "initials": "P"}, {"family": "Delanghe", "given": "Joris", "initials": "J", "orcid": "0000-0002-5702-6792", "researcher": {"href": "https://publications.scilifelab.se/researcher/bc00e2044f7246578cbea5abdf98e844.json"}}, {"family": "Stoneking", "given": "Mark", "initials": "M"}, {"family": "Barham", "given": "Lawrence", "initials": "L", "orcid": "0000-0002-5474-4668", "researcher": {"href": "https://publications.scilifelab.se/researcher/2f2502e25e9047bc811c878c90289cfa.json"}}, {"family": "Lombard", "given": "Marlize", "initials": "M", "orcid": "0000-0002-0675-0414", "researcher": {"href": "https://publications.scilifelab.se/researcher/e04e97bbc9914f358864988174b9b58d.json"}}, {"family": "Meyer", "given": "Anja", "initials": "A", "orcid": "0000-0002-5275-9276", "researcher": {"href": "https://publications.scilifelab.se/researcher/67901afbd54943c3997b3c6348bfb94f.json"}}, {"family": "Steyn", "given": "Maryna", "initials": "M"}, {"family": "Malmstr\u00f6m", "given": "Helena", "initials": "H", "orcid": "0000-0002-6456-8055", "researcher": {"href": "https://publications.scilifelab.se/researcher/3b3397b2842142bea34c222f6683c0eb.json"}}, {"family": "Rocha", "given": "Jorge", "initials": "J", "orcid": "0000-0001-5460-7615", "researcher": {"href": "https://publications.scilifelab.se/researcher/37e0a929cf884352bbdc844b4db86f28.json"}}, {"family": "Soodyall", "given": "Himla", "initials": "H"}, {"family": "Pakendorf", "given": "Brigitte", "initials": "B"}, {"family": "Bostoen", "given": "Koen", "initials": "K", "orcid": "0000-0003-2284-6165", "researcher": {"href": "https://publications.scilifelab.se/researcher/026b51a02da64bc99d42f6df582b29d4.json"}}, {"family": "Schlebusch", "given": "Carina M", "initials": "CM", "orcid": "0000-0002-8160-9621", "researcher": {"href": "https://publications.scilifelab.se/researcher/682f10853c1145649b8c76680605dd9b.json"}}], "type": "journal article", "published": "2024-01-00", "journal": {"title": "Nature", "issn": "1476-4687", "volume": "625", "issue": "7995", "pages": "540-547", "issn-l": "0028-0836"}, "abstract": "The expansion of people speaking Bantu languages is the most dramatic demographic event in Late Holocene Africa and fundamentally reshaped the linguistic, cultural and biological landscape of the continent1-7. With a comprehensive genomic dataset, including newly generated data of modern-day and ancient DNA from previously unsampled regions in Africa, we contribute insights into this expansion that started 6,000-4,000 years ago in western Africa. We genotyped 1,763 participants, including 1,526 Bantu speakers from 147 populations across 14 African countries, and generated whole-genome sequences from 12 Late Iron Age individuals8. We show that genetic diversity amongst Bantu-speaking populations declines with distance from western Africa, with current-day Zambia and the Democratic Republic of Congo as possible crossroads of interaction. Using spatially explicit methods9 and correlating genetic, linguistic and geographical data, we provide cross-disciplinary support for a serial-founder migration model. We further show that Bantu speakers received significant gene flow from local groups in regions they expanded into. Our genetic dataset provides an exhaustive modern-day African comparative dataset for ancient DNA studies10 and will be important to a wide range of disciplines from science and humanities, as well as to the medical sector studying human genetic variation and health in African and African-descendant populations.", "doi": "10.1038/s41586-023-06770-6", "pmid": "38030719", "labels": {"NGI Short read": "Service", "NGI SNP genotyping": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10794141"}, {"db": "pii", "key": "10.1038/s41586-023-06770-6"}], "notes": [], "created": "2023-12-01T06:47:49.351Z", "modified": "2024-11-25T10:19:18.159Z"}, {"entity": "publication", "iuid": "c7dc193c604c4e5fa865e49344129528", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c7dc193c604c4e5fa865e49344129528.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c7dc193c604c4e5fa865e49344129528"}}, "title": "New chemical and microbial perspectives on vitamin B1 and vitamer dynamics of a coastal system.", "authors": [{"family": "Bittner", "given": "Meriel J", "initials": "MJ", "orcid": "0000-0002-3798-6315", "researcher": {"href": "https://publications.scilifelab.se/researcher/5abcc332fec3408f996fff6e2470f304.json"}}, {"family": "Bannon", "given": "Catherine C", "initials": "CC", "orcid": "0000-0002-8581-1069", "researcher": {"href": "https://publications.scilifelab.se/researcher/176684868401463e8e36980a8f297ab8.json"}}, {"family": "Rowland", "given": "Elden", "initials": "E", "orcid": "0000-0003-4756-9125", "researcher": {"href": "https://publications.scilifelab.se/researcher/7c1d771d5585492681b9c2a296a78914.json"}}, {"family": "Sundh", "given": "John", "initials": "J", "orcid": "0000-0003-3053-9392", "researcher": {"href": "https://publications.scilifelab.se/researcher/655b68ac26af42ad9fb4dfe0869e15ea.json"}}, {"family": "Bertrand", "given": "Erin M", "initials": "EM", "orcid": "0000-0002-5950-6810", "researcher": {"href": "https://publications.scilifelab.se/researcher/bc79515185fc4304bb690324be48adf2.json"}}, {"family": "Andersson", "given": "Anders F", "initials": "AF", "orcid": "0000-0002-3627-6899", "researcher": {"href": "https://publications.scilifelab.se/researcher/caa76ee4438d4b4aad386ba8a90448c2.json"}}, {"family": "Paerl", "given": "Ryan W", "initials": "RW", "orcid": "0000-0003-3980-8181", "researcher": {"href": "https://publications.scilifelab.se/researcher/1267dafcedd84e77aa550169e4340998.json"}}, {"family": "Riemann", "given": "Lasse", "initials": "L", "orcid": "0000-0001-9207-2543", "researcher": {"href": "https://publications.scilifelab.se/researcher/9fc561d1d5694c4c9fbc9a05dd741e17.json"}}], "type": "journal article", "published": "2024-01-00", "journal": {"title": "ISME COMMUN.", "issn": "2730-6151", "issn-l": null, "volume": "4", "issue": "1", "pages": "ycad016"}, "abstract": "Vitamin B1 (thiamin, B1) is an essential micronutrient for cells, yet intriguingly in aquatic systems most bacterioplankton are unable to synthesize it de novo (auxotrophy), requiring an exogenous source. Cycling of this valuable metabolite in aquatic systems has not been fully investigated and vitamers (B1-related compounds) have only begun to be measured and incorporated into the B1 cycle. Here, we identify potential key producers and consumers of B1 and gain new insights into the dynamics of B1 cycling through measurements of B1 and vitamers (HMP: 4-amino-5-hydroxymethyl-2-methylpyrimidine, HET: 4-methyl-5-thiazoleethanol, FAMP: N-formyl-4-amino-5-aminomethyl-2-methylpyrimidine) in the particulate and dissolved pool in a temperate coastal system. Dissolved B1 was not the primary limiting nutrient for bacterial production and was relatively stable across seasons with concentrations ranging from 74-117 pM, indicating a balance of supply and demand. However, vitamer concentration changed markedly with season as did transcripts related to vitamer salvage and transport suggesting use of vitamers by certain bacterioplankton, e.g. Pelagibacterales. Genomic and transcriptomic analyses showed that up to 78% of the bacterioplankton taxa were B1 auxotrophs. Notably, de novo B1 production was restricted to a few abundant bacterioplankton (e.g. Vulcanococcus, BACL14 (Burkholderiales), Verrucomicrobiales) across seasons. In summer, abundant picocyanobacteria were important putative B1 sources, based on transcriptional activity, leading to an increase in the B1 pool. Our results provide a new dynamic view of the players and processes involved in B1 cycling over time in coastal waters, and identify specific priority populations and processes for future study.", "doi": "10.1093/ismeco/ycad016", "pmid": "38390520", "labels": {"NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support and Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10881298"}, {"db": "pii", "key": "ycad016"}, {"db": "figshare", "key": "10.6084/m9.figshare.23634429"}], "notes": [], "created": "2024-03-14T11:11:47.095Z", "modified": "2025-02-28T14:18:29.377Z"}, {"entity": "publication", "iuid": "0e680eec7e28428ba9cc34cfcdb773fe", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0e680eec7e28428ba9cc34cfcdb773fe.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0e680eec7e28428ba9cc34cfcdb773fe"}}, "title": "Population genomic data reveal low genetic diversity, divergence and local adaptation among threatened Reeves's Pheasant (Syrmaticus reevesii)", "authors": [{"family": "Lu", "given": "Qi", "initials": "Q"}, {"family": "Wang", "given": "Pengcheng", "initials": "P"}, {"family": "Chang", "given": "Jiang", "initials": "J"}, {"family": "Chen", "given": "De", "initials": "D"}, {"family": "Gao", "given": "Shenghan", "initials": "S"}, {"family": "H\u00f6glund", "given": "Jacob", "initials": "J"}, {"family": "Zhang", "given": "Zhengwang", "initials": "Z"}], "type": "journal-article", "published": "2024-00-00", "journal": {"title": "Avian Research", "issn": "2053-7166", "volume": "15", "pages": "100156", "issn-l": null}, "abstract": null, "doi": "10.1016/j.avrs.2023.100156", "pmid": null, "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [], "notes": [], "created": "2024-03-21T08:49:30.981Z", "modified": "2025-12-04T17:15:18.325Z"}, {"entity": "publication", "iuid": "5646472bef1e4cf5a38babba13f39b12", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5646472bef1e4cf5a38babba13f39b12.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5646472bef1e4cf5a38babba13f39b12"}}, "title": "Effect of anode material and dispersal limitation on the performance and biofilm community in microbial electrolysis cells.", "authors": [{"family": "Abadikhah", "given": "Marie", "initials": "M"}, {"family": "Liu", "given": "Ming", "initials": "M"}, {"family": "Persson", "given": "Frank", "initials": "F"}, {"family": "Wil\u00e9n", "given": "Britt-Marie", "initials": "BM"}, {"family": "Farewell", "given": "Anne", "initials": "A"}, {"family": "Sun", "given": "Jie", "initials": "J"}, {"family": "Modin", "given": "Oskar", "initials": "O"}], "type": "journal article", "published": "2023-12-15", "journal": {"title": "Biofilm", "issn": "2590-2075", "volume": "6", "pages": "100161", "issn-l": null}, "abstract": "In a microbial electrolysis cell (MEC), the oxidization of organic compounds is facilitated by an electrogenic biofilm on the anode surface. The biofilm community composition determines the function of the system. Both deterministic and stochastic factors affect the community, but the relative importance of different factors is poorly understood. Anode material is a deterministic factor as materials with different properties may select for different microorganisms. Ecological drift is a stochastic factor, which is amplified by dispersal limitation between communities. Here, we compared the effects of three anode materials (graphene, carbon cloth, and nickel) with the effect of dispersal limitation on the function and biofilm community assembly. Twelve MECs were operated for 56 days in four hydraulically connected loops and shotgun metagenomic sequencing was used to analyse the microbial community composition on the anode surfaces at the end of the experiment. The anode material was the most important factor affecting the performance of the MECs, explaining 54-80 % of the variance observed in peak current density, total electric charge generation, and start-up lag time, while dispersal limitation explained 10-16 % of the variance. Carbon cloth anodes had the highest current generation and shortest lag time. However, dispersal limitation was the most important factor affecting microbial community structure, explaining 61-98 % of the variance in community diversity, evenness, and the relative abundance of the most abundant taxa, while anode material explained 0-20 % of the variance. The biofilms contained nine Desulfobacterota metagenome-assembled genomes (MAGs), which made up 64-89 % of the communities and were likely responsible for electricity generation in the MECs. Different MAGs dominated in different MECs. Particularly two different genotypes related to Geobacter benzoatilyticus competed for dominance on the anodes and reached relative abundances up to 83 %. The winning genotype was the same in all MECs that were hydraulically connected irrespective of anode material used.", "doi": "10.1016/j.bioflm.2023.100161", "pmid": "37859795", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10582064"}, {"db": "pii", "key": "S2590-2075(23)00058-8"}], "notes": [], "created": "2023-11-29T11:35:13.039Z", "modified": "2023-11-29T11:35:13.056Z"}, {"entity": "publication", "iuid": "eab4268374624f2ab14306ca0d1dd3b0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/eab4268374624f2ab14306ca0d1dd3b0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/eab4268374624f2ab14306ca0d1dd3b0"}}, "title": "Haplotype-resolved genome of heterozygous African cassava cultivar TMEB117 (Manihot esculenta).", "authors": [{"family": "Landi", "given": "Michael", "initials": "M", "orcid": "0000-0001-5597-7802", "researcher": {"href": "https://publications.scilifelab.se/researcher/0a48329b81f14ff191ed7a8c8cb562b8.json"}}, {"family": "Shah", "given": "Trushar", "initials": "T", "orcid": "0000-0002-0091-7981", "researcher": {"href": "https://publications.scilifelab.se/researcher/6db73454fcb34150bd72bcc5e850cb5e.json"}}, {"family": "Falquet", "given": "Laurent", "initials": "L", "orcid": "0000-0001-8102-7579", "researcher": {"href": "https://publications.scilifelab.se/researcher/bba0eeebd71e4f6ca50a2751f898fc6a.json"}}, {"family": "Niazi", "given": "Adnan", "initials": "A", "orcid": "0000-0003-0311-5279", "researcher": {"href": "https://publications.scilifelab.se/researcher/c9e07c9891804a60980eb07956a7cd0d.json"}}, {"family": "Stavolone", "given": "Livia", "initials": "L"}, {"family": "Bongcam-Rudloff", "given": "Erik", "initials": "E", "orcid": "0000-0002-1947-8288", "researcher": {"href": "https://publications.scilifelab.se/researcher/6970ca57259d498588ecf9e1ad28a9b0.json"}}, {"family": "Gisel", "given": "Andreas", "initials": "A", "orcid": "0000-0001-7218-9488", "researcher": {"href": "https://publications.scilifelab.se/researcher/b2eb91acead14ec58845e9eda08742fa.json"}}], "type": "dataset", "published": "2023-12-09", "journal": {"title": "Sci Data", "issn": "2052-4463", "volume": "10", "issue": "1", "pages": "887", "issn-l": "2052-4463"}, "abstract": "Cassava (Manihot esculenta Crantz) is a vital tropical root crop providing essential dietary energy to over 800 million people in tropical and subtropical regions. As a climate-resilient crop, its significance grows as the human population expands. However, yield improvement faces challenges from biotic and abiotic stress and limited breeding. Advanced sequencing and assembly techniques enabled the generation of a highly accurate, nearly complete, haplotype-resolved genome of the African cassava cultivar TMEB117. It is the most accurate cassava genome sequence to date with a base-level accuracy of QV > 64, N50 > 35 Mbp, and 98.9% BUSCO completeness. Over 60% of the genome comprises repetitive elements. We predicted over 45,000 gene models for both haplotypes. This achievement offers valuable insights into the heterozygosity genome organization of the cassava genome, with improved accuracy, completeness, and phased genomes. Due to its high susceptibility to African Cassava Mosaic Virus (ACMV) infections compared to other cassava varieties, TMEB117 provides an ideal reference for studying virus resistance mechanisms, including epigenetic variations and smallRNA expressions.", "doi": "10.1038/s41597-023-02800-0", "pmid": "38071206", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "NGI Uppsala (Uppsala Genome Center)": "Service", "NGI Long read": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC10710486"}, {"db": "pii", "key": "10.1038/s41597-023-02800-0"}], "notes": [], "created": "2023-12-11T06:42:02.155Z", "modified": "2024-01-05T16:18:41.036Z"}, {"entity": "publication", "iuid": "c7fce16085b242e4a0c1e4d445e7cc5f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c7fce16085b242e4a0c1e4d445e7cc5f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c7fce16085b242e4a0c1e4d445e7cc5f"}}, "title": "Multimodal classification of molecular subtypes in pediatric acute lymphoblastic leukemia.", "authors": [{"family": "Krali", "given": "Olga", "initials": "O", "orcid": "0000-0002-6436-9531", "researcher": {"href": "https://publications.scilifelab.se/researcher/14a6e2f99d3b4758a10af78b93777779.json"}}, {"family": "Marincevic-Zuniga", "given": "Yanara", "initials": "Y"}, {"family": "Arvidsson", "given": "Gustav", "initials": "G"}, {"family": "Enblad", "given": "Anna Pia", "initials": "AP"}, {"family": "Lundmark", "given": "Anders", "initials": "A"}, {"family": "Sayyab", "given": "Shumaila", "initials": "S"}, {"family": "Zachariadis", "given": "Vasilios", "initials": "V"}, {"family": "Hein\u00e4niemi", "given": "Merja", "initials": "M"}, {"family": "Suhonen", "given": "Janne", "initials": "J"}, {"family": "Oksa", "given": "Laura", "initials": "L", "orcid": "0000-0003-4468-9877", "researcher": {"href": "https://publications.scilifelab.se/researcher/5526f0f44427441bb2a49f27f00b5683.json"}}, {"family": "Veps\u00e4l\u00e4inen", "given": "Kaisa", "initials": "K"}, {"family": "\u00d6fverholm", "given": "Ingegerd", "initials": "I"}, {"family": "Barbany", "given": "Gisela", "initials": "G", "orcid": "0000-0003-3185-2962", "researcher": {"href": "https://publications.scilifelab.se/researcher/13fda0d702d543f981898ebd53849817.json"}}, {"family": "Nordgren", "given": "Ann", "initials": "A"}, {"family": "Lilljebj\u00f6rn", "given": "Henrik", "initials": "H"}, {"family": "Fioretos", "given": "Thoas", "initials": "T"}, {"family": "Madsen", "given": "Hans O", "initials": "HO"}, {"family": "Marquart", "given": "Hanne Vibeke", "initials": "HV"}, {"family": "Flaegstad", "given": "Trond", "initials": "T"}, {"family": "Forestier", "given": "Erik", "initials": "E"}, {"family": "J\u00f3nsson", "given": "\u00d3lafur G", "initials": "\u00d3G"}, {"family": "Kanerva", "given": "Jukka", "initials": "J"}, {"family": "Lohi", "given": "Olli", "initials": "O"}, {"family": "Nor\u00e9n-Nystr\u00f6m", "given": "Ulrika", "initials": "U"}, {"family": "Schmiegelow", "given": "Kjeld", "initials": "K"}, {"family": "Harila", "given": "Arja", "initials": "A"}, {"family": "Heyman", "given": "Mats", "initials": "M"}, {"family": "L\u00f6nnerholm", "given": "Gudmar", "initials": "G"}, {"family": "Syv\u00e4nen", "given": "Ann-Christine", "initials": "AC", "orcid": "0000-0002-9681-9146", "researcher": {"href": "https://publications.scilifelab.se/researcher/f7012e35025543379380cb90efd71243.json"}}, {"family": "Nordlund", "given": "Jessica", "initials": "J", "orcid": "0000-0001-8699-9959", "researcher": {"href": "https://publications.scilifelab.se/researcher/ddf48c9262134821bcc6ce1180049753.json"}}], "type": "journal article", "published": "2023-12-08", "journal": {"title": "NPJ Precis Oncol", "issn": "2397-768X", "volume": "7", "issue": "1", "pages": "131", "issn-l": null}, "abstract": "Genomic analyses have redefined the molecular subgrouping of pediatric acute lymphoblastic leukemia (ALL). Molecular subgroups guide risk-stratification and targeted therapies, but outcomes of recently identified subtypes are often unclear, owing to limited cases with comprehensive profiling and cross-protocol studies. We developed a machine learning tool (ALLIUM) for the molecular subclassification of ALL in retrospective cohorts as well as for up-front diagnostics. ALLIUM uses DNA methylation and gene expression data from 1131 Nordic ALL patients to predict 17 ALL subtypes with high accuracy. ALLIUM was used to revise and verify the molecular subtype of 281 B-cell precursor ALL (BCP-ALL) cases with previously undefined molecular phenotype, resulting in a single revised subtype for 81.5% of these cases. Our study shows the power of combining DNA methylation and gene expression data for resolving ALL subtypes and provides a comprehensive population-based retrospective cohort study of molecular subtype frequencies in the Nordic countries.", "doi": "10.1038/s41698-023-00479-5", "pmid": "38066241", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "NGI SNP genotyping": "Service", "Clinical Genomics Stockholm": "Service", "Clinical Genomics": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10709574"}, {"db": "pii", "key": "10.1038/s41698-023-00479-5"}], "notes": [], "created": "2024-11-05T18:15:42.686Z", "modified": "2024-11-21T08:31:51.959Z"}, {"entity": "publication", "iuid": "fa0c81dcc024441fa1eeb827056ba874", "links": {"self": {"href": "https://publications.scilifelab.se/publication/fa0c81dcc024441fa1eeb827056ba874.json"}, "display": {"href": "https://publications.scilifelab.se/publication/fa0c81dcc024441fa1eeb827056ba874"}}, "title": "Shared and distinct pathways and networks genetically linked to coronary artery disease between human and mouse.", "authors": [{"family": "Kurt", "given": "Zeyneb", "initials": "Z", "orcid": "0000-0003-3186-8091", "researcher": {"href": "https://publications.scilifelab.se/researcher/64250f1d007945c3897e7698e2dabf55.json"}}, {"family": "Cheng", "given": "Jenny", "initials": "J", "orcid": "0009-0009-2248-1697", "researcher": {"href": "https://publications.scilifelab.se/researcher/d2b5c909f04a4bce9d13a29d39f0e00b.json"}}, {"family": "Barrere-Cain", "given": "Rio", "initials": "R"}, {"family": "McQuillen", "given": "Caden N", "initials": "CN", "orcid": "0000-0002-7762-9283", "researcher": {"href": "https://publications.scilifelab.se/researcher/107d075ac0ff498cbc0d1571db912569.json"}}, {"family": "Saleem", "given": "Zara", "initials": "Z"}, {"family": "Hsu", "given": "Neil", "initials": "N"}, {"family": "Jiang", "given": "Nuoya", "initials": "N"}, {"family": "Pan", "given": "Calvin", "initials": "C"}, {"family": "Franz\u00e9n", "given": "Oscar", "initials": "O", "orcid": "0000-0002-7573-0812", "researcher": {"href": "https://publications.scilifelab.se/researcher/da9f587e682f433dbcdbe932861d1a69.json"}}, {"family": "Koplev", "given": "Simon", "initials": "S"}, {"family": "Wang", "given": "Susanna", "initials": "S", "orcid": "0009-0006-0254-8418", "researcher": {"href": "https://publications.scilifelab.se/researcher/d94dc3b61cff49288601993fed78788c.json"}}, {"family": "Bj\u00f6rkegren", "given": "Johan", "initials": "J"}, {"family": "Lusis", "given": "Aldons J", "initials": "AJ", "orcid": "0000-0001-9013-0228", "researcher": {"href": "https://publications.scilifelab.se/researcher/534cbc36b84f44ddbdbb7e5cc78c11a9.json"}}, {"family": "Blencowe", "given": "Montgomery", "initials": "M", "orcid": "0000-0001-7147-1895", "researcher": {"href": "https://publications.scilifelab.se/researcher/d6456f51239c473685cf9af4ad7e7e0e.json"}}, {"family": "Yang", "given": "Xia", "initials": "X", "orcid": "0000-0002-3971-038X", "researcher": {"href": "https://publications.scilifelab.se/researcher/71b78d5687ba491d8c1dddd171483557.json"}}], "type": "journal article", "published": "2023-12-07", "journal": {"title": "Elife", "issn": "2050-084X", "volume": "12", "issn-l": "2050-084X"}, "abstract": "Mouse models have been used extensively to study human coronary artery disease (CAD) or atherosclerosis and to test therapeutic targets. However, whether mouse and human share similar genetic factors and pathogenic mechanisms of atherosclerosis has not been thoroughly investigated in a data-driven manner. We conducted a cross-species comparison study to better understand atherosclerosis pathogenesis between species by leveraging multiomics data. Specifically, we compared genetically driven and thus CAD-causal gene networks and pathways, by using human GWAS of CAD from the CARDIoGRAMplusC4D consortium and mouse GWAS of atherosclerosis from the Hybrid Mouse Diversity Panel (HMDP) followed by integration with functional multiomics human (STARNET and GTEx) and mouse (HMDP) databases. We found that mouse and human shared >75% of CAD causal pathways. Based on network topology, we then predicted key regulatory genes for both the shared pathways and species-specific pathways, which were further validated through the use of single cell data and the latest CAD GWAS. In sum, our results should serve as a much-needed guidance for which human CAD-causal pathways can or cannot be further evaluated for novel CAD therapies using mouse models.", "doi": "10.7554/eLife.88266", "pmid": "38060277", "labels": {"NGI Short read": "Service", "NGI SNP genotyping": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10703441"}, {"db": "pii", "key": "88266"}], "notes": [], "created": "2024-01-08T15:29:00.638Z", "modified": "2024-01-08T15:29:01.015Z"}, {"entity": "publication", "iuid": "81b93732cab9499a9aa99d87d2b3d294", "links": {"self": {"href": "https://publications.scilifelab.se/publication/81b93732cab9499a9aa99d87d2b3d294.json"}, "display": {"href": "https://publications.scilifelab.se/publication/81b93732cab9499a9aa99d87d2b3d294"}}, "title": "Meta-Analyses of Genome-Wide Association Studies for Postpartum Depression.", "authors": [{"family": "Guintivano", "given": "Jerry", "initials": "J"}, {"family": "Byrne", "given": "Enda M", "initials": "EM"}, {"family": "Kiewa", "given": "Jacqueline", "initials": "J"}, {"family": "Yao", "given": "Shuyang", "initials": "S"}, {"family": "Bauer", "given": "Anna E", "initials": "AE"}, {"family": "Aberg", "given": "Karolina A", "initials": "KA"}, {"family": "Adams", "given": "Mark J", "initials": "MJ"}, {"family": "Campbell", "given": "Archie", "initials": "A"}, {"family": "Campbell", "given": "Megan L", "initials": "ML"}, {"family": "Choi", "given": "Karmel W", "initials": "KW"}, {"family": "Corfield", "given": "Elizabeth C", "initials": "EC"}, {"family": "Havdahl", "given": "Alexandra", "initials": "A"}, {"family": "Hucks", "given": "Donald", "initials": "D"}, {"family": "Koen", "given": "Nastassja", "initials": "N"}, {"family": "Lu", "given": "Yi", "initials": "Y"}, {"family": "M\u00e6gb\u00e6k", "given": "Merete L", "initials": "ML"}, {"family": "Mullaert", "given": "Jimmy", "initials": "J"}, {"family": "Peterson", "given": "Roseann E", "initials": "RE"}, {"family": "Raffield", "given": "Laura M", "initials": "LM"}, {"family": "Sallis", "given": "Hannah M", "initials": "HM"}, {"family": "Sealock", "given": "Julia M", "initials": "JM"}, {"family": "Walker", "given": "Alicia", "initials": "A"}, {"family": "Watson", "given": "Hunna J", "initials": "HJ"}, {"family": "Xiong", "given": "Ying", "initials": "Y"}, {"family": "Yang", "given": "Jessica M K", "initials": "JMK"}, {"family": "Anney", "given": "Richard J L", "initials": "RJL"}, {"family": "Gordon-Smith", "given": "Katherine", "initials": "K"}, {"family": "Hubbard", "given": "Leon", "initials": "L"}, {"family": "Jones", "given": "Lisa A", "initials": "LA"}, {"family": "Mihaescu", "given": "Raluca", "initials": "R"}, {"family": "Nyegaard", "given": "Mette", "initials": "M"}, {"family": "Pardi\u00f1as", "given": "Antonio F", "initials": "AF"}, {"family": "Perry", "given": "Amy", "initials": "A"}, {"family": "Saquib", "given": "Nazmus", "initials": "N"}, {"family": "Shadyab", "given": "Aladdin H", "initials": "AH"}, {"family": "Viktorin", "given": "Alexander", "initials": "A"}, {"family": "Andreassen", "given": "Ole A", "initials": "OA"}, {"family": "Bigdeli", "given": "Tim B", "initials": "TB"}, {"family": "Davis", "given": "Lea K", "initials": "LK"}, {"family": "Dennis", "given": "Cindy-Lee", "initials": "CL"}, {"family": "Di Florio", "given": "Arianna", "initials": "A"}, {"family": "Dubertret", "given": "Caroline", "initials": "C"}, {"family": "Feng", "given": "Yen-Chen A", "initials": "YA"}, {"family": "Frey", "given": "Benicio N", "initials": "BN"}, {"family": "Grigoriadis", "given": "Sophie", "initials": "S"}, {"family": "Gloaguen", "given": "Emilie", "initials": "E"}, {"family": "Jones", "given": "Ian", "initials": "I"}, {"family": "Kennedy", "given": "James L", "initials": "JL"}, {"family": "Krohn", "given": "Holly", "initials": "H"}, {"family": "Kunovac Kallak", "given": "Theodora", "initials": "T"}, {"family": "Li", "given": "Yun", "initials": "Y"}, {"family": "Martin", "given": "Nicholas G", "initials": "NG"}, {"family": "McIntosh", "given": "Andrew M", "initials": "AM"}, {"family": "Milgrom", "given": "Jeannette", "initials": "J"}, {"family": "Munk-Olsen", "given": "Trine", "initials": "T"}, {"family": "Oberlander", "given": "Tim", "initials": "T"}, {"family": "Olsen", "given": "Catherine M", "initials": "CM"}, {"family": "Ramoz", "given": "Nicolas", "initials": "N"}, {"family": "Reichborn-Kjennerud", "given": "Ted", "initials": "T"}, {"family": "Robertson Blackmore", "given": "Emma", "initials": "E"}, {"family": "Rubinow", "given": "David", "initials": "D"}, {"family": "Skalkidou", "given": "Alkistis", "initials": "A"}, {"family": "Smoller", "given": "Jordan W", "initials": "JW"}, {"family": "Stein", "given": "Dan J", "initials": "DJ"}, {"family": "Stowe", "given": "Zachary N", "initials": "ZN"}, {"family": "Taylor", "given": "Valerie", "initials": "V"}, {"family": "Tebeka", "given": "Sarah", "initials": "S"}, {"family": "Tesli", "given": "Martin", "initials": "M"}, {"family": "Van Lieshout", "given": "Ryan J", "initials": "RJ"}, {"family": "van den Oord", "given": "Edwin J C G", "initials": "EJCG"}, {"family": "Vigod", "given": "Simone N", "initials": "SN"}, {"family": "Werge", "given": "Thomas", "initials": "T"}, {"family": "Westlye", "given": "Lars T", "initials": "LT"}, {"family": "Whiteman", "given": "David C", "initials": "DC"}, {"family": "Zar", "given": "Heather J", "initials": "HJ"}, {"family": "Major Depressive Disorder Working Group of the Psychiatric Genomics Consortium", "given": "", "initials": ""}, {"family": "Wray", "given": "Naomi", "initials": "N"}, {"family": "Meltzer-Brody", "given": "Samantha", "initials": "S"}, {"family": "Sullivan", "given": "Patrick", "initials": "P"}], "type": "journal article", "published": "2023-12-01", "journal": {"title": "Am J Psychiatry", "issn": "1535-7228", "volume": "180", "issue": "12", "pages": "884-895", "issn-l": "0002-953X"}, "abstract": "Postpartum depression (PPD) is a common subtype of major depressive disorder (MDD) that is more heritable, yet is understudied in psychiatric genetics. The authors conducted meta-analyses of genome-wide association studies (GWASs) to investigate the genetic architecture of PPD.\n\nMeta-analyses were conducted on 18 cohorts of European ancestry (17,339 PPD cases and 53,426 controls), one cohort of East Asian ancestry (975 cases and 3,780 controls), and one cohort of African ancestry (456 cases and 1,255 controls), totaling 18,770 PPD cases and 58,461 controls. Post-GWAS analyses included 1) single-nucleotide polymorphism (SNP)-based heritability ([Formula: see text]), 2) genetic correlations between PPD and other phenotypes, and 3) enrichment of the PPD GWAS findings in 27 human tissues and 265 cell types from the mouse central and peripheral nervous system.\n\nNo SNP achieved genome-wide significance in the European or the trans-ancestry meta-analyses. The [Formula: see text] of PPD was 0.14 (SE=0.02). Significant genetic correlations were estimated for PPD with MDD, bipolar disorder, anxiety disorders, posttraumatic stress disorder, insomnia, age at menarche, and polycystic ovary syndrome. Cell-type enrichment analyses implicate inhibitory neurons in the thalamus and cholinergic neurons within septal nuclei of the hypothalamus, a pattern that differs from MDD.\n\nWhile more samples are needed to reach genome-wide levels of significance, the results presented confirm PPD as a polygenic and heritable phenotype. There is also evidence that despite a high correlation with MDD, PPD may have unique genetic components. Cell enrichment results suggest GABAergic neurons, which converge on a common mechanism with the only medication approved by the U.S. Food and Drug Administration for PPD (brexanolone).", "doi": "10.1176/appi.ajp.20230053", "pmid": "37849304", "labels": {"NGI SNP genotyping": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [], "notes": [], "created": "2024-01-08T15:58:42.328Z", "modified": "2024-01-08T15:58:42.332Z"}, {"entity": "publication", "iuid": "7d6870c445a44b8e9a55a8424dfa6383", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7d6870c445a44b8e9a55a8424dfa6383.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7d6870c445a44b8e9a55a8424dfa6383"}}, "title": "Complex Evolutionary History With Extensive Ancestral Gene Flow in an African Primate Radiation.", "authors": [{"family": "Jensen", "given": "Axel", "initials": "A", "orcid": "0000-0003-1766-560X", "researcher": {"href": "https://publications.scilifelab.se/researcher/7f139b7f3dac49e28ef6430637d88592.json"}}, {"family": "Swift", "given": "Frances", "initials": "F"}, {"family": "de Vries", "given": "Dorien", "initials": "D"}, {"family": "Beck", "given": "Robin M D", "initials": "RMD"}, {"family": "Kuderna", "given": "Lukas F K", "initials": "LFK"}, {"family": "Knauf", "given": "Sascha", "initials": "S"}, {"family": "Chuma", "given": "Idrissa S", "initials": "IS"}, {"family": "Keyyu", "given": "Julius D", "initials": "JD"}, {"family": "Kitchener", "given": "Andrew C", "initials": "AC", "orcid": "0000-0003-2594-0827", "researcher": {"href": "https://publications.scilifelab.se/researcher/0e8441bdcd504f7ebcc29c55337dd5ac.json"}}, {"family": "Farh", "given": "Kyle", "initials": "K"}, {"family": "Rogers", "given": "Jeffrey", "initials": "J", "orcid": "0000-0002-7374-6490", "researcher": {"href": "https://publications.scilifelab.se/researcher/18b3aaf283e443feb46f08e2aba6dc3d.json"}}, {"family": "Marques-Bonet", "given": "Tomas", "initials": "T"}, {"family": "Detwiler", "given": "Kate M", "initials": "KM"}, {"family": "Roos", "given": "Christian", "initials": "C"}, {"family": "Guschanski", "given": "Katerina", "initials": "K", "orcid": "0000-0002-8493-5457", "researcher": {"href": "https://publications.scilifelab.se/researcher/84b8b0757f02429b9bd419acb42ab6a3.json"}}], "type": "journal article", "published": "2023-12-01", "journal": {"title": "Mol. Biol. Evol.", "issn": "1537-1719", "volume": "40", "issue": "12", "issn-l": "0737-4038"}, "abstract": "Understanding the drivers of speciation is fundamental in evolutionary biology, and recent studies highlight hybridization as an important evolutionary force. Using whole-genome sequencing data from 22 species of guenons (tribe Cercopithecini), one of the world's largest primate radiations, we show that rampant gene flow characterizes their evolutionary history and identify ancient hybridization across deeply divergent lineages that differ in ecology, morphology, and karyotypes. Some hybridization events resulted in mitochondrial introgression between distant lineages, likely facilitated by cointrogression of coadapted nuclear variants. Although the genomic landscapes of introgression were largely lineage specific, we found that genes with immune functions were overrepresented in introgressing regions, in line with adaptive introgression, whereas genes involved in pigmentation and morphology may contribute to reproductive isolation. In line with reports from other systems that hybridization might facilitate diversification, we find that some of the most species-rich guenon clades are of admixed origin. This study provides important insights into the prevalence, role, and outcomes of ancestral hybridization in a large mammalian radiation.", "doi": "10.1093/molbev/msad247", "pmid": "37987553", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10691879"}, {"db": "pii", "key": "7439455"}], "notes": [], "created": "2024-01-08T15:46:27.376Z", "modified": "2024-01-16T13:48:31.531Z"}, {"entity": "publication", "iuid": "c02d8f92e64b4166ac3dc11da08b0eaa", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c02d8f92e64b4166ac3dc11da08b0eaa.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c02d8f92e64b4166ac3dc11da08b0eaa"}}, "title": "An epigenome-wide analysis of sex hormone levels and DNA methylation in male blood samples.", "authors": [{"family": "Harbs", "given": "Justin", "initials": "J"}, {"family": "Rinaldi", "given": "Sabina", "initials": "S"}, {"family": "Keski-Rahkonen", "given": "Pekka", "initials": "P"}, {"family": "Liu", "given": "Xijia", "initials": "X"}, {"family": "Palmqvist", "given": "Richard", "initials": "R"}, {"family": "Van Guelpen", "given": "Bethany", "initials": "B"}, {"family": "Harlid", "given": "Sophia", "initials": "S"}], "type": "journal article", "published": "2023-12-00", "journal": {"title": "Epigenetics", "issn": "1559-2308", "volume": "18", "issue": "1", "pages": "2196759", "issn-l": "1559-2294"}, "abstract": "Endogenous sex hormones and DNA methylation both play important roles in various diseases. However, their interplay is largely unknown. A deeper understanding of their interrelationships could provide new insights into the pathology of disease development. We, therefore, investigated associations between circulating sex hormones, sex hormone binding globulin (SHBG), and DNA methylation in blood, using samples from 77 men (65 with repeated samples), from the population-based Northern Sweden Health and Disease Study (NSHDS). DNA methylation was measured in buffy coat using the Infinium Methylation EPIC BeadChip (Illumina). Sex hormone (oestradiol, oestrone, testosterone, androstenedione, dehydroepiandrosterone, and progesterone) and SHBG concentrations were measured in plasma using a high-performance liquid chromatography tandem mass spectrometry (LC/MS-MS) method and an enzyme-linked immunoassay, respectively. Associations between sex hormones, SHBG, and DNA methylation were estimated using both linear regression and mixed-effects models. Additionally, we used the comb-p method to identify differentially methylated regions based on nearby P values. We identified one novel CpG site (cg14319657), at which DNA methylation was associated with dehydroepiandrosterone, surpassing a genome-wide significance level. In addition, more than 40 differentially methylated regions were associated with levels of sex hormones and SHBG and several of these mapped to genes involved in hormone-related diseases. Our findings support a relationship between circulating sex hormones and DNA methylation and suggest that further investigation is warranted, both for validation, further exploration and to gain a deeper understanding of the mechanisms and potential consequences for health and disease.", "doi": "10.1080/15592294.2023.2196759", "pmid": "36994855", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "NGI SNP genotyping": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10072117"}], "notes": [], "created": "2023-04-06T13:49:55.228Z", "modified": "2023-04-06T13:49:55.241Z"}, {"entity": "publication", "iuid": "d839b4f76f8f43aa9477e6790297fb62", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d839b4f76f8f43aa9477e6790297fb62.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d839b4f76f8f43aa9477e6790297fb62"}}, "title": "Using trials of caloric restriction and bariatric surgery to explore the effects of body mass index on the circulating proteome.", "authors": [{"family": "Goudswaard", "given": "Lucy J", "initials": "LJ"}, {"family": "Smith", "given": "Madeleine L", "initials": "ML"}, {"family": "Hughes", "given": "David A", "initials": "DA"}, {"family": "Taylor", "given": "Roy", "initials": "R"}, {"family": "Lean", "given": "Michael", "initials": "M"}, {"family": "Sattar", "given": "Naveed", "initials": "N"}, {"family": "Welsh", "given": "Paul", "initials": "P"}, {"family": "McConnachie", "given": "Alex", "initials": "A"}, {"family": "Blazeby", "given": "Jane M", "initials": "JM"}, {"family": "Rogers", "given": "Chris A", "initials": "CA"}, {"family": "Suhre", "given": "Karsten", "initials": "K"}, {"family": "Zaghlool", "given": "Shaza B", "initials": "SB"}, {"family": "Hers", "given": "Ingeborg", "initials": "I"}, {"family": "Timpson", "given": "Nicholas J", "initials": "NJ"}, {"family": "Corbin", "given": "Laura J", "initials": "LJ"}], "type": "journal article", "published": "2023-11-29", "journal": {"title": "Sci Rep", "issn": "2045-2322", "issn-l": "2045-2322", "volume": "13", "issue": "1", "pages": "21077"}, "abstract": "Thousands of proteins circulate in the bloodstream; identifying those which associate with weight and intervention-induced weight loss may help explain mechanisms of diseases associated with adiposity. We aimed to identify consistent protein signatures of weight loss across independent studies capturing changes in body mass index (BMI). We analysed proteomic data from studies implementing caloric restriction (Diabetes Remission Clinical trial) and bariatric surgery (By-Band-Sleeve), using SomaLogic and Olink Explore1536 technologies, respectively. Linear mixed models were used to estimate the effect of the interventions on circulating proteins. Twenty-three proteins were altered in a consistent direction after both bariatric surgery and caloric restriction, suggesting that these proteins are modulated by weight change, independent of intervention type. We also integrated Mendelian randomisation (MR) estimates of the effect of BMI on proteins measured by SomaLogic from a UK blood donor cohort as a third line of causal evidence. These MR estimates provided further corroborative evidence for a role of BMI in regulating the levels of six proteins including alcohol dehydrogenase-4, nogo receptor and interleukin-1 receptor antagonist protein. These results indicate the importance of triangulation in interrogating causal relationships; further study into the role of proteins modulated by weight in disease is now warranted.", "doi": "10.1038/s41598-023-47030-x", "pmid": "38030643", "labels": {"Affinity Proteomics Uppsala": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Proteomics": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10686974"}, {"db": "pii", "key": "10.1038/s41598-023-47030-x"}], "notes": [], "created": "2024-11-27T16:10:08.369Z", "modified": "2024-11-27T19:28:55.863Z"}, {"entity": "publication", "iuid": "c02a90250e024d3ea85719e8d9a55e17", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c02a90250e024d3ea85719e8d9a55e17.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c02a90250e024d3ea85719e8d9a55e17"}}, "title": "Infants' looking preferences for social versus non-social objects reflect genetic variation.", "authors": [{"family": "Portugal", "given": "Ana Maria", "initials": "AM", "orcid": "0000-0002-3627-0753", "researcher": {"href": "https://publications.scilifelab.se/researcher/1a54163213cc46f88ba1a6d31ac9dc66.json"}}, {"family": "Viktorsson", "given": "Charlotte", "initials": "C", "orcid": "0000-0003-2727-2957", "researcher": {"href": "https://publications.scilifelab.se/researcher/465e2969410c4109aaa466735d26002b.json"}}, {"family": "Taylor", "given": "Mark J", "initials": "MJ"}, {"family": "Mason", "given": "Luke", "initials": "L"}, {"family": "Tammimies", "given": "Kristiina", "initials": "K", "orcid": "0000-0002-8324-4697", "researcher": {"href": "https://publications.scilifelab.se/researcher/ba19ec07147743c6942ea10c9a92482a.json"}}, {"family": "Ronald", "given": "Angelica", "initials": "A", "orcid": "0000-0002-9576-2176", "researcher": {"href": "https://publications.scilifelab.se/researcher/8eba7a8ff11f40c088e0817c11ab702a.json"}}, {"family": "Falck-Ytter", "given": "Terje", "initials": "T", "orcid": "0000-0001-9714-0197", "researcher": {"href": "https://publications.scilifelab.se/researcher/ead33894d8054f2291e0be7cbb47e015.json"}}], "type": "journal article", "published": "2023-11-27", "journal": {"title": "Nat Hum Behav", "issn": "2397-3374", "issn-l": null}, "abstract": "To what extent do individual differences in infants' early preference for faces versus non-facial objects reflect genetic and environmental factors? Here in a sample of 536 5-month-old same-sex twins, we assessed attention to faces using eye tracking in two ways: initial orienting to faces at the start of the trial (thought to reflect subcortical processing) and sustained face preference throughout the trial (thought to reflect emerging attention control). Twin model fitting suggested an influence of genetic and unique environmental effects, but there was no evidence for an effect of shared environment. The heritability of face orienting and preference were 0.19 (95% confidence interval (CI) 0.04 to 0.33) and 0.46 (95% CI 0.33 to 0.57), respectively. Face preference was associated positively with later parent-reported verbal competence (\u03b2 = 0.14, 95% CI 0.03 to 0.25, P = 0.014, R2 = 0.018, N = 420). This study suggests that individual differences in young infants' selection of perceptual input-social versus non-social-are heritable, providing a developmental perspective on gene-environment interplay occurring at the level of eye movements.", "doi": "10.1038/s41562-023-01764-w", "pmid": "38012276", "labels": {"NGI SNP genotyping": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41562-023-01764-w"}], "notes": [], "created": "2023-11-29T12:37:24.462Z", "modified": "2023-11-29T12:37:24.578Z"}, {"entity": "publication", "iuid": "24281e6606fc498595f006d4846e5c40", "links": {"self": {"href": "https://publications.scilifelab.se/publication/24281e6606fc498595f006d4846e5c40.json"}, "display": {"href": "https://publications.scilifelab.se/publication/24281e6606fc498595f006d4846e5c40"}}, "title": "DNA elements tether canonical Polycomb Repressive Complex 1 to human genes.", "authors": [{"family": "Barrasa", "given": "Juan I", "initials": "JI"}, {"family": "Kahn", "given": "Tatyana G", "initials": "TG"}, {"family": "Lundkvist", "given": "Moa J", "initials": "MJ"}, {"family": "Schwartz", "given": "Yuri B", "initials": "YB", "orcid": "0000-0003-4790-3920", "researcher": {"href": "https://publications.scilifelab.se/researcher/2751a236629d4b8bb9fff42cad6ff614.json"}}], "type": "journal article", "published": "2023-11-27", "journal": {"title": "Nucleic Acids Res.", "issn": "1362-4962", "volume": "51", "issue": "21", "pages": "11613-11633", "issn-l": "0305-1048"}, "abstract": "Development of multicellular animals requires epigenetic repression by Polycomb group proteins. The latter assemble in multi-subunit complexes, of which two kinds, Polycomb Repressive Complex 1 (PRC1) and Polycomb Repressive Complex 2 (PRC2), act together to repress key developmental genes. How PRC1 and PRC2 recognize specific genes remains an open question. Here we report the identification of several hundreds of DNA elements that tether canonical PRC1 to human developmental genes. We use the term tether to describe a process leading to a prominent presence of canonical PRC1 at certain genomic sites, although the complex is unlikely to interact with DNA directly. Detailed analysis indicates that sequence features associated with PRC1 tethering differ from those that favour PRC2 binding. Throughout the genome, the two kinds of sequence features mix in different proportions to yield a gamut of DNA elements that range from those tethering predominantly PRC1 or PRC2 to ones capable of tethering both complexes. The emerging picture is similar to the paradigmatic targeting of Polycomb complexes by Polycomb Response Elements (PREs) of Drosophila but providing for greater plasticity.", "doi": "10.1093/nar/gkad889", "pmid": "37855680", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pii", "key": "7321990"}, {"db": "pmc", "key": "PMC10681801"}], "notes": [], "created": "2023-11-29T11:38:28.542Z", "modified": "2023-11-29T11:38:28.552Z"}, {"entity": "publication", "iuid": "644ff655a61e46c08a5438a23c82830c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/644ff655a61e46c08a5438a23c82830c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/644ff655a61e46c08a5438a23c82830c"}}, "title": "RecView: an interactive R application for locating recombination positions using pedigree data.", "authors": [{"family": "Zhang", "given": "Hongkai", "initials": "H", "orcid": "0000-0001-7371-9612", "researcher": {"href": "https://publications.scilifelab.se/researcher/33b4db2c681b400c9106f8d27b6fb714.json"}}, {"family": "Hansson", "given": "Bengt", "initials": "B", "orcid": "0000-0001-6694-8169", "researcher": {"href": "https://publications.scilifelab.se/researcher/01f0144e207c41dcbc4d5aec68690e4b.json"}}], "type": "journal article", "published": "2023-11-25", "journal": {"title": "BMC Genomics", "issn": "1471-2164", "volume": "24", "issue": "1", "pages": "712", "issn-l": "1471-2164"}, "abstract": "Recombination reshuffles alleles at linked loci, allowing genes to evolve independently and consequently enhancing the efficiency of selection. This makes quantifying recombination along chromosomes an important goal for understanding how selection and drift are acting on genes and chromosomes.\n\nWe present RecView, an interactive R application and its homonymous R package, to facilitate locating recombination positions along chromosomes or scaffolds using whole-genome genotype data of a three-generation pedigree. RecView analyses and plots the grandparent-of-origin of all informative alleles along each chromosome of the offspring in the pedigree, and infers recombination positions with either of two built-in algorithms: one based on change in the proportion of the alleles with specific grandparent-of-origin, and one on the degree of continuity of alleles with the same grandparent-of-origin. RecView handles multiple offspring and chromosomes simultaneously, and all putative recombination positions are reported in base pairs together with an estimated precision based on the local density of informative alleles. We demonstrate RecView using genotype data of a passerine bird with an available reference genome, the great reed warbler (Acrocephalus arundinaceus), and show that recombination events can be located to specific positions.\n\nRecView is an easy-to-use and highly effective application for locating recombination positions with high precision. RecView is available on GitHub ( https://github.com/HKyleZhang/RecView.git ).", "doi": "10.1186/s12864-023-09807-2", "pmid": "38007417", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10676570"}, {"db": "pii", "key": "10.1186/s12864-023-09807-2"}], "notes": [], "created": "2024-01-08T16:11:18.459Z", "modified": "2024-01-16T13:48:31.644Z"}, {"entity": "publication", "iuid": "f8aa1479eff8415b950c15e1654bdec9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f8aa1479eff8415b950c15e1654bdec9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f8aa1479eff8415b950c15e1654bdec9"}}, "title": "Dysregulations in hemostasis, metabolism, immune response, and angiogenesis in post-acute COVID-19 syndrome with and without postural orthostatic tachycardia syndrome: a multi-omic profiling study.", "authors": [{"family": "Mahdi", "given": "Ali", "initials": "A"}, {"family": "Zhao", "given": "Allan", "initials": "A"}, {"family": "Fredengren", "given": "Emelie", "initials": "E"}, {"family": "Fedorowski", "given": "Artur", "initials": "A"}, {"family": "Braunschweig", "given": "Frieder", "initials": "F"}, {"family": "Nygren-Bonnier", "given": "Malin", "initials": "M"}, {"family": "Runold", "given": "Michael", "initials": "M"}, {"family": "Bruchfeld", "given": "Judith", "initials": "J"}, {"family": "Nickander", "given": "Jannike", "initials": "J"}, {"family": "Deng", "given": "Qiaolin", "initials": "Q"}, {"family": "Checa", "given": "Antonio", "initials": "A"}, {"family": "Desta", "given": "Liyew", "initials": "L"}, {"family": "Pernow", "given": "John", "initials": "J"}, {"family": "St\u00e5hlberg", "given": "Marcus", "initials": "M"}], "type": "journal article", "published": "2023-11-19", "journal": {"title": "Sci Rep", "issn": "2045-2322", "issn-l": "2045-2322", "volume": "13", "issue": "1", "pages": "20230"}, "abstract": "Post-acute COVID-19 (PACS) are associated with cardiovascular dysfunction, especially postural orthostatic tachycardia syndrome (POTS). Patients with PACS, both in the absence or presence of POTS, exhibit a wide range of persisting symptoms long after the acute infection. Some of these symptoms may stem from alterations in cardiovascular homeostasis, but the exact mechanisms are poorly understood. The aim of this study was to provide a broad molecular characterization of patients with PACS with (PACS + POTS) and without (PACS-POTS) POTS compared to healthy subjects, including a broad proteomic characterization with a focus on plasma cardiometabolic proteins, quantification of cytokines/chemokines and determination of plasma sphingolipid levels. Twenty-one healthy subjects without a prior COVID-19 infection (mean age 43 years, 95% females), 20 non-hospitalized patients with PACS + POTS (mean age 39 years, 95% females) and 22 non-hospitalized patients with PACS-POTS (mean age 44 years, 100% females) were studied. PACS patients were non-hospitalized and recruited \u224818 months after the acute infection. Cardiometabolic proteomic analyses revealed a dysregulation of \u2248200 out of 700 analyzed proteins in both PACS groups vs. healthy subjects with the majority (> 90%) being upregulated. There was a large overlap (> 90%) with no major differences between the PACS groups. Gene ontology enrichment analysis revealed alterations in hemostasis/coagulation, metabolism, immune responses, and angiogenesis in PACS vs. healthy controls. Furthermore, 11 out of 33 cytokines/chemokines were significantly upregulated both in PACS + POTS and PACS-POTS vs. healthy controls and none of the cytokines were downregulated. There were no differences in between the PACS groups in the cytokine levels. Lastly, 16 and 19 out of 88 sphingolipids were significantly dysregulated in PACS + POTS and PACS-POTS, respectively, compared to controls with no differences between the groups. Collectively, these observations suggest a clear and distinct dysregulation in the proteome, cytokines/chemokines, and sphingolipid levels in PACS patients compared to healthy subjects without any clear signature associated with POTS. This enhances our understanding and might pave the way for future experimental and clinical investigations to elucidate and/or target resolution of inflammation and micro-clots and restore the hemostasis and immunity in PACS.", "doi": "10.1038/s41598-023-47539-1", "pmid": "37981644", "labels": {"Affinity Proteomics Uppsala": "Service", "NGI Proteomics": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10658082"}, {"db": "pii", "key": "10.1038/s41598-023-47539-1"}], "notes": [], "created": "2023-11-29T18:45:17.584Z", "modified": "2023-12-04T06:42:15.974Z"}, {"entity": "publication", "iuid": "7e7ba23c03714d3d9b58baa6d2f778a3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7e7ba23c03714d3d9b58baa6d2f778a3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7e7ba23c03714d3d9b58baa6d2f778a3"}}, "title": "Novel PNKP mutations associated with reduced DNA single-strand break repair and severe microcephaly, seizures, and developmental delay.", "authors": [{"family": "Thuresson", "given": "Ann-Charlotte", "initials": "A"}, {"family": "Brazina", "given": "Jan", "initials": "J"}, {"family": "Akram", "given": "Talia", "initials": "T"}, {"family": "Albrecht", "given": "Julia", "initials": "J"}, {"family": "Dahl", "given": "Niklas", "initials": "N"}, {"family": "Soussi Zander", "given": "Cecilia", "initials": "C"}, {"family": "Caldecott", "given": "Keith W", "initials": "KW"}], "type": "journal article", "published": "2023-11-02", "journal": {"title": "Mol Genet Genomic Med", "issn": "2324-9269", "issn-l": "2324-9269", "volume": null, "issue": null, "pages": "e2295"}, "abstract": "Microcephaly with early-onset seizures (MCSZ) is a neurodevelopmental disorder caused by pathogenic variants in the DNA strand break repair protein, polynucleotide kinase 3'-phosphatase (PNKP).\r\n\r\nWe have used whole genome sequencing and Sanger sequencing to identify disease-causing variants, followed by a minigene assay, Western blotting, alkaline comet assay, \u03b3H2AX, and ADP-ribose immunofluorescence.\r\n\r\nHere, we describe a patient with compound heterozygous variants in PNKP, including a missense variant in the DNA phosphatase domain (T323M) and a novel splice acceptor site variant within the DNA kinase domain that we show leads to exon skipping. We show that primary fibroblasts derived from the patient exhibit greatly reduced levels of PNKP protein and reduced rates of DNA single-strand break repair, confirming that the mutated PNKP alleles are dysfunctional.\r\n\r\nThe data presented show that the detected compound heterozygous variants result in reduced levels of PNKP protein, which affect the repair of both oxidative and TOP1-induced single-strand breaks, and most likely causes MCSZ in this patient.", "doi": "10.1002/mgg3.2295", "pmid": "37916443", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2023-11-29T11:00:34.255Z", "modified": "2024-01-16T13:48:31.746Z"}, {"entity": "publication", "iuid": "f361c17689bc48929bd23e7d629f9f1b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f361c17689bc48929bd23e7d629f9f1b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f361c17689bc48929bd23e7d629f9f1b"}}, "title": "Evidence of Site-Specific and Male-Biased Germline Mutation Rate in a Wild Songbird.", "authors": [{"family": "Zhang", "given": "Hongkai", "initials": "H", "orcid": "0000-0001-7371-9612", "researcher": {"href": "https://publications.scilifelab.se/researcher/33b4db2c681b400c9106f8d27b6fb714.json"}}, {"family": "Lundberg", "given": "Max", "initials": "M", "orcid": "0000-0002-1895-3622", "researcher": {"href": "https://publications.scilifelab.se/researcher/5b6a6dafa8fe4371ab26ed02ca5a550c.json"}}, {"family": "Tarka", "given": "Maja", "initials": "M", "orcid": "0000-0001-9651-1101", "researcher": {"href": "https://publications.scilifelab.se/researcher/7a0abfbfc5bb4d5fb77f356c6ad80a34.json"}}, {"family": "Hasselquist", "given": "Dennis", "initials": "D", "orcid": "0000-0002-0056-6616", "researcher": {"href": "https://publications.scilifelab.se/researcher/73a24d358af64f22b81735f577c33bbb.json"}}, {"family": "Hansson", "given": "Bengt", "initials": "B", "orcid": "0000-0001-6694-8169", "researcher": {"href": "https://publications.scilifelab.se/researcher/01f0144e207c41dcbc4d5aec68690e4b.json"}}], "type": "journal article", "published": "2023-11-01", "journal": {"title": "Genome Biol Evol", "issn": "1759-6653", "volume": "15", "issue": "11", "issn-l": "1759-6653"}, "abstract": "Germline mutations are the ultimate source of genetic variation and the raw material for organismal evolution. Despite their significance, the frequency and genomic locations of mutations, as well as potential sex bias, are yet to be widely investigated in most species. To address these gaps, we conducted whole-genome sequencing of 12 great reed warblers (Acrocephalus arundinaceus) in a pedigree spanning 3 generations to identify single-nucleotide de novo mutations (DNMs) and estimate the germline mutation rate. We detected 82 DNMs within the pedigree, primarily enriched at CpG sites but otherwise randomly located along the chromosomes. Furthermore, we observed a pronounced sex bias in DNM occurrence, with male warblers exhibiting three times more mutations than females. After correction for false negatives and adjusting for callable sites, we obtained a mutation rate of 7.16 \u00d7 10-9 mutations per site per generation (m/s/g) for the autosomes and 5.10 \u00d7 10-9 m/s/g for the Z chromosome. To demonstrate the utility of species-specific mutation rates, we applied our autosomal mutation rate in models reconstructing the demographic history of the great reed warbler. We uncovered signs of drastic population size reductions predating the last glacial period (LGP) and reduced gene flow between western and eastern populations during the LGP. In conclusion, our results provide one of the few direct estimates of the mutation rate in wild songbirds and evidence for male-driven mutations in accordance with theoretical expectations.", "doi": "10.1093/gbe/evad180", "pmid": "37793164", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10627410"}, {"db": "pii", "key": "7289221"}], "notes": [], "created": "2023-11-29T10:54:38.925Z", "modified": "2024-01-16T13:48:31.754Z"}, {"entity": "publication", "iuid": "f5629195f2e24508b64dc207bc2842ce", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f5629195f2e24508b64dc207bc2842ce.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f5629195f2e24508b64dc207bc2842ce"}}, "title": "Smoking affects epigenetic ageing of lung bronchoalveolar lavage cells in Multiple Sclerosis.", "authors": [{"family": "Klose", "given": "Dennis", "initials": "D"}, {"family": "Needhamsen", "given": "Maria", "initials": "M"}, {"family": "Ringh", "given": "Mikael V", "initials": "MV"}, {"family": "Hagemann-Jensen", "given": "Michael", "initials": "M"}, {"family": "Jagodic", "given": "Maja", "initials": "M"}, {"family": "Kular", "given": "Lara", "initials": "L"}], "type": "journal article", "published": "2023-11-00", "journal": {"title": "Mult Scler Relat Disord", "issn": "2211-0356", "volume": "79", "pages": "104991", "issn-l": null}, "abstract": "A compelling body of evidence implicates cigarette smoking and lung inflammation in Multiple Sclerosis (MS) susceptibility and progression. Previous studies have reported epigenetic age (DNAm age) acceleration in blood immune cells and in glial cells of people with MS (pwMS) compared to healthy controls (HC).\n\nWe aimed to examine biological ageing in lung immune cells in the context of MS and smoking.\n\nWe analyzed age acceleration residuals in lung bronchoalveolar lavage (BAL) cells, constituted of mainly alveolar macrophages, from 17 pwMS and 22 HC in relation to smoking using eight DNA methylation-based clocks, namely AltumAge, Horvath, GrimAge, PhenoAge, Zhang, SkinBlood, Hannum, Monocyte clock as well as two RNA-based clocks, which capture different aspects of biological ageing.\n\nAfter adjustment for covariates, five epigenetic clocks showed significant differences between the groups. Four of them, Horvath (Padj = 0.028), GrimAge (Padj = 4.28 \u00d7 10-7), SkinBlood (Padj = 0.001) and Zhang (Padj = 0.02), uncovered the sole effect of smoking on ageing estimates, irrespective of the clinical group. The Horvath, SkinBlood and Zhang clocks showed a negative impact of smoking while GrimAge detected smoking-associated age acceleration in BAL cells. On the contrary, the AltumAge clock revealed differences between pwMS and HC and indicated that, in the absence of smoking, BAL cells of pwMS were epigenetically 5.4 years older compared to HC (Padj = 0.028). Smoking further affected epigenetic ageing in BAL cells of pwMS specifically as non-smoking pwMS exhibited a 10.2-year AltumAge acceleration compared to pwMS smokers (Padj = 0.0049). Of note, blood-derived monocytes did not show any MS-specific or smoking-related AltumAge differences. The difference between BAL cells of pwMS smokers and non-smokers was attributable to the differential methylation of 114 AltumAge-CpGs (Padj < 0.05) affecting genes involved in innate immune processes such as cytokine production, defense response and cell motility. These changes functionally translated into transcriptional differences in BAL cells between pwMS smokers and non-smokers.\n\nBAL cells of pwMS display inflammation-related and smoking-dependent changes associated to epigenetic ageing captured by the AltumAge clock. Future studies examining potential confounders, such as the distribution of distinct BAL myeloid cell types in pwMS compared to control individuals in relation to smoking may clarify the varying performance and DNAm age estimations among epigenetic clocks.", "doi": "10.1016/j.msard.2023.104991", "pmid": "37708820", "labels": {"NGI SNP genotyping": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "S2211-0348(23)00492-3"}], "notes": [], "created": "2023-11-29T11:14:21.697Z", "modified": "2024-01-16T13:48:31.774Z"}, {"entity": "publication", "iuid": "551fd99639b84ce0a81b1e975a93fbcd", "links": {"self": {"href": "https://publications.scilifelab.se/publication/551fd99639b84ce0a81b1e975a93fbcd.json"}, "display": {"href": "https://publications.scilifelab.se/publication/551fd99639b84ce0a81b1e975a93fbcd"}}, "title": "Nutrient availability and grazing influence the strength of priority effects during freshwater bacterial community coalescence.", "authors": [{"family": "Lumpi", "given": "Theresa", "initials": "T", "orcid": "0000-0002-1202-7222", "researcher": {"href": "https://publications.scilifelab.se/researcher/bdcba53ace234cb9b8ad49d220abf665.json"}}, {"family": "Guo", "given": "Xin", "initials": "X"}, {"family": "Lindstr\u00f6m", "given": "Eva S", "initials": "ES", "orcid": "0000-0001-8920-3071", "researcher": {"href": "https://publications.scilifelab.se/researcher/9290d334ce5a4488b8afd2af511e02ad.json"}}], "type": "journal article", "published": "2023-11-00", "journal": {"title": "Environ. Microbiol.", "issn": "1462-2920", "volume": "25", "issue": "11", "pages": "2289-2302", "issn-l": "1462-2912"}, "abstract": "When bacterial communities mix, immigration history can fundamentally affect the community composition as a result of priority effects. Priority effects arise when an early immigrant exhausts resources and/or alters habitat conditions, thereby influencing the establishment success of the late arriver. The strength of priority effects is context-dependent and expected to be stronger if environmental conditions favour the growth of the first arriver. In this study, we conducted a two-factorial experiment testing the importance of nutrient availability and grazing on the strength of priority effects in complex aquatic bacterial communities. We did so by mixing two dissimilar communities, simultaneously, and with a 38 h time-delay. Priority effects were measured as the invasion resistance of the first community to the invading second community. We found stronger priority effects in treatments with high nutrient availability and absence of grazing, but in general, the arrival timing was less important than the selection by nutrients and grazing. At the population level, the results were complex, but priority effects may have been driven by bacteria belonging to for example, the genera Rhodoferax and Herbaspirillum. Our study highlights the importance of arrival timing in complex bacterial communities, especially if environmental conditions favour rapid community growth.", "doi": "10.1111/1462-2920.16450", "pmid": "37381117", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2023-11-29T12:43:22.827Z", "modified": "2024-01-16T13:48:31.783Z"}, {"entity": "publication", "iuid": "df5638c2c3d442cd861fa36a108950d6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/df5638c2c3d442cd861fa36a108950d6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/df5638c2c3d442cd861fa36a108950d6"}}, "title": "Proteomics reveal biomarkers for diagnosis, disease activity and long-term disability outcomes in multiple sclerosis.", "authors": [{"family": "\u00c5kesson", "given": "Julia", "initials": "J", "orcid": "0000-0002-9276-0546", "researcher": {"href": "https://publications.scilifelab.se/researcher/ba1adc3a1e614b87808e3b1b5d4d9cb1.json"}}, {"family": "Hojjati", "given": "Sara", "initials": "S"}, {"family": "Hellberg", "given": "Sandra", "initials": "S"}, {"family": "Raffetseder", "given": "Johanna", "initials": "J", "orcid": "0000-0001-8871-2560", "researcher": {"href": "https://publications.scilifelab.se/researcher/604da06820f542ef84b97cf0e4641e2c.json"}}, {"family": "Khademi", "given": "Mohsen", "initials": "M", "orcid": "0000-0003-0801-1444", "researcher": {"href": "https://publications.scilifelab.se/researcher/5446d6d754bc4c429d0e48ade419413c.json"}}, {"family": "Rynkowski", "given": "Robert", "initials": "R"}, {"family": "Kockum", "given": "Ingrid", "initials": "I", "orcid": "0000-0002-0867-4726", "researcher": {"href": "https://publications.scilifelab.se/researcher/03ebcc6a01ef4d0db4e4673aff8de5d8.json"}}, {"family": "Altafini", "given": "Claudio", "initials": "C", "orcid": "0000-0003-4142-6502", "researcher": {"href": "https://publications.scilifelab.se/researcher/397523f1994046fdb4c462d5127e4c1d.json"}}, {"family": "Lubovac-Pilav", "given": "Zelmina", "initials": "Z", "orcid": "0000-0001-6427-0315", "researcher": {"href": "https://publications.scilifelab.se/researcher/af98c65fa2964875bd6d46f9c2488e6b.json"}}, {"family": "Mellerg\u00e5rd", "given": "Johan", "initials": "J", "orcid": "0000-0003-0120-3734", "researcher": {"href": "https://publications.scilifelab.se/researcher/f471bdcfc7fc4c2fb282484ac7e148bd.json"}}, {"family": "Jenmalm", "given": "Maria C", "initials": "MC", "orcid": "0000-0002-2117-5366", "researcher": {"href": "https://publications.scilifelab.se/researcher/bf1f485192744e0c95ccecdb5471b577.json"}}, {"family": "Piehl", "given": "Fredrik", "initials": "F", "orcid": "0000-0001-8329-5219", "researcher": {"href": "https://publications.scilifelab.se/researcher/ee04062fbee34836a4fa3f4d2e8076cd.json"}}, {"family": "Olsson", "given": "Tomas", "initials": "T"}, {"family": "Ernerudh", "given": "Jan", "initials": "J", "orcid": "0000-0001-9456-2044", "researcher": {"href": "https://publications.scilifelab.se/researcher/dc016a1ad2b14e91b97b65d5aaae7f59.json"}}, {"family": "Gustafsson", "given": "Mika", "initials": "M", "orcid": "0000-0002-0048-4063", "researcher": {"href": "https://publications.scilifelab.se/researcher/466661ecb9274ecc8f1a832b95ef19b2.json"}}], "type": "journal article", "published": "2023-10-30", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "14", "issue": "1", "pages": "6903", "issn-l": "2041-1723"}, "abstract": "Sensitive and reliable protein biomarkers are needed to predict disease trajectory and personalize treatment strategies for multiple sclerosis (MS). Here, we use the highly sensitive proximity-extension assay combined with next-generation sequencing (Olink Explore) to quantify 1463 proteins in cerebrospinal fluid (CSF) and plasma from 143 people with early-stage MS and 43 healthy controls. With longitudinally followed discovery and replication cohorts, we identify CSF proteins that consistently predicted both short- and long-term disease progression. Lower levels of neurofilament light chain (NfL) in CSF is superior in predicting the absence of disease activity two years after sampling (replication AUC = 0.77) compared to all other tested proteins. Importantly, we also identify a combination of 11 CSF proteins (CXCL13, LTA, FCN2, ICAM3, LY9, SLAMF7, TYMP, CHI3L1, FYB1, TNFRSF1B and NfL) that predict the severity of disability worsening according to the normalized age-related MS severity score (replication AUC = 0.90). The identification of these proteins may help elucidate pathogenetic processes and might aid decisions on treatment strategies for persons with MS.", "doi": "10.1038/s41467-023-42682-9", "pmid": "37903821", "labels": {"NGI Proteomics": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Affinity Proteomics Uppsala": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10616092"}, {"db": "pii", "key": "10.1038/s41467-023-42682-9"}], "notes": [], "created": "2023-11-23T07:26:00.330Z", "modified": "2023-11-29T18:44:34.331Z"}, {"entity": "publication", "iuid": "3be027fad7744b0f91376a35ec831490", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3be027fad7744b0f91376a35ec831490.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3be027fad7744b0f91376a35ec831490"}}, "title": "Complete Mitochondrial DNA Genome Variation in the Swedish Population.", "authors": [{"family": "Sturk-Andreaggi", "given": "Kimberly", "initials": "K", "orcid": "0000-0001-6857-923X", "researcher": {"href": "https://publications.scilifelab.se/researcher/3f1cbf7b4fd94b17b1c37712634b7638.json"}}, {"family": "Bodner", "given": "Martin", "initials": "M", "orcid": "0000-0002-3870-9862", "researcher": {"href": "https://publications.scilifelab.se/researcher/455fefcf430d4b7e8433b3c7b3856b4b.json"}}, {"family": "Ring", "given": "Joseph D", "initials": "JD"}, {"family": "Ameur", "given": "Adam", "initials": "A", "orcid": "0000-0001-6085-6749", "researcher": {"href": "https://publications.scilifelab.se/researcher/e960811513664a78b2804a00ee70f7c3.json"}}, {"family": "Gyllensten", "given": "Ulf", "initials": "U"}, {"family": "Parson", "given": "Walther", "initials": "W", "orcid": "0000-0002-5692-2392", "researcher": {"href": "https://publications.scilifelab.se/researcher/84574a9a6f03419ea3a37a6dd0470082.json"}}, {"family": "Marshall", "given": "Charla", "initials": "C"}, {"family": "Allen", "given": "Marie", "initials": "M"}], "type": "journal article", "published": "2023-10-25", "journal": {"title": "Genes", "issn": "2073-4425", "volume": "14", "issue": "11", "issn-l": "2073-4425"}, "abstract": "The development of complete mitochondrial genome (mitogenome) reference data for inclusion in publicly available population databases is currently underway, and the generation of more high-quality mitogenomes will only enhance the statistical power of this forensically useful locus. To characterize mitogenome variation in Sweden, the mitochondrial DNA (mtDNA) reads from the SweGen whole genome sequencing (WGS) dataset were analyzed. To overcome the interference from low-frequency nuclear mtDNA segments (NUMTs), a 10% variant frequency threshold was applied for the analysis. In total, 934 forensic-quality mitogenome haplotypes were characterized. Almost 45% of the SweGen haplotypes belonged to haplogroup H. Nearly all mitogenome haplotypes (99.1%) were assigned to European haplogroups, which was expected based on previous mtDNA studies of the Swedish population. There were signature northern Swedish and Finnish haplogroups observed in the dataset (e.g., U5b1, W1a), consistent with the nuclear DNA analyses of the SweGen data. The complete mitogenome analysis resulted in high haplotype diversity (0.9996) with a random match probability of 0.15%. Overall, the SweGen mitogenomes provide a large mtDNA reference dataset for the Swedish population and also contribute to the effort to estimate global mitogenome haplotype frequencies.", "doi": "10.3390/genes14111989", "pmid": "38002932", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10671102"}, {"db": "pii", "key": "genes14111989"}], "notes": [], "created": "2023-11-30T13:00:25.373Z", "modified": "2023-11-30T13:00:25.400Z"}, {"entity": "publication", "iuid": "dfc74d55aa694120a0e496375231c4dc", "links": {"self": {"href": "https://publications.scilifelab.se/publication/dfc74d55aa694120a0e496375231c4dc.json"}, "display": {"href": "https://publications.scilifelab.se/publication/dfc74d55aa694120a0e496375231c4dc"}}, "title": "Polymorphic parasitic larvae cooperate to build swimming colonies luring hosts.", "authors": [{"family": "Krupenko", "given": "Darya", "initials": "D"}, {"family": "Miroliubov", "given": "Aleksei", "initials": "A"}, {"family": "Kryukov", "given": "Emil", "initials": "E"}, {"family": "Faure", "given": "Louis", "initials": "L"}, {"family": "Minemizu", "given": "Ryo", "initials": "R"}, {"family": "Haag", "given": "Lars", "initials": "L"}, {"family": "Lundgren", "given": "Magnus", "initials": "M"}, {"family": "Kameneva", "given": "Polina", "initials": "P"}, {"family": "Kastriti", "given": "Maria Eleni", "initials": "ME"}, {"family": "Adameyko", "given": "Igor", "initials": "I"}], "type": "journal article", "published": "2023-10-23", "journal": {"title": "Curr. Biol.", "issn": "1879-0445", "volume": "33", "issue": "20", "pages": "4524-4531.e4", "issn-l": "0960-9822"}, "abstract": "Parasites have evolved a variety of astonishing strategies to survive within their hosts, yet the most challenging event in their personal chronicles is the passage from one host to another. It becomes even more complex when a parasite needs to pass through the external environment. Therefore, the free-living stages of parasites present a wide range of adaptations for transmission. Parasitic flatworms from the group Digenea (flukes) have free-living larvae, cercariae, which are remarkably diverse in structure and behavior.1,2 One of the cercariae transmission strategies is to attain a prey-like appearance for the host.3 This can be done through the formation of a swimming aggregate of several cercariae adjoined together by their tails.4 Through the use of live observations and light, electron, and confocal microscopy, we described such a supposedly prey-mimetic colony comprising cercariae of two distinct morphotypes. They are functionally specialized: larger morphotype (sailors) enable motility, and smaller morphotype (passengers) presumably facilitate infection. The analysis of local read alignments between the two samples reveals that both cercaria types have identical 18S, 28S, and 5.8S rRNA genes. Further phylogenetic analysis of these ribosomal sequences indicates that our specimen belongs to the digenean family Acanthocolpidae, likely genus Pleorchis. This discovery provides a unique example and a novel insight into how morphologically and functionally heterogeneous individuals of the same species cooperate to build colonial organisms for the purpose of infection. This strategy bears resemblance to the cooperating castes of the same species found among insects.5.", "doi": "10.1016/j.cub.2023.08.090", "pmid": "37741283", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Ancient DNA": "Collaborative"}, "xrefs": [{"db": "pii", "key": "S0960-9822(23)01170-3"}], "notes": [], "created": "2023-11-29T13:25:24.376Z", "modified": "2025-02-27T04:14:54.724Z"}, {"entity": "publication", "iuid": "335442be797344c78004c386eda66ecf", "links": {"self": {"href": "https://publications.scilifelab.se/publication/335442be797344c78004c386eda66ecf.json"}, "display": {"href": "https://publications.scilifelab.se/publication/335442be797344c78004c386eda66ecf"}}, "title": "Screening for atypical porcine pestivirus in Swedish boar semen used for artificial insemination and a characterisation of the seminal RNA microbiome including the virome.", "authors": [{"family": "Stenberg", "given": "Hedvig", "initials": "H"}, {"family": "Malmberg", "given": "Maja", "initials": "M"}, {"family": "Hayer", "given": "Juliette", "initials": "J"}], "type": "journal article", "published": "2023-10-20", "journal": {"title": "BMC Vet Res", "issn": "1746-6148", "volume": "19", "issue": "1", "pages": "219", "issn-l": null}, "abstract": "This study aimed to characterise the RNA microbiome, including the virome of extended semen from Swedish breeding boars, with particular focus on Atypical porcine pestivirus (APPV). This neurotropic virus, associated with congenital tremor type A-II in piglets, was recently demonstrated to induce the disease through insemination with semen from infected boars.\n\nFrom 124 Artificial Insemination (AI) doses from Swedish breeding boars, APPV was detected in one dose in addition to a sparse seminal RNA virome, characterised by retroviruses, phages, and some fecal-associated contaminants. The detected seminal microbiome was large and characterized by Gram-negative bacteria from the phylum Proteobacteria, mainly consisting of apathogenic or opportunistic bacteria. The proportion of bacteria with a pathogenic potential was low, and no antimicrobial resistance genes (ARGs) were detected in the datasets.\n\nOverall, the results indicate a good health status among Swedish breeding boars. The detection of APPV in semen raises the question of whether routine screening for APPV in breeding boars should be instigated.", "doi": "10.1186/s12917-023-03762-6", "pmid": "37864222", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10588136"}, {"db": "pii", "key": "10.1186/s12917-023-03762-6"}], "notes": [], "created": "2023-11-29T11:41:20.114Z", "modified": "2024-01-16T13:48:31.917Z"}, {"entity": "publication", "iuid": "467d9682bec746ed878a1bacf430dbca", "links": {"self": {"href": "https://publications.scilifelab.se/publication/467d9682bec746ed878a1bacf430dbca.json"}, "display": {"href": "https://publications.scilifelab.se/publication/467d9682bec746ed878a1bacf430dbca"}}, "title": "Single-Cell RNA Analysis Reveals Cell-Intrinsic Functions of CAR T Cells Correlating with Response in a Phase II Study of Lymphoma Patients.", "authors": [{"family": "Sar\u00e9n", "given": "Tina", "initials": "T", "orcid": "0000-0001-5227-6779", "researcher": {"href": "https://publications.scilifelab.se/researcher/b8f06b113565445f8dc2882a926229b6.json"}}, {"family": "Ramachandran", "given": "Mohanraj", "initials": "M", "orcid": "0000-0003-2685-0575", "researcher": {"href": "https://publications.scilifelab.se/researcher/f3fefc78a0b040faa998efb8fde7b920.json"}}, {"family": "Gammelg\u00e5rd", "given": "Gustav", "initials": "G", "orcid": "0009-0008-5522-0103", "researcher": {"href": "https://publications.scilifelab.se/researcher/7f8652afc79e4fe39e82bb49a5dc5307.json"}}, {"family": "L\u00f6vgren", "given": "Tanja", "initials": "T", "orcid": "0000-0003-2170-0682", "researcher": {"href": "https://publications.scilifelab.se/researcher/a578be87e95941fe8d59d344d03d1dd2.json"}}, {"family": "Mirabello", "given": "Claudio", "initials": "C", "orcid": "0000-0001-7868-034X", "researcher": {"href": "https://publications.scilifelab.se/researcher/00052b54a3d24fd4a6e648f987d15e5f.json"}}, {"family": "Bj\u00f6rklund", "given": "\u00c5sa K", "initials": "\u00c5K", "orcid": "0000-0003-2224-7090", "researcher": {"href": "https://publications.scilifelab.se/researcher/8eb8c1fc5f704cbfb87471226485ae1f.json"}}, {"family": "Wikstr\u00f6m", "given": "Kristina", "initials": "K", "orcid": "0009-0000-1027-2534", "researcher": {"href": "https://publications.scilifelab.se/researcher/0922ad45252045e9b2ac4d8ad264a718.json"}}, {"family": "Hashemi", "given": "Jamileh", "initials": "J", "orcid": "0000-0002-4997-3765", "researcher": {"href": "https://publications.scilifelab.se/researcher/d1dd38f2d9644c1c8a9bf870fc69ef2a.json"}}, {"family": "Freyhult", "given": "Eva", "initials": "E", "orcid": "0000-0003-0226-1047", "researcher": {"href": "https://publications.scilifelab.se/researcher/be110f11a53d4dcfa3bfd1657167895e.json"}}, {"family": "Ahlstr\u00f6m", "given": "H\u00e5kan", "initials": "H", "orcid": "0000-0002-8701-969X", "researcher": {"href": "https://publications.scilifelab.se/researcher/53e4a209929642ceaadf3e0aed6b8c69.json"}}, {"family": "Amini", "given": "Rose-Marie", "initials": "RM", "orcid": "0000-0003-0901-5252", "researcher": {"href": "https://publications.scilifelab.se/researcher/c157abcd61fa4900b5ad502b408d6d95.json"}}, {"family": "Hagberg", "given": "Hans", "initials": "H", "orcid": "0000-0001-7855-2452", "researcher": {"href": "https://publications.scilifelab.se/researcher/7ec21157056f48e49cb2f7c528d16b1d.json"}}, {"family": "Loskog", "given": "Angelica", "initials": "A", "orcid": "0000-0001-8583-6138", "researcher": {"href": "https://publications.scilifelab.se/researcher/5730068a851041ecb0bce96c2954bb28.json"}}, {"family": "Enblad", "given": "Gunilla", "initials": "G", "orcid": "0000-0002-0594-724X", "researcher": {"href": "https://publications.scilifelab.se/researcher/11313af3f4a241ecb93af23ab2652195.json"}}, {"family": "Essand", "given": "Magnus", "initials": "M", "orcid": "0000-0002-9725-0422", "researcher": {"href": "https://publications.scilifelab.se/researcher/c5afc47ab0814c09909af3c66217a3a6.json"}}], "type": "journal article", "published": "2023-10-13", "journal": {"title": "Clin. Cancer Res.", "issn": "1557-3265", "issn-l": "1078-0432", "volume": "29", "issue": "20", "pages": "4139-4152"}, "abstract": "Although CD19 chimeric antigen receptor T cells (CAR-T) therapy has shown remarkable success in B-cell malignancies, a substantial fraction of patients do not obtain a long-term clinical response. This could be influenced by the quality of the individual CAR-T infusion product. To shed some light on this, clinical outcome was correlated to characteristics of CAR-T infusion products.\n\nIn this phase II study, patients with B-cell lymphoma (n = 23) or leukemia (n = 1) received one or two infusions of third-generation CD19-directed CAR-Ts (2 \u00d7 108/m2). The clinical trial was registered at clinicaltrials.gov: NCT03068416. We investigated the transcriptional profile of individual CD19 CAR-T infusion products using targeted single-cell RNA sequencing and multicolor flow cytometry.\n\nTwo CAR-T infusions were not better than one in the settings used in this study. As for the CAR-T infusion products, we found that effector-like CD8+CAR-Ts with a high polyfunctionality, high cytotoxic and cytokine production profile, and low dysfunctional signature were associated with clinical response. An extended ex vivo expansion time during CAR-T manufacturing negatively influenced the proportion of effector CD8+CAR-Ts in the infusion product.\n\nWe identified cell-intrinsic characteristics of effector CD8+CAR-Ts correlating with response that could be used as an indicator for clinical outcome. The results in the study also serve as a guide to CAR-T manufacturing practices.", "doi": "10.1158/1078-0432.CCR-23-0178", "pmid": "37540566", "labels": {"Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Affinity Proteomics Uppsala": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC10570681"}, {"db": "pii", "key": "728314"}, {"db": "ClinicalTrials.gov", "key": "NCT03068416"}], "notes": [], "created": "2023-09-20T16:40:48.854Z", "modified": "2024-11-12T12:30:30.156Z"}, {"entity": "publication", "iuid": "dc9a30bd8f0e49a59ae2fc54afee5c1c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/dc9a30bd8f0e49a59ae2fc54afee5c1c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/dc9a30bd8f0e49a59ae2fc54afee5c1c"}}, "title": "Genomic, transcriptomic and epigenomic sequencing data of the B-cell leukemia cell line REH.", "authors": [{"family": "Lysenkova Wiklander", "given": "Mariya", "initials": "M"}, {"family": "\u00d6vern\u00e4s", "given": "Elin", "initials": "E"}, {"family": "Lagensj\u00f6", "given": "Johanna", "initials": "J"}, {"family": "Raine", "given": "Amanda", "initials": "A"}, {"family": "Petri", "given": "Anna", "initials": "A"}, {"family": "Wiman", "given": "Ann-Christin", "initials": "A"}, {"family": "Ramsell", "given": "Jon", "initials": "J"}, {"family": "Marincevic-Zuniga", "given": "Yanara", "initials": "Y"}, {"family": "Gezelius", "given": "Henrik", "initials": "H"}, {"family": "Martin", "given": "Tom", "initials": "T"}, {"family": "Bunikis", "given": "Ignas", "initials": "I"}, {"family": "Ekberg", "given": "Sara", "initials": "S"}, {"family": "Erlandsson", "given": "Rikard", "initials": "R"}, {"family": "Larsson", "given": "Pontus", "initials": "P"}, {"family": "Mosbech", "given": "Mai-Britt", "initials": "M"}, {"family": "H\u00e4ggqvist", "given": "Susana", "initials": "S"}, {"family": "Hellstedt Kerje", "given": "Susanne", "initials": "S"}, {"family": "Feuk", "given": "Lars", "initials": "L"}, {"family": "Ameur", "given": "Adam", "initials": "A"}, {"family": "Liljedahl", "given": "Ulrika", "initials": "U"}, {"family": "Nordlund", "given": "Jessica", "initials": "J"}], "type": "journal article", "published": "2023-10-10", "journal": {"title": "BMC Res Notes", "issn": "1756-0500", "issn-l": "1756-0500", "volume": "16", "issue": "1", "pages": "265"}, "abstract": "The aim of this data paper is to describe a collection of 33 genomic, transcriptomic and epigenomic sequencing datasets of the B-cell acute lymphoblastic leukemia (ALL) cell line REH. REH is one of the most frequently used cell lines for functional studies of pediatric ALL, and these data provide a multi-faceted characterization of its molecular features. The datasets described herein, generated with short- and long-read sequencing technologies, can both provide insights into the complex aberrant karyotype of REH, and be used as reference datasets for sequencing data quality assessment or for methods development.\r\n\r\nThis paper describes 33 datasets corresponding to 867 gigabases of raw sequencing data generated from the REH cell line. These datasets include five different approaches for whole genome sequencing (WGS) on four sequencing platforms, two RNA sequencing (RNA-seq) techniques on two different sequencing platforms, DNA methylation sequencing, and single-cell ATAC-sequencing.", "doi": "10.1186/s13104-023-06537-2", "pmid": "37817248", "labels": {"National Genomics Infrastructure": "Collaborative", "NGI Uppsala (Uppsala Genome Center)": "Collaborative", "NGI Short read": "Collaborative", "NGI Uppsala (SNP&SEQ Technology Platform)": "Collaborative", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10566058"}, {"db": "pii", "key": "10.1186/s13104-023-06537-2"}], "notes": [], "created": "2023-10-12T11:13:24.427Z", "modified": "2024-01-16T13:48:31.989Z"}, {"entity": "publication", "iuid": "57d336fde81e4a409b232134a6c24a50", "links": {"self": {"href": "https://publications.scilifelab.se/publication/57d336fde81e4a409b232134a6c24a50.json"}, "display": {"href": "https://publications.scilifelab.se/publication/57d336fde81e4a409b232134a6c24a50"}}, "title": "Low mutation load in a supergene underpinning alternative male mating strategies in ruff (Calidris pugnax).", "authors": [{"family": "Hill", "given": "Jason", "initials": "J", "orcid": "0000-0002-0151-8931", "researcher": {"href": "https://publications.scilifelab.se/researcher/a2cb6f3cce5f4919959e18074d51256d.json"}}, {"family": "Enbody", "given": "Erik D", "initials": "ED", "orcid": "0000-0003-1349-628X", "researcher": {"href": "https://publications.scilifelab.se/researcher/7a4df51b279746539cae2fa83c37456d.json"}}, {"family": "Bi", "given": "Huijuan", "initials": "H"}, {"family": "Lamichhaney", "given": "Sangeet", "initials": "S"}, {"family": "Lei", "given": "Weipan", "initials": "W"}, {"family": "Chen", "given": "Juexin", "initials": "J"}, {"family": "Wei", "given": "Chentao", "initials": "C"}, {"family": "Liu", "given": "Yang", "initials": "Y", "orcid": "0000-0003-4580-5518", "researcher": {"href": "https://publications.scilifelab.se/researcher/abd2de623f33467b89b1cf800db4b3f5.json"}}, {"family": "Schwochow", "given": "Doreen", "initials": "D"}, {"family": "Younis", "given": "Shady", "initials": "S"}, {"family": "Widemo", "given": "Fredrik", "initials": "F"}, {"family": "Andersson", "given": "Leif", "initials": "L", "orcid": "0000-0002-4085-6968", "researcher": {"href": "https://publications.scilifelab.se/researcher/bd3343c12f994b1fabcae23027d3a76d.json"}}], "type": "journal article", "published": "2023-10-06", "journal": {"title": "Mol. Biol. Evol.", "issn": "1537-1719", "issn-l": "0737-4038", "volume": "40", "issue": "12", "pages": "msad224"}, "abstract": "A paradox in evolutionary biology is how supergenes can maintain high fitness despite reduced effective population size, the suppression of recombination, and the expected accumulation of mutational load. The ruff supergene involves two rare inversion haplotypes (Satellite and Faeder). These are recessive lethals but with dominant effects on male mating strategies, plumage, and body size. Sequence divergence to the wild-type (Independent) haplotype indicates that the inversion could be as old as 4 million years. Here we have constructed a highly contiguous genome assembly of the inversion region for both the Independent and Satellite haplotypes. Based on the new data we estimate that the recombination event(s) creating the Satellite haplotype occurred only about 70,000 years ago. Contrary to expectations for supergenes, we find no substantial expansion of repeats and only a modest mutation load on the Satellite and Faeder haplotypes despite high sequence divergence to the non-inverted haplotype (1.46%). The essential centromere protein N gene CENPN is disrupted by the inversion, and is as well conserved on the inversion haplotypes as on the noninversion haplotype. These results suggest that the inversion may be much younger than previously thought. The low mutation load, despite recessive lethality, may be explained by the introgression of the inversion from a now extinct lineage.", "doi": "10.1093/molbev/msad224", "pmid": "37804117", "labels": {"NGI Long read": "Service", "National Genomics Infrastructure": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service", "NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "7296052"}], "notes": [], "created": "2023-10-10T08:45:20.886Z", "modified": "2024-01-16T13:48:31.996Z"}, {"entity": "publication", "iuid": "838e0b3db3344e009deafc5bec93347c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/838e0b3db3344e009deafc5bec93347c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/838e0b3db3344e009deafc5bec93347c"}}, "title": "Introgression underlies phylogenetic uncertainty but not parallel plumage evolution in a recent songbird radiation.", "authors": [{"family": "Rancilhac", "given": "Lo\u00efs", "initials": "L", "orcid": "0000-0002-9859-1448", "researcher": {"href": "https://publications.scilifelab.se/researcher/c3a53ef0421c4c0990fbf9ef20f6bd3b.json"}}, {"family": "Enbody", "given": "Erik D", "initials": "ED"}, {"family": "Harris", "given": "Rebecca", "initials": "R"}, {"family": "Saitoh", "given": "Takema", "initials": "T"}, {"family": "Irestedt", "given": "Martin", "initials": "M"}, {"family": "Liu", "given": "Yang", "initials": "Y", "orcid": "0000-0003-4580-5518", "researcher": {"href": "https://publications.scilifelab.se/researcher/abd2de623f33467b89b1cf800db4b3f5.json"}}, {"family": "Lei", "given": "Fumin", "initials": "F"}, {"family": "Andersson", "given": "Leif", "initials": "L", "orcid": "0000-0002-4085-6968", "researcher": {"href": "https://publications.scilifelab.se/researcher/bd3343c12f994b1fabcae23027d3a76d.json"}}, {"family": "Alstr\u00f6m", "given": "Per", "initials": "P", "orcid": "0000-0001-7182-2763", "researcher": {"href": "https://publications.scilifelab.se/researcher/f426ea7151c546939b707d5ed71e7d04.json"}}], "type": "journal article", "published": "2023-10-06", "journal": {"title": "Syst. Biol.", "issn": "1076-836X", "issn-l": "1063-5157", "volume": null, "issue": null, "pages": null}, "abstract": "Instances of parallel phenotypic evolution offer great opportunities to understand the evolutionary processes underlying phenotypic changes. However, confirming parallel phenotypic evolution and studying its causes requires a robust phylogenetic framework. One such example is the \"black-and-white wagtails\", a group of five species in the songbird genus Motacilla: one species, Motacilla alba, shows wide intra-specific plumage variation, while the four others form two pairs of very similar-looking species (M. aguimp + M. samveasnae and M. grandis + M. maderaspatensis, respectively). However, the two species in each of these pairs were not recovered as sisters in previous phylogenetic inferences. Their relationships varied depending on the markers used, suggesting that gene tree heterogeneity might have hampered accurate phylogenetic inference. Here, we use whole genome resequencing data to explore the phylogenetic relationships within this group, with a special emphasis on characterizing the extent of gene tree heterogeneity and its underlying causes. We first used multispecies coalescent methods to generate a \"complete evidence\" phylogenetic hypothesis based on genome-wide variants, while accounting for incomplete lineage sorting (ILS) and introgression. We then investigated the variation in phylogenetic signal across the genome, to quantify the extent of discordance across genomic regions, and test its underlying causes. We found that wagtail genomes are mosaics of regions supporting variable genealogies, because of ILS and inter-specific introgression. The most common topology across the genome, supporting M. alba and M. aguimp as sister species, appears to be influenced by ancient introgression. Additionally, we inferred another ancient introgression event, between M. alba and M. grandis. By combining results from multiple analyses, we propose a phylogenetic network for the black-and-white wagtails that confirms that similar phenotypes evolved in non-sister lineages, supporting parallel plumage evolution. Furthermore, the inferred reticulations do not connect species with similar plumage coloration, suggesting that introgression does not underlie parallel plumage evolution in this group. Our results demonstrate the importance of investigation of genome-wide patterns of gene tree heterogeneity to help understanding the mechanisms underlying phenotypic evolution.", "doi": "10.1093/sysbio/syad062", "pmid": "37801684", "labels": {"NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "7294611"}], "notes": [], "created": "2023-10-19T13:54:24.722Z", "modified": "2024-01-16T13:48:32.004Z"}, {"entity": "publication", "iuid": "97328d83a5ff458481fbad51e7615b21", "links": {"self": {"href": "https://publications.scilifelab.se/publication/97328d83a5ff458481fbad51e7615b21.json"}, "display": {"href": "https://publications.scilifelab.se/publication/97328d83a5ff458481fbad51e7615b21"}}, "title": "Metabolomic and transcriptomic analyses identify external conditions and key genes underlying high levels of toxic glycoalkaloids in tubers of stress-sensitive potato cultivars.", "authors": [{"family": "Merino", "given": "Irene", "initials": "I"}, {"family": "Guasca", "given": "Alexandra Olarte", "initials": "AO"}, {"family": "Krmela", "given": "Ales", "initials": "A"}, {"family": "Arif", "given": "Usman", "initials": "U"}, {"family": "Ali", "given": "Ashfaq", "initials": "A"}, {"family": "Westerberg", "given": "Erik", "initials": "E"}, {"family": "Jalmi", "given": "Siddhi Kashinanth", "initials": "SK"}, {"family": "Hajslova", "given": "Jana", "initials": "J"}, {"family": "Schulzova", "given": "Vera", "initials": "V"}, {"family": "Sitbon", "given": "Folke", "initials": "F"}], "type": "journal article", "published": "2023-10-04", "journal": {"title": "Front Plant Sci", "issn": "1664-462X", "issn-l": "1664-462X", "volume": "14", "issue": null, "pages": "1210850"}, "abstract": "High levels of toxic steroidal glycoalkaloids (SGAs) in potato tubers constitute a recognized food quality problem. Tuber SGA levels vary between potato cultivars and can increase after post-harvest stresses such as wounding and light exposure. A few cultivars, e.g., 'Magnum Bonum' and 'Lenape,' have been withdrawn from commercial sales due to excessive SGA levels during some cultivation years. However, these sudden SGA increases are diffucult to predict, and their causes are not understood. To identify external and genetic factors that underlie sudden SGA increases in certain potato cultivars, we have here in a 2-year study investigated 'Magnum Bonum' and five additional table potato cultivars for their SGA levels after wounding and light exposure.\r\n\r\nResults showed that 'Magnum Bonum' has an unusual strong SGA response to light exposure, but not to wounding, whereas 'Bintje' displayed an opposite regulation. Levels of calystegine alkaloids were not significantly altered by treatments, implicating independent metabolic regulation of SGA and calystegine levels also under conditions of high SGA accumulation. Metabolomic and transcriptomic analyses identified a small number of key genes whose expression correlated with SGA differences between cultivars. Overexpression of two key genes in transgenic low-SGA potato cultivars increased their leaf SGA levels significantly.\r\n\r\nThe results show that a strong response to light can underlie the SGA peaks that occasionally occur in certain potato cultivars and indicate that a between-cultivar variation in the expression of single SGA key genes can account for cultivar SGA differerences. We propose that current attempts to mitigate the SGA hazard will benefit from an increased consideration of cultivar-dependent SGA responses to post-harvest conditions, particularly light exposure. The identified key SGA genes can now be used as a molecular tool in this work.", "doi": "10.3389/fpls.2023.1210850", "pmid": "37860257", "labels": {"Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC10582707"}], "notes": [], "created": "2023-11-16T12:04:12.160Z", "modified": "2024-01-16T13:48:32.011Z"}, {"entity": "publication", "iuid": "8c04317c16bd45aa87bc68c221982ad6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8c04317c16bd45aa87bc68c221982ad6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8c04317c16bd45aa87bc68c221982ad6"}}, "title": "Similarity in milk microbiota in replicates.", "authors": [{"family": "Dahlberg", "given": "Josef", "initials": "J", "orcid": "0000-0001-8131-6725", "researcher": {"href": "https://publications.scilifelab.se/researcher/090cf8219ee047be97d9b75b104d8b7c.json"}}, {"family": "Pelve", "given": "Erik", "initials": "E"}, {"family": "Dicksved", "given": "Johan", "initials": "J"}], "type": "journal article", "published": "2023-10-00", "journal": {"title": "Microbiologyopen", "issn": "2045-8827", "issn-l": "2045-8827", "volume": "12", "issue": "5", "pages": "e1383"}, "abstract": "Receiving the same results from repeated analysis of the same sample is a basic principle in science. The inability to reproduce previously published results has led to discussions of a reproducibility crisis within science. For studies of microbial communities, the problem of reproducibility is more pronounced and has, in some fields, led to a discussion on the very existence of a constantly present microbiota. In this study, DNA from 44 bovine milk samples were extracted twice and the V3-V4 region of the 16S rRNA gene was sequenced in two separate runs. The FASTQ files from the two data sets were run through the same bioinformatics pipeline using the same settings and results from the two data sets were compared. Milk samples collected maximally 2 h apart were used as replicates and permitted comparisons to be made within the same run. Results show a significant difference in species richness between the two sequencing runs although Shannon and Simpson's diversity was the same. Multivariate analyses of all samples demonstrate that the sequencing run was a driver for variation. Direct comparison of similarity between samples and sequencing run showed an average similarity of 42%-45% depending on whether binary or abundance-based similarity indices were used. Within-run comparisons of milk samples collected maximally 2 h apart showed an average similarity of 39%-47% depending on the similarity index used and that similarity differed significantly between runs. We conclude that repeated DNA extraction and sequencing significantly can affect the results of a low microbial biomass microbiota study.", "doi": "10.1002/mbo3.1383", "pmid": "37877657", "labels": {"NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10542097"}], "notes": [], "created": "2023-11-24T18:10:29.818Z", "modified": "2024-01-16T13:48:32.027Z"}, {"entity": "publication", "iuid": "140f39a4f52a49ea9d0aa0492554e858", "links": {"self": {"href": "https://publications.scilifelab.se/publication/140f39a4f52a49ea9d0aa0492554e858.json"}, "display": {"href": "https://publications.scilifelab.se/publication/140f39a4f52a49ea9d0aa0492554e858"}}, "title": "Increased MYB alternative promoter usage is associated with relapse in acute lymphoblastic leukemia.", "authors": [{"family": "Fehr", "given": "Andr\u00e9", "initials": "A", "orcid": "0000-0002-2657-1392", "researcher": {"href": "https://publications.scilifelab.se/researcher/c833fc4136e34aa29e70836e5206875e.json"}}, {"family": "Arvidsson", "given": "Gustav", "initials": "G"}, {"family": "Nordlund", "given": "Jessica", "initials": "J"}, {"family": "L\u00f6nnerholm", "given": "Gudmar", "initials": "G"}, {"family": "Stenman", "given": "G\u00f6ran", "initials": "G", "orcid": "0000-0003-1017-7363", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ccb9761a5d6409095e090cf9a1edd9c.json"}}, {"family": "Andersson", "given": "Mattias K", "initials": "MK", "orcid": "0000-0001-6391-2048", "researcher": {"href": "https://publications.scilifelab.se/researcher/95c9dacff6854c5e968b9b615ef34956.json"}}], "type": "journal article", "published": "2023-10-00", "journal": {"title": "Genes Chromosomes Cancer", "issn": "1098-2264", "volume": "62", "issue": "10", "pages": "597-606", "issn-l": "1045-2257"}, "abstract": "Therapy-resistant disease is a major cause of death in patients with acute lymphoblastic leukemia (ALL). Activation of the MYB oncogene is associated with ALL and leads to uncontrolled neoplastic cell proliferation and blocked differentiation. Here, we used RNA-seq to study the clinical significance of MYB expression and MYB alternative promoter (TSS2) usage in 133 pediatric ALLs. RNA-seq revealed that all cases analyzed overexpressed MYB and demonstrated MYB TSS2 activity. qPCR analyses confirmed the expression of the alternative MYB promoter also in seven ALL cell lines. Notably, high MYB TSS2 activity was significantly associated with relapse (p = 0.007). Moreover, cases with high MYB TSS2 usage showed evidence of therapy-resistant disease with increased expression of ABC multidrug resistance transporter genes (e.g., ABCA2, ABCB5, and ABCC10) and enzymes catalyzing drug degradation (e.g., CYP1A2, CYP2C9, and CYP3A5). Elevated MYB TSS2 activity was further associated with augmented KRAS signaling (p < 0.05) and decreased methylation of the conventional MYB promoter (p < 0.01). Taken together, our results suggest that MYB alternative promoter usage is a novel potential prognostic biomarker for relapse and therapy resistance in pediatric ALL.", "doi": "10.1002/gcc.23151", "pmid": "37218648", "labels": {"NGI SNP genotyping": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [], "notes": [], "created": "2023-11-29T10:47:51.587Z", "modified": "2023-11-29T10:47:51.684Z"}, {"entity": "publication", "iuid": "9aef338ade194b078421af40a611fa5a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9aef338ade194b078421af40a611fa5a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9aef338ade194b078421af40a611fa5a"}}, "title": "B cell polygenic risk scores associate with anti-dsDNA antibodies and nephritis in systemic lupus erythematosus.", "authors": [{"family": "Hedenstedt", "given": "Anna", "initials": "A", "orcid": "0009-0007-1596-1233", "researcher": {"href": "https://publications.scilifelab.se/researcher/83ae75c2cfd64c9488ea2a07119d0f4d.json"}}, {"family": "Reid", "given": "Sarah", "initials": "S"}, {"family": "Sayadi", "given": "Ahmed", "initials": "A"}, {"family": "Eloranta", "given": "Maija-Leena", "initials": "ML", "orcid": "0000-0002-8454-1351", "researcher": {"href": "https://publications.scilifelab.se/researcher/d162e060954d420e825884f254886dcd.json"}}, {"family": "Skoglund", "given": "Elisabeth", "initials": "E"}, {"family": "Bolin", "given": "Karin", "initials": "K"}, {"family": "Frodlund", "given": "Martina", "initials": "M"}, {"family": "Lerang", "given": "Karoline", "initials": "K"}, {"family": "J\u00f6nsen", "given": "Andreas", "initials": "A"}, {"family": "Rantap\u00e4\u00e4-Dahlqvist", "given": "Solbritt", "initials": "S"}, {"family": "Bengtsson", "given": "Anders A", "initials": "AA"}, {"family": "Rudin", "given": "Anna", "initials": "A"}, {"family": "Molberg", "given": "\u00d8yvind", "initials": "\u00d8"}, {"family": "Sj\u00f6wall", "given": "Christopher", "initials": "C", "orcid": "0000-0003-0900-2048", "researcher": {"href": "https://publications.scilifelab.se/researcher/fe4dd47b8ca1436e8a26fdea33f5e7f6.json"}}, {"family": "Sandling", "given": "Johanna K", "initials": "JK", "orcid": "0000-0003-1382-2321", "researcher": {"href": "https://publications.scilifelab.se/researcher/9c7bae5a05ac47eeac96547ca7336767.json"}}, {"family": "Leonard", "given": "Dag", "initials": "D", "orcid": "0000-0002-6275-7282", "researcher": {"href": "https://publications.scilifelab.se/researcher/42ed25c2f495484db4757f4fef51abae.json"}}], "type": "journal article", "published": "2023-10-00", "journal": {"title": "Lupus Sci Med", "issn": "2053-8790", "volume": "10", "issue": "2", "issn-l": "2053-8790"}, "abstract": "B cell function and autoantibodies are important in SLE pathogenesis. In this work, we aimed to investigate the impact of cumulative SLE B cell genetics on SLE subphenotype and autoantibody profile.\n\nFemale patients with SLE (n=1248) and healthy controls (n=400) were genotyped using Illumina's Global Screening Array. Two polygenic risk scores (PRSs), one representing B cell genes and the other B cell activation genes, were calculated for each individual using risk loci for SLE in genes assigned to B cell-related pathways according to the Kyoto Encyclopedia of Genes and Genomes, Gene Ontology and Reactome Databases.\n\nDouble-stranded DNA (dsDNA) antibodies were more prevalent among patients with a high compared with a low SLE B cell PRS (OR 1.47 (1.07 to 2.01), p=0.018), and effect sizes were augmented in patients with human leucocyte antigen (HLA) risk haplotypes HLA-DRB1*03:01 and HLA-DRB1*15:01 (DRB1*03/15 -/- (OR 0.99 (0.56 to 1.77), p=0.98; DRB1*03/15 +/- or -/+ (OR 1.64 (1.06 to 2.54), p=0.028; and DRB1*03/15 +/+ (OR 4.47 (1.21 to 16.47), p=0.024). Further, a high compared with a low B cell PRS was associated with low complement levels in DRB1*03/15 +/+ patients (OR 3.92 (1.22 to 12.64), p=0.022). The prevalence of lupus nephritis (LN) was higher in patients with a B cell activation PRS above the third quartile compared with patients below (OR 1.32 (1.00 to 1.74), p=0.048).\n\nHigh genetic burden related to B cell function is associated with dsDNA antibody development and LN. Assessing B cell PRSs may be important in order to determine immunological pathways influencing SLE and to predict clinical phenotype.", "doi": "10.1136/lupus-2023-000926", "pmid": "37844960", "labels": {"NGI Short read": "Service", "NGI SNP genotyping": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10582984"}, {"db": "pii", "key": "10/2/e000926"}], "notes": [], "created": "2023-11-29T10:59:36.253Z", "modified": "2023-11-29T10:59:36.317Z"}, {"entity": "publication", "iuid": "5f84008ef37d4592a6744d625c3bcab6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5f84008ef37d4592a6744d625c3bcab6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5f84008ef37d4592a6744d625c3bcab6"}}, "title": "Whole genome sequence of the deep-sea sponge Geodia barretti (Metazoa, Porifera, Demospongiae).", "authors": [{"family": "Steffen", "given": "Karin", "initials": "K"}, {"family": "Proux-W\u00e9ra", "given": "Estelle", "initials": "E"}, {"family": "Soler", "given": "Lucile", "initials": "L"}, {"family": "Churcher", "given": "Allison", "initials": "A"}, {"family": "Sundh", "given": "John", "initials": "J"}, {"family": "C\u00e1rdenas", "given": "Paco", "initials": "P"}], "type": "journal article", "published": "2023-09-30", "journal": {"title": "G3 (Bethesda)", "issn": "2160-1836", "issn-l": "2160-1836", "volume": "13", "issue": "10", "pages": null}, "abstract": "Sponges are among the earliest branching extant animals. As such, genetic data from this group are valuable for understanding the evolution of various traits and processes in other animals. However, like many marine organisms, they are notoriously difficult to sequence, and hence, genomic data are scarce. Here, we present the draft genome assembly for the North Atlantic deep-sea high microbial abundance species Geodia barretti Bowerbank 1858, from a single individual collected on the West Coast of Sweden. The nuclear genome assembly has 4,535 scaffolds, an N50 of 48,447 bp and a total length of 144 Mb; the mitochondrial genome is 17,996 bp long. BUSCO completeness was 71.5%. The genome was annotated using a combination of ab initio and evidence-based methods finding 31,884 protein-coding genes.", "doi": "10.1093/g3journal/jkad192", "pmid": "37619978", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service", "NGI Long read": "Service", "Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC10542158"}, {"db": "pii", "key": "7250426"}], "notes": [], "created": "2023-09-04T12:08:12.851Z", "modified": "2024-01-16T13:48:32.035Z"}, {"entity": "publication", "iuid": "0e6c5f5e44e3406b9d3f38f57c040da5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0e6c5f5e44e3406b9d3f38f57c040da5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0e6c5f5e44e3406b9d3f38f57c040da5"}}, "title": "Community-wide genome sequencing reveals 30 years of Darwin's finch evolution.", "authors": [{"family": "Enbody", "given": "Erik D", "initials": "ED", "orcid": "0000-0003-1349-628X", "researcher": {"href": "https://publications.scilifelab.se/researcher/7a4df51b279746539cae2fa83c37456d.json"}}, {"family": "Sendell-Price", "given": "Ashley T", "initials": "AT"}, {"family": "Sprehn", "given": "C Grace", "initials": "CG", "orcid": "0000-0002-4164-4246", "researcher": {"href": "https://publications.scilifelab.se/researcher/b51f6d45361e4aa187fc74870a38ac3f.json"}}, {"family": "Rubin", "given": "Carl-Johan", "initials": "C"}, {"family": "Visscher", "given": "Peter M", "initials": "PM", "orcid": "0000-0002-2143-8760", "researcher": {"href": "https://publications.scilifelab.se/researcher/dcdb41d4720b436494304f74e33206ae.json"}}, {"family": "Grant", "given": "B Rosemary", "initials": "BR"}, {"family": "Grant", "given": "Peter R", "initials": "PR", "orcid": "0000-0002-7347-5758", "researcher": {"href": "https://publications.scilifelab.se/researcher/18a184c706054257a130b2ae0694d858.json"}}, {"family": "Andersson", "given": "Leif", "initials": "L", "orcid": "0000-0002-4085-6968", "researcher": {"href": "https://publications.scilifelab.se/researcher/bd3343c12f994b1fabcae23027d3a76d.json"}}], "type": "journal article", "published": "2023-09-29", "journal": {"title": "Science", "issn": "1095-9203", "issn-l": "0036-8075", "volume": "381", "issue": "6665", "pages": "eadf6218"}, "abstract": "A fundamental goal in evolutionary biology is to understand the genetic architecture of adaptive traits. Using whole-genome data of 3955 of Darwin's finches on the Gal\u00e1pagos Island of Daphne Major, we identified six loci of large effect that explain 45% of the variation in the highly heritable beak size of Geospiza fortis, a key ecological trait. The major locus is a supergene comprising four genes. Abrupt changes in allele frequencies at the loci accompanied a strong change in beak size caused by natural selection during a drought. A gradual change in Geospiza scandens occurred across 30 years as a result of introgressive hybridization with G. fortis. This study shows how a few loci with large effect on a fitness-related trait contribute to the genetic potential for rapid adaptive radiation.", "doi": "10.1126/science.adf6218", "pmid": "37769091", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service", "NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2023-10-12T11:14:44.927Z", "modified": "2024-01-16T13:48:32.043Z"}, {"entity": "publication", "iuid": "cfad3d491ac3446ca70f18e88f73c834", "links": {"self": {"href": "https://publications.scilifelab.se/publication/cfad3d491ac3446ca70f18e88f73c834.json"}, "display": {"href": "https://publications.scilifelab.se/publication/cfad3d491ac3446ca70f18e88f73c834"}}, "title": "Single-cell transcriptomics delineates the immune cell landscape in equine lower airways and reveals upregulation of FKBP5 in horses with asthma.", "authors": [{"family": "Riihim\u00e4ki", "given": "Miia", "initials": "M"}, {"family": "Fegraeus", "given": "Kim", "initials": "K"}, {"family": "Nordlund", "given": "Jessica", "initials": "J"}, {"family": "Waern", "given": "Ida", "initials": "I"}, {"family": "Wernersson", "given": "Sara", "initials": "S"}, {"family": "Akula", "given": "Srinivas", "initials": "S"}, {"family": "Hellman", "given": "Lars", "initials": "L"}, {"family": "Raine", "given": "Amanda", "initials": "A"}], "type": "journal article", "published": "2023-09-27", "journal": {"title": "Sci Rep", "issn": "2045-2322", "issn-l": "2045-2322", "volume": "13", "issue": "1", "pages": "16261"}, "abstract": "Equine asthma (EA) is a heterogenous, complex disease, with a significant negative impact on horse welfare and performance. EA and human asthma share fundamental similarities, making EA a useful model for studying the disease. One relevant sample type for investigating chronic lung inflammation is bronchoalveolar lavage fluid (BALF), which provides a snapshot of the immune cells present in the alveolar space. To investigate the immune cell landscape of the respiratory tract in horses with mild-to-moderate equine asthma (mEA) and healthy controls, single-cell RNA sequencing was conducted on equine BALF cells. We characterized the major immune cell populations present in equine BALF, as well as subtypes thereof. Interestingly, the most significantly upregulated gene discovered in cases of mEA was FKBP5, a chaperone protein involved in regulating the activity of the glucocorticoid receptor.", "doi": "10.1038/s41598-023-43368-4", "pmid": "37758813", "labels": {"NGI Short read": "Collaborative", "NGI Uppsala (SNP&SEQ Technology Platform)": "Collaborative", "National Genomics Infrastructure": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "NGI Single cell": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC10533524"}, {"db": "pii", "key": "10.1038/s41598-023-43368-4"}], "notes": [], "created": "2023-11-27T21:49:44.494Z", "modified": "2024-02-27T08:16:23.788Z"}, {"entity": "publication", "iuid": "a7779ca0e6794082a6fb16d84f023606", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a7779ca0e6794082a6fb16d84f023606.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a7779ca0e6794082a6fb16d84f023606"}}, "title": "Identification of motif-based interactions between SARS-CoV-2 protein domains and human peptide ligands pinpoint antiviral targets.", "authors": [{"family": "Mihali\u010d", "given": "Filip", "initials": "F", "orcid": "0000-0002-6840-2319", "researcher": {"href": "https://publications.scilifelab.se/researcher/5f57a961e98e4e15b1b96ec8efc95d4f.json"}}, {"family": "Benz", "given": "Caroline", "initials": "C", "orcid": "0000-0002-5166-3598", "researcher": {"href": "https://publications.scilifelab.se/researcher/86628e15252f4dd98f08759d59fad848.json"}}, {"family": "Kassa", "given": "Eszter", "initials": "E"}, {"family": "Lindqvist", "given": "Richard", "initials": "R"}, {"family": "Simonetti", "given": "Leandro", "initials": "L", "orcid": "0000-0003-1283-9770", "researcher": {"href": "https://publications.scilifelab.se/researcher/23530c1a3cef4f499a460ac59c674261.json"}}, {"family": "Inturi", "given": "Raviteja", "initials": "R"}, {"family": "Aronsson", "given": "Hanna", "initials": "H"}, {"family": "Andersson", "given": "Eva", "initials": "E"}, {"family": "Chi", "given": "Celestine N", "initials": "CN"}, {"family": "Davey", "given": "Norman E", "initials": "NE"}, {"family": "\u00d6verby", "given": "Anna K", "initials": "AK", "orcid": "0000-0001-6553-0940", "researcher": {"href": "https://publications.scilifelab.se/researcher/506b0e2b2d884f868df73c7663b9ffb7.json"}}, {"family": "Jemth", "given": "Per", "initials": "P", "orcid": "0000-0003-1516-7228", "researcher": {"href": "https://publications.scilifelab.se/researcher/91bb46ceba74462498354a328886b982.json"}}, {"family": "Ivarsson", "given": "Ylva", "initials": "Y", "orcid": "0000-0002-7081-3846", "researcher": {"href": "https://publications.scilifelab.se/researcher/f51534acce8c4214a55a3e7387850d53.json"}}], "type": "journal article", "published": "2023-09-13", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "14", "issue": "1", "pages": "5636", "issn-l": "2041-1723"}, "abstract": "The virus life cycle depends on host-virus protein-protein interactions, which often involve a disordered protein region binding to a folded protein domain. Here, we used proteomic peptide phage display (ProP-PD) to identify peptides from the intrinsically disordered regions of the human proteome that bind to folded protein domains encoded by the SARS-CoV-2 genome. Eleven folded domains of SARS-CoV-2 proteins were found to bind 281 peptides from human proteins, and affinities of 31 interactions involving eight SARS-CoV-2 protein domains were determined (KD \u223c 7-300 \u03bcM). Key specificity residues of the peptides were established for six of the interactions. Two of the peptides, binding Nsp9 and Nsp16, respectively, inhibited viral replication. Our findings demonstrate how high-throughput peptide binding screens simultaneously identify potential host-virus interactions and peptides with antiviral properties. Furthermore, the high number of low-affinity interactions suggest that overexpression of viral proteins during infection may perturb multiple cellular pathways.", "doi": "10.1038/s41467-023-41312-8", "pmid": "37704626", "labels": {"NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10499821"}, {"db": "pii", "key": "10.1038/s41467-023-41312-8"}], "notes": [], "created": "2023-10-19T13:57:45.671Z", "modified": "2024-11-12T10:39:14.679Z"}, {"entity": "publication", "iuid": "2e31abdf99b245178c96a47d5696b8da", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2e31abdf99b245178c96a47d5696b8da.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2e31abdf99b245178c96a47d5696b8da"}}, "title": "Seasonal and age-related changes in sperm quality of farmed arctic charr (Salvelinus alpinus).", "authors": [{"family": "Kurta", "given": "Khrystyna", "initials": "K"}, {"family": "Jeuthe", "given": "Henrik", "initials": "H"}, {"family": "Naboulsi", "given": "Rakan", "initials": "R"}, {"family": "de Koning", "given": "Dirk-Jan", "initials": "DJ"}, {"family": "Palaiokostas", "given": "Christos", "initials": "C"}], "type": "journal article", "published": "2023-09-04", "journal": {"title": "BMC Genomics", "issn": "1471-2164", "volume": "24", "issue": "1", "pages": "519", "issn-l": "1471-2164"}, "abstract": "Substantial variation in male fertility is regularly observed in farmed Arctic charr. However, detailed investigations of its fluctuation during a reproductive season and across years are lacking. Furthermore, information about the effect of underlying genetic factors influencing sperm quality is scarce. The current study focused on seasonal and age-related factors that may affect sperm quality characteristics in males reared in natural and delayed photoperiods. Animals were sampled three times for two consecutive years, and sperm quality parameters were recorded using a computer-assisted sperm analysis (CASA) system. Thereafter, high-throughput sequencing technologies were applied, aiming to identify genomic regions related to the variation of sperm quality throughout the reproductive season.\n\nAn across-season variation in the recorded sperm quality parameters was evident. Overall, 29% and 42% of males from the natural and delayed spawning groups had a highly variable total progressive motility. Males at four years of age showed significantly higher sperm motility and velocities during the early October and November recordings compared to the following year when the same animals were five years of age. On the other hand, the opposite was observed regarding sperm concentration during the last sampling. A genome-wide FST scan detected SNP differentiation among males with high and low variability in total progressive motility (PM) on eight chromosomes (FST > 0.17), Genome wide windows with the highest FST contained SNPs in proximity (within 250 kb up- and downstream distance) to 16 genes with sperm quality biological functions in mammalian species.\n\nOur findings provide a detailed view of seasonal, age-related, and genetic effects on sperm quality and can be used to guide decisions on broodstock selection and hatchery management.", "doi": "10.1186/s12864-023-09614-9", "pmid": "37667174", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10478403"}, {"db": "pii", "key": "10.1186/s12864-023-09614-9"}], "notes": [], "created": "2023-11-29T10:58:03.579Z", "modified": "2023-11-29T10:58:03.583Z"}, {"entity": "publication", "iuid": "20bb1b4554cb4d499841f007d0b0230a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/20bb1b4554cb4d499841f007d0b0230a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/20bb1b4554cb4d499841f007d0b0230a"}}, "title": "Stratified genetic analysis reveals sex differences in MPO-ANCA-associated vasculitis.", "authors": [{"family": "Ekman", "given": "Diana", "initials": "D"}, {"family": "Sennblad", "given": "Bengt", "initials": "B"}, {"family": "Knight", "given": "Ann", "initials": "A"}, {"family": "Karlsson", "given": "\u00c5sa", "initials": "\u00c5"}, {"family": "Rantap\u00e4\u00e4-Dahlqvist", "given": "Solbritt", "initials": "S", "orcid": "0000-0001-8259-3863", "researcher": {"href": "https://publications.scilifelab.se/researcher/dfca4bfdcf3946fda64397d3b7debc59.json"}}, {"family": "Berglin", "given": "Ewa", "initials": "E"}, {"family": "Stegmayr", "given": "Bernd", "initials": "B"}, {"family": "Baslund", "given": "Bo", "initials": "B"}, {"family": "Palm", "given": "\u00d8yvind", "initials": "\u00d8"}, {"family": "Haukeland", "given": "Hilde", "initials": "H"}, {"family": "Gunnarsson", "given": "Iva", "initials": "I"}, {"family": "Bruchfeld", "given": "Annette", "initials": "A", "orcid": "0000-0002-9752-9941", "researcher": {"href": "https://publications.scilifelab.se/researcher/dc6ee3e8a4124c5f8d6506ab762949ae.json"}}, {"family": "Segelmark", "given": "M\u00e5rten", "initials": "M"}, {"family": "Ohlsson", "given": "Sophie", "initials": "S"}, {"family": "Mohammad", "given": "Aladdin J", "initials": "AJ", "orcid": "0000-0002-7169-6936", "researcher": {"href": "https://publications.scilifelab.se/researcher/d7010c3f5b91415dbc26c87d6a923f68.json"}}, {"family": "Sv\u00e4rd", "given": "Anna", "initials": "A"}, {"family": "Pullerits", "given": "Rille", "initials": "R"}, {"family": "Herlitz", "given": "Hans", "initials": "H"}, {"family": "S\u00f6derbergh", "given": "Annika", "initials": "A"}, {"family": "Omdal", "given": "Roald", "initials": "R"}, {"family": "Jonsson", "given": "Roland", "initials": "R"}, {"family": "R\u00f6nnblom", "given": "Lars", "initials": "L"}, {"family": "Eriksson", "given": "Per", "initials": "P"}, {"family": "Lindblad-Toh", "given": "Kerstin", "initials": "K"}, {"family": "Dahlqvist", "given": "Johanna", "initials": "J", "orcid": "0000-0002-6283-644X", "researcher": {"href": "https://publications.scilifelab.se/researcher/8fb2ab2d83b6437f9918f330e5fb81b2.json"}}], "type": "journal article", "published": "2023-09-01", "journal": {"title": "Rheumatology (Oxford)", "issn": "1462-0332", "issn-l": "1462-0324", "volume": "62", "issue": "9", "pages": "3213-3218"}, "abstract": "To identify and genetically characterize subgroups of patients with ANCA-associated vasculitides (AAV) based on sex and ANCA subtype.\n\nA previously established SNP dataset derived from DNA sequencing of 1853 genes and genotyping of 1088 Scandinavian cases with AAV and 1589 controls was stratified for sex and ANCA subtype and analysed for association with five top AAV SNPs. rs9274619, a lead variant at the HLA-DQB1/HLA-DQA2 locus previously associated with AAV positive for myeloperoxidase (MPO)-ANCA, was analysed for association with the cumulative disease involvement of ten different organ systems.\n\nrs9274619 showed a significantly stronger association to MPO-ANCA-positive females than males [P = 2.0 \u00d7 10-4, OR = 2.3 (95% CI 1.5, 3.5)], whereas proteinase 3 (PR3)-ANCA-associated variants rs1042335, rs9277341 (HLA-DPB1/A1) and rs28929474 (SERPINA1) were equally associated with females and males with PR3-ANCA. In MPO-ANCA-positive cases, carriers of the rs9274619 risk allele were more prone to disease engagement of eyes [P = 0.021, OR = 11 (95% CI 2.2, 205)] but less prone to pulmonary involvement [P = 0.026, OR = 0.52 (95% CI 0.30, 0.92)]. Moreover, AAV with both MPO-ANCA and PR3-ANCA was associated with the PR3-ANCA lead SNP rs1042335 [P = 0.0015, OR = 0.091 (95% CI 0.0022, 0.55)] but not with rs9274619.\n\nFemales and males with MPO-ANCA-positive AAV differ in genetic predisposition to disease, suggesting at least partially distinct disease mechanisms between the sexes. Double ANCA-positive AAV cases are genetically similar to PR3-ANCA-positive cases, providing clues to the clinical follow-up and treatment of these patients.", "doi": "10.1093/rheumatology/kead152", "pmid": "37004177", "labels": {"Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "NGI SNP genotyping": "Service", "NGI Short read": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC10473270"}, {"db": "pii", "key": "7099616"}], "notes": [], "created": "2023-04-04T12:12:11.801Z", "modified": "2024-01-16T13:48:32.331Z"}, {"entity": "publication", "iuid": "a66d093637414a70b17413710bda1d35", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a66d093637414a70b17413710bda1d35.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a66d093637414a70b17413710bda1d35"}}, "title": "Mosaic Loss of Chromosome Y Is Associated With Functional Outcome After Ischemic Stroke.", "authors": [{"family": "Dorvall", "given": "Malin", "initials": "M", "orcid": "0009-0009-4646-5130", "researcher": {"href": "https://publications.scilifelab.se/researcher/fc024352284b481180f888ff19d03627.json"}}, {"family": "Pedersen", "given": "Annie", "initials": "A", "orcid": "0000-0002-7498-7755", "researcher": {"href": "https://publications.scilifelab.se/researcher/596f0e19af284f1b83c1e3de24f64526.json"}}, {"family": "Dumanski", "given": "Jan P", "initials": "JP", "orcid": "0000-0002-1489-1452", "researcher": {"href": "https://publications.scilifelab.se/researcher/15b14282209342cfa9c82cdbf02999f6.json"}}, {"family": "S\u00f6derholm", "given": "Martin", "initials": "M", "orcid": "0009-0001-3129-9581", "researcher": {"href": "https://publications.scilifelab.se/researcher/c7c0a66eb28644deb98160c4c94fe737.json"}}, {"family": "Lindgren", "given": "Arne G", "initials": "AG", "orcid": "0000-0003-1942-7330", "researcher": {"href": "https://publications.scilifelab.se/researcher/94b604b14f1f4776a19010f5ac2a575c.json"}}, {"family": "Stanne", "given": "Tara M", "initials": "TM", "orcid": "0000-0001-9668-0407", "researcher": {"href": "https://publications.scilifelab.se/researcher/f3c967b386124a3199b2373de1111d03.json"}}, {"family": "Jern", "given": "Christina", "initials": "C", "orcid": "0000-0002-7531-2354", "researcher": {"href": "https://publications.scilifelab.se/researcher/13e58d6c4a2e44cd9067f38a2ff2ea32.json"}}], "type": "journal article", "published": "2023-09-00", "journal": {"title": "Stroke", "issn": "1524-4628", "volume": "54", "issue": "9", "pages": "2434-2437", "issn-l": "0039-2499"}, "abstract": "Mosaic loss of chromosome Y (LOY) is associated with cardiovascular and neurodegenerative diseases in men, and genetic predisposition to LOY is associated with poor poststroke outcome. We, therefore, tested the hypothesis that LOY itself is associated with functional outcome after ischemic stroke.\n\nThe study comprised male patients with ischemic stroke from the cohort studies SAHLSIS2 (Sahlgrenska Academy Study on Ischemic Stroke Phase 2; n=588) and LSR (Lund Stroke Register; n=735). We used binary logistic regression to analyze associations between LOY, determined by DNA microarray intensity data, and poor 3-month functional outcome (modified Rankin Scale score, >2) in each cohort separately and combined. Patients who received recanalization therapy were excluded from sensitivity analyses.\n\nLOY was associated with about 2.5-fold increased risk of poor outcome in univariable analyses (P<0.001). This association withstood separate adjustment for stroke severity and diabetes in both cohorts but not age. In sensitivity analyses restricted to the nonrecanalization group (n=987 in the combined cohort), the association was significant also after separate adjustment for age (odds ratio, 1.6 [95% CI, 1.1-2.4]) and when additionally adjusting for stroke severity and diabetes (odds ratio, 1.6 [95% CI, 1.1-2.5]).\n\nWe observed an association between LOY and poor outcome after ischemic stroke in patients not receiving recanalization therapy. Future studies on LOY and other somatic genetic alterations in larger stroke cohorts are warranted.", "doi": "10.1161/STROKEAHA.123.043551", "pmid": "37465995", "labels": {"NGI SNP genotyping": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Clinical Genomics Gothenburg": "Service", "Clinical Genomics": "Service"}, "xrefs": [{"db": "mid", "key": "NIHMS1915501"}, {"db": "pmc", "key": "PMC10453343"}], "notes": [], "created": "2023-11-29T11:19:36.243Z", "modified": "2023-11-30T22:29:53.328Z"}, {"entity": "publication", "iuid": "574c8505fa834097a975bfc1cdc70d36", "links": {"self": {"href": "https://publications.scilifelab.se/publication/574c8505fa834097a975bfc1cdc70d36.json"}, "display": {"href": "https://publications.scilifelab.se/publication/574c8505fa834097a975bfc1cdc70d36"}}, "title": "Milder Autumns May Increase Risk for Infection of Crops with Turnip Yellows Virus.", "authors": [{"family": "Puthanveed", "given": "Vinitha", "initials": "V"}, {"family": "Singh", "given": "Khushwant", "initials": "K"}, {"family": "Poimenopoulou", "given": "Efstratia", "initials": "E"}, {"family": "Pettersson", "given": "Josefin", "initials": "J"}, {"family": "Siddique", "given": "Abu Bakar", "initials": "AB"}, {"family": "Kvarnheden", "given": "Anders", "initials": "A", "orcid": "0000-0001-9394-7700", "researcher": {"href": "https://publications.scilifelab.se/researcher/bf67998333e74016847b7a6d3f121e7b.json"}}], "type": "journal article", "published": "2023-09-00", "journal": {"title": "Phytopathology", "issn": "0031-949X", "issn-l": null, "volume": "113", "issue": "9", "pages": "1788-1798"}, "abstract": "Climate change has increased the risk for infection of crops with insect-transmitted viruses. Mild autumns provide prolonged active periods to insects, which may spread viruses to winter crops. In autumn 2018, green peach aphids (Myzus persicae) were found in suction traps in southern Sweden that presented infection risk for winter oilseed rape (OSR; Brassica napus) with turnip yellows virus (TuYV). A survey was carried out in spring 2019 with random leaf samples from 46 OSR fields in southern and central Sweden using DAS-ELISA, and TuYV was detected in all fields except one. In the counties of Sk\u00e5ne, Kalmar, and \u00d6sterg\u00f6tland, the average incidence of TuYV-infected plants was 75%, and the incidence reached 100% for nine fields. Sequence analyses of the coat protein gene revealed a close relationship between TuYV isolates from Sweden and other parts of the world. High-throughput sequencing for one of the OSR samples confirmed the presence of TuYV and revealed coinfection with TuYV-associated RNA. Molecular analyses of seven sugar beet (Beta vulgaris) plants with yellowing, collected in 2019, revealed that two of them were infected by TuYV, together with two other poleroviruses: beet mild yellowing virus and beet chlorosis virus. The presence of TuYV in sugar beet suggests a spillover from other hosts. Poleroviruses are prone to recombination, and mixed infection with three poleroviruses in the same plant poses a risk for the emergence of new polerovirus genotypes. [Formula: see text] Copyright \u00a9 2023 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.", "doi": "10.1094/PHYTO-11-22-0446-V", "pmid": "36802872", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2023-11-27T21:54:07.736Z", "modified": "2024-01-16T13:48:32.357Z"}, {"entity": "publication", "iuid": "155b51259682437faf22ad2c6fa5b409", "links": {"self": {"href": "https://publications.scilifelab.se/publication/155b51259682437faf22ad2c6fa5b409.json"}, "display": {"href": "https://publications.scilifelab.se/publication/155b51259682437faf22ad2c6fa5b409"}}, "title": "Chromatin accessibility, not 5mC methylation covaries with partial dosage compensation in crows.", "authors": [{"family": "Catal\u00e1n", "given": "Ana", "initials": "A", "orcid": "0000-0002-4543-748X", "researcher": {"href": "https://publications.scilifelab.se/researcher/f5edac0f763941e29cbe9595b998023b.json"}}, {"family": "Merondun", "given": "Justin", "initials": "J"}, {"family": "Knief", "given": "Ulrich", "initials": "U", "orcid": "0000-0001-6959-3033", "researcher": {"href": "https://publications.scilifelab.se/researcher/5d8858c7c7b44a008a172bc637957ce1.json"}}, {"family": "Wolf", "given": "Jochen B W", "initials": "JBW"}], "type": "journal article", "published": "2023-09-00", "journal": {"title": "PLoS Genet.", "issn": "1553-7404", "volume": "19", "issue": "9", "pages": "e1010901", "issn-l": "1553-7390"}, "abstract": "The evolution of genetic sex determination is often accompanied by degradation of the sex-limited chromosome. Male heterogametic systems have evolved convergent, epigenetic mechanisms restoring the resulting imbalance in gene dosage between diploid autosomes (AA) and the hemizygous sex chromosome (X). Female heterogametic systems (AAf Zf, AAm ZZm) tend to only show partial dosage compensation (0.5 < Zf:AAf < 1) and dosage balance (0.5<Zf:ZZm<1). The underlying mechanism remains largely elusive. Here, we quantified gene expression for a total of 15 male and female Eurasian crows (Corvus (corone) spp.) raised under common garden conditions. In addition, we characterized aspects of the regulatory epigenetic landscape quantifying chromatin accessibility (ATAC-seq) and 5mC methylation profiles. Partial dosage balance and compensation was due to female upregulation of Z-linked genes which covaried significantly with increased chromatin accessibility of the female Z chromosome. 5mC methylation was tissue and sex chromosome-specific, but unrelated to dosage. With the exception of the pseudo-autosomal region (PAR), female upregulation of gene expression was evenly spread across the Z chromosome without evidence for regional centers of epigenetic regulation, as has, for example, been suggested for the male hypermethylated region (MHM) in chicken. Our results suggest that partial dosage balance and compensation in female heterogametic systems are tightly linked to chromosome-wide, epigenetic control of the female Z chromosome mediated by differential chromatin accessibility.", "doi": "10.1371/journal.pgen.1010901", "pmid": "37747941", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10575545"}, {"db": "pii", "key": "PGENETICS-D-23-00282"}], "notes": [], "created": "2023-11-29T11:12:52.573Z", "modified": "2023-11-29T11:12:52.615Z"}, {"entity": "publication", "iuid": "9fb879c926904883b9330093264e5427", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9fb879c926904883b9330093264e5427.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9fb879c926904883b9330093264e5427"}}, "title": "Inhibition of high level E2F in a RB1 proficient MYCN overexpressing chicken retinoblastoma model normalizes neoplastic behaviour.", "authors": [{"family": "Zhang", "given": "Hanzhao", "initials": "H"}, {"family": "Konjusha", "given": "Dardan", "initials": "D"}, {"family": "Rafati", "given": "Nima", "initials": "N"}, {"family": "Tararuk", "given": "Tatsiana", "initials": "T"}, {"family": "Hallb\u00f6\u00f6k", "given": "Finn", "initials": "F"}], "type": "journal article", "published": "2023-08-22", "journal": {"title": "Cell Oncol (Dordr)", "issn": "2211-3436", "issn-l": null, "volume": null, "issue": null, "pages": null}, "abstract": "Retinoblastoma, a childhood cancer, is most frequently caused by bi-allelic inactivation of RB1 gene. However, other oncogenic mutations such as MYCN amplification can induce retinoblastoma with proficient RB1. Previously, we established RB1-proficient MYCN-overexpressing retinoblastoma models both in human organoids and chicken. Here, we investigate the regulatory events in MYCN-induced retinoblastoma carcinogenesis based on the model in chicken.\r\n\r\nMYCN transformed retinal cells in culture were obtained from in vivo MYCN electroporated chicken embryo retina. The expression profiles were analysed by RNA sequencing. Chemical treatments, qRT-PCR, flow cytometry, immunohisto- and immunocytochemistry and western blot were applied to study the properties and function of these cells.\r\n\r\nThe expression profile of MYCN-transformed retinal cells in culture showed cone photoreceptor progenitor signature and robustly increased levels of E2Fs. This expression profile was consistently observed in long-term culture. Chemical treatments confirmed RB1 proficiency in these cells. The cells were insensitive to p53 activation but inhibition of E2f efficiently induced cell cycle arrest followed by apoptosis.\r\n\r\nIn conclusion, with proficient RB1, MYCN-induced high level of E2F expression dysregulates the cell cycle and contributes to retinoblastoma carcinogenesis. The increased level of E2f renders the cells to adopt a similar mechanistic phenotype to a RB1-deficient tumour.", "doi": "10.1007/s13402-023-00863-0", "pmid": "37606819", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1007/s13402-023-00863-0"}], "notes": [], "created": "2023-11-02T09:10:58.573Z", "modified": "2024-01-16T13:48:32.442Z"}, {"entity": "publication", "iuid": "b0fc64bb3f354c23a4cefe81c8290ef8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b0fc64bb3f354c23a4cefe81c8290ef8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b0fc64bb3f354c23a4cefe81c8290ef8"}}, "title": "Contrasting response of microeukaryotic and bacterial communities to the interplay of seasonality and local stressors in shallow soda lakes.", "authors": [{"family": "M\u00e1rton", "given": "Zsuzsanna", "initials": "Z"}, {"family": "Csit\u00e1ri", "given": "Bianka", "initials": "B"}, {"family": "Felf\u00f6ldi", "given": "Tam\u00e1s", "initials": "T", "orcid": "0000-0003-2009-2478", "researcher": {"href": "https://publications.scilifelab.se/researcher/3a452e1d353649bc860f59485fc8bf03.json"}}, {"family": "Hidas", "given": "Andr\u00e1s", "initials": "A"}, {"family": "Jord\u00e1n", "given": "Ferenc", "initials": "F"}, {"family": "Szab\u00f3", "given": "Attila", "initials": "A"}, {"family": "Sz\u00e9kely", "given": "Anna J", "initials": "AJ", "orcid": "0000-0001-8063-7156", "researcher": {"href": "https://publications.scilifelab.se/researcher/c9b2d69cfd6a4f41a978b38ddf66c8d5.json"}}], "type": "journal article", "published": "2023-08-22", "journal": {"title": "FEMS Microbiol. Ecol.", "issn": "1574-6941", "volume": "99", "issue": "9", "issn-l": "0168-6496"}, "abstract": "Seasonal environmental variation is a leading driver of microbial planktonic community assembly and interactions. However, departures from usual seasonal trends are often reported. To understand the role of local stressors in modifying seasonal succession, we sampled fortnightly, throughout three seasons, five nearby shallow soda lakes exposed to identical seasonal and meteorological changes. We characterised their microeukaryotic and bacterial communities by amplicon sequencing of the 16S and 18S rRNA gene, respectively. Biological interactions were inferred by analyses of synchronous and time-shifted interaction networks, and the keystone taxa of the communities were topologically identified. The lakes showed similar succession patterns during the study period with spring being characterised by the relevance of trophic interactions and a certain level of community stability followed by a more dynamic and variable summer-autumn period. Adaptation to general seasonal changes happened through shared core microbiome of the lakes. Stochastic events such as desiccation disrupted common network attributes and introduced shifts from the prevalent seasonal trajectory. Our results demonstrated that, despite being extreme and highly variable habitats, shallow soda lakes exhibit certain similarities in the seasonality of their planktonic communities, yet local stressors such as droughts instigate deviations from prevalent trends to a greater extent for microeukaryotic than for bacterial communities.", "doi": "10.1093/femsec/fiad095", "pmid": "37586889", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10449373"}, {"db": "pii", "key": "7243381"}], "notes": [], "created": "2023-11-29T11:26:09.024Z", "modified": "2024-01-16T13:48:32.450Z"}, {"entity": "publication", "iuid": "9343655379b04dd9a0b4d89466148dab", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9343655379b04dd9a0b4d89466148dab.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9343655379b04dd9a0b4d89466148dab"}}, "title": "Bacterial bioindicators enable biological status classification along the continental Danube river.", "authors": [{"family": "Fontaine", "given": "Laurent", "initials": "L"}, {"family": "Pin", "given": "Lorenzo", "initials": "L"}, {"family": "Savio", "given": "Domenico", "initials": "D"}, {"family": "Friberg", "given": "Nikolai", "initials": "N"}, {"family": "Kirschner", "given": "Alexander K T", "initials": "AKT"}, {"family": "Farnleitner", "given": "Andreas H", "initials": "AH"}, {"family": "Eiler", "given": "Alexander", "initials": "A", "orcid": "0000-0001-9916-9567", "researcher": {"href": "https://publications.scilifelab.se/researcher/e7286785c9334dcba90273b69f81c018.json"}}], "type": "journal article", "published": "2023-08-18", "journal": {"title": "Commun Biol", "issn": "2399-3642", "volume": "6", "issue": "1", "pages": "862", "issn-l": "2399-3642"}, "abstract": "Despite the importance of bacteria in aquatic ecosystems and their predictable diversity patterns across space and time, biomonitoring tools for status assessment relying on these organisms are widely lacking. This is partly due to insufficient data and models to identify reliable microbial predictors. Here, we show metabarcoding in combination with multivariate statistics and machine learning allows to identify bacterial bioindicators for existing biological status classification systems. Bacterial beta-diversity dynamics follow environmental gradients and the observed associations highlight potential bioindicators for ecological outcomes. Spatio-temporal links spanning the microbial communities along the river allow accurate prediction of downstream biological status from upstream information. Network analysis on amplicon sequence veariants identify as good indicators genera Fluviicola, Acinetobacter, Flavobacterium, and Rhodoluna, and reveal informational redundancy among taxa, which coincides with taxonomic relatedness. The redundancy among bacterial bioindicators reveals mutually exclusive taxa, which allow accurate biological status modeling using as few as 2-3 amplicon sequence variants. As such our models show that using a few bacterial amplicon sequence variants from globally distributed genera allows for biological status assessment along river systems.", "doi": "10.1038/s42003-023-05237-8", "pmid": "37596339", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s42003-023-05237-8"}, {"db": "pmc", "key": "PMC10439154"}], "notes": [], "created": "2023-08-21T05:58:55.824Z", "modified": "2023-08-21T05:58:55.835Z"}, {"entity": "publication", "iuid": "ec41cb3ea29c430eb8044c7b6d1c640b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ec41cb3ea29c430eb8044c7b6d1c640b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ec41cb3ea29c430eb8044c7b6d1c640b"}}, "title": "Environmental effects rather than relatedness determine gut microbiome similarity in a social mammal.", "authors": [{"family": "Bensch", "given": "Hanna M", "initials": "HM", "orcid": "0000-0002-8449-9843", "researcher": {"href": "https://publications.scilifelab.se/researcher/9a204f1b0fe34b8999893abe65fb3e8c.json"}}, {"family": "Lundin", "given": "Daniel", "initials": "D", "orcid": "0000-0002-8779-6464", "researcher": {"href": "https://publications.scilifelab.se/researcher/227cc90e084348a193fee05eb23a6bf3.json"}}, {"family": "Tolf", "given": "Conny", "initials": "C"}, {"family": "Waldenstr\u00f6m", "given": "Jonas", "initials": "J", "orcid": "0000-0002-1152-4235", "researcher": {"href": "https://publications.scilifelab.se/researcher/53013aa313214e26abdb18ea0199371f.json"}}, {"family": "Z\u00f6ttl", "given": "Markus", "initials": "M", "orcid": "0000-0002-5582-2306", "researcher": {"href": "https://publications.scilifelab.se/researcher/e262a41c07044bd88a4bd6f1dcc2f1eb.json"}}], "type": "journal article", "published": "2023-08-16", "journal": {"title": "J. Evol. Biol.", "issn": "1420-9101", "issn-l": "1010-061X"}, "abstract": "In social species, group members commonly show substantial similarity in gut microbiome composition. Such similarities have been hypothesized to arise either by shared environmental effects or by host relatedness. However, disentangling these factors is difficult, because group members are often related, and social groups typically share similar environmental conditions. In this study, we conducted a cross-foster experiment under controlled laboratory conditions in group-living Damaraland mole-rats (Fukomys damarensis) and used 16S amplicon sequencing to disentangle the effects of the environment and relatedness on gut microbiome similarity and diversity. Our results show that a shared environment is the main factor explaining gut microbiome similarity, overshadowing any effect of host relatedness. Together with studies in wild animal populations, our results suggest that among conspecifics environmental factors are more powerful drivers of gut microbiome composition similarity than host genetics.", "doi": "10.1111/jeb.14208", "pmid": "37584218", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [], "notes": [], "created": "2023-11-29T11:41:57.913Z", "modified": "2023-11-29T11:41:58.018Z"}, {"entity": "publication", "iuid": "3964f1e7f99c42f09a08ee5fd125ad18", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3964f1e7f99c42f09a08ee5fd125ad18.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3964f1e7f99c42f09a08ee5fd125ad18"}}, "title": "Feasibility to use whole-genome sequencing as a sole diagnostic method to detect genomic aberrations in pediatric B-cell acute lymphoblastic leukemia.", "authors": [{"family": "Rezayee", "given": "Fatemah", "initials": "F"}, {"family": "Eisfeldt", "given": "Jesper", "initials": "J"}, {"family": "Skaftason", "given": "Aron", "initials": "A"}, {"family": "\u00d6fverholm", "given": "Ingegerd", "initials": "I"}, {"family": "Sayyab", "given": "Shumaila", "initials": "S"}, {"family": "Syv\u00e4nen", "given": "Ann Christine", "initials": "AC"}, {"family": "Maqbool", "given": "Khurram", "initials": "K"}, {"family": "Lilljebj\u00f6rn", "given": "Henrik", "initials": "H"}, {"family": "Johansson", "given": "Bertil", "initials": "B"}, {"family": "Olsson-Arvidsson", "given": "Linda", "initials": "L"}, {"family": "Pietras", "given": "Christina Orsmark", "initials": "CO"}, {"family": "Staffas", "given": "Anna", "initials": "A"}, {"family": "Palmqvist", "given": "Lars", "initials": "L"}, {"family": "Fioretos", "given": "Thoas", "initials": "T"}, {"family": "Cavelier", "given": "Lucia", "initials": "L"}, {"family": "Fogelstrand", "given": "Linda", "initials": "L"}, {"family": "Nordlund", "given": "Jessica", "initials": "J"}, {"family": "Wirta", "given": "Valtteri", "initials": "V"}, {"family": "Rosenquist", "given": "Richard", "initials": "R"}, {"family": "Barbany", "given": "Gisela", "initials": "G"}], "type": "journal article", "published": "2023-08-14", "journal": {"title": "Front Oncol", "issn": "2234-943X", "issn-l": "2234-943X", "volume": "13", "issue": null, "pages": "1217712"}, "abstract": "The suitability of whole-genome sequencing (WGS) as the sole method to detect clinically relevant genomic aberrations in B-cell acute lymphoblastic leukemia (ALL) was investigated with the aim of replacing current diagnostic methods.\n\nFor this purpose, we assessed the analytical performance of 150 bp paired-end WGS (90x leukemia/30x germline). A set of 88 retrospective B-cell ALL samples were selected to represent established ALL subgroups as well as ALL lacking stratifying markers by standard-of-care (SoC), so-called B-other ALL.\n\nBoth the analysis of paired leukemia/germline (L/N)(n=64) as well as leukemia-only (L-only)(n=88) detected all types of aberrations mandatory in the current ALLTogether trial protocol, i.e., aneuploidies, structural variants, and focal copy-number aberrations. Moreover, comparison to SoC revealed 100% concordance and that all patients had been assigned to the correct genetic subgroup using both approaches. Notably, WGS could allocate 35 out of 39 B-other ALL samples to one of the emerging genetic subgroups considered in the most recent classifications of ALL. We further investigated the impact of high (90x; n=58) vs low (30x; n=30) coverage on the diagnostic yield and observed an equally perfect concordance with SoC; low coverage detected all relevant lesions.\n\nThe filtration of the WGS findings with a short list of genes recurrently rearranged in ALL was instrumental to extract the clinically relevant information efficiently. Nonetheless, the detection of DUX4 rearrangements required an additional customized analysis, due to multiple copies of this gene embedded in the highly repetitive D4Z4 region. We conclude that the diagnostic performance of WGS as the standalone method was remarkable and allowed detection of all clinically relevant genomic events in the diagnostic setting of B-cell ALL.", "doi": "10.3389/fonc.2023.1217712", "pmid": "37664045", "labels": {"Clinical Genomics Stockholm": "Service", "NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Clinical Genomics Gothenburg": "Collaborative", "Clinical Genomics": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC10470829"}], "notes": [], "created": "2023-11-22T21:44:19.108Z", "modified": "2024-11-20T20:05:01.286Z"}, {"entity": "publication", "iuid": "3bc1aebcc63f41edbfce850538cda6c4", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3bc1aebcc63f41edbfce850538cda6c4.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3bc1aebcc63f41edbfce850538cda6c4"}}, "title": "Genetic continuity, isolation, and gene flow in Stone Age Central and Eastern Europe.", "authors": [{"family": "Mattila", "given": "Tiina M", "initials": "TM", "orcid": "0000-0002-1298-7370", "researcher": {"href": "https://publications.scilifelab.se/researcher/0dbb4f417ab0440fb02a305aaf81b3d5.json"}}, {"family": "Svensson", "given": "Emma M", "initials": "EM"}, {"family": "Juras", "given": "Anna", "initials": "A", "orcid": "0000-0002-2585-127X", "researcher": {"href": "https://publications.scilifelab.se/researcher/21890fe291bb4e8e913c5eb5963bcdce.json"}}, {"family": "G\u00fcnther", "given": "Torsten", "initials": "T"}, {"family": "Kashuba", "given": "Natalija", "initials": "N", "orcid": "0000-0002-3744-4073", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a321904793d47399adc5f73b0f58dcc.json"}}, {"family": "Ala-Hulkko", "given": "Terhi", "initials": "T", "orcid": "0000-0002-0884-2152", "researcher": {"href": "https://publications.scilifelab.se/researcher/c9f4036f2bc54136a489b22aaba390d7.json"}}, {"family": "Chyle\u0144ski", "given": "Maciej", "initials": "M", "orcid": "0000-0003-1347-1904", "researcher": {"href": "https://publications.scilifelab.se/researcher/e211127b50ca4ed8ab6b2ae9bede0102.json"}}, {"family": "McKenna", "given": "James", "initials": "J"}, {"family": "Pospieszny", "given": "\u0141ukasz", "initials": "\u0141"}, {"family": "Constantinescu", "given": "Mihai", "initials": "M"}, {"family": "Rotea", "given": "Mihai", "initials": "M"}, {"family": "Palinca\u0219", "given": "Nona", "initials": "N", "orcid": "0000-0001-5308-4349", "researcher": {"href": "https://publications.scilifelab.se/researcher/f4275405ad5045da8909e05ac7fb9dd9.json"}}, {"family": "Wilk", "given": "Stanis\u0142aw", "initials": "S"}, {"family": "Czerniak", "given": "Lech", "initials": "L", "orcid": "0000-0002-0352-5385", "researcher": {"href": "https://publications.scilifelab.se/researcher/73f2691cdc7f424784c4a7d1dbb2957e.json"}}, {"family": "Kruk", "given": "Janusz", "initials": "J"}, {"family": "\u0141apo", "given": "Jerzy", "initials": "J"}, {"family": "Makarowicz", "given": "Przemys\u0142aw", "initials": "P", "orcid": "0000-0003-4452-7704", "researcher": {"href": "https://publications.scilifelab.se/researcher/035ae0d32cf649f6a82c6e4df78cc122.json"}}, {"family": "Potekhina", "given": "Inna", "initials": "I"}, {"family": "Soficaru", "given": "Andrei", "initials": "A"}, {"family": "Szmyt", "given": "Marzena", "initials": "M"}, {"family": "Szostek", "given": "Krzysztof", "initials": "K"}, {"family": "G\u00f6therstr\u00f6m", "given": "Anders", "initials": "A"}, {"family": "Stor\u00e5", "given": "Jan", "initials": "J"}, {"family": "Netea", "given": "Mihai G", "initials": "MG", "orcid": "0000-0003-2421-6052", "researcher": {"href": "https://publications.scilifelab.se/researcher/f0b25efbd9ee43e7a873baaaec4cf34c.json"}}, {"family": "Nikitin", "given": "Alexey G", "initials": "AG", "orcid": "0000-0002-3897-4607", "researcher": {"href": "https://publications.scilifelab.se/researcher/7f103c7d36c24ac981fbd8291fea853c.json"}}, {"family": "Persson", "given": "Per", "initials": "P", "orcid": "0009-0007-4490-2494", "researcher": {"href": "https://publications.scilifelab.se/researcher/178194b694e04e8d9520328ddda9bd11.json"}}, {"family": "Malmstr\u00f6m", "given": "Helena", "initials": "H", "orcid": "0000-0002-6456-8055", "researcher": {"href": "https://publications.scilifelab.se/researcher/3b3397b2842142bea34c222f6683c0eb.json"}}, {"family": "Jakobsson", "given": "Mattias", "initials": "M", "orcid": "0000-0001-7840-7853", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a4abe0fcb20492d9ec849c9fbf58a71.json"}}], "type": "journal article", "published": "2023-08-09", "journal": {"title": "Commun Biol", "issn": "2399-3642", "volume": "6", "issue": "1", "pages": "793", "issn-l": "2399-3642"}, "abstract": "The genomic landscape of Stone Age Europe was shaped by multiple migratory waves and population replacements, but different regions do not all show similar patterns. To refine our understanding of the population dynamics before and after the dawn of the Neolithic, we generated and analyzed genomic sequence data from human remains of 56 individuals from the Mesolithic, Neolithic, and Eneolithic across Central and Eastern Europe. We found that Mesolithic European populations formed a geographically widespread isolation-by-distance zone ranging from Central Europe to Siberia, which was already established 10,000 years ago. We found contrasting patterns of population continuity during the Neolithic transition: people around the lower Dnipro Valley region, Ukraine, showed continuity over 4000 years, from the Mesolithic to the end of the Neolithic, in contrast to almost all other parts of Europe where population turnover drove this cultural change, including vast areas of Central Europe and around the Danube River.", "doi": "10.1038/s42003-023-05131-3", "pmid": "37558731", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10412644"}, {"db": "pii", "key": "10.1038/s42003-023-05131-3"}], "notes": [], "created": "2023-08-14T06:19:02.423Z", "modified": "2024-01-16T13:48:32.510Z"}, {"entity": "publication", "iuid": "9390f83757d84114bb03a1e646722167", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9390f83757d84114bb03a1e646722167.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9390f83757d84114bb03a1e646722167"}}, "title": "DNA Methylation Signatures of Multiple Sclerosis Occur Independently of Known Genetic Risk and Are Primarily Attributed to B Cells and Monocytes.", "authors": [{"family": "Xavier", "given": "Alexandre", "initials": "A", "orcid": "0000-0002-6397-051X", "researcher": {"href": "https://publications.scilifelab.se/researcher/8894ebe0300644019b1608029fab4bbd.json"}}, {"family": "Maltby", "given": "Vicki E", "initials": "VE"}, {"family": "Ewing", "given": "Ewoud", "initials": "E", "orcid": "0000-0001-8644-366X", "researcher": {"href": "https://publications.scilifelab.se/researcher/aea9350a4f864d8e8781ab111b4f9273.json"}}, {"family": "Campagna", "given": "Maria Pia", "initials": "MP", "orcid": "0000-0001-8148-8228", "researcher": {"href": "https://publications.scilifelab.se/researcher/db0eb83d578341019f77e4c9b946b127.json"}}, {"family": "Burnard", "given": "Sean M", "initials": "SM", "orcid": "0000-0003-2149-3556", "researcher": {"href": "https://publications.scilifelab.se/researcher/9931628e8de440b8a76dbbadddaa0d67.json"}}, {"family": "Tegner", "given": "Jesper N", "initials": "JN"}, {"family": "Slee", "given": "Mark", "initials": "M", "orcid": "0000-0003-4323-2453", "researcher": {"href": "https://publications.scilifelab.se/researcher/a058e51f23ff477685966f04e57b10bc.json"}}, {"family": "Butzkueven", "given": "Helmut", "initials": "H", "orcid": "0000-0003-3940-8727", "researcher": {"href": "https://publications.scilifelab.se/researcher/56ccbf40dcc04d189a8789ec56f76644.json"}}, {"family": "Kockum", "given": "Ingrid", "initials": "I"}, {"family": "Kular", "given": "Lara", "initials": "L", "orcid": "0000-0002-2907-6071", "researcher": {"href": "https://publications.scilifelab.se/researcher/09563004a20543dc934dd4d3b1ceebd7.json"}}, {"family": "Jokubaitis", "given": "Vilija G", "initials": "VG", "orcid": "0000-0002-3942-4340", "researcher": {"href": "https://publications.scilifelab.se/researcher/1f672603d0824a428a280b352aa0ade7.json"}}, {"family": "Kilpatrick", "given": "Trevor", "initials": "T"}, {"family": "Alfredsson", "given": "Lars", "initials": "L", "orcid": "0000-0003-1688-6697", "researcher": {"href": "https://publications.scilifelab.se/researcher/6df230614a8a448e8607e03480169658.json"}}, {"family": "Jagodic", "given": "Maja", "initials": "M"}, {"family": "Ponsonby", "given": "Anne-Louise", "initials": "AL", "orcid": "0000-0002-6581-3657", "researcher": {"href": "https://publications.scilifelab.se/researcher/25b82fd1df8947ee96863dd6f09d7a3d.json"}}, {"family": "Taylor", "given": "Bruce V", "initials": "BV", "orcid": "0000-0003-2807-0070", "researcher": {"href": "https://publications.scilifelab.se/researcher/dda9895ba1d445dea2d0604e2e0bfff1.json"}}, {"family": "Scott", "given": "Rodney J", "initials": "RJ", "orcid": "0000-0001-7724-3404", "researcher": {"href": "https://publications.scilifelab.se/researcher/d7645133eea749cea02da335cec8f00e.json"}}, {"family": "Lea", "given": "Rodney A", "initials": "RA"}, {"family": "Lechner-Scott", "given": "Jeannette", "initials": "J"}], "type": "journal article", "published": "2023-08-08", "journal": {"title": "Int J Mol Sci", "issn": "1422-0067", "volume": "24", "issue": "16", "issn-l": null}, "abstract": "Epigenetic mechanisms can regulate how DNA is expressed independently of sequence and are known to be associated with various diseases. Among those epigenetic mechanisms, DNA methylation (DNAm) is influenced by genotype and the environment, making it an important molecular interface for studying disease etiology and progression. In this study, we examined the whole blood DNA methylation profiles of a large group of people with (pw) multiple sclerosis (MS) compared to those of controls. We reveal that methylation differences in pwMS occur independently of known genetic risk loci and show that they more strongly differentiate disease (AUC = 0.85, 95% CI 0.82-0.89, p = 1.22 \u00d7 10-29) than known genetic risk loci (AUC = 0.72, 95% CI: 0.66-0.76, p = 9.07 \u00d7 10-17). We also show that methylation differences in MS occur predominantly in B cells and monocytes and indicate the involvement of cell-specific biological pathways. Overall, this study comprehensively characterizes the immune cell-specific epigenetic architecture of MS.", "doi": "10.3390/ijms241612576", "pmid": "37628757", "labels": {"NGI SNP genotyping": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10454485"}, {"db": "pii", "key": "ijms241612576"}], "notes": [], "created": "2023-11-29T11:14:24.111Z", "modified": "2023-11-29T11:14:24.426Z"}, {"entity": "publication", "iuid": "070b694696014ed78f1f2be943ae1025", "links": {"self": {"href": "https://publications.scilifelab.se/publication/070b694696014ed78f1f2be943ae1025.json"}, "display": {"href": "https://publications.scilifelab.se/publication/070b694696014ed78f1f2be943ae1025"}}, "title": "Relation between HLA and copy number variation of steroid 21-hydroxylase in a Swedish cohort of patients with autoimmune Addison's disease.", "authors": [{"family": "Lundtoft", "given": "Christian", "initials": "C", "orcid": "0000-0001-5872-4253", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a05532d3aad4e2dbe00a4724e8dddd8.json"}}, {"family": "Eriksson", "given": "Daniel", "initials": "D"}, {"family": "Bianchi", "given": "Matteo", "initials": "M"}, {"family": "Aranda-Guill\u00e9n", "given": "Maribel", "initials": "M"}, {"family": "Landegren", "given": "Nils", "initials": "N"}, {"family": "Rantap\u00e4\u00e4-Dahlqvist", "given": "Solbritt", "initials": "S", "orcid": "0000-0001-8259-3863", "researcher": {"href": "https://publications.scilifelab.se/researcher/dfca4bfdcf3946fda64397d3b7debc59.json"}}, {"family": "S\u00f6derkvist", "given": "Peter", "initials": "P"}, {"family": "Meadows", "given": "Jennifer R S", "initials": "JRS"}, {"family": "Consortium", "given": "DISSECT", "initials": "D"}, {"family": ",,", "given": "", "initials": ""}, {"family": "Consortium", "given": "ImmunoArray", "initials": "I"}, {"family": ",,", "given": "", "initials": ""}, {"family": "Group", "given": "Swedish Addison Registry Study", "initials": "SARS"}, {"family": ",,", "given": "", "initials": ""}, {"family": "Bensing", "given": "Sophie", "initials": "S", "orcid": "0000-0002-9193-2860", "researcher": {"href": "https://publications.scilifelab.se/researcher/acae2ad8ca844588b2b850c863034b7b.json"}}, {"family": "Pielberg", "given": "Gerli Rosengren", "initials": "GR"}, {"family": "Lindblad-Toh", "given": "Kerstin", "initials": "K"}, {"family": "R\u00f6nnblom", "given": "Lars", "initials": "L"}, {"family": "K\u00e4mpe", "given": "Olle", "initials": "O", "orcid": "0000-0001-6091-9914", "researcher": {"href": "https://publications.scilifelab.se/researcher/2c547dc809a14cdaa47b623cf638162b.json"}}], "type": "journal article", "published": "2023-08-02", "journal": {"title": "Eur. J. Endocrinol.", "issn": "1479-683X", "issn-l": "0804-4643", "volume": "189", "issue": "2", "pages": "235-241"}, "abstract": "Autoantibodies against the adrenal enzyme 21-hydroxylase is a hallmark manifestation in autoimmune Addison's disease (AAD). Steroid 21-hydroxylase is encoded by CYP21A2, which is located in the human leucocyte antigen (HLA) region together with the highly similar pseudogene CYP21A1P. A high level of copy number variation is seen for the 2 genes, and therefore, we asked whether genetic variation of the CYP21 genes is associated with AAD.\r\n\r\nCase-control study on patients with AAD and healthy controls.\r\n\r\nUsing next-generation DNA sequencing, we estimated the copy number of CYP21A2 and CYP21A1P, together with HLA alleles, in 479 Swedish patients with AAD and autoantibodies against 21-hydroxylase and in 1393 healthy controls.\r\n\r\nWith 95% of individuals carrying 2 functional 21-hydroxylase genes, no difference in CYP21A2 copy number was found when comparing patients and controls. In contrast, we discovered a lower copy number of the pseudogene CYP21A1P among AAD patients (P = 5 \u00d7 10-44), together with associations of additional nucleotide variants, in the CYP21 region. However, the strongest association was found for HLA-DQB1*02:01 (P = 9 \u00d7 10-63), which, in combination with the DRB1*04:04-DQB1*03:02 haplotype, imposed the greatest risk of AAD.\r\n\r\nWe identified strong associations between copy number variants in the CYP21 region and risk of AAD, although these associations most likely are due to linkage disequilibrium with disease-associated HLA class II alleles.", "doi": "10.1093/ejendo/lvad102", "pmid": "37553728", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "NGI SNP genotyping": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "7239340"}], "notes": [], "created": "2023-11-27T21:51:56.107Z", "modified": "2024-01-16T13:48:32.542Z"}, {"entity": "publication", "iuid": "f33c20d74f204c0e85888aad80e6bae6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f33c20d74f204c0e85888aad80e6bae6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f33c20d74f204c0e85888aad80e6bae6"}}, "title": "Genetic insights into resting heart rate and its role in cardiovascular disease.", "authors": [{"family": "van de Vegte", "given": "Yordi J", "initials": "YJ", "orcid": "0000-0002-6689-0144", "researcher": {"href": "https://publications.scilifelab.se/researcher/9edbd70a05e140da86f8a115a8cfa913.json"}}, {"family": "Eppinga", "given": "Ruben N", "initials": "RN"}, {"family": "van der Ende", "given": "M Yldau", "initials": "MY"}, {"family": "Hagemeijer", "given": "Yanick P", "initials": "YP", "orcid": "0000-0001-6036-3741", "researcher": {"href": "https://publications.scilifelab.se/researcher/f3c9fe93b0e04102b0298e2d08a7503c.json"}}, {"family": "Mahendran", "given": "Yuvaraj", "initials": "Y"}, {"family": "Salfati", "given": "Elias", "initials": "E"}, {"family": "Smith", "given": "Albert 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"https://publications.scilifelab.se/researcher/4a0f019dcb7a453a84480953a5514dd5.json"}}, {"family": "Ohlsson", "given": "Claes", "initials": "C", "orcid": "0000-0002-9633-2805", "researcher": {"href": "https://publications.scilifelab.se/researcher/995dac358caa4a169fc889b7a3eef44a.json"}}, {"family": "Porteous", "given": "David J", "initials": "DJ", "orcid": "0000-0003-1249-6106", "researcher": {"href": "https://publications.scilifelab.se/researcher/b6e3ae11c02e4cb89e638e1e5ae0f50a.json"}}, {"family": "Eriksson", "given": "Johan G", "initials": "JG"}, {"family": "Bouchard", "given": "Claude", "initials": "C", "orcid": "0000-0002-0048-491X", "researcher": {"href": "https://publications.scilifelab.se/researcher/516e35bcb46449469c44596ac2c260b8.json"}}, {"family": "Moebus", "given": "Susanne", "initials": "S", "orcid": "0000-0002-0072-5410", "researcher": {"href": "https://publications.scilifelab.se/researcher/3897666b2c0847e4a9208b62d48a3a72.json"}}, {"family": "Kraft", "given": "Peter", "initials": "P", "orcid": "0000-0002-4472-8103", "researcher": {"href": "https://publications.scilifelab.se/researcher/5af0cbcc64e54601944c6e881d8ce4d9.json"}}, {"family": "Weir", "given": "David R", "initials": "DR", "orcid": "0000-0002-1661-2402", "researcher": {"href": "https://publications.scilifelab.se/researcher/f90b7cfe829845fb8cbea9558a5c82a7.json"}}, {"family": "Cusi", "given": "Daniele", "initials": "D"}, {"family": "Ferrucci", "given": "Luigi", "initials": "L", "orcid": "0000-0002-6273-1613", "researcher": {"href": "https://publications.scilifelab.se/researcher/8d07f761257c4e59b462acf360461fe3.json"}}, {"family": "Ulivi", "given": "Sheila", "initials": "S"}, {"family": "Girotto", "given": "Giorgia", "initials": "G", "orcid": "0000-0003-4507-6589", "researcher": {"href": "https://publications.scilifelab.se/researcher/1bc5f25ecc414d5d9e4855217c1da506.json"}}, {"family": "Correa", "given": "Adolfo", "initials": "A", "orcid": "0000-0002-9501-600X", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a12b716143c4156b060f87d5373b87d.json"}}, {"family": "K\u00e4\u00e4b", "given": "Stefan", "initials": "S", "orcid": "0000-0001-8824-3581", "researcher": {"href": "https://publications.scilifelab.se/researcher/e32358c306304e359aa5df0ab67ee31c.json"}}, {"family": "Peters", "given": "Annette", "initials": "A", "orcid": "0000-0001-6645-0985", "researcher": {"href": "https://publications.scilifelab.se/researcher/05465e52a0f6412e81752d2249af30de.json"}}, {"family": "Chambers", "given": "John C", "initials": "JC"}, {"family": "Kooner", "given": "Jaspal S", "initials": "JS", "orcid": "0000-0003-2086-4837", "researcher": {"href": "https://publications.scilifelab.se/researcher/73c5749dbce143f3aaf7e80b89ec9dd6.json"}}, {"family": "M\u00e4rz", "given": "Winfried", "initials": "W"}, {"family": "Rotter", "given": "Jerome I", "initials": "JI", "orcid": "0000-0001-7191-1723", "researcher": {"href": "https://publications.scilifelab.se/researcher/7e9bdbf58ae94fc8b455bbbcbcaa50ce.json"}}, {"family": "Hicks", "given": "Andrew A", "initials": "AA", "orcid": "0000-0001-6320-0411", "researcher": {"href": "https://publications.scilifelab.se/researcher/a679db3cfdb6408b8f1a009534d7b902.json"}}, {"family": "Smith", "given": "J Gustav", "initials": "JG"}, {"family": "Kiemeney", "given": "Lambertus A L M", "initials": "LALM", "orcid": "0000-0002-2368-1326", "researcher": {"href": "https://publications.scilifelab.se/researcher/b174fc0d7ae44de6bba97a2f816ba695.json"}}, {"family": "Mook-Kanamori", "given": "Dennis O", "initials": "DO"}, {"family": "Penninx", "given": "Brenda W J H", "initials": "BWJH"}, {"family": "Gyllensten", "given": "Ulf", "initials": "U", "orcid": "0000-0002-6316-3355", "researcher": {"href": "https://publications.scilifelab.se/researcher/e8739f0f42c44019ab88a49db350a4f2.json"}}, {"family": "Wilson", "given": "James F", "initials": "JF", "orcid": "0000-0001-5751-9178", "researcher": {"href": "https://publications.scilifelab.se/researcher/b39e6e0f7210494cb4f80be0f7413b6f.json"}}, {"family": "Burgess", "given": "Stephen", "initials": "S", "orcid": "0000-0001-5365-8760", "researcher": {"href": "https://publications.scilifelab.se/researcher/6fd2dcaf4dbb4e4c91c2af460b8fa98f.json"}}, {"family": "Sundstr\u00f6m", "given": "Johan", "initials": "J", "orcid": "0000-0003-2247-8454", "researcher": {"href": "https://publications.scilifelab.se/researcher/91a40d3c138d43f2b0d38f66be4b71c7.json"}}, {"family": "Lieb", "given": "Wolfgang", "initials": "W", "orcid": "0000-0003-2544-4460", "researcher": {"href": "https://publications.scilifelab.se/researcher/b6b229457c2c4b25ae9c7d2cf029b82b.json"}}, {"family": "Jukema", "given": "J Wouter", "initials": "JW", "orcid": "0000-0002-3246-8359", "researcher": {"href": "https://publications.scilifelab.se/researcher/0479b794031d4df7bed96340b3470c19.json"}}, {"family": "Eijgelsheim", "given": "Mark", "initials": "M"}, {"family": "Lakatta", "given": "Edward L M", "initials": "ELM", "orcid": "0000-0002-4772-0035", "researcher": {"href": "https://publications.scilifelab.se/researcher/bc797241e3fa45d7b9d8438568414f2a.json"}}, {"family": "Cheng", "given": "Ching-Yu", "initials": "C"}, {"family": "D\u00f6rr", "given": "Marcus", "initials": "M", "orcid": "0000-0001-7471-475X", "researcher": {"href": "https://publications.scilifelab.se/researcher/346fa1fbeb2e474b94f189d52d7cfb1c.json"}}, {"family": "Wong", "given": "Tien-Yin", "initials": "T"}, {"family": "Sabanayagam", "given": "Charumathi", "initials": "C", "orcid": "0000-0002-4042-4719", "researcher": {"href": "https://publications.scilifelab.se/researcher/a5ac2397f6b14194949f4dbb92a21eba.json"}}, {"family": "Oldehinkel", "given": "Albertine J", "initials": "AJ", "orcid": "0000-0003-3925-3913", "researcher": {"href": "https://publications.scilifelab.se/researcher/65ee5f9938f547bcbe51cbaf5fd7a9ba.json"}}, {"family": "Riese", "given": "Harriette", "initials": "H"}, {"family": "Lehtim\u00e4ki", "given": "Terho", "initials": "T", "orcid": "0000-0002-2555-4427", "researcher": {"href": "https://publications.scilifelab.se/researcher/03ed59707dae4c8fb9e63ac1f7c398e3.json"}}, {"family": "Verweij", "given": "Niek", "initials": "N"}, {"family": "van der Harst", "given": "Pim", "initials": "P"}], "type": "meta-analysis", "published": "2023-08-02", "journal": {"title": "Nat Commun", "issn": "2041-1723", "issn-l": "2041-1723", "volume": "14", "issue": "1", "pages": "4646"}, "abstract": "Resting heart rate is associated with cardiovascular diseases and mortality in observational and Mendelian randomization studies. The aims of this study are to extend the number of resting heart rate associated genetic variants and to obtain further insights in resting heart rate biology and its clinical consequences. A genome-wide meta-analysis of 100 studies in up to 835,465 individuals reveals 493 independent genetic variants in 352 loci, including 68 genetic variants outside previously identified resting heart rate associated loci. We prioritize 670 genes and in silico annotations point to their enrichment in cardiomyocytes and provide insights in their ECG signature. Two-sample Mendelian randomization analyses indicate that higher genetically predicted resting heart rate increases risk of dilated cardiomyopathy, but decreases risk of developing atrial fibrillation, ischemic stroke, and cardio-embolic stroke. We do not find evidence for a linear or non-linear genetic association between resting heart rate and all-cause mortality in contrast to our previous Mendelian randomization study. Systematic alteration of key differences between the current and previous Mendelian randomization study indicates that the most likely cause of the discrepancy between these studies arises from false positive findings in previous one-sample MR analyses caused by weak-instrument bias at lower P-value thresholds. The results extend our understanding of resting heart rate biology and give additional insights in its role in cardiovascular disease development.", "doi": "10.1038/s41467-023-39521-2", "pmid": "37532724", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "NGI SNP genotyping": "Service", "Clinical Genomics Gothenburg": "Collaborative", "Clinical Genomics": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC10397318"}, {"db": "pii", "key": "10.1038/s41467-023-39521-2"}], "notes": [], "created": "2023-08-14T06:18:27.304Z", "modified": "2023-11-30T22:39:21.180Z"}, {"entity": "publication", "iuid": "6fac894c455046668ab3f18eed8a7f8d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6fac894c455046668ab3f18eed8a7f8d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6fac894c455046668ab3f18eed8a7f8d"}}, "title": "Somatic Exonic Deletions in RUNX1 Constitutes a Novel Recurrent Genomic Abnormality in Acute Myeloid Leukemia.", "authors": [{"family": "Eriksson", "given": "Anna", "initials": "A", "orcid": "0000-0002-8853-1863", "researcher": {"href": "https://publications.scilifelab.se/researcher/53cfc6bb334e455d9f64172ff43e3428.json"}}, {"family": "Engvall", "given": "Marie", "initials": "M", "orcid": "0000-0002-7394-9191", "researcher": {"href": "https://publications.scilifelab.se/researcher/0be7a9a5a518448ba7afb6f7a2cb3ca1.json"}}, {"family": "Mathot", "given": "Lucy", "initials": "L", "orcid": "0000-0002-2990-2038", "researcher": {"href": "https://publications.scilifelab.se/researcher/c9f3bfe35ddf41e5beb4312d3408a7ea.json"}}, {"family": "\u00d6sterroos", "given": "Albin", "initials": "A", "orcid": "0000-0001-8749-7299", "researcher": {"href": "https://publications.scilifelab.se/researcher/47a3ea9e722b4c72a7f00a61b5c9fe0a.json"}}, {"family": "Rippin", "given": "Martin", "initials": "M", "orcid": "0000-0003-4362-0122", "researcher": {"href": "https://publications.scilifelab.se/researcher/9b30009265224c56b99e1afd024b5240.json"}}, {"family": "Cavelier", "given": "Lucia", "initials": "L", "orcid": "0009-0003-8195-370X", "researcher": {"href": "https://publications.scilifelab.se/researcher/f01226edb140436da0c9d166c1f5fe51.json"}}, {"family": "Ladenvall", "given": "Claes", "initials": "C", "orcid": "0000-0002-7501-6598", "researcher": {"href": "https://publications.scilifelab.se/researcher/4c5c362dc308476195eb55d2e588ba60.json"}}, {"family": "Baliakas", "given": "Panagiotis", "initials": "P", "orcid": "0000-0002-5634-7156", "researcher": {"href": "https://publications.scilifelab.se/researcher/17370bd509dc4b1081af5aed9e5117c7.json"}}], "type": "research support, non-u.s. gov't", "published": "2023-08-01", "journal": {"title": "Clin. Cancer Res.", "issn": "1557-3265", "issn-l": "1078-0432", "volume": "29", "issue": "15", "pages": "2826-2834"}, "abstract": "In acute myeloid leukemia (AML), somatic mutations (commonly missense, nonsense, and frameshift indels) in RUNX1 are associated with a dismal clinical outcome. Inherited RUNX1 mutations cause familial platelet disorder. As approximately 5%-10% of germline RUNX1 mutations are large exonic deletions, we hypothesized that such exonic RUNX1 aberrations may also be acquired during the development of AML.\n\nSixty patients with well-characterized AML were analyzed with multiplex ligation-dependent probe amplification (n = 60), microarray (n = 11), and/or whole-genome sequencing (n = 8).\n\nIn total, 25 (42% of the cohort) RUNX1-aberrant patients (defined by the presence of classical mutations and/or exonic deletions) were identified. Sixteen patients (27%) carried only exonic deletions, 5 (8%) carried classical mutations, and 4 (7%) carried both exonic deletions and mutations. No significant difference was observed between patients with classical RUNX1 mutations and RUNX1 exonic deletions in median overall survival (OS, 53.1 vs. 38.8 months, respectively, P = 0.63). When applying the European Leukemia Net (ELN) classification including the RUNX1-aberrant group, 20% of the patients initially stratified as intermediate-risk (5% of the whole cohort) were reassigned to the high-risk group, which improved the performance of ELN classification regarding OS between intermediate- and high-risk groups (18.9 vs. 9.6 months, P = 0.09).\n\nSomatic RUNX1 exonic deletions constitute a novel recurrent aberration in AML. Our findings have important clinical implications regarding AML classification, risk stratification, and treatment decision. Moreover, they argue in favor of further investigating such genomic aberrations not only in RUNX1 but also in other genes implicated in cancer biology and management. See related commentary by Chakraborty and Stengel, p. 2742.", "doi": "10.1158/1078-0432.CCR-23-0122", "pmid": "37022349", "labels": {"Clinical Genomics Uppsala": "Collaborative", "NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service", "Clinical Genomics": "Collaborative"}, "xrefs": [{"db": "pii", "key": "725154"}], "notes": [], "created": "2023-11-29T08:28:02.202Z", "modified": "2024-01-16T13:48:32.633Z"}, {"entity": "publication", "iuid": "cac2b2a5dca44746b91a68788dce04df", "links": {"self": {"href": "https://publications.scilifelab.se/publication/cac2b2a5dca44746b91a68788dce04df.json"}, "display": {"href": "https://publications.scilifelab.se/publication/cac2b2a5dca44746b91a68788dce04df"}}, "title": "Patrilocality and hunter-gatherer-related ancestry of populations in East-Central Europe during the Middle Bronze Age.", "authors": [{"family": "Chyle\u0144ski", "given": "Maciej", "initials": "M", "orcid": "0000-0003-1347-1904", "researcher": {"href": "https://publications.scilifelab.se/researcher/e211127b50ca4ed8ab6b2ae9bede0102.json"}}, {"family": "Makarowicz", "given": "Przemys\u0142aw", "initials": "P", "orcid": "0000-0003-4452-7704", "researcher": {"href": "https://publications.scilifelab.se/researcher/035ae0d32cf649f6a82c6e4df78cc122.json"}}, {"family": "Juras", "given": "Anna", "initials": "A"}, {"family": "Krzewi\u0144ska", "given": "Maja", "initials": "M", "orcid": "0000-0002-6702-8724", "researcher": {"href": "https://publications.scilifelab.se/researcher/c483febf380c4d9db683e5a73ba89816.json"}}, {"family": "Pospieszny", "given": "\u0141ukasz", "initials": "\u0141"}, {"family": "Ehler", "given": "Edvard", "initials": "E", "orcid": "0000-0003-1774-0091", "researcher": {"href": "https://publications.scilifelab.se/researcher/6d5e30a4e46e47d8b800d5242e23d7de.json"}}, {"family": "Breszka", "given": "Agnieszka", "initials": "A"}, {"family": "G\u00f3rski", "given": "Jacek", "initials": "J"}, {"family": "Taras", "given": "Halina", "initials": "H"}, {"family": "Szczepanek", "given": "Anita", "initials": "A"}, {"family": "Pola\u0144ska", "given": "Marta", "initials": "M"}, {"family": "W\u0142odarczak", "given": "Piotr", "initials": "P", "orcid": "0000-0003-0359-7386", "researcher": {"href": "https://publications.scilifelab.se/researcher/a4581e4213be44969693180b26b3f263.json"}}, {"family": "Lasota-Ku\u015b", "given": "Anna", "initials": "A", "orcid": "0000-0002-0603-846X", "researcher": {"href": "https://publications.scilifelab.se/researcher/8716e836f3894e28bee1bcacffb7245a.json"}}, {"family": "W\u00f3jcik", "given": "Irena", "initials": "I"}, {"family": "Romaniszyn", "given": "Jan", "initials": "J"}, {"family": "Szmyt", "given": "Marzena", "initials": "M"}, {"family": "Ko\u015bko", "given": "Aleksander", "initials": "A"}, {"family": "Ignaczak", "given": "Marcin", "initials": "M"}, {"family": "Sadowski", "given": "Sylwester", "initials": "S"}, {"family": "Matoga", "given": "Andrzej", "initials": "A"}, {"family": "Grossman", "given": "Anna", "initials": "A"}, {"family": "Ilchyshyn", "given": "Vasyl", "initials": "V"}, {"family": "Yahodinska", "given": "Maryna O", "initials": "MO"}, {"family": "Roma\u0144ska", "given": "Adriana", "initials": "A"}, {"family": "Tunia", "given": "Krzysztof", "initials": "K"}, {"family": "Przyby\u0142a", "given": "Marcin", "initials": "M"}, {"family": "Grygiel", "given": "Ryszard", "initials": "R"}, {"family": "Szostek", "given": "Krzysztof", "initials": "K"}, {"family": "Dabert", "given": "Miroslawa", "initials": "M"}, {"family": "G\u00f6therstr\u00f6m", "given": "Anders", "initials": "A"}, {"family": "Jakobsson", "given": "Mattias", "initials": "M", "orcid": "0000-0001-7840-7853", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a4abe0fcb20492d9ec849c9fbf58a71.json"}}, {"family": "Malmstr\u00f6m", "given": "Helena", "initials": "H", "orcid": "0000-0002-6456-8055", "researcher": {"href": "https://publications.scilifelab.se/researcher/3b3397b2842142bea34c222f6683c0eb.json"}}], "type": "historical article", "published": "2023-08-01", "journal": {"title": "Nat Commun", "issn": "2041-1723", "issn-l": "2041-1723", "volume": "14", "issue": "1", "pages": "4395"}, "abstract": "The demographic history of East-Central Europe after the Neolithic period remains poorly explored, despite this region being on the confluence of various ecological zones and cultural entities. Here, the descendants of societies associated with steppe pastoralists form Early Bronze Age were followed by Middle Bronze Age populations displaying unique characteristics. Particularly, the predominance of collective burials, the scale of which, was previously seen only in the Neolithic. The extent to which this re-emergence of older traditions is a result of genetic shift or social changes in the MBA is a subject of debate. Here by analysing 91 newly generated genomes from Bronze Age individuals from present Poland and Ukraine, we discovered that Middle Bronze Age populations were formed by an additional admixture event involving a population with relatively high proportions of genetic component associated with European hunter-gatherers and that their social structure was based on, primarily patrilocal, multigenerational kin-groups.", "doi": "10.1038/s41467-023-40072-9", "pmid": "37528090", "labels": {"NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10393988"}, {"db": "pii", "key": "10.1038/s41467-023-40072-9"}], "notes": [], "created": "2023-10-19T12:43:53.699Z", "modified": "2024-01-16T13:48:32.641Z"}, {"entity": "publication", "iuid": "45b263a5d46c47de9e46a6d662722b6c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/45b263a5d46c47de9e46a6d662722b6c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/45b263a5d46c47de9e46a6d662722b6c"}}, "title": "Examining neurodevelopmental problems in 15q11.2 (BP1-BP2) copy number variation carriers at ages 9/12 and 18 in a Swedish twin sample.", "authors": [{"family": "Jonsson", "given": "Lina", "initials": "L", "orcid": "0000-0002-3175-103X", "researcher": {"href": "https://publications.scilifelab.se/researcher/f251f15f93bb4aaa8a4e858cdb7d6d65.json"}}, {"family": "Martin", "given": "Joanna", "initials": "J"}, {"family": "Lichtenstein", "given": "Paul", "initials": "P"}, {"family": "Magnusson", "given": "Patrik K E", "initials": "PKE"}, {"family": "Lundstr\u00f6m", "given": "Sebastian", "initials": "S"}, {"family": "Westberg", "given": "Lars", "initials": "L"}, {"family": "Tammimies", "given": "Kristiina", "initials": "K", "orcid": "0000-0002-8324-4697", "researcher": {"href": "https://publications.scilifelab.se/researcher/ba19ec07147743c6942ea10c9a92482a.json"}}], "type": "twin study", "published": "2023-08-00", "journal": {"title": "Mol Genet Genomic Med", "issn": "2324-9269", "issn-l": "2324-9269", "volume": "11", "issue": "8", "pages": "e2191"}, "abstract": "Several copy number variations (CNVs) are associated with increased risk for neurodevelopmental and psychiatric disorders. The CNV 15q11.2 (BP1-BP2) deletion has been associated with learning difficulties, attention deficit hyperactivity disorder (ADHD), epilepsy, and brain morphology; however, many carriers present mild or no symptoms. Carrying the reciprocal duplication does not seem to confer risk for these disorders or traits. Our aim was to examine the impact of carrying either 15q11.2 deletion and reciprocal duplication on neurodevelopmental problems in a population-based sample of children.\n\nTwins with genotype and phenotype information in the Child and Adolescent Twin Study in Sweden (CATSS) were included (N = 12,040). We included measures of neurodevelopmental problems (NDPs), including learning problems, from the questionnaire Autism-Tics, ADHD, and other Comorbidities inventory (A-TAC) at age 9/12, ADHD and autism spectrum disorder (ASD) questionnaires at age 18, as well as information about lifetime psychiatric diagnoses and epileptic seizures. We tested the association between these phenotypic measurements and carrying the 15q11.2 deletion, the reciprocal duplication, and other CNVs with previously reported strong associations with neurodevelopmental and psychiatric disorders (i.e., psychiatric CNVs).\n\nWe identified 57 carriers of the 15q11.2 deletion, 75 carriers of the reciprocal duplication, and 67 carriers of other psychiatric CNVs. We did not find an increased risk for NDPs or psychiatric diagnoses in the 15q11.2 deletion carriers. For 15q11.2 duplication carriers, we found an increased risk for math learning problems and fewer self-reported ADHD symptoms at age 18 but not for other NDPs. In line with previous studies, we found an increased risk of NDPs and other evaluated phenotypes in carriers of psychiatric CNVs.\n\nOur results support previous findings that carrying 15q11.2 deletion does not have a large effect on NDPs in children.", "doi": "10.1002/mgg3.2191", "pmid": "37156729", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI SNP genotyping": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10422071"}], "notes": [], "created": "2023-05-15T11:41:50.020Z", "modified": "2024-01-16T13:48:32.763Z"}, {"entity": "publication", "iuid": "eb2054fcd72f4e85a7d459c134350840", "links": {"self": {"href": "https://publications.scilifelab.se/publication/eb2054fcd72f4e85a7d459c134350840.json"}, "display": {"href": "https://publications.scilifelab.se/publication/eb2054fcd72f4e85a7d459c134350840"}}, "title": "Clones on the run: The genomics of a recently expanded partially clonal species.", "authors": [{"family": "Pereyra", "given": "Ricardo T", "initials": "RT"}, {"family": "Rafajlovi\u0107", "given": "Marina", "initials": "M"}, {"family": "De Wit", "given": "Pierre", "initials": "P", "orcid": "0000-0003-4709-3438", "researcher": {"href": "https://publications.scilifelab.se/researcher/95b69d4724ce4b69819c0a1578cd56eb.json"}}, {"family": "Pinder", "given": "Matthew", "initials": "M"}, {"family": "Kinnby", "given": "Alexandra", "initials": "A"}, {"family": "T\u00f6pel", "given": "Mats", "initials": "M"}, {"family": "Johannesson", "given": "Kerstin", "initials": "K", "orcid": "0000-0003-0176-7986", "researcher": {"href": "https://publications.scilifelab.se/researcher/a376951d80cd405183f4ff8606df8bbc.json"}}], "type": "journal article", "published": "2023-08-00", "journal": {"title": "Mol. Ecol.", "issn": "1365-294X", "volume": "32", "issue": "15", "pages": "4209-4223", "issn-l": "0962-1083"}, "abstract": "Why species that in their core areas mainly reproduce sexually become enriched with clones in marginal populations (\"geographic parthenogenesis\") remains unclear. Earlier hypotheses have emphasized that selection might promote clonality because it protects locally adapted genotypes. On the other hand, it also hampers recombination and adaptation to changing conditions. The aim of the present study was to investigate the early stages of range expansion in a partially clonal species and what drives an increase in cloning during such expansion. We used genome-wide sequencing to investigate the origin and evolution of large clones formed in a macroalgal species (Fucus vesiculosus) during a recent expansion into the postglacial Baltic Sea. We found low but persistent clonality in core populations, while at range margins, large dominant clonal lineages had evolved repeatedly from different sexual populations. A range expansion model showed that even when asexual recruitment is less favourable than sexual recruitment in core populations, repeated bottlenecks at the expansion front can establish a genetically eroded clonal wave that spreads ahead of a sexual wave into the new area. Genetic variation decreases by drift following repeated bottlenecks at the expansion front. This results in the emerging clones having low expected heterozygosity, which corroborated our empirical observations. We conclude that Baker's Law (clones being favoured by uniparental reproductive assurance in new areas) can play an important role during range expansion in partially clonal species, resulting in a complex spatiotemporal mosaic of clonal and sexual lineages that might persist during thousands of generations.", "doi": "10.1111/mec.16996", "pmid": "37199478", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [], "notes": [], "created": "2023-11-29T09:04:27.425Z", "modified": "2023-11-29T09:04:27.440Z"}, {"entity": "publication", "iuid": "1d3400d45b8b493d905352f554009969", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1d3400d45b8b493d905352f554009969.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1d3400d45b8b493d905352f554009969"}}, "title": "Characterisation of a low methane emission rice cultivar suitable for cultivation in high latitude light and temperature conditions.", "authors": [{"family": "Hu", "given": "Jia", "initials": "J", "orcid": "0000-0002-5829-2638", "researcher": {"href": "https://publications.scilifelab.se/researcher/e3313b4e4add403ea9242b01eef55796.json"}}, {"family": "Bettembourg", "given": "Mathilde", "initials": "M"}, {"family": "Moreno", "given": "Silvana", "initials": "S"}, {"family": "Zhang", "given": "Ai", "initials": "A"}, {"family": "Schn\u00fcrer", "given": "Anna", "initials": "A"}, {"family": "Sun", "given": "Chuanxin", "initials": "C"}, {"family": "Sundstr\u00f6m", "given": "Jens", "initials": "J"}, {"family": "Jin", "given": "Yunkai", "initials": "Y"}], "type": "journal article", "published": "2023-08-00", "journal": {"title": "Environ Sci Pollut Res", "issn": "1614-7499", "issn-l": "0944-1344", "volume": "30", "issue": "40", "pages": "92950-92962"}, "abstract": "Rice cultivation on paddy soil is commonly associated with emissions of methane, a greenhouse gas, but rice varieties may differ in their actual level of emissions. This study analysed methane emissions associated with 22 distinct rice genotypes, using gas chromatography, and identified the cultivar Heijing 5 from northern China as a potential low-methane rice variety. To confirm this and to examine whether Heijing 5 can perform similarly at higher latitudes, Heijing 5 was cultivated in field trials in China (lat. 32\u00b0 N) and Sweden (lat. 59\u00b0 N) where (i) methane emissions were measured, (ii) methanogen abundance in the rhizosphere was determined using quantitative PCR, and (iii) the concentrations of nutrients in water and of heavy metals in rice grain and paddy soil were analysed. The results demonstrated that the low-methane rice cultivar Heijing 5 can successfully complete an entire growth period at high-latitude locations such as central Sweden. Massively parallel sequencing of mRNAs identified candidate genes involved in day length and cold acclimatisation. Cultivation of Heijing 5 in central Sweden was also associated with relatively low heavy metal accumulation in rice grains and lowered nutrient losses to neighbouring water bodies.", "doi": "10.1007/s11356-023-28985-w", "pmid": "37501024", "labels": {"NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10447601"}, {"db": "pii", "key": "10.1007/s11356-023-28985-w"}], "notes": [], "created": "2023-10-19T12:57:19.310Z", "modified": "2024-01-16T13:48:32.778Z"}, {"entity": "publication", "iuid": "b5090ee7f17e4311876f2e97125ba47d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b5090ee7f17e4311876f2e97125ba47d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b5090ee7f17e4311876f2e97125ba47d"}}, "title": "Cutaneous squamous cell carcinoma-derived extracellular vesicles exert an oncogenic role by activating cancer-associated fibroblasts.", "authors": [{"family": "Li", "given": "Chen", "initials": "C", "orcid": "0000-0002-7199-4298", "researcher": {"href": "https://publications.scilifelab.se/researcher/acadd10dfac94eda9e9c951a8c04d6cb.json"}}, {"family": "Sun", "given": "Chengxi", "initials": "C", "orcid": "0000-0002-1050-5956", "researcher": {"href": "https://publications.scilifelab.se/researcher/8b42a5450dfd4211981fee0603acf321.json"}}, {"family": "Lohcharoenkal", "given": "Warangkana", "initials": "W"}, {"family": "Ali", "given": "Mohamad Moustafa", "initials": "MM", "orcid": "0000-0002-4902-0550", "researcher": {"href": "https://publications.scilifelab.se/researcher/780c944670ff4d7489410895569ac257.json"}}, {"family": "Xing", "given": "Pengwei", "initials": "P"}, {"family": "Zheng", "given": "Wenyi", "initials": "W"}, {"family": "G\u00f6rgens", "given": "Andr\u00e9", "initials": "A", "orcid": "0000-0001-9198-0857", "researcher": {"href": "https://publications.scilifelab.se/researcher/ea5f85e2c23a4515a39a2fa23d665a99.json"}}, {"family": "Gustafsson", "given": "Manuela O", "initials": "MO"}, {"family": "El Andaloussi", "given": "Samir", "initials": "S"}, {"family": "Sonkoly", "given": "Enik\u00f6", "initials": "E"}, {"family": "Pivarcsi", "given": "Andor", "initials": "A", "orcid": "0000-0003-2196-1102", "researcher": {"href": "https://publications.scilifelab.se/researcher/77ca870317234573a3da5dffb24bb268.json"}}], "type": "journal article", "published": "2023-07-26", "journal": {"title": "Cell Death Discov", "issn": "2058-7716", "volume": "9", "issue": "1", "pages": "260", "issn-l": "2058-7716"}, "abstract": "Cutaneous squamous cell carcinoma (cSCC) is a fast-increasing cancer with metastatic potential. Extracellular vesicles (EVs) are small membrane-bound vesicles that play important roles in intercellular communication, particularly in the tumor microenvironment (TME). Here we report that cSCC cells secrete an increased number of EVs relative to normal human epidermal keratinocytes (NHEKs) and that interfering with the capacity of cSCC to secrete EVs inhibits tumor growth in vivo in a xenograft model of human cSCC. Transcriptome analysis of tumor xenografts by RNA-sequencing enabling the simultaneous quantification of both the human and the mouse transcripts revealed that impaired EV-production of cSCC cells prominently altered the phenotype of stromal cells, in particular genes related to extracellular matrix (ECM)-formation and epithelial-mesenchymal transition (EMT). In line with these results, co-culturing of human dermal fibroblasts (HDFs) with cSCC cells, but not with normal keratinocytes in vitro resulted in acquisition of cancer-associated fibroblast (CAF) phenotype. Interestingly, EVs derived from metastatic cSCC cells, but not primary cSCCs or NHEKs, were efficient in converting HDFs to CAFs. Multiplex bead-based flow cytometry assay and mass-spectrometry (MS)-based proteomic analyses revealed the heterogenous cargo of cSCC-derived EVs and that especially EVs derived from metastatic cSCCs carry proteins associated with EV-biogenesis, EMT, and cell migration. Mechanistically, EVs from metastatic cSCC cells result in the activation of TGF\u03b2 signaling in HDFs. Altogether, our study suggests that cSCC-derived EVs mediate cancer-stroma communication, in particular the conversion of fibroblasts to CAFs, which eventually contribute to cSCC progression.", "doi": "10.1038/s41420-023-01555-2", "pmid": "37495566", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10372068"}, {"db": "pii", "key": "10.1038/s41420-023-01555-2"}], "notes": [], "created": "2023-11-29T11:23:30.604Z", "modified": "2024-01-16T13:48:32.858Z"}, {"entity": "publication", "iuid": "bd7e4686333d489495edae6e2cb9e54a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/bd7e4686333d489495edae6e2cb9e54a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/bd7e4686333d489495edae6e2cb9e54a"}}, "title": "Next generation pan-cancer blood proteome profiling using proximity extension assay.", "authors": [{"family": "\u00c1lvez", "given": "Mar\u00eda Bueno", "initials": "MB", "orcid": "0000-0002-2669-7796", "researcher": {"href": "https://publications.scilifelab.se/researcher/b6a18cc0ce34429a91758206cedb5d60.json"}}, {"family": "Edfors", "given": "Fredrik", "initials": "F", "orcid": "0000-0002-0017-7987", "researcher": {"href": "https://publications.scilifelab.se/researcher/3f0e8af0b9144bcd9fd566d316008a62.json"}}, {"family": "von Feilitzen", "given": "Kalle", "initials": "K", "orcid": "0000-0002-0257-7554", "researcher": {"href": "https://publications.scilifelab.se/researcher/9f1e309f8d9247458c59e2ecfbd0c079.json"}}, {"family": "Zwahlen", "given": "Martin", "initials": "M", "orcid": "0000-0002-0064-4776", "researcher": {"href": "https://publications.scilifelab.se/researcher/04fb4e913dfb47b9bee48531db50d64c.json"}}, {"family": "Mardinoglu", "given": "Adil", "initials": "A", "orcid": "0000-0002-4254-6090", "researcher": {"href": "https://publications.scilifelab.se/researcher/da756265658c4ed2a8911644583e07a3.json"}}, {"family": "Edqvist", "given": "Per-Henrik", "initials": "PH", "orcid": "0000-0002-8330-0134", "researcher": {"href": "https://publications.scilifelab.se/researcher/dd5ff31463cd4345a1fc8351e797ac7f.json"}}, {"family": "Sj\u00f6blom", "given": "Tobias", "initials": "T", "orcid": "0000-0001-6668-4140", "researcher": {"href": "https://publications.scilifelab.se/researcher/909f00a5bf6e465f9ff560b12bcd863a.json"}}, {"family": "Lundin", "given": "Emma", "initials": "E", "orcid": "0009-0000-7711-1962", "researcher": {"href": "https://publications.scilifelab.se/researcher/06761839da88443e9098d9562810fb7f.json"}}, {"family": "Rameika", "given": "Natallia", "initials": "N", "orcid": "0000-0002-7835-4357", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a1b2d0ce6ea452b82a35c603a073eb1.json"}}, {"family": "Enblad", "given": "Gunilla", "initials": "G", "orcid": "0000-0002-0594-724X", "researcher": {"href": "https://publications.scilifelab.se/researcher/11313af3f4a241ecb93af23ab2652195.json"}}, {"family": "Lindman", "given": "Henrik", "initials": "H"}, {"family": "H\u00f6glund", "given": "Martin", "initials": "M", "orcid": "0000-0003-2468-0226", "researcher": {"href": "https://publications.scilifelab.se/researcher/8717164448ee4e2797fefd365103ddc8.json"}}, {"family": "Hesselager", "given": "G\u00f6ran", "initials": "G", "orcid": "0000-0001-9613-1344", "researcher": {"href": "https://publications.scilifelab.se/researcher/978fc6fea7d54f5b81a8b5a87efa083a.json"}}, {"family": "St\u00e5lberg", "given": "Karin", "initials": "K", "orcid": "0000-0001-5527-8796", "researcher": {"href": "https://publications.scilifelab.se/researcher/47a9c8e243994dccb4730266b0431d6d.json"}}, {"family": "Enblad", "given": "Malin", "initials": "M", "orcid": "0000-0001-5900-0900", "researcher": {"href": "https://publications.scilifelab.se/researcher/1e801966db544e6286fb2b4037980dba.json"}}, {"family": "Simonson", "given": "Oscar E", "initials": "OE", "orcid": "0000-0002-3552-5558", "researcher": {"href": "https://publications.scilifelab.se/researcher/0a52b4426da84787aeb56b8d6232ba87.json"}}, {"family": "H\u00e4ggman", "given": "Michael", "initials": "M"}, {"family": "Axelsson", "given": "Tomas", "initials": "T"}, {"family": "\u00c5berg", "given": "Mikael", "initials": "M", "orcid": "0000-0002-7858-8233", "researcher": {"href": "https://publications.scilifelab.se/researcher/90fa86e9aeaa43ea9547e48b4f3f24e3.json"}}, {"family": "Nordlund", "given": "Jessica", "initials": "J", "orcid": "0000-0001-8699-9959", "researcher": {"href": "https://publications.scilifelab.se/researcher/ddf48c9262134821bcc6ce1180049753.json"}}, {"family": "Zhong", "given": "Wen", "initials": "W", "orcid": "0000-0002-7422-6104", "researcher": {"href": "https://publications.scilifelab.se/researcher/a82c3b7da3b8472392d39ca5f6d5bedb.json"}}, {"family": "Karlsson", "given": "Max", "initials": "M", "orcid": "0000-0002-7000-4416", "researcher": {"href": "https://publications.scilifelab.se/researcher/6e1bd9a99e5648c3998c6e0106a07fbc.json"}}, {"family": "Gyllensten", "given": "Ulf", "initials": "U", "orcid": "0000-0002-6316-3355", "researcher": {"href": "https://publications.scilifelab.se/researcher/e8739f0f42c44019ab88a49db350a4f2.json"}}, {"family": "Ponten", "given": "Fredrik", "initials": "F", "orcid": "0000-0003-0703-3940", "researcher": {"href": "https://publications.scilifelab.se/researcher/a8b56979a6c74891aa277fb28848b6ce.json"}}, {"family": "Fagerberg", "given": "Linn", "initials": "L", "orcid": "0000-0003-0198-7137", "researcher": {"href": "https://publications.scilifelab.se/researcher/e8db0663a10a4d9e9241457609d5952e.json"}}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}], "type": "journal article", "published": "2023-07-18", "journal": {"title": "Nat Commun", "issn": "2041-1723", "issn-l": "2041-1723", "volume": "14", "issue": "1", "pages": "4308"}, "abstract": "A comprehensive characterization of blood proteome profiles in cancer patients can contribute to a better understanding of the disease etiology, resulting in earlier diagnosis, risk stratification and better monitoring of the different cancer subtypes. Here, we describe the use of next generation protein profiling to explore the proteome signature in blood across patients representing many of the major cancer types. Plasma profiles of 1463 proteins from more than 1400 cancer patients are measured in minute amounts of blood collected at the time of diagnosis and before treatment. An open access Disease Blood Atlas resource allows the exploration of the individual protein profiles in blood collected from the individual cancer patients. We also present studies in which classification models based on machine learning have been used for the identification of a set of proteins associated with each of the analyzed cancers. The implication for cancer precision medicine of next generation plasma profiling is discussed.", "doi": "10.1038/s41467-023-39765-y", "pmid": "37463882", "labels": {"Affinity Proteomics Uppsala": "Collaborative", "NGI Proteomics": "Collaborative", "NGI Uppsala (SNP&SEQ Technology Platform)": "Collaborative", "National Genomics Infrastructure": "Collaborative", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10354027"}, {"db": "pii", "key": "10.1038/s41467-023-39765-y"}], "notes": [], "created": "2023-11-29T19:16:18.991Z", "modified": "2024-01-16T13:48:32.880Z"}, {"entity": "publication", "iuid": "b736476c34b9439da7adaec3604dbd0c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b736476c34b9439da7adaec3604dbd0c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b736476c34b9439da7adaec3604dbd0c"}}, "title": "Vascular endothelial growth factor-D plasma levels and VEGFD genetic variants are independently associated with outcomes in patients with cardiovascular disease.", "authors": [{"family": "Davidsson", "given": "Pia", "initials": "P", "orcid": "0000-0002-4775-5828", "researcher": {"href": "https://publications.scilifelab.se/researcher/23f2792fe59f463dba3e347ff1efb2bc.json"}}, {"family": "Eketj\u00e4ll", "given": "Susanna", "initials": "S"}, {"family": "Eriksson", "given": "Niclas", "initials": "N", "orcid": "0000-0002-2152-4343", "researcher": {"href": "https://publications.scilifelab.se/researcher/64611a83caba46d597f45371b77de26b.json"}}, {"family": "Walentinsson", "given": "Anna", "initials": "A"}, {"family": "Becker", "given": "Richard C", "initials": "RC"}, {"family": "Cavallin", "given": "Anders", "initials": "A"}, {"family": "Bogstedt", "given": "Anna", "initials": "A"}, {"family": "Coll\u00e9n", "given": "Anna", "initials": "A"}, {"family": "Held", "given": "Claes", "initials": "C", "orcid": "0000-0001-9402-7404", "researcher": {"href": "https://publications.scilifelab.se/researcher/88c69f319fce4852aab37e02a75ed525.json"}}, {"family": "James", "given": "Stefan", "initials": "S"}, {"family": "Siegbahn", "given": "Agneta", "initials": "A"}, {"family": "Stewart", "given": "Ralph", "initials": "R", "orcid": "0000-0002-6167-1225", "researcher": {"href": "https://publications.scilifelab.se/researcher/493d2ac878264e0d98736945d8fdbb4d.json"}}, {"family": "Storey", "given": "Robert F", "initials": "RF"}, {"family": "White", "given": "Harvey", "initials": "H"}, {"family": "Wallentin", "given": "Lars", "initials": "L", "orcid": "0000-0003-0378-6531", "researcher": {"href": "https://publications.scilifelab.se/researcher/388a76db2e4d423882d1cf2bf6b7d985.json"}}], "type": "journal article", "published": "2023-07-04", "journal": {"title": "Cardiovasc. Res.", "issn": "1755-3245", "volume": "119", "issue": "7", "pages": "1596-1605", "issn-l": "0008-6363"}, "abstract": "The vascular endothelial growth factor (VEGF) family is involved in pathophysiological mechanisms underlying cardiovascular (CV) diseases. The aim of this study was to investigate the associations between circulating VEGF ligands and/or soluble receptors and CV outcome in patients with acute coronary syndrome (ACS) and chronic coronary syndrome (CCS).\n\nLevels of VEGF biomarkers, including bFGF, Flt-1, KDR (VEGFR2), PlGF, Tie-2, VEGF-A, VEGF-C, and VEGF-D, were measured in the PLATO ACS cohort (n = 2091, discovery cohort). Subsequently, VEGF-D was also measured in the STABILITY CCS cohort (n = 4015, confirmation cohort) to verify associations with CV outcomes. Associations between plasma VEGF-D and outcomes were analysed by multiple Cox regression models with hazard ratios (HR [95% CI]) comparing the upper vs. the lower quartile of VEGF-D. Genome-wide association study (GWAS) of VEGF-D in PLATO identified SNPs that were used as genetic instruments in Mendelian randomization (MR) meta-analyses vs. clinical endpoints. GWAS and MR were performed in patients with ACS from PLATO (n = 10 013) and FRISC-II (n = 2952), and with CCS from the STABILITY trial (n = 10 786). VEGF-D, KDR, Flt-1, and PlGF showed significant association with CV outcomes. VEGF-D was most strongly associated with CV death (P = 3.73e-05, HR 1.892 [1.419, 2.522]). Genome-wide significant associations with VEGF-D levels were identified at the VEGFD locus on chromosome Xp22. MR analyses of the combined top ranked SNPs (GWAS P-values; rs192812042, P = 5.82e-20; rs234500, P = 1.97e-14) demonstrated a significant effect on CV mortality [P = 0.0257, HR 1.81 (1.07, 3.04) per increase of one unit in log VEGF-D].\n\nThis is the first large-scale cohort study to demonstrate that both VEGF-D plasma levels and VEGFD genetic variants are independently associated with CV outcomes in patients with ACS and CCS. Measurements of VEGF-D levels and/or VEGFD genetic variants may provide incremental prognostic information in patients with ACS and CCS.", "doi": "10.1093/cvr/cvad039", "pmid": "36869765", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "NGI SNP genotyping": "Service", "Affinity Proteomics Uppsala": "Service"}, "xrefs": [{"db": "pii", "key": "7069262"}], "notes": [], "created": "2023-04-06T13:50:07.167Z", "modified": "2023-11-29T19:15:31.361Z"}, {"entity": "publication", "iuid": "3a1a5b9ee3754ffbb4b6a74c5b1396cd", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3a1a5b9ee3754ffbb4b6a74c5b1396cd.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3a1a5b9ee3754ffbb4b6a74c5b1396cd"}}, "title": "Forest Fire Influence on Tomicus piniperda-Associated Fungal Communities and Phloem Nutrient Availability of Colonized Pinus sylvestris.", "authors": [{"family": "Kluting", "given": "Kerri", "initials": "K"}, {"family": "Strid", "given": "Ylva", "initials": "Y"}, {"family": "Six", "given": "Diana", "initials": "D"}, {"family": "Rosling", "given": "Anna", "initials": "A", "orcid": "0000-0002-7003-5941", "researcher": {"href": "https://publications.scilifelab.se/researcher/c4c4bbb9e6c343808e8fa9345b7c05b2.json"}}], "type": "journal article", "published": "2023-07-00", "journal": {"title": "Microb. Ecol.", "issn": "1432-184X", "issn-l": "0095-3628", "volume": "86", "issue": "1", "pages": "224-239"}, "abstract": "Forest fire is known to positively affect bark beetle populations by providing fire-damaged trees with impaired defenses for infestation. Tomicus piniperda, the common pine shoot beetle, breeds and lays eggs under the bark of stressed pine trees and is considered a serious forest pest within its native range. Wood-colonizing fungi have been hypothesized to improve substrate quality and detoxify tree defensive chemistry to indirectly facilitate tree colonization by beetles. While some bark beetle species form symbiotic associations with fungi and actively vector their partners when colonizing new trees, T. piniperda does not have mycangia or body hairs for specific vectoring of fungi. To explore the T. piniperda-associated fungal community for signs of specific association, we used ITS metabarcoding to separately characterize fungal communities associated with surface and gut of male and female beetles. We also characterized the temporal changes in fungal community and nutrient status of pine phloem with and without beetle galleries. Sampling was performed 2 years after a natural forest fire and included both burnt and unburnt sites. In our study system, we find that forest fire significantly impacts the fungal community composition associated with T. piniperda and that fire may also indirectly change nutrient availability in phloem to beetle galleries. We conclude that T. piniperda can vector fungi to newly colonized trees but the absence of positive effects on substrate quality and minimal effects of sex indicate that vectoring of associated fungal communities is not a strategy associated with the T. piniperda life cycle.", "doi": "10.1007/s00248-022-02066-w", "pmid": "35831642", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service", "NGI Long read": "Service", "NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10293462"}, {"db": "pii", "key": "10.1007/s00248-022-02066-w"}], "notes": [], "created": "2023-09-04T12:09:36.897Z", "modified": "2024-01-16T13:48:33.043Z"}, {"entity": "publication", "iuid": "afa40fcfd6c54ca29a3c2a528fb202b6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/afa40fcfd6c54ca29a3c2a528fb202b6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/afa40fcfd6c54ca29a3c2a528fb202b6"}}, "title": "Forensic prediction of sex, age, height, body mass index, hip-to-waist ratio, smoking status and lipid lowering drugs using epigenetic markers and plasma proteins.", "authors": [{"family": "Llobet", "given": "M\u00f2nica Ortega", "initials": "MO"}, {"family": "Johansson", "given": "\u00c5sa", "initials": "\u00c5"}, {"family": "Gyllensten", "given": "Ulf", "initials": "U"}, {"family": "Allen", "given": "Marie", "initials": "M"}, {"family": "Enroth", "given": "Stefan", "initials": "S"}], "type": "journal article", "published": "2023-07-00", "journal": {"title": "Forensic Sci Int Genet", "issn": "1878-0326", "issn-l": "1872-4973", "volume": "65", "issue": null, "pages": "102871"}, "abstract": "The prediction of human characteristics from blood using molecular markers would be very helpful in forensic science. Such information can be particularly important in providing investigative leads in police casework from, for example, blood found at crime scenes in cases without a suspect. Here, we investigated the possibilities and limitations of predicting seven phenotypic traits (sex, age, height, body mass index [BMI], hip-to-waist [WTH] ratio, smoking status and lipid-lowering drug use) using either DNA methylation or plasma proteins separately or in combination. We developed a prediction pipeline starting with the prediction of sex followed by sex-specific, stepwise, individual age, sex-specific anthropometric traits and, finally, lifestyle-related traits. Our data revealed that age, sex and smoking status can be accurately predicted from DNA methylation alone, while the use of plasma proteins was highly accurate for prediction of the WTH ratio, and a combined analysis of the best predictions for BMI and lipid-lowering drug use. In unseen individuals, age was predicted with a standard error of 3.3 years for women and 6.5 years for men, while the accuracy in smoking prediction across both men and women was 0.86. In conclusion, we have developed a stepwise approach for the de-novo prediction of individual characteristics from plasma proteins and DNA methylation markers. These models are accurate and may provide valuable information and investigative leads in future forensic casework.", "doi": "10.1016/j.fsigen.2023.102871", "pmid": "37054667", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI SNP genotyping": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "S1872-4973(23)00046-7"}], "notes": [], "created": "2023-05-15T11:41:55.175Z", "modified": "2024-01-16T13:48:33.052Z"}, {"entity": "publication", "iuid": "c7a01707163a492680ecdd4294d2c2b0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c7a01707163a492680ecdd4294d2c2b0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c7a01707163a492680ecdd4294d2c2b0"}}, "title": "Environmental stress during larval development induces DNA methylation shifts in the migratory painted lady butterfly (Vanessa cardui).", "authors": [{"family": "Boman", "given": "Jesper", "initials": "J", "orcid": "0000-0002-0537-8219", "researcher": {"href": "https://publications.scilifelab.se/researcher/669c974e6e284e94bfb6009f49ffc06d.json"}}, {"family": "Zhu", "given": "Yishu", "initials": "Y"}, {"family": "H\u00f6\u00f6k", "given": "Lars", "initials": "L"}, {"family": "Vila", "given": "Roger", "initials": "R", "orcid": "0000-0002-2447-4388", "researcher": {"href": "https://publications.scilifelab.se/researcher/12f9f7ce050d463bb9a67d6970b9428a.json"}}, {"family": "Talavera", "given": "Gerard", "initials": "G", "orcid": "0000-0003-1112-1345", "researcher": {"href": "https://publications.scilifelab.se/researcher/1081486b2353478b8dba3388e819822b.json"}}, {"family": "Backstr\u00f6m", "given": "Niclas", "initials": "N", "orcid": "0000-0002-0961-8427", "researcher": {"href": "https://publications.scilifelab.se/researcher/674a0756dcf44e79ac6a6a2499b01760.json"}}], "type": "journal article", "published": "2023-07-00", "journal": {"title": "Mol. Ecol.", "issn": "1365-294X", "issn-l": "0962-1083", "volume": "32", "issue": "13", "pages": "3513-3523"}, "abstract": "Seasonal environmental fluctuations provide formidable challenges for living organisms, especially small ectotherms such as butterflies. A common strategy to cope with harsh environments is to enter diapause, but some species avoid unsuitable conditions by migrating. Despite a growing understanding of migration in the life cycles of some butterfly species, it remains unknown how individuals register and store environmental cues to determine whether and where to migrate. Here, we explored how competition and host plant availability during larval development affect patterns of DNA methylation in the migratory painted lady (Vanessa cardui) butterfly. We identify a set of potentially functional methylome shifts associated with differences in the environment, indicating that DNA methylation is involved in the response to different conditions during larval development. By analysing the transcriptome for the same samples used for methylation profiling, we also uncovered a non-monotonic relationship between gene body methylation and gene expression. Our results provide a starting point for understanding the interplay between DNA methylation and gene expression in butterflies in general and how differences in environmental conditions during development can trigger unique epigenetic marks that might be important for behavioural decisions in the adult stage.", "doi": "10.1111/mec.16957", "pmid": "37088782", "labels": {"NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2023-10-04T12:44:28.636Z", "modified": "2024-01-16T13:48:33.060Z"}, {"entity": "publication", "iuid": "961f1a0909c14017aba5c52b861cd8c2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/961f1a0909c14017aba5c52b861cd8c2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/961f1a0909c14017aba5c52b861cd8c2"}}, "title": "Genetic markers associated with bone composition in Rhode Island Red laying hens.", "authors": [{"family": "Sallam", "given": "Moh", "initials": "M", "orcid": "0000-0002-4485-7626", "researcher": {"href": "https://publications.scilifelab.se/researcher/877cf4417612438797238e303a8de163.json"}}, {"family": "Wilson", "given": "Peter W", "initials": "PW"}, {"family": "Andersson", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Schmutz", "given": "Matthias", "initials": "M"}, {"family": "Benavides", "given": "Cristina", "initials": "C"}, {"family": "Dominguez-Gasca", "given": "Nazaret", "initials": "N"}, {"family": "Sanchez-Rodriguez", "given": "Estefania", "initials": "E"}, {"family": "Rodriguez-Navarro", "given": "Alejandro B", "initials": "AB"}, {"family": "Dunn", "given": "Ian C", "initials": "IC"}, {"family": "De Koning", "given": "Dirk-Jan", "initials": "DJ"}, {"family": "Johnsson", "given": "Martin", "initials": "M"}], "type": "journal article", "published": "2023-06-29", "journal": {"title": "Genet. Sel. Evol.", "issn": "1297-9686", "volume": "55", "issue": "1", "pages": "44", "issn-l": "0999-193X"}, "abstract": "Bone damage has welfare and economic impacts on modern commercial poultry and is known as one of the major challenges in the poultry industry. Bone damage is particularly common in laying hens and is probably due to the physiological link between bone and the egg laying process. Previous studies identified and validated quantitative trait loci (QTL) for bone strength in White Leghorn laying hens based on several measurements, including bone composition measurements on the cortex and medulla of the tibia bone. In a previous pedigree-based analysis, bone composition measurements showed heritabilities ranging from 0.18 to 0.41 and moderate to strong genetic correlations with tibia strength and density. Bone composition was measured using infrared spectroscopy and thermogravimetry. The aim of this study was to combine these bone composition measurements with genotyping data via a genome-wide association study (GWAS) to investigate genetic markers that contribute to genetic variance in bone composition in Rhode Island Red laying hens. In addition, we investigated the genetic correlations between bone composition and bone strength.\n\nWe found novel genetic markers that are significantly associated with cortical lipid, cortical mineral scattering, medullary organic matter, and medullary mineralization. Composition of the bone organic matter showed more significant associations than bone mineral composition. We also found interesting overlaps between the GWAS results for tibia composition traits, particularly for cortical lipid and tibia strength. Bone composition measurements by infrared spectroscopy showed more significant associations than thermogravimetry measurements. Based on the results of infrared spectroscopy, cortical lipid showed the highest genetic correlations with tibia density, which was negative (- 0.20 \u00b1 0.04), followed by cortical CO3/PO4 (0.18 \u00b1 0.04). Based on the results of thermogravimetry, medullary organic matter% and mineral% showed the highest genetic correlations with tibia density (- 0.25 \u00b1 0.04 and 0.25 \u00b1 0.04, respectively).\n\nThis study detected novel genetic associations for bone composition traits, particularly those involving organic matter, that could be used as a basis for further molecular genetic investigations. Tibia cortical lipids displayed the strongest genetic associations of all the composition measurements, including a significantly high genetic correlation with tibia density and strength. Our results also highlighted that cortical lipid may be a key measurement for further avian bone studies.", "doi": "10.1186/s12711-023-00818-x", "pmid": "37386416", "labels": {"NGI SNP genotyping": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10311847"}, {"db": "pii", "key": "10.1186/s12711-023-00818-x"}], "notes": [], "created": "2023-11-29T10:57:27.612Z", "modified": "2023-11-29T10:57:27.651Z"}, {"entity": "publication", "iuid": "48bf04137ea64df1b6b70285f4f67cd2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/48bf04137ea64df1b6b70285f4f67cd2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/48bf04137ea64df1b6b70285f4f67cd2"}}, "title": "Mutations in the CYP27B1 gene cause vitamin D dependent rickets in pugs.", "authors": [{"family": "Rohdin", "given": "Cecilia", "initials": "C", "orcid": "0000-0002-7698-550X", "researcher": {"href": "https://publications.scilifelab.se/researcher/c17d3c315f7149bb93ac86f48a18ab99.json"}}, {"family": "Wang", "given": "Chao", "initials": "C"}, {"family": "Brander", "given": "Gustaf", "initials": "G"}, {"family": "Rondahl", "given": "Veronica", "initials": "V"}, {"family": "Karlsson", "given": "\u00c5sa", "initials": "\u00c5"}, {"family": "Friling", "given": "Lisa", "initials": "L"}, {"family": "Fischetti", "given": "Anthony", "initials": "A"}, {"family": "Meadows", "given": "Jennifer", "initials": "J"}, {"family": "H\u00e4ggstr\u00f6m", "given": "Jens", "initials": "J", "orcid": "0000-0003-3402-023X", "researcher": {"href": "https://publications.scilifelab.se/researcher/5e1779188e20402294f12861a8232e71.json"}}, {"family": "J\u00e4derlund", "given": "Karin Hultin", "initials": "KH"}, {"family": "Ljungvall", "given": "Ingrid", "initials": "I", "orcid": "0000-0002-6617-0454", "researcher": {"href": "https://publications.scilifelab.se/researcher/12b19ecb541c4d13a685b574390e8104.json"}}, {"family": "Lindblad-Toh", "given": "Kerstin", "initials": "K"}], "type": "case reports", "published": "2023-06-09", "journal": {"title": "J. Vet. Intern. Med.", "issn": "1939-1676", "volume": "37", "issue": "4", "pages": "1507-1513", "issn-l": "0891-6640"}, "abstract": "Rickets is a disorder of bone development and can be the result of either dietary or genetic causes. Here, related pugs from 2 litters were included. Three pugs had clinical signs including, lameness, bone deformities, and dyspnea. One other pug was found dead. Radiographs of 2 affected pugs, 5 and 6 months old, showed generalized widening, and irregular margination of the physes of both the appendicular and the axial skeleton with generalized decrease in bone opacity and bulbous swelling of the costochondral junctions. Two pugs had low serum calcium and 1,25 (OH)2 D3 concentrations. Test results further indicated secondary hyperparathyroidism with adequate concentrations of 25-hydroxyvitamin D. Necropsy revealed tongue-like projections of cartilage extending into the metaphysis consistent with rickets, loss of metaphyseal mineralization and lung pathology. Vitamin D-dependent rickets was diagnosed. A truncating mutation in the 1\u03b1-hydroxylase gene (CYP27B1) was identified by genome sequence analysis of the pugs with VDDR type 1A. Vitamin D-dependent rickets type 1A can occur in young pugs, and if left untreated is a life-threatening condition. Early medical intervention can reverse clinical signs and should be instituted as soon as possible.", "doi": "10.1111/jvim.16791", "pmid": "37293695", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10365047"}], "notes": [], "created": "2023-11-29T10:49:54.098Z", "modified": "2024-01-16T13:48:33.185Z"}, {"entity": "publication", "iuid": "4ab0b7f2d3b44dedbf4230ac6274f925", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4ab0b7f2d3b44dedbf4230ac6274f925.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4ab0b7f2d3b44dedbf4230ac6274f925"}}, "title": "Ablation of ZC3H11A causes early embryonic lethality and dysregulation of metabolic processes.", "authors": [{"family": "Younis", "given": "Shady", "initials": "S"}, {"family": "Jouneau", "given": "Alice", "initials": "A"}, {"family": "Larsson", "given": "M\u00e5rten", "initials": "M"}, {"family": "Oudin", "given": "Jean-Francois", "initials": "JF"}, {"family": "Adenot", "given": "Pierre", "initials": "P"}, {"family": "Omar", "given": "Jihad", "initials": "J"}, {"family": "Brochard", "given": "Vincent", "initials": "V"}, {"family": "Andersson", "given": "Leif", "initials": "L", "orcid": "0000-0002-4085-6968", "researcher": {"href": "https://publications.scilifelab.se/researcher/bd3343c12f994b1fabcae23027d3a76d.json"}}], "type": "journal article", "published": "2023-06-06", "journal": {"title": "Proc. Natl. Acad. Sci. U.S.A.", "issn": "1091-6490", "volume": "120", "issue": "23", "pages": "e2216799120", "issn-l": "0027-8424"}, "abstract": "ZC3H11A (zinc finger CCCH domain-containing protein 11A) is a stress-induced mRNA-binding protein required for efficient growth of nuclear-replicating viruses. The cellular functions of ZC3H11A during embryonic development are unknown. Here, we report the generation and phenotypic characterization of Zc3h11a knockout (KO) mice. Heterozygous null Zc3h11a mice were born at the expected frequency without distinguishable phenotypic differences compared with wild-type mice. In contrast, homozygous null Zc3h11a mice were missing, indicating that Zc3h11a is crucial for embryonic viability and survival. Zc3h11a -/- embryos were detected at the expected Mendelian ratios up to late preimplantation stage (E4.5). However, phenotypic characterization at E6.5 revealed degeneration of Zc3h11a -/- embryos, indicating developmental defects around the time of implantation. Transcriptomic analyses documented a dysregulation of glycolysis and fatty acid metabolic pathways in Zc3h11a-/- embryos at E4.5. Proteomic analysis indicated a tight interaction between ZC3H11A and mRNA-export proteins in embryonic stem cells. CLIP-seq analysis demonstrated that ZC3H11A binds a subset of mRNA transcripts that are critical for metabolic regulation of embryonic cells. Furthermore, embryonic stem cells with an induced deletion of Zc3h11a display an impaired differentiation toward epiblast-like cells and impaired mitochondrial membrane potential. Altogether, the results show that ZC3H11A is participating in export and posttranscriptional regulation of selected mRNA transcripts required to maintain metabolic processes in embryonic cells. While ZC3H11A is essential for the viability of the early mouse embryo, inactivation of Zc3h11a expression in adult tissues using a conditional KO did not lead to obvious phenotypic defects.", "doi": "10.1073/pnas.2216799120", "pmid": "37252988", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10266022"}], "notes": [], "created": "2023-11-29T11:18:46.020Z", "modified": "2023-11-29T11:18:46.029Z"}, {"entity": "publication", "iuid": "b72895f9bcf545a6a05e8b4ba0657679", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b72895f9bcf545a6a05e8b4ba0657679.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b72895f9bcf545a6a05e8b4ba0657679"}}, "title": "Phenotypic and transcriptomic acclimation of the green microalga Raphidocelis subcapitata to high environmental levels of the herbicide diflufenican.", "authors": [{"family": "G\u00f3mez-Mart\u00ednez", "given": "Daniela", "initials": "D"}, {"family": "Bengtson", "given": "Johanna", "initials": "J"}, {"family": "Nilsson", "given": "Anders K", "initials": "AK"}, {"family": "Clarke", "given": "Adrian K", "initials": "AK"}, {"family": "Nilsson", "given": "Rolf Henrik", "initials": "RH"}, {"family": "Kristiansson", "given": "Erik", "initials": "E"}, {"family": "Corcoll", "given": "Nat\u00e0lia", "initials": "N"}], "type": "journal article", "published": "2023-06-01", "journal": {"title": "Sci. Total Environ.", "issn": "1879-1026", "volume": "875", "pages": "162604", "issn-l": "0048-9697"}, "abstract": "Herbicide pollution poses a worldwide threat to plants and freshwater ecosystems. However, the understanding of how organisms develop tolerance to these chemicals and the associated trade-off expenses are largely unknown. This study aims to investigate the physiological and transcriptional mechanisms underlying the acclimation of the green microalgal model species Raphidocelis subcapitata (Selenastraceae) towards the herbicide diflufenican, and the fitness costs associated with tolerance development. Algae were exposed for 12 weeks (corresponding to 100 generations) to diflufenican at the two environmental concentrations 10 and 310 ng/L. The monitoring of growth, pigment composition, and photosynthetic performance throughout the experiment revealed an initial dose-dependent stress phase (week 1) with an EC50 of 397 ng/L, followed by a time-dependent recovery phase during weeks 2 to 4. After week 4, R. subcapitata was acclimated to diflufenican exposure with a similar growth rate, content of carotenoids, and photosynthetic performance as the unexposed control algae. This acclimation state of the algae was explored in terms of tolerance acquisition, changes in the fatty acids composition, diflufenican removal rate, cell size, and changes in mRNA gene expression profile, revealing potential fitness costs associated with acclimation, such as up-regulation of genes related to cell division, structure, morphology, and reduction of cell size. Overall, this study demonstrates that R. subcapitata can quickly acclimate to environmental but toxic levels of diflufenican; however, the acclimation is associated with trade-off expenses that result in smaller cell size.", "doi": "10.1016/j.scitotenv.2023.162604", "pmid": "36878298", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pii", "key": "S0048-9697(23)01220-2"}], "notes": [], "created": "2023-11-29T13:30:43.924Z", "modified": "2023-11-29T13:30:43.928Z"}, {"entity": "publication", "iuid": "a4df06e9148b4e4a95aae401ff4a8016", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a4df06e9148b4e4a95aae401ff4a8016.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a4df06e9148b4e4a95aae401ff4a8016"}}, "title": "Chromosome-level genome assembly of Lilford's wall lizard, Podarcis lilfordi (G\u00fcnther, 1874) from the Balearic Islands (Spain).", "authors": [{"family": "Gomez-Garrido", "given": "Jessica", "initials": "J"}, {"family": "Cruz", "given": "Fernando", "initials": "F"}, {"family": "Alioto", "given": "Tyler S", "initials": "TS"}, {"family": "Feiner", "given": "Nathalie", "initials": "N"}, {"family": "Uller", "given": "Tobias", "initials": "T", "orcid": "0000-0003-1293-5842", "researcher": {"href": "https://publications.scilifelab.se/researcher/6346267a5c3e41c6a6825b7b20a53fa5.json"}}, {"family": "Gut", "given": "Marta", "initials": "M"}, {"family": "Sanchez Escudero", "given": "Ignacio", "initials": "I"}, {"family": "Tavecchia", "given": "Giacomo", "initials": "G"}, {"family": "Rotger", "given": "Andreu", "initials": "A"}, {"family": "Otalora Acevedo", "given": "Katherin Eliana", "initials": "KE"}, {"family": "Baldo", "given": "Laura", "initials": "L", "orcid": "0000-0003-4528-6674", "researcher": {"href": "https://publications.scilifelab.se/researcher/8c72ce0ae73a4909a4bdeb49ab722d58.json"}}], "type": "journal article", "published": "2023-06-01", "journal": {"title": "DNA Res.", "issn": "1756-1663", "issn-l": "1340-2838", "volume": "30", "issue": "3", "pages": null}, "abstract": "The Mediterranean lizard Podarcis lilfordi is an emblematic species of the Balearic Islands. The extensive phenotypic diversity among extant isolated populations makes the species a great insular model system for eco-evolutionary studies, as well as a challenging target for conservation management plans. Here we report the first high-quality chromosome-level assembly and annotation of the P. lilfordi genome, along with its mitogenome, based on a mixed sequencing strategy (10X Genomics linked reads, Oxford Nanopore Technologies long reads and Hi-C scaffolding) coupled with extensive transcriptomic data (Illumina and PacBio). The genome assembly (1.5 Gb) is highly contiguous (N50 = 90 Mb) and complete, with 99% of the sequence assigned to candidate chromosomal sequences and >97% gene completeness. We annotated a total of 25,663 protein-coding genes translating into 38,615 proteins. Comparison to the genome of the related species Podarcis muralis revealed substantial similarity in genome size, annotation metrics, repeat content, and a strong collinearity, despite their evolutionary distance (~18-20 MYA). This genome expands the repertoire of available reptilian genomes and will facilitate the exploration of the molecular and evolutionary processes underlying the extraordinary phenotypic diversity of this insular species, while providing a critical resource for conservation genomics.", "doi": "10.1093/dnares/dsad008", "pmid": "37137526", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service", "NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Other": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10214862"}, {"db": "pii", "key": "7151100"}], "notes": [], "created": "2023-10-10T08:47:32.990Z", "modified": "2023-11-29T11:43:27.568Z"}, {"entity": "publication", "iuid": "8d34b82577f64f6b877c9b79fd1ede24", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8d34b82577f64f6b877c9b79fd1ede24.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8d34b82577f64f6b877c9b79fd1ede24"}}, "title": "The genomic basis and environmental correlates of local adaptation in the Atlantic horse mackerel (Trachurus trachurus).", "authors": [{"family": "Fuentes-Pardo", "given": "Angela P", "initials": "AP", "orcid": "0000-0002-5734-9030", "researcher": {"href": "https://publications.scilifelab.se/researcher/f08a3b9b781b4ef9971a667a40b62d93.json"}}, {"family": "Farrell", "given": "Edward D", "initials": "ED", "orcid": "0000-0002-0070-9154", "researcher": {"href": "https://publications.scilifelab.se/researcher/941224a45e9242398fbcd4dacbe812c1.json"}}, {"family": "Pettersson", "given": "Mats E", "initials": "ME", "orcid": "0000-0002-7372-9076", "researcher": {"href": "https://publications.scilifelab.se/researcher/27011c7fbb8a44dda536a4fc876675b0.json"}}, {"family": "Sprehn", "given": "C Grace", "initials": "CG", "orcid": "0000-0002-4164-4246", "researcher": {"href": "https://publications.scilifelab.se/researcher/b51f6d45361e4aa187fc74870a38ac3f.json"}}, {"family": "Andersson", "given": "Leif", "initials": "L", "orcid": "0000-0002-4085-6968", "researcher": {"href": "https://publications.scilifelab.se/researcher/bd3343c12f994b1fabcae23027d3a76d.json"}}], "type": "journal article", "published": "2023-06-00", "journal": {"title": "Evol Appl", "issn": "1752-4571", "volume": "16", "issue": "6", "pages": "1201-1219", "issn-l": "1752-4571"}, "abstract": "Understanding how populations adapt to their environment is increasingly important to prevent biodiversity loss due to overexploitation and climate change. Here we studied the population structure and genetic basis of local adaptation of Atlantic horse mackerel, a commercially and ecologically important marine fish that has one of the widest distributions in the eastern Atlantic. We analyzed whole-genome sequencing and environmental data of samples collected from the North Sea to North Africa and the western Mediterranean Sea. Our genomic approach indicated low population structure with a major split between the Mediterranean Sea and the Atlantic Ocean and between locations north and south of mid-Portugal. Populations from the North Sea are the most genetically distinct in the Atlantic. We discovered that most population structure patterns are driven by a few highly differentiated putatively adaptive loci. Seven loci discriminate the North Sea, two the Mediterranean Sea, and a large putative inversion (9.9 Mb) on chromosome 21 underlines the north-south divide and distinguishes North Africa. A genome-environment association analysis indicates that mean seawater temperature and temperature range, or factors correlated to them, are likely the main environmental drivers of local adaptation. Our genomic data broadly support the current stock divisions, but highlight areas of potential mixing, which require further investigation. Moreover, we demonstrate that as few as 17 highly informative SNPs can genetically discriminate the North Sea and North African samples from neighboring populations. Our study highlights the importance of both, life history and climate-related selective pressures in shaping population structure patterns in marine fish. It also supports that chromosomal rearrangements play a key role in local adaptation with gene flow. This study provides the basis for more accurate delineation of the horse mackerel stocks and paves the way for improving stock assessments.", "doi": "10.1111/eva.13559", "pmid": "37360028", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10286234"}, {"db": "pii", "key": "EVA13559"}], "notes": [], "created": "2023-08-14T06:20:40.908Z", "modified": "2024-01-16T13:48:33.272Z"}, {"entity": "publication", "iuid": "2aed043e07494edeb8d66c6047ca7cfd", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2aed043e07494edeb8d66c6047ca7cfd.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2aed043e07494edeb8d66c6047ca7cfd"}}, "title": "Northwest African Neolithic initiated by migrants from Iberia and Levant.", "authors": [{"family": "Sim\u00f5es", "given": "Luciana G", "initials": "LG", "orcid": "0000-0002-6119-9776", "researcher": {"href": "https://publications.scilifelab.se/researcher/eea5b7ccd8f84d44b2e0be03f5c4e762.json"}}, {"family": "G\u00fcnther", "given": "Torsten", "initials": "T", "orcid": "0000-0001-9460-390X", "researcher": {"href": "https://publications.scilifelab.se/researcher/84159bff82a64a938bcff107f550c901.json"}}, {"family": "Mart\u00ednez-S\u00e1nchez", "given": "Rafael M", "initials": "RM"}, {"family": "Vera-Rodr\u00edguez", "given": "Juan Carlos", "initials": "JC"}, {"family": "Iriarte", "given": "Eneko", "initials": "E", "orcid": "0000-0001-8365-5616", "researcher": {"href": "https://publications.scilifelab.se/researcher/112f0c5761e84deea89b2b7cb68521ce.json"}}, {"family": "Rodr\u00edguez-Varela", "given": "Ricardo", "initials": "R"}, {"family": "Bokbot", "given": "Youssef", "initials": "Y"}, {"family": "Valdiosera", "given": "Cristina", "initials": "C", "orcid": "0000-0003-4948-2226", "researcher": {"href": "https://publications.scilifelab.se/researcher/113ef0dde1dd48e388f75c43bd672005.json"}}, {"family": "Jakobsson", "given": "Mattias", "initials": "M", "orcid": "0000-0001-7840-7853", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a4abe0fcb20492d9ec849c9fbf58a71.json"}}], "type": "comparative study", "published": "2023-06-00", "journal": {"title": "Nature", "issn": "1476-4687", "issn-l": "0028-0836", "volume": "618", "issue": "7965", "pages": "550-556"}, "abstract": "In northwestern Africa, lifestyle transitioned from foraging to food production around 7,400 years ago but what sparked that change remains unclear. Archaeological data support conflicting views: (1) that migrant European Neolithic farmers brought the new way of life to North Africa1-3 or (2) that local hunter-gatherers adopted technological innovations4,5. The latter view is also supported by archaeogenetic data6. Here we fill key chronological and archaeogenetic gaps for the Maghreb, from Epipalaeolithic to Middle Neolithic, by sequencing the genomes of nine individuals (to between 45.8- and 0.2-fold genome coverage). Notably, we trace 8,000 years of population continuity and isolation from the Upper Palaeolithic, via the Epipaleolithic, to some Maghrebi Neolithic farming groups. However, remains from the earliest Neolithic contexts showed mostly European Neolithic ancestry. We suggest that farming was introduced by European migrants and was then rapidly adopted by local groups. During the Middle Neolithic a new ancestry from the Levant appears in the Maghreb, coinciding with the arrival of pastoralism in the region, and all three ancestries blend together during the Late Neolithic. Our results show ancestry shifts in the Neolithization of northwestern Africa that probably mirrored a heterogeneous economic and cultural landscape, in a more multifaceted process than observed in other regions.", "doi": "10.1038/s41586-023-06166-6", "pmid": "37286608", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10266975"}, {"db": "pii", "key": "10.1038/s41586-023-06166-6"}], "notes": [], "created": "2023-11-29T10:51:14.891Z", "modified": "2024-01-16T13:48:33.294Z"}, {"entity": "publication", "iuid": "9100a2388b73463d97cf05a0164a759e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9100a2388b73463d97cf05a0164a759e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9100a2388b73463d97cf05a0164a759e"}}, "title": "Genome-wide association study and functional characterization identifies candidate genes for insulin-stimulated glucose uptake.", "authors": [{"family": "Williamson", "given": "Alice", "initials": "A", "orcid": "0000-0002-7599-9301", "researcher": {"href": "https://publications.scilifelab.se/researcher/c202432e49b84fe59c9fdea5ffc8b3e6.json"}}, {"family": "Norris", "given": "Dougall M", "initials": "DM"}, {"family": "Yin", "given": "Xianyong", "initials": "X"}, {"family": "Broadaway", "given": "K Alaine", "initials": "KA"}, {"family": "Moxley", "given": "Anne H", "initials": "AH"}, {"family": "Vadlamudi", "given": "Swarooparani", "initials": "S"}, {"family": "Wilson", "given": "Emma P", "initials": "EP"}, {"family": "Jackson", "given": "Anne U", "initials": "AU", "orcid": "0000-0002-9672-2547", "researcher": {"href": "https://publications.scilifelab.se/researcher/b8230afabb0b4dcda8dc58ead349aea0.json"}}, {"family": "Ahuja", "given": "Vasudha", "initials": "V"}, {"family": "Andersen", "given": "Mette K", "initials": "MK", "orcid": "0000-0001-8227-1469", "researcher": {"href": "https://publications.scilifelab.se/researcher/dac5dfaabb5d49a29f4251e63d4c5a07.json"}}, {"family": "Arzumanyan", "given": "Zorayr", "initials": "Z"}, {"family": "Bonnycastle", "given": "Lori L", "initials": "LL"}, {"family": "Bornstein", "given": "Stefan R", "initials": "SR"}, {"family": "Bretschneider", "given": "Maxi P", "initials": "MP"}, {"family": "Buchanan", "given": "Thomas A", "initials": "TA", "orcid": "0000-0001-7892-5132", "researcher": {"href": "https://publications.scilifelab.se/researcher/05527c66312645efbf21e15fad4fce60.json"}}, {"family": "Chang", "given": "Yi-Cheng", "initials": "YC"}, {"family": "Chuang", "given": "Lee-Ming", "initials": "LM", "orcid": "0000-0003-0978-2662", "researcher": {"href": "https://publications.scilifelab.se/researcher/60cc72f48610453199321c06f5008d7c.json"}}, {"family": "Chung", "given": "Ren-Hua", "initials": "RH", "orcid": "0000-0002-9835-6333", "researcher": {"href": 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"https://publications.scilifelab.se/researcher/c2dc6be9aa194bdc9a161e551d5e6747.json"}}, {"family": "Walker", "given": "Mark", "initials": "M"}, {"family": "Grarup", "given": "Niels", "initials": "N", "orcid": "0000-0001-5526-1070", "researcher": {"href": "https://publications.scilifelab.se/researcher/eefb6d29ce1b4e319e9495734175036d.json"}}, {"family": "Boehnke", "given": "Michael", "initials": "M", "orcid": "0000-0002-6442-7754", "researcher": {"href": "https://publications.scilifelab.se/researcher/b8cb72bdcea4492199a1b9d8ac406ac7.json"}}, {"family": "Wareham", "given": "Nicholas J", "initials": "NJ", "orcid": "0000-0003-1422-2993", "researcher": {"href": "https://publications.scilifelab.se/researcher/176d8605b9ac4ecbbd5c197335769814.json"}}, {"family": "Mohlke", "given": "Karen L", "initials": "KL", "orcid": "0000-0001-6721-153X", "researcher": {"href": "https://publications.scilifelab.se/researcher/7c11d7ab911243edb9e2696efd95ecd4.json"}}, {"family": "Wheeler", "given": "Eleanor", "initials": "E", "orcid": "0000-0002-8616-6444", "researcher": {"href": "https://publications.scilifelab.se/researcher/f7ed362ab4ba4b76b0ee743de84370c4.json"}}, {"family": "O'Rahilly", "given": "Stephen", "initials": "S", "orcid": "0000-0003-2199-4449", "researcher": {"href": "https://publications.scilifelab.se/researcher/c599d6c6dd044335aa326acda778096f.json"}}, {"family": "Fazakerley", "given": "Daniel J", "initials": "DJ", "orcid": "0000-0001-8241-2903", "researcher": {"href": "https://publications.scilifelab.se/researcher/4f41c07e336349e4b3c69d93535e2508.json"}}, {"family": "Langenberg", "given": "Claudia", "initials": "C", "orcid": "0000-0002-5017-7344", "researcher": {"href": "https://publications.scilifelab.se/researcher/ca19370bb4d6437aa9df3905db9d3dd2.json"}}], "type": "journal article", "published": "2023-06-00", "journal": {"title": "Nat. Genet.", "issn": "1546-1718", "volume": "55", "issue": "6", "pages": "973-983", "issn-l": "1061-4036"}, "abstract": "Distinct tissue-specific mechanisms mediate insulin action in fasting and postprandial states. Previous genetic studies have largely focused on insulin resistance in the fasting state, where hepatic insulin action dominates. Here we studied genetic variants influencing insulin levels measured 2 h after a glucose challenge in >55,000 participants from three ancestry groups. We identified ten new loci (P < 5 \u00d7 10-8) not previously associated with postchallenge insulin resistance, eight of which were shown to share their genetic architecture with type 2 diabetes in colocalization analyses. We investigated candidate genes at a subset of associated loci in cultured cells and identified nine candidate genes newly implicated in the expression or trafficking of GLUT4, the key glucose transporter in postprandial glucose uptake in muscle and fat. By focusing on postprandial insulin resistance, we highlighted the mechanisms of action at type 2 diabetes loci that are not adequately captured by studies of fasting glycemic traits.", "doi": "10.1038/s41588-023-01408-9", "pmid": "37291194", "labels": {"NGI SNP genotyping": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "mid", "key": "EMS178611"}, {"db": "pmc", "key": "PMC7614755"}, {"db": "pii", "key": "10.1038/s41588-023-01408-9"}], "notes": [], "created": "2023-11-29T10:58:43.096Z", "modified": "2023-11-29T10:58:43.909Z"}, {"entity": "publication", "iuid": "2ace00d184224d9a8da1fe7ded82ae91", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2ace00d184224d9a8da1fe7ded82ae91.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2ace00d184224d9a8da1fe7ded82ae91"}}, "title": "The Swedish childhood tumor biobank: systematic collection and molecular characterization of all pediatric CNS and other solid tumors in Sweden.", "authors": [{"family": "D\u00edaz de St\u00e5hl", "given": "Teresita", "initials": "T", "orcid": "0000-0001-5933-6623", "researcher": {"href": "https://publications.scilifelab.se/researcher/2f51158ce6e14f3b96bf16a214689d1d.json"}}, {"family": "Shamikh", "given": "Alia", "initials": "A"}, {"family": "Mayrhofer", "given": "Markus", "initials": "M"}, {"family": "Juhos", "given": "Szilvester", "initials": "S"}, {"family": "Basmaci", "given": "Elisa", "initials": "E"}, {"family": "Prochazka", "given": "Gabriela", "initials": "G"}, {"family": "Garcia", "given": "Maxime", "initials": "M"}, {"family": "Somarajan", "given": "Praveen Raj", "initials": "PR"}, {"family": "Zielinska-Chomej", "given": "Katarzyna", "initials": "K"}, {"family": "Illies", "given": "Christopher", "initials": "C"}, {"family": "\u00d8ra", "given": "Ingrid", "initials": "I"}, {"family": "Siesj\u00f6", "given": "Peter", "initials": "P"}, {"family": "Sandstr\u00f6m", "given": "Per-Erik", "initials": "P"}, {"family": "Stenman", "given": "Jakob", "initials": "J"}, {"family": "Sabel", "given": "Magnus", "initials": "M"}, {"family": "Gustavsson", "given": "Bengt", "initials": "B"}, {"family": "Kogner", "given": "Per", "initials": "P"}, {"family": "Pfeifer", "given": "Susan", "initials": "S"}, {"family": "Ljungman", "given": "Gustaf", "initials": "G"}, {"family": "Sandgren", "given": "Johanna", "initials": "J"}, {"family": "Nist\u00e9r", "given": "Monica", "initials": "M"}], "type": "journal article", "published": "2023-05-23", "journal": {"title": "J Transl Med", "issn": "1479-5876", "issn-l": "1479-5876", "volume": "21", "issue": "1", "pages": "342"}, "abstract": "The Swedish Childhood Tumor Biobank (BTB) is a nonprofit national infrastructure for collecting tissue samples and genomic data from pediatric patients diagnosed with central nervous system (CNS) and other solid tumors. The BTB is built on a multidisciplinary network established to provide the scientific community with standardized biospecimens and genomic data, thereby improving knowledge of the biology, treatment and outcome of childhood tumors. As of 2022, over 1100 fresh-frozen tumor samples are available for researchers. We present the workflow of the BTB from sample collection and processing to the generation of genomic data and services offered. To determine the research and clinical utility of the data, we performed bioinformatics analyses on next-generation sequencing (NGS) data obtained from a subset of 82 brain tumors and patient blood-derived DNA combined with methylation profiling to enhance the diagnostic accuracy and identified germline and somatic alterations with potential biological or clinical significance. The BTB procedures for collection, processing, sequencing, and bioinformatics deliver high-quality data. We observed that the findings could impact patient management by confirming or clarifying the diagnosis in 79 of the 82 tumors and detecting known or likely driver mutations in 68 of 79 patients. In addition to revealing known mutations in a broad spectrum of genes implicated in pediatric cancer, we discovered numerous alterations that may represent novel driver events and specific tumor entities. In summary, these examples reveal the power of NGS to identify a wide number of actionable gene alterations. Making the power of NGS available in healthcare is a challenging task requiring the integration of the work of clinical specialists and cancer biologists; this approach requires a dedicated infrastructure, as exemplified here by the BTB.", "doi": "10.1186/s12967-023-04178-4", "pmid": "37221626", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Collaborative", "NGI Short read": "Collaborative", "NGI Stockholm (Genomics Production)": "Collaborative", "NGI SNP genotyping": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC10204274"}, {"db": "pii", "key": "10.1186/s12967-023-04178-4"}], "notes": [], "created": "2023-07-07T10:40:17.052Z", "modified": "2024-01-16T13:48:33.377Z"}, {"entity": "publication", "iuid": "b1ca32c9035c4f99ba117f53cb7df654", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b1ca32c9035c4f99ba117f53cb7df654.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b1ca32c9035c4f99ba117f53cb7df654"}}, "title": "SAG-RAD: A Method for Single-Cell Population Genomics of Unicellular Eukaryotes.", "authors": [{"family": "Gollnisch", "given": "Raphael", "initials": "R", "orcid": "0000-0001-6177-8877", "researcher": {"href": "https://publications.scilifelab.se/researcher/4f78f6e8cacf4eba9104fbfd2ab26f66.json"}}, {"family": "Wallenius", "given": "Joel", "initials": "J"}, {"family": "Gribble", "given": "Kristin E", "initials": "KE"}, {"family": "Ahr\u00e9n", "given": "Dag", "initials": "D"}, {"family": "Rengefors", "given": "Karin", "initials": "K"}], "type": "journal article", "published": "2023-05-02", "journal": {"title": "Mol. Biol. Evol.", "issn": "1537-1719", "issn-l": "0737-4038", "volume": "40", "issue": "5", "pages": null}, "abstract": "Sequencing of reduced representation libraries enables genotyping of many individuals for population genomic studies. However, high amounts of DNA are required, and the method cannot be applied directly on single cells, preventing its use on most microbes. We developed and implemented the analysis of single amplified genomes followed by restriction-site-associated DNA sequencing to bypass labor-intensive culturing and to avoid culturing bias in population genomic studies of unicellular eukaryotes. This method thus opens the way for addressing important questions about the genetic diversity, gene flow, adaptation, dispersal, and biogeography of hitherto unexplored species.", "doi": "10.1093/molbev/msad095", "pmid": "37079883", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC10202595"}, {"db": "pii", "key": "7133828"}], "notes": [], "created": "2023-05-24T12:59:17.974Z", "modified": "2024-01-16T13:48:33.441Z"}, {"entity": "publication", "iuid": "2110e1a811fc4f6db742533b43bdd50a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2110e1a811fc4f6db742533b43bdd50a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2110e1a811fc4f6db742533b43bdd50a"}}, "title": "Comparative assessment of the bacterial communities associated with Anopheles darlingi immature stages and their breeding sites in the Brazilian Amazon.", "authors": [{"family": "Mosquera", "given": "Katherine D", "initials": "KD"}, {"family": "Nilsson", "given": "Louise K J", "initials": "LKJ"}, {"family": "de Oliveira", "given": "Marta Rodrigues", "initials": "MR"}, {"family": "Rocha", "given": "Elerson Matos", "initials": "EM"}, {"family": "Marinotti", "given": "Osvaldo", "initials": "O"}, {"family": "H\u00e5kansson", "given": "Sebastian", "initials": "S"}, {"family": "Tadei", "given": "Wanderli P", "initials": "WP"}, {"family": "de Souza", "given": "Antonia Queiroz Lima", "initials": "AQL"}, {"family": "Terenius", "given": "Olle", "initials": "O"}], "type": "journal article", "published": "2023-05-01", "journal": {"title": "Parasit Vectors", "issn": "1756-3305", "volume": "16", "issue": "1", "pages": "156", "issn-l": "1756-3305"}, "abstract": "The neotropical anopheline mosquito Anopheles darlingi is a major malaria vector in the Americas. Studies on mosquito-associated microbiota have shown that symbiotic bacteria play a major role in host biology. Mosquitoes acquire and transmit microorganisms over their life cycle. Specifically, the microbiota of immature forms is largely acquired from their aquatic environment. Therefore, our study aimed to describe the microbial communities associated with An. darlingi immature forms and their breeding sites in the Coari municipality, Brazilian Amazon.\n\nLarvae, pupae, and breeding water were collected in two different geographical locations. Samples were submitted for DNA extraction and high-throughput 16S rRNA gene sequencing was conducted. Microbial ecology analyses were performed to explore and compare the bacterial profiles of An. darlingi and their aquatic habitats.\n\nWe found lower richness and diversity in An. darlingi microbiota than in water samples, which suggests that larvae are colonized by a subset of the bacterial community present in their breeding sites. Moreover, the bacterial community composition of the immature mosquitoes and their breeding water differed according to their collection sites, i.e., the microbiota associated with An. darlingi reflected that in the aquatic habitats where they developed. The three most abundant bacterial classes across the An. darlingi samples were Betaproteobacteria, Clostridia, and Gammaproteobacteria, while across the water samples they were Gammaproteobacteria, Bacilli, and Alphaproteobacteria.\n\nOur findings reinforce the current evidence that the environment strongly shapes the composition and diversity of mosquito microbiota. A better understanding of mosquito-microbe interactions will contribute to identifying microbial candidates impacting host fitness and disease transmission.", "doi": "10.1186/s13071-023-05749-6", "pmid": "37127597", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10150499"}, {"db": "pii", "key": "10.1186/s13071-023-05749-6"}], "notes": [], "created": "2023-05-05T06:04:21.836Z", "modified": "2024-01-16T13:48:33.490Z"}, {"entity": "publication", "iuid": "63814c2828f14ee58cef696374d723d9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/63814c2828f14ee58cef696374d723d9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/63814c2828f14ee58cef696374d723d9"}}, "title": "Trophozoite fitness dictates the intestinal epithelial cell response to Giardia intestinalis infection.", "authors": [{"family": "Gr\u00fcttner", "given": "Jana", "initials": "J", "orcid": "0000-0002-2507-3375", "researcher": {"href": "https://publications.scilifelab.se/researcher/28fb027f36d94b85afb5e1325fd0ed7b.json"}}, {"family": "van Rijn", "given": "Jorik M", "initials": "JM", "orcid": "0000-0003-2865-4455", "researcher": {"href": "https://publications.scilifelab.se/researcher/8f2defce179d4632a4e7d60666417ab2.json"}}, {"family": "Geiser", "given": "Petra", "initials": "P", "orcid": "0000-0003-2785-4201", "researcher": {"href": "https://publications.scilifelab.se/researcher/ae0bf10f41dc4698b19288809bae2dd6.json"}}, {"family": "Florbrant", "given": "Alexandra", "initials": "A", "orcid": "0000-0002-1630-4442", "researcher": {"href": "https://publications.scilifelab.se/researcher/360f8004f9394dabb68f1f9e0725e42c.json"}}, {"family": "Webb", "given": "Dominic-Luc", "initials": "DL", "orcid": "0000-0002-6979-9194", "researcher": {"href": "https://publications.scilifelab.se/researcher/868fca24b48f440eb2417acdb04e73d3.json"}}, {"family": "Hellstr\u00f6m", "given": "Per M", "initials": "PM", "orcid": "0000-0001-8428-0772", "researcher": {"href": "https://publications.scilifelab.se/researcher/e85863b505f34d7e95a23ac127b9d6dc.json"}}, {"family": "Sundbom", "given": "Magnus", "initials": "M", "orcid": "0000-0002-6243-2859", "researcher": {"href": "https://publications.scilifelab.se/researcher/a54316faa45947bd92615d27a38c2b87.json"}}, {"family": "Sellin", "given": "Mikael E", "initials": "ME", "orcid": "0000-0002-8355-0803", "researcher": {"href": "https://publications.scilifelab.se/researcher/f797357bcd3d4447bff96c20873dd500.json"}}, {"family": "Sv\u00e4rd", "given": "Staffan G", "initials": "SG", "orcid": "0000-0002-7392-1746", "researcher": {"href": "https://publications.scilifelab.se/researcher/b01942d70ef84a1db3aaccab65af9c57.json"}}], "type": "journal article", "published": "2023-05-00", "journal": {"title": "PLoS Pathog.", "issn": "1553-7374", "volume": "19", "issue": "5", "pages": "e1011372", "issn-l": "1553-7366"}, "abstract": "Giardia intestinalis is a non-invasive, protozoan parasite infecting the upper small intestine of most mammals. Symptomatic infections cause the diarrhoeal disease giardiasis in humans and animals, but at least half of the infections are asymptomatic. However, the molecular underpinnings of these different outcomes of the infection are still poorly defined. Here, we studied the early transcriptional response to G. intestinalis trophozoites, the disease-causing life-cycle stage, in human enteroid-derived, 2-dimensional intestinal epithelial cell (IEC) monolayers. Trophozoites preconditioned in media that maximise parasite fitness triggered only neglectable inflammatory transcription in the IECs during the first hours of co-incubation. By sharp contrast, \"non-fit\" or lysed trophozoites induced a vigorous IEC transcriptional response, including high up-regulation of many inflammatory cytokines and chemokines. Furthermore, \"fit\" trophozoites could even suppress the stimulatory effect of lysed trophozoites in mixed infections, suggesting active G. intestinalis suppression of the IEC response. By dual-species RNA-sequencing, we defined the IEC and G. intestinalis gene expression programs associated with these differential outcomes of the infection. Taken together, our results inform on how G. intestinalis infection can lead to such highly variable effects on the host, and pinpoints trophozoite fitness as a key determinant of the IEC response to this common parasite.", "doi": "10.1371/journal.ppat.1011372", "pmid": "37141303", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10187934"}, {"db": "pii", "key": "PPATHOGENS-D-22-02213"}], "notes": [], "created": "2023-05-22T07:22:26.525Z", "modified": "2023-05-22T07:22:26.821Z"}, {"entity": "publication", "iuid": "975c24b0b06442ffa2f3706d774f15a8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/975c24b0b06442ffa2f3706d774f15a8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/975c24b0b06442ffa2f3706d774f15a8"}}, "title": "\u200bComparative genomics of Balto, a famous historic dog, captures lost diversity of 1920s sled dogs.", "authors": [{"family": "Moon", "given": "Katherine L", "initials": "KL", "orcid": "0000-0002-0795-3096", "researcher": {"href": "https://publications.scilifelab.se/researcher/4761aeff839047fb977b0a347da4b2cb.json"}}, {"family": "Huson", "given": "Heather J", "initials": "HJ", "orcid": "0000-0001-8299-0447", "researcher": {"href": "https://publications.scilifelab.se/researcher/1d550f894cde4251b5b8e7b41022db7c.json"}}, {"family": "Morrill", "given": "Kathleen", "initials": "K", "orcid": "0000-0002-9139-453X", "researcher": {"href": "https://publications.scilifelab.se/researcher/16283fa15c524fe69225a6b86822f0e3.json"}}, {"family": "Wang", "given": "Ming-Shan", "initials": "M"}, {"family": "Li", "given": "Xue", "initials": "X", "orcid": "0000-0002-9126-2692", "researcher": {"href": "https://publications.scilifelab.se/researcher/bfa777bbc9d34c0e9f4920decc7cdcb3.json"}}, {"family": "Srikanth", "given": "Krishnamoorthy", "initials": "K", "orcid": "0000-0002-5205-193X", "researcher": {"href": "https://publications.scilifelab.se/researcher/ba9ba40f2c594bc18d5ab34ba55d6e6f.json"}}, {"family": "Zoonomia Consortium", "given": "", "initials": ""}, {"family": "Lindblad-Toh", "given": "Kerstin", "initials": "K", "orcid": "0000-0001-8338-0253", "researcher": {"href": "https://publications.scilifelab.se/researcher/e0063145f7d6476f80ab42f94833f4cf.json"}}, {"family": "Svenson", "given": "Gavin J", "initials": "GJ", "orcid": "0000-0003-0207-6458", "researcher": {"href": "https://publications.scilifelab.se/researcher/703555ba027b4719a036ef315366377a.json"}}, {"family": "Karlsson", "given": "Elinor K", "initials": "EK", "orcid": "0000-0002-4343-3776", "researcher": {"href": "https://publications.scilifelab.se/researcher/2bd97378a1cc403db0923895adde15e3.json"}}, {"family": "Shapiro", "given": "Beth", "initials": "B", "orcid": "0000-0002-2733-7776", "researcher": {"href": "https://publications.scilifelab.se/researcher/7e998b6760594d43b00e50c4f6a27d05.json"}}], "type": "journal article", "published": "2023-04-28", "journal": {"title": "Science", "issn": "1095-9203", "issn-l": "0036-8075", "volume": "380", "issue": "6643", "pages": "eabn5887"}, "abstract": "We reconstruct the phenotype of Balto, the heroic sled dog renowned for transporting diphtheria antitoxin to Nome, Alaska, in 1925, using evolutionary constraint estimates from the Zoonomia alignment of 240 mammals and 682 genomes from dogs and wolves of the 21st century. Balto shares just part of his diverse ancestry with the eponymous Siberian husky breed. Balto's genotype predicts a combination of coat features atypical for modern sled dog breeds, and a slightly smaller stature. He had enhanced starch digestion compared with Greenland sled dogs and a compendium of derived homozygous coding variants at constrained positions in genes connected to bone and skin development. We propose that Balto's population of origin, which was less inbred and genetically healthier than that of modern breeds, was adapted to the extreme environment of 1920s Alaska.", "doi": "10.1126/science.abn5887", "pmid": "37104591", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "mid", "key": "NIHMS1893725"}, {"db": "pmc", "key": "PMC10184777"}], "notes": [], "created": "2023-12-01T09:07:28.377Z", "modified": "2024-01-16T13:48:33.546Z"}, {"entity": "publication", "iuid": "8ee42fe5c10a4a589cf92177bcc10041", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8ee42fe5c10a4a589cf92177bcc10041.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8ee42fe5c10a4a589cf92177bcc10041"}}, "title": "Three-dimensional genome rewiring in loci with human accelerated regions.", "authors": [{"family": "Keough", "given": "Kathleen C", "initials": "KC", "orcid": "0000-0002-7481-0511", "researcher": {"href": "https://publications.scilifelab.se/researcher/60254d61d3d64a8e80eee17c1e3d24db.json"}}, {"family": "Whalen", "given": "Sean", "initials": "S", "orcid": "0000-0002-6648-3610", "researcher": {"href": "https://publications.scilifelab.se/researcher/1a791e66720648dd817179e8626dfe69.json"}}, {"family": "Inoue", "given": "Fumitaka", "initials": "F", "orcid": "0000-0003-0657-434X", "researcher": {"href": "https://publications.scilifelab.se/researcher/c48d37d0d68e4b0a96010704bb7d2136.json"}}, {"family": "Przytycki", "given": "Pawel F", "initials": "PF", "orcid": "0000-0002-3360-6936", "researcher": {"href": "https://publications.scilifelab.se/researcher/cdeddfa32b3e41318e8cd6fea8b619f1.json"}}, {"family": "Fair", "given": "Tyler", "initials": "T"}, {"family": "Deng", "given": "Chengyu", "initials": "C", "orcid": "0000-0003-3595-9935", "researcher": {"href": "https://publications.scilifelab.se/researcher/25f79619fa6f46ce9bb13a6abcad6165.json"}}, {"family": "Steyert", "given": "Marilyn", "initials": "M", "orcid": "0000-0003-4095-4776", "researcher": {"href": "https://publications.scilifelab.se/researcher/9940f9ae5fcd43ed8582432bfe8588d5.json"}}, {"family": "Ryu", "given": "Hane", "initials": "H"}, {"family": "Lindblad-Toh", "given": "Kerstin", "initials": "K", "orcid": "0000-0001-8338-0253", "researcher": {"href": "https://publications.scilifelab.se/researcher/e0063145f7d6476f80ab42f94833f4cf.json"}}, {"family": "Karlsson", "given": "Elinor", "initials": "E", "orcid": "0000-0002-4343-3776", "researcher": {"href": "https://publications.scilifelab.se/researcher/2bd97378a1cc403db0923895adde15e3.json"}}, {"family": "Zoonomia Consortium\u00a7", "given": "", "initials": ""}, {"family": "Nowakowski", "given": "Tomasz", "initials": "T", "orcid": "0000-0003-2345-4964", "researcher": {"href": "https://publications.scilifelab.se/researcher/9afca838449f4601844b1462c2ceb953.json"}}, {"family": "Ahituv", "given": "Nadav", "initials": "N", "orcid": "0000-0002-7434-8144", "researcher": {"href": "https://publications.scilifelab.se/researcher/24ed3745c2ab498c98cd24d6766c9019.json"}}, {"family": "Pollen", "given": "Alex", "initials": "A", "orcid": "0000-0003-3263-8634", "researcher": {"href": "https://publications.scilifelab.se/researcher/9a70ab2e0b994621b4993fe25baed4fe.json"}}, {"family": "Pollard", "given": "Katherine S", "initials": "KS", "orcid": "0000-0002-9870-6196", "researcher": {"href": "https://publications.scilifelab.se/researcher/bb2a865a28524f55bb5d9df3db79563f.json"}}], "type": "journal article", "published": "2023-04-28", "journal": {"title": "Science", "issn": "1095-9203", "issn-l": "0036-8075", "volume": "380", "issue": "6643", "pages": "eabm1696"}, "abstract": "Human accelerated regions (HARs) are conserved genomic loci that evolved at an accelerated rate in the human lineage and may underlie human-specific traits. We generated HARs and chimpanzee accelerated regions with an automated pipeline and an alignment of 241 mammalian genomes. Combining deep learning with chromatin capture experiments in human and chimpanzee neural progenitor cells, we discovered a significant enrichment of HARs in topologically associating domains containing human-specific genomic variants that change three-dimensional (3D) genome organization. Differential gene expression between humans and chimpanzees at these loci suggests rewiring of regulatory interactions between HARs and neurodevelopmental genes. Thus, comparative genomics together with models of 3D genome folding revealed enhancer hijacking as an explanation for the rapid evolution of HARs.", "doi": "10.1126/science.abm1696", "pmid": "37104607", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2023-12-01T08:54:13.311Z", "modified": "2024-01-16T13:48:33.575Z"}, {"entity": "publication", "iuid": "0c70433579774cc297a55baabec049ea", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0c70433579774cc297a55baabec049ea.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0c70433579774cc297a55baabec049ea"}}, "title": "The functional and evolutionary impacts of human-specific deletions in conserved elements.", "authors": [{"family": "Xue", "given": "James R", "initials": "JR", "orcid": "0000-0002-3332-5747", "researcher": {"href": "https://publications.scilifelab.se/researcher/c910e64598674d5da576b3b5057afb43.json"}}, {"family": "Mackay-Smith", "given": "Ava", "initials": "A", "orcid": "0000-0003-0404-0563", "researcher": {"href": "https://publications.scilifelab.se/researcher/a60ce7b39d8c4b25bfddc8b8cd460970.json"}}, {"family": "Mouri", "given": "Kousuke", "initials": "K", "orcid": "0000-0003-1712-6833", "researcher": {"href": "https://publications.scilifelab.se/researcher/66c28c463e194c4395f03776335db2f1.json"}}, {"family": "Garcia", "given": "Meilin Fernandez", "initials": "MF", "orcid": "0000-0002-8745-9775", "researcher": {"href": "https://publications.scilifelab.se/researcher/c28f08d4f61f4c07ae57f56d220ab158.json"}}, {"family": "Dong", "given": "Michael X", "initials": "MX", "orcid": "0000-0003-4084-3099", "researcher": {"href": "https://publications.scilifelab.se/researcher/d44d219b319346c481c82d69d5055cd8.json"}}, {"family": "Akers", "given": "Jared F", "initials": "JF", "orcid": "0000-0002-9270-0017", "researcher": {"href": "https://publications.scilifelab.se/researcher/11555b05f1914cd8b1a63a07335d9f70.json"}}, {"family": "Noble", "given": "Mark", "initials": "M", "orcid": "0000-0002-9618-120X", "researcher": {"href": "https://publications.scilifelab.se/researcher/4d35842f19164723979bd2e19ae4c470.json"}}, {"family": "Li", "given": "Xue", "initials": "X", "orcid": "0000-0002-9126-2692", "researcher": {"href": "https://publications.scilifelab.se/researcher/bfa777bbc9d34c0e9f4920decc7cdcb3.json"}}, {"family": "Zoonomia Consortium\u2020", "given": "", "initials": ""}, {"family": "Lindblad-Toh", "given": "Kerstin", "initials": "K", "orcid": "0000-0001-8338-0253", "researcher": {"href": "https://publications.scilifelab.se/researcher/e0063145f7d6476f80ab42f94833f4cf.json"}}, {"family": "Karlsson", "given": "Elinor K", "initials": "EK", "orcid": "0000-0002-4343-3776", "researcher": {"href": "https://publications.scilifelab.se/researcher/2bd97378a1cc403db0923895adde15e3.json"}}, {"family": "Noonan", "given": "James P", "initials": "JP", "orcid": "0000-0001-9632-5835", "researcher": {"href": "https://publications.scilifelab.se/researcher/4e35cb8e4ed64e5a8c5583b81c29bb65.json"}}, {"family": "Capellini", "given": "Terence D", "initials": "TD", "orcid": "0000-0003-3842-8478", "researcher": {"href": "https://publications.scilifelab.se/researcher/8ca4d388b3314861afe8593858bac9ab.json"}}, {"family": "Brennand", "given": "Kristen J", "initials": "KJ", "orcid": "0000-0003-0993-5956", "researcher": {"href": "https://publications.scilifelab.se/researcher/79ac89080d28492ab5fb4012939b0994.json"}}, {"family": "Tewhey", "given": "Ryan", "initials": "R", "orcid": "0000-0002-4607-8001", "researcher": {"href": "https://publications.scilifelab.se/researcher/08c06e4a031147ec8e0a4692b86a8198.json"}}, {"family": "Sabeti", "given": "Pardis C", "initials": "PC", "orcid": "0000-0002-9843-1890", "researcher": {"href": "https://publications.scilifelab.se/researcher/7a05c59f83114ac68c7bd1a0930fa0c9.json"}}, {"family": "Reilly", "given": "Steven K", "initials": "SK", "orcid": "0000-0003-3140-1483", "researcher": {"href": "https://publications.scilifelab.se/researcher/0c12bcf707394bb5b9c34075aba19f13.json"}}], "type": "journal article", "published": "2023-04-28", "journal": {"title": "Science", "issn": "1095-9203", "issn-l": "0036-8075", "volume": "380", "issue": "6643", "pages": "eabn2253"}, "abstract": "Conserved genomic sequences disrupted in humans may underlie uniquely human phenotypic traits. We identified and characterized 10,032 human-specific conserved deletions (hCONDELs). These short (average 2.56 base pairs) deletions are enriched for human brain functions across genetic, epigenomic, and transcriptomic datasets. Using massively parallel reporter assays in six cell types, we discovered 800 hCONDELs conferring significant differences in regulatory activity, half of which enhance rather than disrupt regulatory function. We highlight several hCONDELs with putative human-specific effects on brain development, including HDAC5, CPEB4, and PPP2CA. Reverting an hCONDEL to the ancestral sequence alters the expression of LOXL2 and developmental genes involved in myelination and synaptic function. Our data provide a rich resource to investigate the evolutionary mechanisms driving new traits in humans and other species.", "doi": "10.1126/science.abn2253", "pmid": "37104592", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "mid", "key": "NIHMS1897409"}, {"db": "pmc", "key": "PMC10202372"}], "notes": [], "created": "2023-12-01T09:07:31.011Z", "modified": "2024-01-16T13:48:33.587Z"}, {"entity": "publication", "iuid": "44039aa0a48d4c0caad589efc02597cf", "links": {"self": {"href": "https://publications.scilifelab.se/publication/44039aa0a48d4c0caad589efc02597cf.json"}, "display": {"href": "https://publications.scilifelab.se/publication/44039aa0a48d4c0caad589efc02597cf"}}, "title": "The contribution of historical processes to contemporary extinction risk in placental mammals.", "authors": [{"family": "Wilder", "given": "Aryn P", "initials": "AP", "orcid": "0000-0003-4970-6891", "researcher": {"href": "https://publications.scilifelab.se/researcher/582a7c9cf0214c8b9063df22f49910d5.json"}}, {"family": "Supple", "given": "Megan A", "initials": "MA", "orcid": "0000-0002-0204-7852", "researcher": {"href": "https://publications.scilifelab.se/researcher/68aab878c786406da6d8810c1ca6eb04.json"}}, {"family": "Subramanian", "given": "Ayshwarya", "initials": "A", "orcid": "0000-0002-4134-7612", "researcher": {"href": "https://publications.scilifelab.se/researcher/fbf15f9b2bd447f49e0bbc5c8d4d3b21.json"}}, {"family": "Mudide", "given": "Anish", "initials": "A", "orcid": "0000-0002-6174-2345", "researcher": {"href": "https://publications.scilifelab.se/researcher/99494338a7704bad94a32a59b2357181.json"}}, {"family": "Swofford", "given": "Ross", "initials": "R", "orcid": "0000-0003-3676-8479", "researcher": {"href": "https://publications.scilifelab.se/researcher/5bf782e1d8b646daa53455586d8bf706.json"}}, {"family": "Serres-Armero", "given": "Aitor", "initials": "A"}, {"family": "Steiner", "given": "Cynthia", "initials": "C", "orcid": "0000-0002-2131-8072", "researcher": {"href": "https://publications.scilifelab.se/researcher/74c6c6b31d4e49628a2a74a1f7377ce5.json"}}, {"family": "Koepfli", "given": "Klaus-Peter", "initials": "K"}, {"family": "Genereux", "given": "Diane P", "initials": "DP", "orcid": "0000-0001-5770-0989", "researcher": {"href": "https://publications.scilifelab.se/researcher/0dedda53aab044eabd09ae377084ff9d.json"}}, {"family": "Karlsson", "given": "Elinor K", "initials": "EK", "orcid": "0000-0002-4343-3776", "researcher": {"href": "https://publications.scilifelab.se/researcher/2bd97378a1cc403db0923895adde15e3.json"}}, {"family": "Lindblad-Toh", "given": "Kerstin", "initials": "K", "orcid": "0000-0001-8338-0253", "researcher": {"href": "https://publications.scilifelab.se/researcher/e0063145f7d6476f80ab42f94833f4cf.json"}}, {"family": "Marques-Bonet", "given": "Tomas", "initials": "T", "orcid": "0000-0002-5597-3075", "researcher": {"href": "https://publications.scilifelab.se/researcher/b4ea50a4fe3147f3b979ccaa8a2a0de4.json"}}, {"family": "Munoz Fuentes", "given": "Violeta", "initials": "V", "orcid": "0000-0003-3574-546X", "researcher": {"href": "https://publications.scilifelab.se/researcher/8f2bdc1125af4e71b43d057c36e76967.json"}}, {"family": "Foley", "given": "Kathleen", "initials": "K", "orcid": "0000-0003-0923-1326", "researcher": {"href": "https://publications.scilifelab.se/researcher/03f76d7e48d843d39046582156da3615.json"}}, {"family": "Meyer", "given": "Wynn K", "initials": "WK", "orcid": "0000-0001-7978-3877", "researcher": {"href": "https://publications.scilifelab.se/researcher/d168f23b63994217b3b082c3cd70561b.json"}}, {"family": "Zoonomia Consortium\u2021", "given": "", "initials": ""}, {"family": "Ryder", "given": "Oliver A", "initials": "OA", "orcid": "0000-0003-2427-763X", "researcher": {"href": "https://publications.scilifelab.se/researcher/7a55f8ea442f4168a8426ae4a2c43a46.json"}}, {"family": "Shapiro", "given": "Beth", "initials": "B", "orcid": "0000-0002-2733-7776", "researcher": {"href": "https://publications.scilifelab.se/researcher/7e998b6760594d43b00e50c4f6a27d05.json"}}], "type": "journal article", "published": "2023-04-28", "journal": {"title": "Science", "issn": "1095-9203", "issn-l": "0036-8075", "volume": "380", "issue": "6643", "pages": "eabn5856"}, "abstract": "Species persistence can be influenced by the amount, type, and distribution of diversity across the genome, suggesting a potential relationship between historical demography and resilience. In this study, we surveyed genetic variation across single genomes of 240 mammals that compose the Zoonomia alignment to evaluate how historical effective population size (Ne) affects heterozygosity and deleterious genetic load and how these factors may contribute to extinction risk. We find that species with smaller historical Ne carry a proportionally larger burden of deleterious alleles owing to long-term accumulation and fixation of genetic load and have a higher risk of extinction. This suggests that historical demography can inform contemporary resilience. Models that included genomic data were predictive of species' conservation status, suggesting that, in the absence of adequate census or ecological data, genomic information may provide an initial risk assessment.", "doi": "10.1126/science.abn5856", "pmid": "37104572", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "mid", "key": "NIHMS1893031"}, {"db": "pmc", "key": "PMC10184782"}], "notes": [], "created": "2023-12-01T08:54:18.907Z", "modified": "2024-01-16T13:48:33.595Z"}, {"entity": "publication", "iuid": "bfb6fdc7339947a692119410b04c42a1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/bfb6fdc7339947a692119410b04c42a1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/bfb6fdc7339947a692119410b04c42a1"}}, "title": "Relating enhancer genetic variation across mammals to complex phenotypes using machine learning.", "authors": [{"family": "Kaplow", "given": "Irene M", "initials": "IM", "orcid": "0000-0002-8924-8269", "researcher": {"href": "https://publications.scilifelab.se/researcher/9bbc94842b1f4195b678beee7cc8cf6e.json"}}, {"family": "Lawler", "given": "Alyssa J", "initials": "AJ", "orcid": "0000-0002-2151-5164", "researcher": {"href": "https://publications.scilifelab.se/researcher/9ac870df8d074925b9956e82fba828eb.json"}}, {"family": "Sch\u00e4ffer", "given": "Daniel E", "initials": "DE", "orcid": "0000-0003-3608-152X", "researcher": {"href": "https://publications.scilifelab.se/researcher/0be4ccbb9fd247eaa3320c4f1a8d64dc.json"}}, {"family": "Srinivasan", "given": "Chaitanya", "initials": "C", "orcid": "0000-0002-1487-541X", "researcher": {"href": "https://publications.scilifelab.se/researcher/a1f3803c67844809b8d460e321034287.json"}}, {"family": "Sestili", "given": "Heather H", "initials": "HH", "orcid": "0000-0002-3944-3429", "researcher": {"href": "https://publications.scilifelab.se/researcher/247a3b572c934443a8b06bf1eeab2e06.json"}}, {"family": "Wirthlin", "given": "Morgan E", "initials": "ME", "orcid": "0000-0001-7967-7070", "researcher": {"href": "https://publications.scilifelab.se/researcher/d37d43eda07f49fa8f44adf0d1f41b5a.json"}}, {"family": "Phan", "given": "BaDoi N", "initials": "BN", "orcid": "0000-0001-6331-5980", "researcher": {"href": "https://publications.scilifelab.se/researcher/b9e37df4e5c54204a19ea394e1f7651e.json"}}, {"family": "Prasad", "given": "Kavya", "initials": "K", "orcid": "0000-0003-3419-5670", "researcher": {"href": "https://publications.scilifelab.se/researcher/68bbc313fcd344e2adb1ab5d8d7f8581.json"}}, {"family": "Brown", "given": "Ashley R", "initials": "AR", "orcid": "0000-0002-3091-3930", "researcher": {"href": "https://publications.scilifelab.se/researcher/31ed0f654aa3485e8b2a02f902981f32.json"}}, {"family": "Zhang", "given": "Xiaomeng", "initials": "X", "orcid": "0000-0002-8536-6460", "researcher": {"href": "https://publications.scilifelab.se/researcher/2f4e1e573fa54ccc88171795e61d2a7a.json"}}, {"family": "Foley", "given": "Kathleen", "initials": "K", "orcid": "0000-0003-0923-1326", "researcher": {"href": "https://publications.scilifelab.se/researcher/03f76d7e48d843d39046582156da3615.json"}}, {"family": "Genereux", "given": "Diane P", "initials": "DP", "orcid": "0000-0001-5770-0989", "researcher": {"href": "https://publications.scilifelab.se/researcher/0dedda53aab044eabd09ae377084ff9d.json"}}, {"family": "Zoonomia Consortium**", "given": "", "initials": ""}, {"family": "Karlsson", "given": "Elinor K", "initials": "EK", "orcid": "0000-0002-4343-3776", "researcher": {"href": "https://publications.scilifelab.se/researcher/2bd97378a1cc403db0923895adde15e3.json"}}, {"family": "Lindblad-Toh", "given": "Kerstin", "initials": "K", "orcid": "0000-0001-8338-0253", "researcher": {"href": "https://publications.scilifelab.se/researcher/e0063145f7d6476f80ab42f94833f4cf.json"}}, {"family": "Meyer", "given": "Wynn K", "initials": "WK", "orcid": "0000-0001-7978-3877", "researcher": {"href": "https://publications.scilifelab.se/researcher/d168f23b63994217b3b082c3cd70561b.json"}}, {"family": "Pfenning", "given": "Andreas R", "initials": "AR", "orcid": "0000-0002-3447-9801", "researcher": {"href": "https://publications.scilifelab.se/researcher/579e32fe57da4d738b7fbf0a57fb6faf.json"}}], "type": "journal article", "published": "2023-04-28", "journal": {"title": "Science", "issn": "1095-9203", "issn-l": "0036-8075", "volume": "380", "issue": "6643", "pages": "eabm7993"}, "abstract": "Protein-coding differences between species often fail to explain phenotypic diversity, suggesting the involvement of genomic elements that regulate gene expression such as enhancers. Identifying associations between enhancers and phenotypes is challenging because enhancer activity can be tissue-dependent and functionally conserved despite low sequence conservation. We developed the Tissue-Aware Conservation Inference Toolkit (TACIT) to associate candidate enhancers with species' phenotypes using predictions from machine learning models trained on specific tissues. Applying TACIT to associate motor cortex and parvalbumin-positive interneuron enhancers with neurological phenotypes revealed dozens of enhancer-phenotype associations, including brain size-associated enhancers that interact with genes implicated in microcephaly or macrocephaly. TACIT provides a foundation for identifying enhancers associated with the evolution of any convergently evolved phenotype in any large group of species with aligned genomes.", "doi": "10.1126/science.abm7993", "pmid": "37104615", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "mid", "key": "NIHMS1897368"}, {"db": "pmc", "key": "PMC10322212"}], "notes": [], "created": "2023-12-01T09:07:36.543Z", "modified": "2024-01-16T13:48:33.603Z"}, {"entity": "publication", "iuid": "c579ad21c5b84f01bac1beeb5e447116", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c579ad21c5b84f01bac1beeb5e447116.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c579ad21c5b84f01bac1beeb5e447116"}}, "title": "Mammalian evolution of human cis-regulatory elements and transcription factor binding sites.", "authors": [{"family": "Andrews", "given": "Gregory", "initials": "G", "orcid": "0000-0002-9880-3965", "researcher": {"href": "https://publications.scilifelab.se/researcher/3f84c888473d45ea8d8e97945d508705.json"}}, {"family": "Fan", "given": "Kaili", "initials": "K", "orcid": "0000-0002-8723-7902", "researcher": {"href": "https://publications.scilifelab.se/researcher/1f65b033be1343e48895a7c99903717c.json"}}, {"family": "Pratt", "given": "Henry E", "initials": "HE", "orcid": "0000-0001-9413-834X", "researcher": {"href": "https://publications.scilifelab.se/researcher/c565845faf8049c6b076a0470fe95b1a.json"}}, {"family": "Phalke", "given": "Nishigandha", "initials": "N"}, {"family": "Zoonomia Consortium\u00a7", "given": "", "initials": ""}, {"family": "Karlsson", "given": "Elinor K", "initials": "EK", "orcid": "0000-0002-4343-3776", "researcher": {"href": "https://publications.scilifelab.se/researcher/2bd97378a1cc403db0923895adde15e3.json"}}, {"family": "Lindblad-Toh", "given": "Kerstin", "initials": "K", "orcid": "0000-0001-8338-0253", "researcher": {"href": "https://publications.scilifelab.se/researcher/e0063145f7d6476f80ab42f94833f4cf.json"}}, {"family": "Gazal", "given": "Steven", "initials": "S", "orcid": "0000-0003-4510-5730", "researcher": {"href": "https://publications.scilifelab.se/researcher/fecc8307017145088589536e3c312515.json"}}, {"family": "Moore", "given": "Jill E", "initials": "JE", "orcid": "0000-0002-3023-0806", "researcher": {"href": "https://publications.scilifelab.se/researcher/cfa6791c7bf0450298988030f7c64667.json"}}, {"family": "Weng", "given": "Zhiping", "initials": "Z", "orcid": "0000-0002-3032-7966", "researcher": {"href": "https://publications.scilifelab.se/researcher/25ad44250cba4b0cba5250b07f764ba3.json"}}], "type": "journal article", "published": "2023-04-28", "journal": {"title": "Science", "issn": "1095-9203", "issn-l": "0036-8075", "volume": "380", "issue": "6643", "pages": "eabn7930"}, "abstract": "Understanding the regulatory landscape of the human genome is a long-standing objective of modern biology. Using the reference-free alignment across 241 mammalian genomes produced by the Zoonomia Consortium, we charted evolutionary trajectories for 0.92 million human candidate cis-regulatory elements (cCREs) and 15.6 million human transcription factor binding sites (TFBSs). We identified 439,461 cCREs and 2,024,062 TFBSs under evolutionary constraint. Genes near constrained elements perform fundamental cellular processes, whereas genes near primate-specific elements are involved in environmental interaction, including odor perception and immune response. About 20% of TFBSs are transposable element-derived and exhibit intricate patterns of gains and losses during primate evolution whereas sequence variants associated with complex traits are enriched in constrained TFBSs. Our annotations illuminate the regulatory functions of the human genome.", "doi": "10.1126/science.abn7930", "pmid": "37104580", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": null}, "xrefs": [], "notes": [], "created": "2023-12-01T08:31:26.561Z", "modified": "2024-01-16T13:48:33.610Z"}, {"entity": "publication", "iuid": "6cea0eb350cd40bba54717d8b627da6b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6cea0eb350cd40bba54717d8b627da6b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6cea0eb350cd40bba54717d8b627da6b"}}, "title": "Leveraging base-pair mammalian constraint to understand genetic variation and human disease.", "authors": [{"family": "Sullivan", "given": "Patrick F", "initials": "PF", "orcid": "0000-0002-6619-873X", "researcher": {"href": "https://publications.scilifelab.se/researcher/4d95de0b5ab14586980a6a13c8299346.json"}}, {"family": "Meadows", "given": "Jennifer R S", "initials": "JRS", "orcid": "0000-0002-0850-230X", "researcher": {"href": "https://publications.scilifelab.se/researcher/86acdca0104c4552880d5a7cb5ac6565.json"}}, {"family": "Gazal", "given": "Steven", "initials": "S", "orcid": "0000-0003-4510-5730", "researcher": {"href": "https://publications.scilifelab.se/researcher/fecc8307017145088589536e3c312515.json"}}, {"family": "Phan", "given": "BaDoi N", "initials": "BN", "orcid": "0000-0001-6331-5980", "researcher": {"href": "https://publications.scilifelab.se/researcher/b9e37df4e5c54204a19ea394e1f7651e.json"}}, {"family": "Li", "given": "Xue", "initials": "X", "orcid": "0000-0002-9126-2692", "researcher": {"href": "https://publications.scilifelab.se/researcher/bfa777bbc9d34c0e9f4920decc7cdcb3.json"}}, {"family": "Genereux", "given": "Diane P", "initials": "DP", "orcid": "0000-0001-5770-0989", "researcher": {"href": "https://publications.scilifelab.se/researcher/0dedda53aab044eabd09ae377084ff9d.json"}}, {"family": "Dong", "given": "Michael X", "initials": "MX", "orcid": "0000-0003-4084-3099", "researcher": {"href": "https://publications.scilifelab.se/researcher/d44d219b319346c481c82d69d5055cd8.json"}}, {"family": "Bianchi", "given": "Matteo", "initials": "M", "orcid": "0000-0003-3394-6495", "researcher": {"href": "https://publications.scilifelab.se/researcher/d645ef0e04a245f0ac9e7d7498b2bd69.json"}}, {"family": "Andrews", "given": "Gregory", "initials": "G", "orcid": "0000-0002-9880-3965", "researcher": {"href": "https://publications.scilifelab.se/researcher/3f84c888473d45ea8d8e97945d508705.json"}}, {"family": "Sakthikumar", "given": "Sharadha", "initials": "S", "orcid": "0000-0002-7746-8264", "researcher": {"href": "https://publications.scilifelab.se/researcher/538c86311b2549d6a5214a5562578cc2.json"}}, {"family": "Nordin", "given": "Jessika", "initials": "J", "orcid": "0000-0002-8414-2190", "researcher": {"href": "https://publications.scilifelab.se/researcher/2603df7f3ff84e6980605b9e8eef4c2f.json"}}, {"family": "Roy", "given": "Ananya", "initials": "A"}, {"family": "Christmas", "given": "Matthew J", "initials": "MJ", "orcid": "0000-0002-6355-7581", "researcher": {"href": "https://publications.scilifelab.se/researcher/76e069a0271e4a1fbc31fd3cb440366f.json"}}, {"family": "Marinescu", "given": "Voichita D", "initials": "VD", "orcid": "0000-0002-4803-4707", "researcher": {"href": "https://publications.scilifelab.se/researcher/087384bb1f8743158b76352c8847d48d.json"}}, {"family": "Wang", "given": "Chao", "initials": "C", "orcid": "0000-0003-3936-4023", "researcher": {"href": "https://publications.scilifelab.se/researcher/202a8fd115e14824809a362a7cfc5a41.json"}}, {"family": "Wallerman", "given": "Ola", "initials": "O", "orcid": "0000-0003-1037-7904", "researcher": {"href": "https://publications.scilifelab.se/researcher/9b32e1cfd3084b10a4c220416a6bc589.json"}}, {"family": "Xue", "given": "James", "initials": "J", "orcid": "0000-0002-3332-5747", "researcher": {"href": "https://publications.scilifelab.se/researcher/c910e64598674d5da576b3b5057afb43.json"}}, {"family": "Yao", "given": "Shuyang", "initials": "S", "orcid": "0000-0001-9669-4470", "researcher": {"href": "https://publications.scilifelab.se/researcher/fcd036ee020e4622ad16d020bfcd7b38.json"}}, {"family": "Sun", "given": "Quan", "initials": "Q", "orcid": "0000-0001-8324-2803", "researcher": {"href": "https://publications.scilifelab.se/researcher/ed5ee3899858449cae82e6be2e6faca6.json"}}, {"family": "Szatkiewicz", "given": "Jin", "initials": "J", "orcid": "0000-0002-4898-7401", "researcher": {"href": "https://publications.scilifelab.se/researcher/eb39edd3c6c14938a47f1e22ecfea080.json"}}, {"family": "Wen", "given": "Jia", "initials": "J"}, {"family": "Huckins", "given": "Laura M", "initials": "LM", "orcid": "0000-0002-5369-6502", "researcher": {"href": "https://publications.scilifelab.se/researcher/aef1cd06be604bc9ac483e888bf2235d.json"}}, {"family": "Lawler", "given": "Alyssa", "initials": "A", "orcid": "0000-0002-2151-5164", "researcher": {"href": "https://publications.scilifelab.se/researcher/9ac870df8d074925b9956e82fba828eb.json"}}, {"family": "Keough", "given": "Kathleen C", "initials": "KC", "orcid": "0000-0002-7481-0511", "researcher": {"href": "https://publications.scilifelab.se/researcher/60254d61d3d64a8e80eee17c1e3d24db.json"}}, {"family": "Zheng", "given": "Zhili", "initials": "Z", "orcid": "0000-0003-2102-221X", "researcher": {"href": "https://publications.scilifelab.se/researcher/d6856724cd504fca8624fc001f9e6381.json"}}, {"family": "Zeng", "given": "Jian", "initials": "J", "orcid": "0000-0001-8801-5220", "researcher": {"href": "https://publications.scilifelab.se/researcher/483f4a2875dd42a68b4f6f4e18c503ec.json"}}, {"family": "Wray", "given": "Naomi R", "initials": "NR", "orcid": "0000-0001-7421-3357", "researcher": {"href": "https://publications.scilifelab.se/researcher/15a175036d9f44f9b4090d7d431f78d7.json"}}, {"family": "Li", "given": "Yun", "initials": "Y", "orcid": "0000-0002-9275-4189", "researcher": {"href": "https://publications.scilifelab.se/researcher/c294ce82ce8946428048b9b4e3e9cad8.json"}}, {"family": "Johnson", "given": "Jessica", "initials": "J", "orcid": "0000-0002-4519-3120", "researcher": {"href": "https://publications.scilifelab.se/researcher/c2cc5da674c44d4cb58c1f98d145043a.json"}}, {"family": "Chen", "given": "Jiawen", "initials": "J", "orcid": "0000-0002-6193-534X", "researcher": {"href": "https://publications.scilifelab.se/researcher/39de15a492f34e4b8e237e748c38524b.json"}}, {"family": "Zoonomia Consortium\u00a7", "given": "", "initials": ""}, {"family": "Paten", "given": "Benedict", "initials": "B", "orcid": "0000-0001-8863-3539", "researcher": {"href": "https://publications.scilifelab.se/researcher/956ebe9c0b6e43d7ac2a568519f43431.json"}}, {"family": "Reilly", "given": "Steven K", "initials": "SK", "orcid": "0000-0003-3140-1483", "researcher": {"href": "https://publications.scilifelab.se/researcher/0c12bcf707394bb5b9c34075aba19f13.json"}}, {"family": "Hughes", "given": "Graham M", "initials": "GM", "orcid": "0000-0003-3088-345X", "researcher": {"href": "https://publications.scilifelab.se/researcher/800da869332a45b9b4c7bd8fd5522666.json"}}, {"family": "Weng", "given": "Zhiping", "initials": "Z", "orcid": "0000-0002-3032-7966", "researcher": {"href": "https://publications.scilifelab.se/researcher/25ad44250cba4b0cba5250b07f764ba3.json"}}, {"family": "Pollard", "given": "Katherine S", "initials": "KS", "orcid": "0000-0002-9870-6196", "researcher": {"href": "https://publications.scilifelab.se/researcher/bb2a865a28524f55bb5d9df3db79563f.json"}}, {"family": "Pfenning", "given": "Andreas R", "initials": "AR", "orcid": "0000-0002-3447-9801", "researcher": {"href": "https://publications.scilifelab.se/researcher/579e32fe57da4d738b7fbf0a57fb6faf.json"}}, {"family": "Forsberg-Nilsson", "given": "Karin", "initials": "K", "orcid": "0000-0003-0692-6245", "researcher": {"href": "https://publications.scilifelab.se/researcher/5da04859250141a0a7271a69c7da9176.json"}}, {"family": "Karlsson", "given": "Elinor K", "initials": "EK", "orcid": "0000-0002-4343-3776", "researcher": {"href": "https://publications.scilifelab.se/researcher/2bd97378a1cc403db0923895adde15e3.json"}}, {"family": "Lindblad-Toh", "given": "Kerstin", "initials": "K", "orcid": "0000-0001-8338-0253", "researcher": {"href": "https://publications.scilifelab.se/researcher/e0063145f7d6476f80ab42f94833f4cf.json"}}], "type": "journal article", "published": "2023-04-28", "journal": {"title": "Science", "issn": "1095-9203", "issn-l": "0036-8075", "volume": "380", "issue": "6643", "pages": "eabn2937"}, "abstract": "Thousands of genomic regions have been associated with heritable human diseases, but attempts to elucidate biological mechanisms are impeded by an inability to discern which genomic positions are functionally important. Evolutionary constraint is a powerful predictor of function, agnostic to cell type or disease mechanism. Single-base phyloP scores from 240 mammals identified 3.3% of the human genome as significantly constrained and likely functional. We compared phyloP scores to genome annotation, association studies, copy-number variation, clinical genetics findings, and cancer data. Constrained positions are enriched for variants that explain common disease heritability more than other functional annotations. Our results improve variant annotation but also highlight that the regulatory landscape of the human genome still needs to be further explored and linked to disease.", "doi": "10.1126/science.abn2937", "pmid": "37104612", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "mid", "key": "NIHMS1897004"}, {"db": "pmc", "key": "PMC10259825"}], "notes": [], "created": "2023-12-01T08:54:10.456Z", "modified": "2024-01-16T13:48:33.619Z"}, {"entity": "publication", "iuid": "048080e8a4d44a78bbecf7078f9d6901", "links": {"self": {"href": "https://publications.scilifelab.se/publication/048080e8a4d44a78bbecf7078f9d6901.json"}, "display": {"href": "https://publications.scilifelab.se/publication/048080e8a4d44a78bbecf7078f9d6901"}}, "title": "Integrating gene annotation with orthology inference at scale.", "authors": [{"family": "Kirilenko", "given": "Bogdan M", "initials": "BM", "orcid": "0000-0002-9394-4275", "researcher": {"href": "https://publications.scilifelab.se/researcher/104f94382f604235ac8edd862204924e.json"}}, {"family": "Munegowda", "given": "Chetan", "initials": "C", "orcid": "0000-0002-3790-2185", "researcher": {"href": "https://publications.scilifelab.se/researcher/5ffdf84352a347a790277d9a7debbe28.json"}}, {"family": "Osipova", "given": "Ekaterina", "initials": "E", "orcid": "0000-0002-6769-7223", "researcher": {"href": "https://publications.scilifelab.se/researcher/f048ee0785094c2fa3e5b79eba6d1900.json"}}, {"family": "Jebb", "given": "David", "initials": "D"}, {"family": "Sharma", "given": "Virag", "initials": "V", "orcid": "0000-0003-4086-4105", "researcher": {"href": "https://publications.scilifelab.se/researcher/5bfd936285cc49c6b40d3c3d0ee4ed26.json"}}, {"family": "Blumer", "given": "Moritz", "initials": "M", "orcid": "0000-0002-5775-1767", "researcher": {"href": "https://publications.scilifelab.se/researcher/58505e8b013b4428bb69b52b1d2f5cf1.json"}}, {"family": "Morales", "given": "Ariadna E", "initials": "AE", "orcid": "0000-0002-0637-7349", "researcher": {"href": "https://publications.scilifelab.se/researcher/0d82eb099b284f068e85ba556ef1cbf5.json"}}, {"family": "Ahmed", "given": "Alexis-Walid", "initials": "A"}, {"family": "Kontopoulos", "given": "Dimitrios-Georgios", "initials": "D"}, {"family": "Hilgers", "given": "Leon", "initials": "L", "orcid": "0000-0002-3539-2513", "researcher": {"href": "https://publications.scilifelab.se/researcher/819689e4085e481b931f20d96a395a27.json"}}, {"family": "Lindblad-Toh", "given": "Kerstin", "initials": "K", "orcid": "0000-0001-8338-0253", "researcher": {"href": "https://publications.scilifelab.se/researcher/e0063145f7d6476f80ab42f94833f4cf.json"}}, {"family": "Karlsson", "given": "Elinor K", "initials": "EK", "orcid": "0000-0002-4343-3776", "researcher": {"href": "https://publications.scilifelab.se/researcher/2bd97378a1cc403db0923895adde15e3.json"}}, {"family": "Zoonomia Consortium\u2021", "given": "", "initials": ""}, {"family": "Hiller", "given": "Michael", "initials": "M", "orcid": "0000-0003-3024-1449", "researcher": {"href": "https://publications.scilifelab.se/researcher/c304600adfb24d45a7bd0c94f55d1f5b.json"}}], "type": "journal article", "published": "2023-04-28", "journal": {"title": "Science", "issn": "1095-9203", "issn-l": "0036-8075", "volume": "380", "issue": "6643", "pages": "eabn3107"}, "abstract": "Annotating coding genes and inferring orthologs are two classical challenges in genomics and evolutionary biology that have traditionally been approached separately, limiting scalability. We present TOGA (Tool to infer Orthologs from Genome Alignments), a method that integrates structural gene annotation and orthology inference. TOGA implements a different paradigm to infer orthologous loci, improves ortholog detection and annotation of conserved genes compared with state-of-the-art methods, and handles even highly fragmented assemblies. TOGA scales to hundreds of genomes, which we demonstrate by applying it to 488 placental mammal and 501 bird assemblies, creating the largest comparative gene resources so far. Additionally, TOGA detects gene losses, enables selection screens, and automatically provides a superior measure of mammalian genome quality. TOGA is a powerful and scalable method to annotate and compare genes in the genomic era.", "doi": "10.1126/science.abn3107", "pmid": "37104600", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "mid", "key": "NIHMS1898035"}, {"db": "pmc", "key": "PMC10193443"}], "notes": [], "created": "2023-12-01T09:07:33.771Z", "modified": "2024-01-16T13:48:33.629Z"}, {"entity": "publication", "iuid": "1b55f000e45e48569ce691e5f288112a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1b55f000e45e48569ce691e5f288112a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1b55f000e45e48569ce691e5f288112a"}}, "title": "Insights into mammalian TE diversity through the curation of 248 genome assemblies.", "authors": [{"family": "Osmanski", "given": "Austin B", "initials": "AB", "orcid": "0000-0002-1485-6446", "researcher": {"href": "https://publications.scilifelab.se/researcher/861bdbbf0e72446795a267d6d0a4cb81.json"}}, {"family": "Paulat", "given": "Nicole S", "initials": "NS", "orcid": "0000-0002-6881-2588", "researcher": {"href": "https://publications.scilifelab.se/researcher/58778de33da041ceba1481ae528dbb0c.json"}}, {"family": "Korstian", "given": "Jenny", "initials": "J", "orcid": "0000-0003-3872-8948", "researcher": {"href": "https://publications.scilifelab.se/researcher/c3541cf73dab433cace7f4e670155278.json"}}, {"family": "Grimshaw", "given": "Jenna R", "initials": "JR", "orcid": "0000-0001-7673-5167", "researcher": {"href": "https://publications.scilifelab.se/researcher/1658aea21a524780b67bfdca293ab1d0.json"}}, {"family": "Halsey", "given": "Michaela", "initials": "M"}, {"family": "Sullivan", "given": "Kevin A M", "initials": "KAM", "orcid": "0000-0001-8499-0491", "researcher": {"href": "https://publications.scilifelab.se/researcher/13f0fe7f177c4422bd5ab25dd2a070c6.json"}}, {"family": "Moreno-Santill\u00e1n", "given": "Diana D", "initials": "DD", "orcid": "0000-0003-2153-0732", "researcher": {"href": "https://publications.scilifelab.se/researcher/460f9988264e4be58157b65c376561b0.json"}}, {"family": "Crookshanks", "given": "Claudia", "initials": "C"}, {"family": "Roberts", "given": "Jacquelyn", "initials": "J"}, {"family": "Garcia", "given": "Carlos", "initials": "C", "orcid": "0000-0001-9194-4514", "researcher": {"href": "https://publications.scilifelab.se/researcher/f836e2eaf97a4f09837704347f112324.json"}}, {"family": "Johnson", "given": "Matthew G", "initials": "MG", "orcid": "0000-0002-1958-6334", "researcher": {"href": "https://publications.scilifelab.se/researcher/5e75a950635a403eb0e34a15cdf0fef2.json"}}, {"family": "Densmore", "given": "Llewellyn D", "initials": "LD", "orcid": "0000-0002-6681-5507", "researcher": {"href": "https://publications.scilifelab.se/researcher/941b0334a8374ec79bfaf95881b370ff.json"}}, {"family": "Stevens", "given": "Richard D", "initials": "RD"}, {"family": "Zoonomia Consortium\u2020", "given": "", "initials": ""}, {"family": "Rosen", "given": "Jeb", "initials": "J", "orcid": "0000-0002-8832-1276", "researcher": {"href": "https://publications.scilifelab.se/researcher/39406330ee844bdbb9476ee472ff44a8.json"}}, {"family": "Storer", "given": "Jessica M", "initials": "JM", "orcid": "0000-0002-9619-5265", "researcher": {"href": "https://publications.scilifelab.se/researcher/17dbab57213847a8b685d1fd7d0885d8.json"}}, {"family": "Hubley", "given": "Robert", "initials": "R", "orcid": "0000-0001-9261-3821", "researcher": {"href": "https://publications.scilifelab.se/researcher/76c6f83d0eb34efc9e50811d6af5a0b1.json"}}, {"family": "Smit", "given": "Arian F A", "initials": "AFA", "orcid": "0000-0003-2088-3165", "researcher": {"href": "https://publications.scilifelab.se/researcher/34068300dba84e9f80ffde962a8ca49b.json"}}, {"family": "D\u00e1valos", "given": "Liliana M", "initials": "LM", "orcid": "0000-0002-4327-7697", "researcher": {"href": "https://publications.scilifelab.se/researcher/3c73133e743c4560a2660c7ab5b036cd.json"}}, {"family": "Karlsson", "given": "Elinor K", "initials": "EK", "orcid": "0000-0002-4343-3776", "researcher": {"href": "https://publications.scilifelab.se/researcher/2bd97378a1cc403db0923895adde15e3.json"}}, {"family": "Lindblad-Toh", "given": "Kerstin", "initials": "K", "orcid": "0000-0001-8338-0253", "researcher": {"href": "https://publications.scilifelab.se/researcher/e0063145f7d6476f80ab42f94833f4cf.json"}}, {"family": "Ray", "given": "David A", "initials": "DA", "orcid": "0000-0002-3340-3987", "researcher": {"href": "https://publications.scilifelab.se/researcher/1637808586b2454190e734d575cf0140.json"}}], "type": "journal article", "published": "2023-04-28", "journal": {"title": "Science", "issn": "1095-9203", "issn-l": "0036-8075", "volume": "380", "issue": "6643", "pages": "eabn1430"}, "abstract": "We examined transposable element (TE) content of 248 placental mammal genome assemblies, the largest de novo TE curation effort in eukaryotes to date. We found that although mammals resemble one another in total TE content and diversity, they show substantial differences with regard to recent TE accumulation. This includes multiple recent expansion and quiescence events across the mammalian tree. Young TEs, particularly long interspersed elements, drive increases in genome size, whereas DNA transposons are associated with smaller genomes. Mammals tend to accumulate only a few types of TEs at any given time, with one TE type dominating. We also found association between dietary habit and the presence of DNA transposon invasions. These detailed annotations will serve as a benchmark for future comparative TE analyses among placental mammals.", "doi": "10.1126/science.abn1430", "pmid": "37104570", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2023-12-01T08:54:16.075Z", "modified": "2024-01-16T13:48:33.640Z"}, {"entity": "publication", "iuid": "d7e4da3ff4c54966b53e2e1210128441", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d7e4da3ff4c54966b53e2e1210128441.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d7e4da3ff4c54966b53e2e1210128441"}}, "title": "Evolutionary constraint and innovation across hundreds of placental mammals.", "authors": [{"family": "Christmas", "given": "Matthew J", "initials": "MJ", "orcid": "0000-0002-6355-7581", "researcher": {"href": "https://publications.scilifelab.se/researcher/76e069a0271e4a1fbc31fd3cb440366f.json"}}, {"family": "Kaplow", "given": "Irene M", "initials": "IM", "orcid": "0000-0002-8924-8269", "researcher": {"href": "https://publications.scilifelab.se/researcher/9bbc94842b1f4195b678beee7cc8cf6e.json"}}, {"family": "Genereux", "given": "Diane P", "initials": "DP", "orcid": "0000-0001-5770-0989", "researcher": {"href": "https://publications.scilifelab.se/researcher/0dedda53aab044eabd09ae377084ff9d.json"}}, {"family": "Dong", "given": "Michael X", "initials": "MX", "orcid": "0000-0003-4084-3099", "researcher": {"href": "https://publications.scilifelab.se/researcher/d44d219b319346c481c82d69d5055cd8.json"}}, {"family": "Hughes", "given": "Graham M", "initials": "GM", "orcid": "0000-0003-3088-345X", "researcher": {"href": "https://publications.scilifelab.se/researcher/800da869332a45b9b4c7bd8fd5522666.json"}}, {"family": "Li", "given": "Xue", "initials": "X", "orcid": "0000-0002-9126-2692", "researcher": 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{"href": "https://publications.scilifelab.se/researcher/b6be89ad73a14d66a3b9439efc9c4099.json"}}, {"family": "Lawler", "given": "Alyssa J", "initials": "AJ", "orcid": "0000-0002-2151-5164", "researcher": {"href": "https://publications.scilifelab.se/researcher/9ac870df8d074925b9956e82fba828eb.json"}}, {"family": "Marinescu", "given": "Voichita D", "initials": "VD", "orcid": "0000-0002-4803-4707", "researcher": {"href": "https://publications.scilifelab.se/researcher/087384bb1f8743158b76352c8847d48d.json"}}, {"family": "Morrill", "given": "Kathleen M", "initials": "KM", "orcid": "0000-0002-9139-453X", "researcher": {"href": "https://publications.scilifelab.se/researcher/16283fa15c524fe69225a6b86822f0e3.json"}}, {"family": "Osmanski", "given": "Austin", "initials": "A", "orcid": "0000-0002-1485-6446", "researcher": {"href": "https://publications.scilifelab.se/researcher/861bdbbf0e72446795a267d6d0a4cb81.json"}}, {"family": "Paulat", "given": "Nicole S", "initials": "NS", "orcid": "0000-0002-6881-2588", "researcher": {"href": "https://publications.scilifelab.se/researcher/58778de33da041ceba1481ae528dbb0c.json"}}, {"family": "Phan", "given": "BaDoi N", "initials": "BN", "orcid": "0000-0001-6331-5980", "researcher": {"href": "https://publications.scilifelab.se/researcher/b9e37df4e5c54204a19ea394e1f7651e.json"}}, {"family": "Reilly", "given": "Steven K", "initials": "SK", "orcid": "0000-0003-3140-1483", "researcher": {"href": "https://publications.scilifelab.se/researcher/0c12bcf707394bb5b9c34075aba19f13.json"}}, {"family": "Sch\u00e4ffer", "given": "Daniel E", "initials": "DE", "orcid": "0000-0003-3608-152X", "researcher": {"href": "https://publications.scilifelab.se/researcher/0be4ccbb9fd247eaa3320c4f1a8d64dc.json"}}, {"family": "Steiner", "given": "Cynthia", "initials": "C", "orcid": "0000-0002-2131-8072", "researcher": {"href": "https://publications.scilifelab.se/researcher/74c6c6b31d4e49628a2a74a1f7377ce5.json"}}, {"family": "Supple", "given": "Megan A", "initials": "MA", "orcid": "0000-0002-0204-7852", "researcher": {"href": "https://publications.scilifelab.se/researcher/68aab878c786406da6d8810c1ca6eb04.json"}}, {"family": "Wilder", "given": "Aryn P", "initials": "AP", "orcid": "0000-0003-4970-6891", "researcher": {"href": "https://publications.scilifelab.se/researcher/582a7c9cf0214c8b9063df22f49910d5.json"}}, {"family": "Wirthlin", "given": "Morgan E", "initials": "ME", "orcid": "0000-0001-7967-7070", "researcher": {"href": "https://publications.scilifelab.se/researcher/d37d43eda07f49fa8f44adf0d1f41b5a.json"}}, {"family": "Xue", "given": "James R", "initials": "JR", "orcid": "0000-0002-3332-5747", "researcher": {"href": "https://publications.scilifelab.se/researcher/c910e64598674d5da576b3b5057afb43.json"}}, {"family": "Zoonomia Consortium\u00a7", "given": "", "initials": ""}, {"family": "Birren", "given": "Bruce W", "initials": "BW"}, {"family": "Gazal", "given": "Steven", "initials": "S", "orcid": "0000-0003-4510-5730", "researcher": {"href": "https://publications.scilifelab.se/researcher/fecc8307017145088589536e3c312515.json"}}, {"family": "Hubley", "given": "Robert M", "initials": "RM", "orcid": "0000-0001-9261-3821", "researcher": {"href": "https://publications.scilifelab.se/researcher/76c6f83d0eb34efc9e50811d6af5a0b1.json"}}, {"family": "Koepfli", "given": "Klaus-Peter", "initials": "K"}, {"family": "Marques-Bonet", "given": "Tomas", "initials": "T", "orcid": "0000-0002-5597-3075", "researcher": {"href": "https://publications.scilifelab.se/researcher/b4ea50a4fe3147f3b979ccaa8a2a0de4.json"}}, {"family": "Meyer", "given": "Wynn K", "initials": "WK", "orcid": "0000-0001-7978-3877", "researcher": {"href": "https://publications.scilifelab.se/researcher/d168f23b63994217b3b082c3cd70561b.json"}}, {"family": "Nweeia", "given": "Martin", "initials": "M", "orcid": "0000-0001-7079-4123", "researcher": {"href": "https://publications.scilifelab.se/researcher/32d99c20badf4462b17eb73d543bd766.json"}}, {"family": "Sabeti", "given": "Pardis C", "initials": "PC", "orcid": "0000-0002-9843-1890", "researcher": {"href": "https://publications.scilifelab.se/researcher/7a05c59f83114ac68c7bd1a0930fa0c9.json"}}, {"family": "Shapiro", "given": "Beth", "initials": "B", "orcid": "0000-0002-2733-7776", "researcher": {"href": "https://publications.scilifelab.se/researcher/7e998b6760594d43b00e50c4f6a27d05.json"}}, {"family": "Smit", "given": "Arian F A", "initials": "AFA", "orcid": "0000-0003-2088-3165", "researcher": {"href": "https://publications.scilifelab.se/researcher/34068300dba84e9f80ffde962a8ca49b.json"}}, {"family": "Springer", "given": "Mark S", "initials": "MS", "orcid": "0000-0001-7335-6946", "researcher": {"href": "https://publications.scilifelab.se/researcher/fb2b4f352f9b4e8b9f20da68caa94912.json"}}, {"family": "Teeling", "given": "Emma C", "initials": "EC", "orcid": "0000-0002-3309-1346", "researcher": {"href": "https://publications.scilifelab.se/researcher/50529df15a684ed68e16de6aa981d3aa.json"}}, {"family": "Weng", "given": "Zhiping", "initials": "Z", "orcid": "0000-0002-3032-7966", "researcher": {"href": "https://publications.scilifelab.se/researcher/25ad44250cba4b0cba5250b07f764ba3.json"}}, {"family": "Hiller", "given": "Michael", "initials": "M", "orcid": "0000-0003-3024-1449", "researcher": {"href": "https://publications.scilifelab.se/researcher/c304600adfb24d45a7bd0c94f55d1f5b.json"}}, {"family": "Levesque", "given": "Danielle L", "initials": "DL", "orcid": "0000-0003-0132-8094", "researcher": {"href": "https://publications.scilifelab.se/researcher/c8f6270f0b104f8ba5d216b052d36a0c.json"}}, {"family": "Lewin", "given": "Harris A", "initials": "HA", "orcid": "0000-0002-1043-7287", "researcher": {"href": "https://publications.scilifelab.se/researcher/a2f6f17d3e4b4b7e8f47349bda4c1bb0.json"}}, {"family": "Murphy", "given": "William J", "initials": "WJ", "orcid": "0000-0003-3699-0723", "researcher": {"href": "https://publications.scilifelab.se/researcher/bedfc4bc5b6e421da56cfe2bebfa21f3.json"}}, {"family": "Navarro", "given": "Arcadi", "initials": "A", "orcid": "0000-0003-2162-8246", "researcher": {"href": "https://publications.scilifelab.se/researcher/c541642111d94cb8a682b1ff8bea41ac.json"}}, {"family": "Paten", "given": "Benedict", "initials": "B", "orcid": "0000-0001-8863-3539", "researcher": {"href": "https://publications.scilifelab.se/researcher/956ebe9c0b6e43d7ac2a568519f43431.json"}}, {"family": "Pollard", "given": "Katherine S", "initials": "KS", "orcid": "0000-0002-9870-6196", "researcher": {"href": "https://publications.scilifelab.se/researcher/bb2a865a28524f55bb5d9df3db79563f.json"}}, {"family": "Ray", "given": "David A", "initials": "DA", "orcid": "0000-0002-3340-3987", "researcher": {"href": "https://publications.scilifelab.se/researcher/1637808586b2454190e734d575cf0140.json"}}, {"family": "Ruf", "given": "Irina", "initials": "I", "orcid": "0000-0002-9728-1210", "researcher": {"href": "https://publications.scilifelab.se/researcher/838b4e91f9484f26a6dcc1404051a38a.json"}}, {"family": "Ryder", "given": "Oliver A", "initials": "OA", "orcid": "0000-0003-2427-763X", "researcher": {"href": "https://publications.scilifelab.se/researcher/7a55f8ea442f4168a8426ae4a2c43a46.json"}}, {"family": "Pfenning", "given": "Andreas R", "initials": "AR", "orcid": "0000-0002-3447-9801", "researcher": {"href": "https://publications.scilifelab.se/researcher/579e32fe57da4d738b7fbf0a57fb6faf.json"}}, {"family": "Lindblad-Toh", "given": "Kerstin", "initials": "K", "orcid": "0000-0001-8338-0253", "researcher": {"href": "https://publications.scilifelab.se/researcher/e0063145f7d6476f80ab42f94833f4cf.json"}}, {"family": "Karlsson", "given": "Elinor K", "initials": "EK", "orcid": "0000-0002-4343-3776", "researcher": {"href": "https://publications.scilifelab.se/researcher/2bd97378a1cc403db0923895adde15e3.json"}}], "type": "journal article", "published": "2023-04-28", "journal": {"title": "Science", "issn": "1095-9203", "issn-l": "0036-8075", "volume": "380", "issue": "6643", "pages": "eabn3943"}, "abstract": "Zoonomia is the largest comparative genomics resource for mammals produced to date. By aligning genomes for 240 species, we identify bases that, when mutated, are likely to affect fitness and alter disease risk. At least 332 million bases (~10.7%) in the human genome are unusually conserved across species (evolutionarily constrained) relative to neutrally evolving repeats, and 4552 ultraconserved elements are nearly perfectly conserved. Of 101 million significantly constrained single bases, 80% are outside protein-coding exons and half have no functional annotations in the Encyclopedia of DNA Elements (ENCODE) resource. Changes in genes and regulatory elements are associated with exceptional mammalian traits, such as hibernation, that could inform therapeutic development. Earth's vast and imperiled biodiversity offers distinctive power for identifying genetic variants that affect genome function and organismal phenotypes.", "doi": "10.1126/science.abn3943", "pmid": "37104599", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "mid", "key": "NIHMS1896905"}, {"db": "pmc", "key": "PMC10250106"}], "notes": [], "created": "2023-12-01T08:40:50.036Z", "modified": "2024-01-16T13:48:33.655Z"}, {"entity": "publication", "iuid": "5da7c081abc141ff8b4814107fd6c56d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5da7c081abc141ff8b4814107fd6c56d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5da7c081abc141ff8b4814107fd6c56d"}}, "title": "A genomic timescale for placental mammal evolution.", "authors": [{"family": "Foley", "given": "Nicole M", "initials": "NM", "orcid": "0000-0002-8169-9436", "researcher": {"href": "https://publications.scilifelab.se/researcher/6a0b5fa8c458409794479e010bdf8425.json"}}, {"family": "Mason", "given": "Victor C", "initials": "VC"}, {"family": "Harris", "given": "Andrew J", "initials": "AJ", "orcid": "0000-0001-6373-7446", "researcher": {"href": "https://publications.scilifelab.se/researcher/2c2b9909ba9147b39741671de325f90f.json"}}, {"family": "Bredemeyer", "given": "Kevin R", "initials": "KR", "orcid": "0000-0002-1374-6050", "researcher": {"href": "https://publications.scilifelab.se/researcher/54402aedeec3424588e9bdffabd77c0f.json"}}, {"family": "Damas", "given": "Joana", "initials": "J", "orcid": "0000-0003-4857-2510", "researcher": {"href": "https://publications.scilifelab.se/researcher/86c0daf03cc84d55a831bfe99448a389.json"}}, {"family": "Lewin", "given": "Harris A", "initials": "HA", "orcid": "0000-0002-1043-7287", "researcher": {"href": "https://publications.scilifelab.se/researcher/a2f6f17d3e4b4b7e8f47349bda4c1bb0.json"}}, {"family": "Eizirik", "given": "Eduardo", "initials": "E", "orcid": "0000-0002-9658-0999", "researcher": {"href": "https://publications.scilifelab.se/researcher/102a98d00d9b4643aafb72e08a273ac9.json"}}, {"family": "Gatesy", "given": "John", "initials": "J", "orcid": "0000-0003-3061-7741", "researcher": {"href": "https://publications.scilifelab.se/researcher/be557f53354548e584381076522b78ba.json"}}, {"family": "Karlsson", "given": "Elinor K", "initials": "EK", "orcid": "0000-0002-4343-3776", "researcher": {"href": "https://publications.scilifelab.se/researcher/2bd97378a1cc403db0923895adde15e3.json"}}, {"family": "Lindblad-Toh", "given": "Kerstin", "initials": "K", "orcid": "0000-0001-8338-0253", "researcher": {"href": "https://publications.scilifelab.se/researcher/e0063145f7d6476f80ab42f94833f4cf.json"}}, {"family": "Zoonomia Consortium\u2021", "given": "", "initials": ""}, {"family": "Springer", "given": "Mark S", "initials": "MS", "orcid": "0000-0001-7335-6946", "researcher": {"href": "https://publications.scilifelab.se/researcher/fb2b4f352f9b4e8b9f20da68caa94912.json"}}, {"family": "Murphy", "given": "William J", "initials": "WJ", "orcid": "0000-0003-3699-0723", "researcher": {"href": "https://publications.scilifelab.se/researcher/bedfc4bc5b6e421da56cfe2bebfa21f3.json"}}], "type": "journal article", "published": "2023-04-28", "journal": {"title": "Science", "issn": "1095-9203", "issn-l": "0036-8075", "volume": "380", "issue": "6643", "pages": "eabl8189"}, "abstract": "The precise pattern and timing of speciation events that gave rise to all living placental mammals remain controversial. We provide a comprehensive phylogenetic analysis of genetic variation across an alignment of 241 placental mammal genome assemblies, addressing prior concerns regarding limited genomic sampling across species. We compared neutral genome-wide phylogenomic signals using concatenation and coalescent-based approaches, interrogated phylogenetic variation across chromosomes, and analyzed extensive catalogs of structural variants. Interordinal relationships exhibit relatively low rates of phylogenomic conflict across diverse datasets and analytical methods. Conversely, X-chromosome versus autosome conflicts characterize multiple independent clades that radiated during the Cenozoic. Genomic time trees reveal an accumulation of cladogenic events before and immediately after the Cretaceous-Paleogene (K-Pg) boundary, implying important roles for Cretaceous continental vicariance and the K-Pg extinction in the placental radiation.", "doi": "10.1126/science.abl8189", "pmid": "37104581", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "mid", "key": "NIHMS1897334"}, {"db": "pmc", "key": "PMC10233747"}], "notes": [], "created": "2023-12-01T08:38:42.154Z", "modified": "2024-01-16T13:48:33.669Z"}, {"entity": "publication", "iuid": "0cbfeedb7a3041fd81710b5b601f31d2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0cbfeedb7a3041fd81710b5b601f31d2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0cbfeedb7a3041fd81710b5b601f31d2"}}, "title": "Prominent epigenetic and transcriptomic changes in CD4+ and CD8+ T cells during and after pregnancy in women with multiple sclerosis and controls.", "authors": [{"family": "Zenere", "given": "Alberto", "initials": "A"}, {"family": "Hellberg", "given": "Sandra", "initials": "S"}, {"family": "Papapavlou Lingehed", "given": "Georgia", "initials": "G"}, {"family": "Svenvik", "given": "Maria", "initials": "M"}, {"family": "Mellerg\u00e5rd", "given": "Johan", "initials": "J"}, {"family": "Dahle", "given": "Charlotte", "initials": "C"}, {"family": "Vrethem", "given": "Magnus", "initials": "M"}, {"family": "Raffetseder", "given": "Johanna", "initials": "J"}, {"family": "Khademi", "given": "Mohsen", "initials": "M"}, {"family": "Olsson", "given": "Tomas", "initials": "T"}, {"family": "Blomberg", "given": "Marie", "initials": "M"}, {"family": "Jenmalm", "given": "Maria C", "initials": "MC"}, {"family": "Altafini", "given": "Claudio", "initials": "C"}, {"family": "Gustafsson", "given": "Mika", "initials": "M"}, {"family": "Ernerudh", "given": "Jan", "initials": "J"}], "type": "journal article", "published": "2023-04-27", "journal": {"title": "J Neuroinflammation", "issn": "1742-2094", "issn-l": "1742-2094", "volume": "20", "issue": "1", "pages": "98"}, "abstract": "Multiple sclerosis (MS) is a neuroinflammatory disease in which pregnancy leads to a temporary amelioration in disease activity as indicated by the profound decrease in relapses rate during the 3rd trimester of pregnancy. CD4+ and CD8+ T cells are implicated in MS pathogenesis as being key regulators of inflammation and brain lesion formation. Although Tcells are prime candidates for the pregnancy-associated improvement of MS, the precise mechanisms are yet unclear, and in particular, a deep characterization of the epigenetic and transcriptomic events that occur in peripheral T cells during pregnancy in MS is lacking.\r\n\r\nWomen with MS and healthy controls were longitudinally sampled before, during (1st, 2nd and 3rd trimesters) and after pregnancy. DNA methylation array and RNA sequencing were performed on paired CD4+ and CD8+ T cells samples. Differential analysis and network-based approaches were used to analyze the global dynamics of epigenetic and transcriptomic changes.\r\n\r\nBoth DNA methylation and RNA sequencing revealed a prominent regulation, mostly peaking in the 3rd trimester and reversing post-partum, thus mirroring the clinical course with improvement followed by a worsening in disease activity. This rebound pattern was found to represent a general adaptation of the maternal immune system, with only minor differences between MS and controls. By using a network-based approach, we highlighted several genes at the core of this pregnancy-induced regulation, which were found to be enriched for genes and pathways previously reported to be involved in MS. Moreover, these pathways were enriched for in vitro stimulated genes and pregnancy hormones targets.\r\n\r\nThis study represents, to our knowledge, the first in-depth investigation of the methylation and expression changes in peripheral CD4+ and CD8+ T cells during pregnancy in MS. Our findings indicate that pregnancy induces profound changes in peripheral T cells, in both MS and healthy controls, which are associated with the modulation of inflammation and MS activity.", "doi": "10.1186/s12974-023-02781-2", "pmid": "37106402", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI SNP genotyping": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10134602"}, {"db": "pii", "key": "10.1186/s12974-023-02781-2"}], "notes": [], "created": "2023-05-15T11:41:52.874Z", "modified": "2023-06-02T15:24:54.894Z"}, {"entity": "publication", "iuid": "03f6f1b4cfe24ceea3859aa58e725308", "links": {"self": {"href": "https://publications.scilifelab.se/publication/03f6f1b4cfe24ceea3859aa58e725308.json"}, "display": {"href": "https://publications.scilifelab.se/publication/03f6f1b4cfe24ceea3859aa58e725308"}}, "title": "Low-grade glioma risk SNP rs11706832 is associated with type I interferon response pathway genes in cell lines.", "authors": [{"family": "Rosenbaum", "given": "Adam", "initials": "A"}, {"family": "Dahlin", "given": "Anna M", "initials": "AM"}, {"family": "Andersson", "given": "Ulrika", "initials": "U"}, {"family": "Bj\u00f6rkblom", "given": "Benny", "initials": "B"}, {"family": "Wu", "given": "Wendy Yi-Ying", "initials": "WY"}, {"family": "Hedman", "given": "H\u00e5kan", "initials": "H"}, {"family": "Wibom", "given": "Carl", "initials": "C"}, {"family": "Melin", "given": "Beatrice", "initials": "B"}], "type": "journal article", "published": "2023-04-25", "journal": {"title": "Sci Rep", "issn": "2045-2322", "issn-l": "2045-2322", "volume": "13", "issue": "1", "pages": "6777"}, "abstract": "Genome-wide association studies (GWAS) have contributed to our understanding of glioma susceptibility. To date, 25 risk loci for development of any of the glioma subtypes are known. However, GWAS studies reveal little about the molecular processes that lead to increased risk, especially for non-coding single nucleotide polymorphisms (SNP). A particular SNP in intron 2 of LRIG1, rs11706832, has been shown to increase the susceptibility for IDH1 mutated low-grade gliomas (LGG). Leucine-rich repeats and immunoglobulin-like domains protein 1 (LRIG1) is important in cancer development as it negatively regulates the epidermal growth factor receptor (EGFR); however, the mechanism responsible for this particular risk SNP and its potential effect on LRIG1 are not known. Using CRISPR-CAS9, we edited rs11706832 in HEK293T cells. Four HEK293T clones with the risk allele were compared to four clones with the non-risk allele for LRIG1 and SLC25A26 gene expression using RT-qPCR, for global gene expression using RNA-seq, and for metabolites using gas chromatography-mass spectrometry (GC-MS). The experiment did not reveal any significant effect of the SNP on the expression levels or splicing patterns of LRIG1 or SLC25A26. The global gene expression analysis revealed that the risk allele C was associated with upregulation of several mitochondrial genes. Gene enrichment analysis of 74 differentially expressed genes in the genome revealed a significant enrichment of type I interferon response genes, where many genes were downregulated for the risk allele C. Gene expression data of IDH1 mutated LGGs from the cancer genome atlas (TCGA) revealed a similar under expression of type I interferon genes associated with the risk allele. This study found the expression levels and splicing patterns of LRIG1 and SLC25A26 were not affected by the SNP in HEK293T cells. However, the risk allele was associated with a downregulation of genes involved in the innate immune response both in the HEK293T cells and in the LGG data from TCGA.", "doi": "10.1038/s41598-023-33923-4", "pmid": "37185361", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service", "Swedish Metabolomics Centre": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10130147"}, {"db": "pii", "key": "10.1038/s41598-023-33923-4"}], "notes": [], "created": "2023-08-30T07:04:23.132Z", "modified": "2025-10-17T13:03:14.040Z"}, {"entity": "publication", "iuid": "b7ade62398f54e0284d41dfed05b1a6e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b7ade62398f54e0284d41dfed05b1a6e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b7ade62398f54e0284d41dfed05b1a6e"}}, "title": "Longitudinal associations between use of antihypertensive, antidiabetic, and lipid-lowering medications and biological aging.", "authors": [{"family": "Tang", "given": "Bowen", "initials": "B"}, {"family": "Li", "given": "Xia", "initials": "X"}, {"family": "Wang", "given": "Yunzhang", "initials": "Y"}, {"family": "Sj\u00f6lander", "given": "Arvid", "initials": "A"}, {"family": "Johnell", "given": "Kristina", "initials": "K"}, {"family": "Thambisetty", "given": "Madhav", "initials": "M"}, {"family": "Ferrucci", "given": "Luigi", "initials": "L"}, {"family": "Reynolds", "given": "Chandra A", "initials": "CA"}, {"family": "Finkel", "given": "Deborah", "initials": "D"}, {"family": "Jylh\u00e4v\u00e4", "given": "Juulia", "initials": "J"}, {"family": "Pedersen", "given": "Nancy L", "initials": "NL"}, {"family": "H\u00e4gg", "given": "Sara", "initials": "S", "orcid": "0000-0002-2452-1500", "researcher": {"href": "https://publications.scilifelab.se/researcher/e1d010dfe5d84a33b6a6c7ec815ca3dc.json"}}], "type": "journal article", "published": "2023-04-10", "journal": {"title": "Geroscience", "issn": "2509-2723", "issn-l": null, "volume": null, "issue": null, "pages": null}, "abstract": "Aging is a major risk factor for many chronic diseases. This study aimed to examine the effects of antihypertensive, lipid-lowering, and antidiabetic drugs on biological aging. We included 672 participants and 2746 repeated measurements from the Swedish Adoption/Twin Study of Aging. Self-reported medicine uses were categorized into antidiabetic, antihypertensive, and lipid-lowering drugs. A total of 12 biomarkers for biological aging (BA biomarkers) were included as outcomes. Conditional generalized estimating equations were applied conditioning on individuals to estimate the drug effect on BA biomarker level within the same person when using or not using the drug. Chronological age, body mass index, smoking status, number of multiple medication uses, blood pressure, blood glucose level, and apoB/apoA ratio were adjusted for as covariates in the model. Overall, using antihypertensive drugs was associated with a decrease in one DNA-methylation age (PCGrimAge: beta = - 0.39, 95%CI = - 0.67 to - 0.12). When looking into drug subcategories, calcium channel blockers (CCBs) were associated with a decrease in several DNA-methylation ages (PCHorvathAge beta = - 1.28, 95%CI = - 2.34 to - 0.21; PCSkin&bloodAge beta = - 1.34, 95%CI = - 2.61 to - 0.07; PCPhenoAge beta = - 1.74, 95%CI = - 2.58 to - 0.89; PCGrimAge beta = - 0.57, 95%CI = - 0.96 to - 0.17) and in functional biological ages (functional age index beta = - 2.18, 95%CI = - 3.65 to - 0.71; frailty index beta = - 1.31, 95%CI = - 2.43 to - 0.18). However, the results within other drug subcategories were inconsistent. Calcium channel blockers may decrease biological aging captured by the BA biomarkers measured at epigenetic and functional level. Future studies are warranted to confirm these effects and understand the underlying biological mechanisms.", "doi": "10.1007/s11357-023-00784-8", "pmid": "37032369", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI SNP genotyping": "Service"}, "xrefs": [{"db": "pii", "key": "10.1007/s11357-023-00784-8"}], "notes": [], "created": "2023-05-15T11:41:57.546Z", "modified": "2023-06-02T15:25:45.521Z"}, {"entity": "publication", "iuid": "f16eb3a1f69d495e98898dc2db501ac5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f16eb3a1f69d495e98898dc2db501ac5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f16eb3a1f69d495e98898dc2db501ac5"}}, "title": "Cross-Sectional Gene-Smoking Interaction Analysis in Relation to Subclinical Atherosclerosis-Results From the IMPROVE Study.", "authors": [{"family": "Maitusong", "given": "Buamina", "initials": "B"}, {"family": "Laguzzi", "given": "Federica", "initials": "F", "orcid": "0000-0003-3551-1348", "researcher": {"href": "https://publications.scilifelab.se/researcher/7da74e51f7ef486db7516914f9e4a8c5.json"}}, {"family": "Strawbridge", "given": "Rona J", "initials": "RJ", "orcid": "0000-0001-8506-3585", "researcher": {"href": "https://publications.scilifelab.se/researcher/8ac5060a3b37466dae002d4ad8f4d0ac.json"}}, {"family": "Baldassarre", "given": "Damiano", "initials": "D", "orcid": "0000-0002-2766-8882", "researcher": {"href": "https://publications.scilifelab.se/researcher/0c131cad5784434eb16cf720f7964ecb.json"}}, {"family": "Veglia", "given": "Fabrizio", "initials": "F", "orcid": "0000-0002-9378-8874", "researcher": {"href": "https://publications.scilifelab.se/researcher/46cd876aad8b495d982cf2a3ac7bb6aa.json"}}, {"family": "Humphries", "given": "Steve E", "initials": "SE", "orcid": "0000-0002-8221-6547", "researcher": {"href": "https://publications.scilifelab.se/researcher/7669b620701f4ebd97f91594c9a4989e.json"}}, {"family": "Savonen", "given": "Kai", "initials": "K", "orcid": "0000-0002-6871-8153", "researcher": {"href": "https://publications.scilifelab.se/researcher/19178127ffff42919e26c230ae50ef05.json"}}, {"family": "Kurl", "given": "Sudhir", "initials": "S"}, {"family": "Pirro", "given": "Matteo", "initials": "M", "orcid": "0000-0002-5527-4821", "researcher": {"href": "https://publications.scilifelab.se/researcher/0e4ee91d24cf4784ab09a25c1a766085.json"}}, {"family": "Smit", "given": "Andries J", "initials": "AJ"}, {"family": "Giral", "given": "Philippe", "initials": "P", "orcid": "0000-0002-1863-1711", "researcher": {"href": "https://publications.scilifelab.se/researcher/0f782e7ead4842fabd2aa461dc253a04.json"}}, {"family": "Silveira", "given": "Angela", "initials": "A", "orcid": "0000-0003-2063-4935", "researcher": {"href": "https://publications.scilifelab.se/researcher/6fd1197769804dd48b9de86f11340ef2.json"}}, {"family": "Tremoli", "given": "Elena", "initials": "E", "orcid": "0000-0002-0929-6106", "researcher": {"href": "https://publications.scilifelab.se/researcher/ce500f9d80404d76ac7c68ac3444db28.json"}}, {"family": "Hamsten", "given": "Anders", "initials": "A"}, {"family": "de Faire", "given": "Ulf", "initials": "U", "orcid": "0000-0002-6000-3698", "researcher": {"href": "https://publications.scilifelab.se/researcher/462b15f7decc4465b09bada73f0a0b7d.json"}}, {"family": "Gigante", "given": "Bruna", "initials": "B", "orcid": "0000-0003-4508-7990", "researcher": {"href": "https://publications.scilifelab.se/researcher/3ac1bdc52e3241ea9eb5645f603229a3.json"}}, {"family": "Leander", "given": "Karin", "initials": "K", "orcid": "0000-0002-1404-9222", "researcher": {"href": "https://publications.scilifelab.se/researcher/d502263c97a744a5a179a16220115db5.json"}}, {"family": "IMPROVE Study group\u2020", "given": "", "initials": ""}], "type": "journal article", "published": "2023-04-06", "journal": {"title": "Circ Genom Precis Med", "issn": "2574-8300", "pages": "e003710", "issn-l": "2574-8300"}, "abstract": "Smoking is associated with carotid intima-media thickness (C-IMT). However, knowledge about how genetics may influence this association is limited. We aimed to perform nonhypothesis driven gene-smoking interaction analyses to identify potential genetic variants, among those included in immune and metabolic platforms, that may modify the effect of smoking on carotid intima-media thickness.\n\nWe used baseline data from 1551 men and 1700 women, aged 55 to 79, included in a European multi-center study. Carotid intima-media thickness maximum, the maximum of values measured at different locations of the carotid tree, was dichotomized with cut point values \u226575, respectively. Genetic data were retrieved through use of the Illumina Cardio-Metabo- and Immuno- Chips. Gene-smoking interactions were evaluated through calculations of Synergy index (S). After adjustments for multiple testing, P values of <2.4\u00d710-7 for S were considered significant. The models were adjusted for age, sex, education, physical activity, type of diet, and population stratification.\n\nOur screening of 207 586 SNPs available for analysis, resulted in the identification of 47 significant gene-smoking synergistic interactions in relation to carotid intima-media thickness maximum. Among the significant SNPs, 28 were in protein coding genes, 2 in noncoding RNA and the remaining 17 in intergenic regions.\n\nThrough nonhypothesis-driven analyses of gene-smoking interactions, several significant results were observed. These may stimulate further research on the role of specific genes in the process that determines the effect of smoking habits on the development of carotid atherosclerosis.", "doi": "10.1161/CIRCGEN.122.003710", "pmid": "37021583", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "NGI SNP genotyping": "Service"}, "xrefs": [], "notes": [], "created": "2023-04-06T13:49:58.020Z", "modified": "2023-04-06T13:49:58.510Z"}, {"entity": "publication", "iuid": "10500fb8067541b5a9afef93fd90136a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/10500fb8067541b5a9afef93fd90136a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/10500fb8067541b5a9afef93fd90136a"}}, "title": "Red clover root-associated microbiota is shaped by geographic location and choice of farming system.", "authors": [{"family": "Jambagi", "given": "Shridhar", "initials": "S", "orcid": "0000-0003-4119-2750", "researcher": {"href": "https://publications.scilifelab.se/researcher/231e180fbd154372ae51411274d9ea00.json"}}, {"family": "Hod\u00e9n", "given": "Kristian Persson", "initials": "KP", "orcid": "0000-0003-0354-0662", "researcher": {"href": "https://publications.scilifelab.se/researcher/e8b41e8e41574ee6bcb55df3b0d145d9.json"}}, {"family": "\u00d6hlund", "given": "Linda", "initials": "L"}, {"family": "Dixelius", "given": "Christina", "initials": "C", "orcid": "0000-0003-0150-0608", "researcher": {"href": "https://publications.scilifelab.se/researcher/197905a68ba24d429fc14a598dc22132.json"}}], "type": "journal article", "published": "2023-04-03", "journal": {"title": "J Appl Microbiol", "issn": "1365-2672", "issn-l": "1364-5072", "volume": "134", "issue": "4", "pages": null}, "abstract": "This study evaluated the red clover (Trifolium pratense) root-associated microbiota to clarify the presence of pathogenic and beneficial microorganisms in 89 Swedish field sites.\r\n\r\n16S rRNA and ITS amplicon sequencing analysis were performed on DNA extracted from the red clover root samples collected to determine the composition of the prokaryotic and eukaryotic root-associated microbe communities. Alpha and beta diversities were calculated and relative abundance of various microbial taxa and their co-occurrence were analyzed. Rhizobium was the most prevalent bacterial genus, followed by Sphingomonas, Mucilaginibacter, Flavobacterium, and the unclassified Chloroflexi group KD4-96. The Leptodontidium, Cladosporium, Clonostachys, and Tetracladium fungal genera known for endophytic, saprotrophic, and mycoparasitic lifestyles were also frequently observed in all samples. Sixty-two potential pathogenic fungi were identified with a bias toward grass pathogens and a higher abundance in samples from conventional farms.\r\n\r\nWe showed that the microbial community was mainly shaped by geographic location and management procedures. Co-occurrence networks revealed that the Rhizobiumleguminosarum bv. trifolii was negatively associated with all fungal pathogenic taxa recognized in this study.", "doi": "10.1093/jambio/lxad067", "pmid": "37012225", "labels": {"NGI Uppsala (Uppsala Genome Center)": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "7100963"}], "notes": [], "created": "2023-05-22T19:56:22.157Z", "modified": "2024-01-16T13:48:33.706Z"}, {"entity": "publication", "iuid": "091bc2001e6e49a1a25c43f310e57220", "links": {"self": {"href": "https://publications.scilifelab.se/publication/091bc2001e6e49a1a25c43f310e57220.json"}, "display": {"href": "https://publications.scilifelab.se/publication/091bc2001e6e49a1a25c43f310e57220"}}, "title": "Whole-genome re-sequencing provides key genomic insights in farmed Arctic charr (Salvelinus alpinus) populations of anadromous and landlocked origin from Scandinavia.", "authors": [{"family": "Pappas", "given": "Fotis", "initials": "F"}, {"family": "Kurta", "given": "Khrystyna", "initials": "K"}, {"family": "Vanhala", "given": "Tytti", "initials": "T"}, {"family": "Jeuthe", "given": "Henrik", "initials": "H"}, {"family": "Hagen", "given": "\u00d8rjan", "initials": "\u00d8"}, {"family": "Beir\u00e3o", "given": "Jos\u00e9", "initials": "J"}, {"family": "Palaiokostas", "given": "Christos", "initials": "C", "orcid": "0000-0002-4480-4612", "researcher": {"href": "https://publications.scilifelab.se/researcher/a1d6c65f53a8434cb1d5dd4c7bf5d444.json"}}], "type": "journal article", "published": "2023-04-00", "journal": {"title": "Evol Appl", "issn": "1752-4571", "volume": "16", "issue": "4", "pages": "797-813", "issn-l": "1752-4571"}, "abstract": "Arctic charr (Salvelinus alpinus) is a niche-market high-value species for Nordic aquaculture. Similar to other salmonids, both anadromous and landlocked populations are encountered. Whole-genome re-sequencing (22X coverage) was performed on two farmed populations of anadromous (Sigerfjord; n = 24) and landlocked (Arctic Superior; n = 24) origin from Norway and Sweden respectively. More than 5 million SNPs were used to study their genetic diversity and to scan for selection signatures. The two populations were clearly distinguished through principal component analysis, with the mean fixation index being ~0.12. Furthermore, the levels of genomic inbreeding estimated from runs of homozygosity were 6.23% and 8.66% for the Norwegian and the Swedish population respectively. Biological processes that could be linked to selection pressure associated primarily with the anadromous background and/or secondarily with domestication were suggested. Overall, our study provided insights regarding the genetic composition of two main strains of farmed Arctic charr from Scandinavia. At the same time, ample genomic resources were produced in the magnitude of millions of SNPs that could assist the transition of Nordic Arctic charr farming in the genomics era.", "doi": "10.1111/eva.13537", "pmid": "37124091", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10130564"}, {"db": "pii", "key": "EVA13537"}], "notes": [], "created": "2023-11-29T11:32:33.735Z", "modified": "2023-11-29T11:32:33.768Z"}, {"entity": "publication", "iuid": "b4a94cb3e0a848b997dafcf6f2d13186", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b4a94cb3e0a848b997dafcf6f2d13186.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b4a94cb3e0a848b997dafcf6f2d13186"}}, "title": "Genetically and environmentally predicted obesity in relation to cardiovascular disease: a nationwide cohort study.", "authors": [{"family": "Ojalehto", "given": "Elsa", "initials": "E"}, {"family": "Zhan", "given": "Yiqiang", "initials": "Y"}, {"family": "Jylh\u00e4v\u00e4", "given": "Juulia", "initials": "J"}, {"family": "Reynolds", "given": "Chandra A", "initials": "CA"}, {"family": "Dahl Aslan", "given": "Anna K", "initials": "AK"}, {"family": "Karlsson", "given": "Ida K", "initials": "IK"}], "type": "journal article", "published": "2023-04-00", "journal": {"title": "EClinicalMedicine", "issn": "2589-5370", "issn-l": null, "volume": "58", "issue": null, "pages": "101943"}, "abstract": "Evidence indicates that the adverse health effects of obesity differ between genetically and environmentally influenced obesity. We examined differences in the association between obesity and cardiovascular disease (CVD) between individuals with a genetically predicted low, medium, or high body mass index (BMI).\r\n\r\nWe used cohort data from Swedish twins born before 1959 who had BMI measured between the ages of 40-64 years (midlife) or at the age of 65 years or later (late-life), or both, and prospective CVD information from nationwide register linkage through 2016. A polygenic score for BMI (PGSBMI) was used to define genetically predicted BMI. Individuals missing BMI or covariate data, or diagnosed with CVD at first BMI measure, were excluded, leaving an analysis sample of 17,988 individuals. We applied Cox proportional hazard models to examine the association between BMI category and incident CVD, stratified by the PGSBMI. Co-twin control models were applied to adjust for genetic influences not captured by the PGSBMI.\r\n\r\nBetween 1984 and 2010, the 17,988 participants were enrolled in sub-studies of the Swedish Twin Registry. Midlife obesity was associated with a higher risk of CVD across all PGSBMI categories, but the association was stronger with genetically predicted lower BMI (hazard ratio from 1.55 to 2.08 for those with high and low PGSBMI, respectively). Within monozygotic twin pairs, the association did not differ by genetically predicted BMI, indicating genetic confounding not captured by the PGSBMI. Results were similar when obesity was measured in late-life, but suffered from low power.\r\n\r\nObesity was associated with CVD regardless of PGSBMI category, but obesity influenced by genetic predisposition (genetically predicted high BMI) was less harmful than obesity influenced by environmental factors (obesity despite genetically predicted low BMI). However, additional genetic factors, not captured by the PGSBMI, still influence the associations.\r\n\r\nThe Strategic Research Program in Epidemiology at Karolinska Institutet; Loo and Hans Osterman's Foundation; Foundation for Geriatric Diseases at Karolinska Institutet; the Swedish Research Council for Health, Working Life and Welfare; the Swedish Research Council; and the National Institutes of Health.", "doi": "10.1016/j.eclinm.2023.101943", "pmid": "37181410", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI SNP genotyping": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10166783"}, {"db": "pii", "key": "S2589-5370(23)00120-7"}], "notes": [], "created": "2023-05-15T11:41:59.928Z", "modified": "2023-06-02T15:27:30.679Z"}, {"entity": "publication", "iuid": "1b64b2e873f440098c5413b843a1c9cf", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1b64b2e873f440098c5413b843a1c9cf.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1b64b2e873f440098c5413b843a1c9cf"}}, "title": "From high masked to high realized genetic load in inbred Scandinavian wolves.", "authors": [{"family": "Smeds", "given": "Linn\u00e9a", "initials": "L", "orcid": "0000-0002-8415-9259", "researcher": {"href": "https://publications.scilifelab.se/researcher/b46a4a275c954de8bb969ef4cda9e33b.json"}}, {"family": "Ellegren", "given": "Hans", "initials": "H", "orcid": "0000-0002-5035-1736", "researcher": {"href": "https://publications.scilifelab.se/researcher/819e68cc7125446baec6165aabd2d19c.json"}}], "type": "journal article", "published": "2023-04-00", "journal": {"title": "Mol. Ecol.", "issn": "1365-294X", "issn-l": "0962-1083", "volume": "32", "issue": "7", "pages": "1567-1580"}, "abstract": "When new mutations arise at functional sites they are more likely to impair than improve fitness. If not removed by purifying selection, such deleterious mutations will generate a genetic load that can have negative fitness effects in small populations and increase the risk of extinction. This is relevant for the highly inbred Scandinavian wolf (Canis lupus) population, founded by only three wolves in the 1980s and suffering from inbreeding depression. We used functional annotation and evolutionary conservation scores to study deleterious variation in a total of 209 genomes from both the Scandinavian and neighbouring wolf populations in northern Europe. The masked load (deleterious mutations in heterozygote state) was highest in Russia and Finland with deleterious alleles segregating at lower frequency than neutral variation. Genetic drift in the Scandinavian population led to the loss of ancestral alleles, fixation of deleterious variants and a significant increase in the per-individual realized load (deleterious mutations in homozygote state; an increase by 45% in protein-coding genes) over five generations of inbreeding. Arrival of immigrants gave a temporary genetic rescue effect with ancestral alleles re-entering the population and thereby shifting deleterious alleles from homozygous into heterozygote genotypes. However, in the absence of permanent connectivity to Finnish and Russian populations, inbreeding has then again led to the exposure of deleterious mutations. These observations provide genome-wide insight into the magnitude of genetic load and genetic rescue at the molecular level, and in relation to population history. They emphasize the importance of securing gene flow in the management of endangered populations.", "doi": "10.1111/mec.16802", "pmid": "36458895", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "Dryad", "key": "10.5061/dryad.7m0cfxpzj"}], "notes": [], "created": "2023-11-29T09:02:42.251Z", "modified": "2024-01-16T13:48:33.734Z"}, {"entity": "publication", "iuid": "16d85a0c24b34671acbb2f2a26072985", "links": {"self": {"href": "https://publications.scilifelab.se/publication/16d85a0c24b34671acbb2f2a26072985.json"}, "display": {"href": "https://publications.scilifelab.se/publication/16d85a0c24b34671acbb2f2a26072985"}}, "title": "Epigenetic changes in the CYP2D6 gene are related to severity of suicide attempt: A cross-sectional study of suicide attempters.", "authors": [{"family": "Bostr\u00f6m", "given": "Adrian E Desai", "initials": "AED"}, {"family": "Jamshidi", "given": "Esmail", "initials": "E"}, {"family": "Manu", "given": "Diana-Maria", "initials": "DM"}, {"family": "Kular", "given": "Lara", "initials": "L"}, {"family": "Schi\u00f6th", "given": "Helgi B", "initials": "HB"}, {"family": "\u00c5sberg", "given": "Marie", "initials": "M"}, {"family": "Jokinen", "given": "Jussi", "initials": "J"}], "type": "journal article", "published": "2023-04-00", "journal": {"title": "J Psychiatr Res", "issn": "1879-1379", "volume": "160", "pages": "217-224", "issn-l": "0022-3956"}, "abstract": "The ability to accurately estimate risk of suicide deaths on an individual level remains elusive.\n\nThis study reports on a case-control study set-up from a well-characterized cohort of 88 predominantly female suicide attempters (SA), stratified into low- (n = 57) and high-risk groups (n = 31) based on reports of later death by suicide, as well as degree of intent-to-die and lethality of SA method. We perform an unbiased analysis of 12,930 whole-blood derived CpG-sites (Illumina Infinium EPIC BeadChip) previously demonstrated to be more conciliable with brain-derived variations. The candidate site was validated by pyrosequencing. External replication was performed in (1) relation to age at index suicide attempt in 97 women with emotionally unstable personality disorder (whole-blood) and (2) death by suicide in a mixed group of 183 prefrontal-cortex (PFC) derived samples who died by suicide or from non-psychiatric etiologies.\n\nCYP2D6-coupled CpG-site cg07016288 was hypomethylated in severe suicidal behavior (p < 10E-06). Results were validated by pyrosequencing (p < 0.01). Replication analyses demonstrate hypomethylation of cg07016288 in relation to age at index SA in females (p < 0.05) and hypermethylation in PFC of male suicide completers (p < 0.05).\n\nGenotyping of CYP2D6 was not performed and CpG-site associations to gene expression were not explored.\n\nCYP2D6-coupled epigenetic markers are hypomethylated in females in dependency of features known to confer increased risk of suicide deaths and hypermethylated in PFC of male suicide completers. Further elucidating the role of CYP2D6 in severe suicidality or suicide deaths hold promise to deduce clinically meaningful results.", "doi": "10.1016/j.jpsychires.2023.02.025", "pmid": "36857986", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "NGI SNP genotyping": "Service"}, "xrefs": [{"db": "pii", "key": "S0022-3956(23)00093-6"}], "notes": [], "created": "2023-04-06T13:50:03.639Z", "modified": "2023-04-06T13:50:03.654Z"}, {"entity": "publication", "iuid": "14f4d2b869aa4a2dabad06efa432aa96", "links": {"self": {"href": "https://publications.scilifelab.se/publication/14f4d2b869aa4a2dabad06efa432aa96.json"}, "display": {"href": "https://publications.scilifelab.se/publication/14f4d2b869aa4a2dabad06efa432aa96"}}, "title": "Simultaneous Ultra-Sensitive Detection of Structural and Single Nucleotide Variants Using Multiplex Droplet Digital PCR in Liquid Biopsies from Children with Medulloblastoma.", "authors": [{"family": "Arthur", "given": "Cecilia", "initials": "C", "orcid": "0000-0002-0645-6530", "researcher": {"href": "https://publications.scilifelab.se/researcher/7b07104d934d413a9c9546e7e9933051.json"}}, {"family": "Jylh\u00e4", "given": "Cecilia", "initials": "C"}, {"family": "de St\u00e5hl", "given": "Teresita D\u00edaz", "initials": "TD", "orcid": "0000-0001-5933-6623", "researcher": {"href": "https://publications.scilifelab.se/researcher/2f51158ce6e14f3b96bf16a214689d1d.json"}}, {"family": "Shamikh", "given": "Alia", "initials": "A"}, {"family": "Sandgren", "given": "Johanna", "initials": "J"}, {"family": "Rosenquist", "given": "Richard", "initials": "R"}, {"family": "Nordenskj\u00f6ld", "given": "Magnus", "initials": "M"}, {"family": "Harila", "given": "Arja", "initials": "A"}, {"family": "Barbany", "given": "Gisela", "initials": "G", "orcid": "0000-0003-3185-2962", "researcher": {"href": "https://publications.scilifelab.se/researcher/13fda0d702d543f981898ebd53849817.json"}}, {"family": "Sandvik", "given": "Ulrika", "initials": "U", "orcid": "0000-0002-9273-2158", "researcher": {"href": "https://publications.scilifelab.se/researcher/72b8c0bf76054dc8ba15fa80fa78918e.json"}}, {"family": "Tham", "given": "Emma", "initials": "E", "orcid": "0000-0001-6079-164X", "researcher": {"href": "https://publications.scilifelab.se/researcher/6689dd9aff584082a57398141a538111.json"}}], "type": "journal article", "published": "2023-03-25", "journal": {"title": "Cancers (Basel)", "issn": "2072-6694", "volume": "15", "issue": "7", "issn-l": "2072-6694"}, "abstract": "Medulloblastoma is a malignant embryonal tumor of the central nervous system (CNS) that mainly affects infants and children. Prognosis is highly variable, and molecular biomarkers for measurable residual disease (MRD) detection are lacking. Analysis of cell-free DNA (cfDNA) in cerebrospinal fluid (CSF) using broad genomic approaches, such as low-coverage whole-genome sequencing, has shown promising prognostic value. However, more sensitive methods are needed for MRD analysis. Here, we show the technical feasibility of capturing medulloblastoma-associated structural variants and point mutations simultaneously in cfDNA using multiplexed droplet digital PCR (ddPCR). Assay sensitivity was assessed with a dilution series of tumor in normal genomic DNA, and the limit of detection was below 100 pg of input DNA for all assays. False positive rates were zero for structural variant assays. Liquid biopsies (CSF and plasma, n = 47) were analyzed from 12 children with medulloblastoma, all with negative CSF cytology. MRD was detected in 75% (9/12) of patients overall. In CSF samples taken before or within 21 days of surgery, MRD was detected in 88% (7/8) of patients with localized disease and in one patient with the metastasized disease. Our results suggest that this approach could expand the utility of ddPCR and complement broader analyses of cfDNA for MRD detection.", "doi": "10.3390/cancers15071972", "pmid": "37046633", "labels": {"NGI SNP genotyping": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10092983"}, {"db": "pii", "key": "cancers15071972"}], "notes": [], "created": "2023-11-29T11:43:56.624Z", "modified": "2024-01-16T13:48:33.819Z"}, {"entity": "publication", "iuid": "3ec4d200a0024c8da044c7667d25768e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3ec4d200a0024c8da044c7667d25768e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3ec4d200a0024c8da044c7667d25768e"}}, "title": "Enhanced glycerol assimilation and lipid production in Rhodotorula toruloides CBS14 upon addition of hemicellulose primarily correlates with early transcription of energy-metabolism-related genes.", "authors": [{"family": "Mart\u00edn-Hern\u00e1ndez", "given": "Giselle C", "initials": "GC"}, {"family": "Chmielarz", "given": "Miko\u0142aj", "initials": "M"}, {"family": "M\u00fcller", "given": "Bettina", "initials": "B"}, {"family": "Brandt", "given": "Christian", "initials": "C"}, {"family": "Viehweger", "given": "Adrian", "initials": "A"}, {"family": "H\u00f6lzer", "given": "Martin", "initials": "M"}, {"family": "Passoth", "given": "Volkmar", "initials": "V"}], "type": "journal article", "published": "2023-03-10", "journal": {"title": "Biotechnol Biofuels Bioprod", "issn": "2731-3654", "volume": "16", "issue": "1", "pages": "42", "issn-l": null}, "abstract": "Lipid formation from glycerol was previously found to be activated in Rhodotorula toruloides when the yeast was cultivated in a mixture of crude glycerol (CG) and hemicellulose hydrolysate (CGHH) compared to CG as the only carbon source. RNA samples from R. toruloides CBS14 cell cultures grown on either CG or CGHH were collected at different timepoints of cultivation, and a differential gene expression analysis was performed between cells grown at a similar physiological situation.\n\nWe observed enhanced transcription of genes involved in oxidative phosphorylation and enzymes localized in mitochondria in CGHH compared to CG. Genes involved in protein turnover, including those encoding ribosomal proteins, translation elongation factors, and genes involved in building the proteasome also showed an enhanced transcription in CGHH compared to CG. At 10 h cultivation, another group of activated genes in CGHH was involved in \u03b2-oxidation, handling oxidative stress and degradation of xylose and aromatic compounds. Potential bypasses of the standard GUT1 and GUT2-glycerol assimilation pathway were also expressed and upregulated in CGHH 10 h. When the additional carbon sources from HH were completely consumed, at CGHH 36 h, their transcription decreased and NAD+-dependent glycerol-3-phosphate dehydrogenase was upregulated compared to CG 60 h, generating NADH instead of NADPH with glycerol catabolism. TPI1 was upregulated in CGHH compared to cells grown on CG in all physiological situations, potentially channeling the DHAP formed through glycerol catabolism into glycolysis. The highest number of upregulated genes encoding glycolytic enzymes was found after 36 h in CGHH, when all additional carbon sources were already consumed.\n\nWe suspect that the physiological reason for the accelerated glycerol assimilation and faster lipid production, was primarily the activation of enzymes that provide energy.", "doi": "10.1186/s13068-023-02294-3", "pmid": "36899390", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9999650"}, {"db": "pii", "key": "10.1186/s13068-023-02294-3"}], "notes": [], "created": "2023-11-30T12:59:39.548Z", "modified": "2023-11-30T12:59:39.563Z"}, {"entity": "publication", "iuid": "07fe9e3eec8b4340aa05343a657ea24d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/07fe9e3eec8b4340aa05343a657ea24d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/07fe9e3eec8b4340aa05343a657ea24d"}}, "title": "Rickettsia felis DNA recovered from a child who lived in southern Africa 2000 years ago.", "authors": [{"family": "Rifkin", "given": "Riaan F", "initials": "RF", "orcid": "0000-0003-1791-3706", "researcher": {"href": "https://publications.scilifelab.se/researcher/9b6691b2d64749e197ef0ddd36fd5af1.json"}}, {"family": "Vikram", "given": "Surendra", "initials": "S", "orcid": "0000-0002-4721-2890", "researcher": {"href": "https://publications.scilifelab.se/researcher/9171a14995cc47de9fb4d70bf4fe9aa9.json"}}, {"family": "Alcorta", "given": "Jaime", "initials": "J"}, {"family": "Ramond", "given": "Jean-Baptiste", "initials": "JB", "orcid": "0000-0003-4790-6232", "researcher": {"href": "https://publications.scilifelab.se/researcher/6f9b3ec176bd489daeeb78e1ef0a1acf.json"}}, {"family": "Cowan", "given": "Don A", "initials": "DA", "orcid": "0000-0001-8059-861X", "researcher": {"href": "https://publications.scilifelab.se/researcher/cc756e07160f4c888fbdc7612936db03.json"}}, {"family": "Jakobsson", "given": "Mattias", "initials": "M", "orcid": "0000-0001-7840-7853", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a4abe0fcb20492d9ec849c9fbf58a71.json"}}, {"family": "Schlebusch", "given": "Carina M", "initials": "CM", "orcid": "0000-0002-8160-9621", "researcher": {"href": "https://publications.scilifelab.se/researcher/682f10853c1145649b8c76680605dd9b.json"}}, {"family": "Lombard", "given": "Marlize", "initials": "M", "orcid": "0000-0002-0675-0414", "researcher": {"href": "https://publications.scilifelab.se/researcher/e04e97bbc9914f358864988174b9b58d.json"}}], "type": "journal article", "published": "2023-03-03", "journal": {"title": "Commun Biol", "issn": "2399-3642", "volume": "6", "issue": "1", "pages": "240", "issn-l": "2399-3642"}, "abstract": "The Stone Age record of South Africa provides some of the earliest evidence for the biological and cultural origins of Homo sapiens. While there is extensive genomic evidence for the selection of polymorphisms in response to pathogen-pressure in sub-Saharan Africa, e.g., the sickle cell trait which provides protection against malaria, there is inadequate direct human genomic evidence for ancient human-pathogen infection in the region. Here, we analysed shotgun metagenome libraries derived from the sequencing of a Later Stone Age hunter-gatherer child who lived near Ballito Bay, South Africa, c. 2000 years ago. This resulted in the identification of ancient DNA sequence reads homologous to Rickettsia felis, the causative agent of typhus-like flea-borne rickettsioses, and the reconstruction of an ancient R. felis genome.", "doi": "10.1038/s42003-023-04582-y", "pmid": "36869137", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9984395"}, {"db": "pii", "key": "10.1038/s42003-023-04582-y"}], "notes": [], "created": "2023-11-29T11:28:26.513Z", "modified": "2023-11-29T11:28:26.659Z"}, {"entity": "publication", "iuid": "feb48652b3a64f24ab3cc30b33e698ab", "links": {"self": {"href": "https://publications.scilifelab.se/publication/feb48652b3a64f24ab3cc30b33e698ab.json"}, "display": {"href": "https://publications.scilifelab.se/publication/feb48652b3a64f24ab3cc30b33e698ab"}}, "title": "Genome-wide analysis identifies genetic effects on reproductive success and ongoing natural selection at the FADS locus.", "authors": [{"family": "Mathieson", "given": "Iain", "initials": "I", "orcid": "0000-0002-4256-3982", "researcher": {"href": "https://publications.scilifelab.se/researcher/ea771b602668431abd1a375ea66c46a6.json"}}, {"family": "Day", "given": "Felix R", "initials": "FR", "orcid": "0000-0003-3789-7651", "researcher": {"href": "https://publications.scilifelab.se/researcher/5d9ffc4d251a4469bcb97dd24dcc4218.json"}}, {"family": "Barban", "given": "Nicola", "initials": "N"}, {"family": "Tropf", "given": "Felix C", "initials": "FC"}, {"family": "Brazel", "given": "David M", "initials": "DM"}, {"family": "eQTLGen Consortium", "given": "", "initials": ""}, {"family": "BIOS Consortium", "given": "", "initials": ""}, {"family": "Vaez", "given": "Ahmad", "initials": "A", "orcid": "0000-0001-9048-3795", "researcher": {"href": "https://publications.scilifelab.se/researcher/34a09aa88bc74e1285ddd71655dbddc3.json"}}, {"family": "van Zuydam", "given": "Natalie", "initials": "N"}, {"family": "Bitarello", "given": "B\u00e1rbara D", "initials": "BD", "orcid": "0000-0001-7676-9367", "researcher": {"href": "https://publications.scilifelab.se/researcher/2c3bdb02b83148c2a929354acb46b668.json"}}, {"family": "Gardner", "given": "Eugene J", "initials": "EJ", "orcid": "0000-0001-9671-1533", "researcher": {"href": "https://publications.scilifelab.se/researcher/bd0b968817d84a9ab2c0c425e8b03f7b.json"}}, {"family": "Akimova", "given": "Evelina T", "initials": "ET", "orcid": "0000-0001-8733-3745", "researcher": {"href": "https://publications.scilifelab.se/researcher/0fbf028b586744b19796cd129eda3801.json"}}, {"family": "Azad", "given": "Ajuna", "initials": "A"}, {"family": "Bergmann", "given": "Sven", "initials": "S", "orcid": "0000-0002-6785-9034", "researcher": {"href": "https://publications.scilifelab.se/researcher/07785d6cc5af460ca1901fe3819808fa.json"}}, {"family": "Bielak", "given": "Lawrence F", "initials": "LF", "orcid": "0000-0002-3443-8030", "researcher": {"href": "https://publications.scilifelab.se/researcher/d1934e3543f14cbe83b95d1c1c3e24c7.json"}}, {"family": "Boomsma", "given": "Dorret I", "initials": "DI", "orcid": "0000-0002-7099-7972", "researcher": {"href": "https://publications.scilifelab.se/researcher/4b66ab2525fd4a468e7a4ad14c955cb4.json"}}, {"family": "Bosak", "given": "Kristina", "initials": "K"}, {"family": "Brumat", "given": "Marco", "initials": "M"}, {"family": "Buring", "given": "Julie E", "initials": "JE"}, {"family": "Cesarini", "given": "David", "initials": "D"}, {"family": "Chasman", "given": "Daniel I", "initials": "DI", "orcid": "0000-0003-3357-0862", "researcher": {"href": "https://publications.scilifelab.se/researcher/1c06690291064fe58836958edbcaafbc.json"}}, {"family": "Chavarro", "given": "Jorge E", "initials": "JE", "orcid": "0000-0002-4436-9630", "researcher": {"href": "https://publications.scilifelab.se/researcher/2dfd7bd45f304d47867bcace25a951af.json"}}, {"family": "Cocca", "given": "Massimiliano", "initials": "M", "orcid": "0000-0002-1127-7596", "researcher": {"href": "https://publications.scilifelab.se/researcher/86431d25a54645e3988674b5e0ef6a59.json"}}, {"family": "Concas", "given": "Maria Pina", "initials": "MP", "orcid": "0000-0003-3598-2537", "researcher": {"href": "https://publications.scilifelab.se/researcher/74f63075f4ce43cc921c658fb353bd25.json"}}, {"family": "Davey Smith", "given": "George", "initials": "G", "orcid": "0000-0002-1407-8314", "researcher": {"href": "https://publications.scilifelab.se/researcher/0790d5850377432087ad3900af0044e0.json"}}, {"family": "Davies", "given": "Gail", "initials": "G", "orcid": "0000-0003-1120-7026", "researcher": {"href": "https://publications.scilifelab.se/researcher/40dfc10ac1f64ff0b2a8efc0171383c5.json"}}, {"family": "Deary", "given": "Ian J", "initials": "IJ"}, {"family": "Esko", "given": "T\u00f5nu", "initials": "T"}, {"family": "Faul", "given": "Jessica D", "initials": "JD"}, {"family": "FinnGen Study", "given": "", "initials": ""}, {"family": "Franco", "given": "Oscar", "initials": "O", "orcid": "0000-0002-4606-4929", "researcher": {"href": "https://publications.scilifelab.se/researcher/fffb8b8696f34f669672e11e5e7843f9.json"}}, {"family": "Ganna", "given": "Andrea", "initials": "A", "orcid": "0000-0002-8147-240X", "researcher": {"href": "https://publications.scilifelab.se/researcher/5e361d3e080246f6b58dcbb603e8c66d.json"}}, {"family": "Gaskins", "given": "Audrey J", "initials": "AJ", "orcid": "0000-0001-9195-646X", "researcher": {"href": "https://publications.scilifelab.se/researcher/703a92ee9c1b4082a81bc334f8cf07cb.json"}}, {"family": "Gelemanovic", "given": "Andrea", "initials": "A"}, {"family": "de Geus", "given": "Eco J C", "initials": "EJC"}, {"family": "Gieger", "given": "Christian", "initials": "C", "orcid": "0000-0001-6986-9554", "researcher": {"href": "https://publications.scilifelab.se/researcher/86f44e76061c403fadd97b768e2a7e62.json"}}, {"family": "Girotto", "given": "Giorgia", "initials": "G", "orcid": "0000-0003-4507-6589", "researcher": {"href": "https://publications.scilifelab.se/researcher/1bc5f25ecc414d5d9e4855217c1da506.json"}}, {"family": "Gopinath", "given": "Bamini", "initials": "B"}, {"family": "Grabe", "given": "Hans J\u00f6rgen", "initials": "HJ", "orcid": "0000-0003-3684-4208", "researcher": {"href": "https://publications.scilifelab.se/researcher/d660f9169e6c4c8485041382ebf71e3d.json"}}, {"family": "Gunderson", "given": "Erica P", "initials": "EP", "orcid": "0000-0002-2039-1964", "researcher": {"href": "https://publications.scilifelab.se/researcher/d8b625d39d684431b348579fc1f35093.json"}}, {"family": "Hayward", "given": "Caroline", "initials": "C"}, {"family": "He", "given": "Chunyan", "initials": "C", "orcid": "0000-0001-9443-4368", "researcher": {"href": "https://publications.scilifelab.se/researcher/154a1f76ec7949b4ab0ab69ca161fd02.json"}}, {"family": "van Heemst", "given": "Diana", "initials": "D"}, {"family": "Hill", "given": "W David", "initials": "WD"}, {"family": "Hoffmann", "given": "Eva R", "initials": "ER", "orcid": "0000-0002-2588-0652", "researcher": {"href": "https://publications.scilifelab.se/researcher/4d5725300d8449e18c06581c63f36807.json"}}, {"family": "Homuth", "given": "Georg", "initials": "G", "orcid": "0000-0001-6839-0605", "researcher": {"href": "https://publications.scilifelab.se/researcher/3ff9df166c2a4643990b250c74c5dad3.json"}}, {"family": "Hottenga", "given": "Jouke Jan", "initials": "JJ", "orcid": "0000-0002-5668-2368", "researcher": {"href": "https://publications.scilifelab.se/researcher/75553b594b1f4255833de730f7f7d170.json"}}, {"family": "Huang", "given": "Hongyang", "initials": "H"}, {"family": "Hypp\u04e7nen", "given": "Elina", "initials": "E", "orcid": "0000-0003-3670-9399", "researcher": {"href": "https://publications.scilifelab.se/researcher/786540ff507c4cb495d11dbb1da72d63.json"}}, {"family": "Ikram", "given": "M Arfan", "initials": "MA", "orcid": "0000-0003-0372-8585", "researcher": {"href": 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"initials": "A", "orcid": "0000-0002-3764-4905", "researcher": {"href": "https://publications.scilifelab.se/researcher/06314200660e45ac9574a570af7b25e8.json"}}, {"family": "Kiiskinen", "given": "Tuomo", "initials": "T", "orcid": "0000-0002-6306-8227", "researcher": {"href": "https://publications.scilifelab.se/researcher/732db23f7f9f4af7b879d405d1f99ee3.json"}}, {"family": "Kraft", "given": "Peter", "initials": "P", "orcid": "0000-0002-4472-8103", "researcher": {"href": "https://publications.scilifelab.se/researcher/5af0cbcc64e54601944c6e881d8ce4d9.json"}}, {"family": "K\u00fchnel", "given": "Brigitte", "initials": "B"}, {"family": "Langenberg", "given": "Claudia", "initials": "C", "orcid": "0000-0002-5017-7344", "researcher": {"href": "https://publications.scilifelab.se/researcher/ca19370bb4d6437aa9df3905db9d3dd2.json"}}, {"family": "Liew", "given": "Gerald", "initials": "G"}, {"family": "Lifelines Cohort Study", "given": "", "initials": ""}, {"family": "Lind", "given": "Penelope A", 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"Weir", "given": "David R", "initials": "DR", "orcid": "0000-0002-1661-2402", "researcher": {"href": "https://publications.scilifelab.se/researcher/f90b7cfe829845fb8cbea9558a5c82a7.json"}}, {"family": "Willemsen", "given": "Gonneke", "initials": "G"}, {"family": "Zhao", "given": "Jing Hau", "initials": "JH"}, {"family": "Zhao", "given": "Wei", "initials": "W", "orcid": "0000-0001-7388-0692", "researcher": {"href": "https://publications.scilifelab.se/researcher/a0c2246e69494086bab7ead8e6f1f717.json"}}, {"family": "Zhao", "given": "Yajie", "initials": "Y", "orcid": "0000-0002-2747-0219", "researcher": {"href": "https://publications.scilifelab.se/researcher/e1f2103cc88e44279543dd6e87783855.json"}}, {"family": "Snieder", "given": "Harold", "initials": "H", "orcid": "0000-0003-1949-2298", "researcher": {"href": "https://publications.scilifelab.se/researcher/e9276827839a4f3cb50dcaa2ad4708a5.json"}}, {"family": "den Hoed", "given": "Marcel", "initials": "M", "orcid": "0000-0001-8081-428X", "researcher": {"href": "https://publications.scilifelab.se/researcher/d712cc087d344b15ab9a7971640acebe.json"}}, {"family": "Ong", "given": "Ken K", "initials": "KK", "orcid": "0000-0003-4689-7530", "researcher": {"href": "https://publications.scilifelab.se/researcher/abdc034f3fa1428d9311a306a5446b35.json"}}, {"family": "Mills", "given": "Melinda C", "initials": "MC", "orcid": "0000-0003-1704-0001", "researcher": {"href": "https://publications.scilifelab.se/researcher/957f1b6833c64bbcb286e383512bc14b.json"}}, {"family": "Perry", "given": "John R B", "initials": "JRB", "orcid": "0000-0001-6483-3771", "researcher": {"href": "https://publications.scilifelab.se/researcher/39d95b143f6849b1b914bca9563218c8.json"}}], "type": "journal article", "published": "2023-03-02", "journal": {"title": "Nat Hum Behav", "issn": "2397-3374", "issn-l": null}, "abstract": "Identifying genetic determinants of reproductive success may highlight mechanisms underlying fertility and identify alleles under present-day selection. Using data in 785,604 individuals of European ancestry, we identified 43 genomic loci associated with either number of children ever born (NEB) or childlessness. These loci span diverse aspects of reproductive biology, including puberty timing, age at first birth, sex hormone regulation, endometriosis and age at menopause. Missense variants in ARHGAP27 were associated with higher NEB but shorter reproductive lifespan, suggesting a trade-off at this locus between reproductive ageing and intensity. Other genes implicated by coding variants include PIK3IP1, ZFP82 and LRP4, and our results suggest a new role for the melanocortin 1 receptor (MC1R) in reproductive biology. As NEB is one component of evolutionary fitness, our identified associations indicate loci under present-day natural selection. Integration with data from historical selection scans highlighted an allele in the FADS1/2 gene locus that has been under selection for thousands of years and remains so today. Collectively, our findings demonstrate that a broad range of biological mechanisms contribute to reproductive success.", "doi": "10.1038/s41562-023-01528-6", "pmid": "36864135", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "NGI SNP genotyping": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41562-023-01528-6"}], "notes": [], "created": "2023-04-06T13:50:09.776Z", "modified": "2023-04-06T13:50:10.709Z"}, {"entity": "publication", "iuid": "944da838dbba4f998547392247fd92d0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/944da838dbba4f998547392247fd92d0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/944da838dbba4f998547392247fd92d0"}}, "title": "Occupational inhalable agents constitute major risk factors for rheumatoid arthritis, particularly in the context of genetic predisposition and smoking.", "authors": [{"family": "Tang", "given": "Bowen", "initials": "B", "orcid": "0000-0002-1391-2522", "researcher": {"href": "https://publications.scilifelab.se/researcher/b3e80f30ad9746229713eb01cb981a16.json"}}, {"family": "Liu", "given": "Qianwen", "initials": "Q"}, {"family": "Ilar", "given": "Anna", "initials": "A"}, {"family": "Wiebert", "given": "Pernilla", "initials": "P"}, {"family": "H\u00e4gg", "given": "Sara", "initials": "S"}, {"family": "Padyukov", "given": "Leonid", "initials": "L"}, {"family": "Klareskog", "given": "Lars", "initials": "L", "orcid": "0000-0001-9601-6186", "researcher": {"href": "https://publications.scilifelab.se/researcher/c89507c56863420b89f9b417a6f44451.json"}}, {"family": "Alfredsson", "given": "Lars", "initials": "L"}, {"family": "Jiang", "given": "Xia", "initials": "X"}], "type": "journal article", "published": "2023-03-00", "journal": {"title": "Ann. Rheum. Dis.", "issn": "1468-2060", "volume": "82", "issue": "3", "pages": "316-323", "issn-l": "0003-4967"}, "abstract": "To assess the effects of occupational inhalable exposures on rheumatoid arthritis (RA) development and their interactions with smoking and RA-risk genes, stratifying by presence of anticitrullinated protein antibodies (ACPA).\n\nData came from the Swedish Epidemiological Investigation of RA, consisting of 4033 incident RA cases and 6485 matched controls. Occupational histories were retrieved, combining with a Swedish national job-exposure matrix, to estimate exposure to 32 inhalable agents. Genetic data were used to define Genetic Risk Score (GRS) or carrying any copy of human leucocyte antigen class II shared epitope (HLA-SE) alleles. Associations were identified with unconditional logistical regression models. Attributable proportion due to interaction was estimated to evaluate presence of interaction.\n\nExposure to any occupational inhalable agents was associated with increased risk for ACPA-positive RA (OR 1.25, 95% CI 1.12 to 1.38). The risk increased as number of exposed agents increased (Ptrend<0.001) or duration of exposure elongated (Ptrend<0.001). When jointly considering exposure to any occupational inhalable agents, smoking and high GRS, a markedly elevated risk for ACPA-positive RA was observed among the triple-exposed group compared with those not exposed to any (OR 18.22, 95% CI 11.77 to 28.19). Significant interactions were found between occupational inhalable agents and smoking/genetic factors (high GRS or HLA-SE) in ACPA-positive RA.\n\nOccupational inhalable agents could act as important environmental triggers in RA development and interact with smoking and RA-risk genes leading to excessive risk for ACPA-positive RA. Future studies are warranted to assess preventive strategies aimed at reducing occupational hazards and smoking, especially among those who are genetically vulnerable.", "doi": "10.1136/ard-2022-223134", "pmid": "36600175", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI SNP genotyping": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9933179"}, {"db": "pii", "key": "ard-2022-223134"}], "notes": [], "created": "2023-02-24T13:14:03.227Z", "modified": "2023-02-24T13:14:03.311Z"}, {"entity": "publication", "iuid": "6f8f6cd1462b4c9e8cef52480dc55daa", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6f8f6cd1462b4c9e8cef52480dc55daa.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6f8f6cd1462b4c9e8cef52480dc55daa"}}, "title": "Multi-ancestry genome-wide association analyses improve resolution of genes and pathways influencing lung function and chronic obstructive pulmonary disease risk.", "authors": [{"family": "Shrine", "given": "Nick", "initials": "N", "orcid": "0000-0003-3641-4371", "researcher": {"href": "https://publications.scilifelab.se/researcher/b7b11702c0a9442f80ec1abe29042d9a.json"}}, {"family": "Izquierdo", "given": "Abril G", "initials": "AG"}, {"family": "Chen", "given": "Jing", "initials": "J", "orcid": "0000-0003-1287-1930", "researcher": {"href": "https://publications.scilifelab.se/researcher/f49b33706e8e487bbc6abc731fbd1959.json"}}, {"family": "Packer", "given": "Richard", "initials": "R"}, {"family": "Hall", "given": "Robert J", "initials": "RJ"}, {"family": "Guyatt", "given": "Anna L", "initials": "AL", "orcid": "0000-0003-1860-6337", "researcher": {"href": "https://publications.scilifelab.se/researcher/e0feeb53925742f49f7ea3eebdc46487.json"}}, {"family": "Batini", "given": "Chiara", "initials": "C"}, {"family": "Thompson", "given": "Rebecca J", "initials": "RJ"}, {"family": "Pavuluri", "given": "Chandan", "initials": "C"}, {"family": "Malik", "given": "Vidhi", "initials": "V"}, {"family": "Hobbs", "given": "Brian D", "initials": "BD", "orcid": "0000-0001-9564-0745", "researcher": {"href": "https://publications.scilifelab.se/researcher/1a83033c1e704b4490747939324b7bec.json"}}, {"family": "Moll", "given": "Matthew", "initials": "M"}, {"family": "Kim", "given": "Wonji", "initials": "W", "orcid": "0000-0002-1249-797X", "researcher": {"href": "https://publications.scilifelab.se/researcher/6dc987897fcc4950b5e06e7eaa940871.json"}}, {"family": "Tal-Singer", "given": "Ruth", "initials": "R"}, {"family": "Bakke", "given": "Per", "initials": "P"}, {"family": "Fawcett", "given": "Katherine A", "initials": "KA"}, {"family": "John", "given": "Catherine", "initials": "C"}, {"family": "Coley", "given": "Kayesha", "initials": "K", "orcid": "0000-0003-4951-6799", "researcher": {"href": "https://publications.scilifelab.se/researcher/6a13beebd6b54183b366c13d4df27748.json"}}, {"family": "Piga", "given": "Noemi Nicole", 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"given": "Emma L", "initials": "EL", "orcid": "0000-0001-7426-3792", "researcher": {"href": "https://publications.scilifelab.se/researcher/004ac30e0f144d13823c979490bb6b44.json"}}, {"family": "Dudbridge", "given": "Frank", "initials": "F", "orcid": "0000-0002-8817-8908", "researcher": {"href": "https://publications.scilifelab.se/researcher/789f2884eb174898bd5620bb0a9cb7c5.json"}}, {"family": "Silverman", "given": "Edwin K", "initials": "EK"}, {"family": "Strachan", "given": "David P", "initials": "DP", "orcid": "0000-0001-7854-1366", "researcher": {"href": "https://publications.scilifelab.se/researcher/7f96a3bb72be4068ad3c3200bf75e50a.json"}}, {"family": "Walters", "given": "Robin G", "initials": "RG", "orcid": "0000-0002-9179-0321", "researcher": {"href": "https://publications.scilifelab.se/researcher/f36254611faa44b782b76da870e89bd3.json"}}, {"family": "Morris", "given": "Andrew P", "initials": "AP", "orcid": "0000-0002-6805-6014", "researcher": {"href": "https://publications.scilifelab.se/researcher/991fd686a4a040a1a197c1f32d5b731b.json"}}, {"family": "London", "given": "Stephanie J", "initials": "SJ", "orcid": "0000-0003-4911-5290", "researcher": {"href": "https://publications.scilifelab.se/researcher/7542ea2dd880470b8f3330e8b74eeb5c.json"}}, {"family": "Cho", "given": "Michael H", "initials": "MH", "orcid": "0000-0002-4907-1657", "researcher": {"href": "https://publications.scilifelab.se/researcher/fa377da2fe604b18babe1ab6475ad942.json"}}, {"family": "Wain", "given": "Louise V", "initials": "LV", "orcid": "0000-0003-4951-1867", "researcher": {"href": "https://publications.scilifelab.se/researcher/f5ac36354ef94bafa622965e847cbae7.json"}}, {"family": "Hall", "given": "Ian P", "initials": "IP", "orcid": "0000-0001-9933-3216", "researcher": {"href": "https://publications.scilifelab.se/researcher/7a31b8b1ed6d42abb9a64b387bb0a414.json"}}, {"family": "Tobin", "given": "Martin D", "initials": "MD", "orcid": "0000-0002-3596-7874", "researcher": {"href": "https://publications.scilifelab.se/researcher/e0664d5fa4c4449681bf3baeac074584.json"}}], "type": "meta-analysis", "published": "2023-03-00", "journal": {"title": "Nat. Genet.", "issn": "1546-1718", "volume": "55", "issue": "3", "pages": "410-422", "issn-l": "1061-4036"}, "abstract": "Lung-function impairment underlies chronic obstructive pulmonary disease (COPD) and predicts mortality. In the largest multi-ancestry genome-wide association meta-analysis of lung function to date, comprising 580,869 participants, we identified 1,020 independent association signals implicating 559 genes supported by \u22652 criteria from a systematic variant-to-gene mapping framework. These genes were enriched in 29 pathways. Individual variants showed heterogeneity across ancestries, age and smoking groups, and collectively as a genetic risk score showed strong association with COPD across ancestry groups. We undertook phenome-wide association studies for selected associated variants as well as trait and pathway-specific genetic risk scores to infer possible consequences of intervening in pathways underlying lung function. We highlight new putative causal variants, genes, proteins and pathways, including those targeted by existing drugs. These findings bring us closer to understanding the mechanisms underlying lung function and COPD, and should inform functional genomics experiments and potentially future COPD therapies.", "doi": "10.1038/s41588-023-01314-0", "pmid": "36914875", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "NGI SNP genotyping": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10011137"}, {"db": "pii", "key": "10.1038/s41588-023-01314-0"}], "notes": [], "created": "2023-04-06T13:50:14.193Z", "modified": "2023-04-06T13:50:15.219Z"}, {"entity": "publication", "iuid": "972a9d48ef104e73a8766b8630ade5af", "links": {"self": {"href": "https://publications.scilifelab.se/publication/972a9d48ef104e73a8766b8630ade5af.json"}, "display": {"href": "https://publications.scilifelab.se/publication/972a9d48ef104e73a8766b8630ade5af"}}, "title": "Reconstructing clonal tree for phylo-phenotypic characterization of cancer using single-cell transcriptomics.", "authors": [{"family": "Jun", "given": "Seong-Hwan", "initials": "S"}, {"family": "Toosi", "given": "Hosein", "initials": "H"}, {"family": "Mold", "given": "Jeff", "initials": "J"}, {"family": "Engblom", "given": "Camilla", "initials": "C", "orcid": "0000-0001-5090-4161", "researcher": {"href": "https://publications.scilifelab.se/researcher/5ae4350efff0421393356f3ff1f2a971.json"}}, {"family": "Chen", "given": "Xinsong", "initials": "X", "orcid": "0000-0002-3214-9075", "researcher": {"href": "https://publications.scilifelab.se/researcher/561d04f60c61426bb790ba83153ba651.json"}}, {"family": "O'Flanagan", "given": "Ciara", "initials": "C"}, {"family": "Hagemann-Jensen", "given": "Michael", "initials": "M", "orcid": "0000-0002-6423-8216", "researcher": {"href": "https://publications.scilifelab.se/researcher/26cb45960bd042c498f4914a342312a0.json"}}, {"family": "Sandberg", "given": "Rickard", "initials": "R", "orcid": "0000-0001-6473-1740", "researcher": {"href": "https://publications.scilifelab.se/researcher/048c7c9b9edb4366bac7873daad461cd.json"}}, {"family": "Aparicio", "given": "Samuel", "initials": "S", "orcid": "0000-0002-0487-9599", "researcher": {"href": "https://publications.scilifelab.se/researcher/8665401549d749ea8c1ab814dbfe5061.json"}}, {"family": "Hartman", "given": "Johan", "initials": "J", "orcid": "0000-0002-6500-8527", "researcher": {"href": "https://publications.scilifelab.se/researcher/da7cefda6e00463d8ba95fc63eeb8f0a.json"}}, {"family": "Roth", "given": "Andrew", "initials": "A", "orcid": "0000-0003-3422-8823", "researcher": {"href": "https://publications.scilifelab.se/researcher/55d6b9360321440ca1bc9199a42b624a.json"}}, {"family": "Lagergren", "given": "Jens", "initials": "J", "orcid": "0000-0002-4552-0240", "researcher": {"href": "https://publications.scilifelab.se/researcher/b956941833b843f6ace483bf4c21e643.json"}}], "type": "journal article", "published": "2023-02-22", "journal": {"title": "Nat Commun", "issn": "2041-1723", "issn-l": "2041-1723", "volume": "14", "issue": "1", "pages": "982"}, "abstract": "Functional characterization of the cancer clones can shed light on the evolutionary mechanisms driving cancer's proliferation and relapse mechanisms. Single-cell RNA sequencing data provide grounds for understanding the functional state of cancer as a whole; however, much research remains to identify and reconstruct clonal relationships toward characterizing the changes in functions of individual clones. We present PhylEx that integrates bulk genomics data with co-occurrences of mutations from single-cell RNA sequencing data to reconstruct high-fidelity clonal trees. We evaluate PhylEx on synthetic and well-characterized high-grade serous ovarian cancer cell line datasets. PhylEx outperforms the state-of-the-art methods both when comparing capacity for clonal tree reconstruction and for identifying clones. We analyze high-grade serous ovarian cancer and breast cancer data to show that PhylEx exploits clonal expression profiles beyond what is possible with expression-based clustering methods and clear the way for accurate inference of clonal trees and robust phylo-phenotypic analysis of cancer.", "doi": "10.1038/s41467-023-36202-y", "pmid": "36813776", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9946941"}, {"db": "pii", "key": "10.1038/s41467-023-36202-y"}], "notes": [], "created": "2023-03-06T13:47:42.947Z", "modified": "2023-11-29T11:39:09.375Z"}, {"entity": "publication", "iuid": "eec4c83790864c44b1c29201e9e0559a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/eec4c83790864c44b1c29201e9e0559a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/eec4c83790864c44b1c29201e9e0559a"}}, "title": "Accelerated epigenetic aging in women with emotionally unstable personality disorder and a history of suicide attempts.", "authors": [{"family": "Bostr\u00f6m", "given": "Adrian Desai E", "initials": "ADE", "orcid": "0000-0001-8604-9638", "researcher": {"href": "https://publications.scilifelab.se/researcher/5ace74b9a4894d82a16e7ff445bbcea6.json"}}, {"family": "Andersson", "given": "Peter", "initials": "P"}, {"family": "Jamshidi", "given": "Esmail", "initials": "E"}, {"family": "Wilczek", "given": "Alexander", "initials": "A"}, {"family": "Nilsonne", "given": "\u00c5sa", "initials": "\u00c5"}, {"family": "Rask-Andersen", "given": "Mathias", "initials": "M"}, {"family": "\u00c5sberg", "given": "Marie", "initials": "M"}, {"family": "Jokinen", "given": "Jussi", "initials": "J"}], "type": "journal article", "published": "2023-02-22", "journal": {"title": "Transl Psychiatry", "issn": "2158-3188", "volume": "13", "issue": "1", "pages": "66", "issn-l": "2158-3188"}, "abstract": "Emotional unstable personality disorder (EUPD; previously borderline personality disorder, BPD) is associated with excess natural-cause mortality, comorbid medical conditions, poor health habits and stress related epigenomic alterations. Previous studies demonstrated that GrimAge - a state-of-the-art epigenetic age (EA) estimator - strongly predicts mortality risk and physiological dysregulation. Herein, we utilize the GrimAge algorithm to investigate whether women with EUPD and a history of recent suicide attempts exhibit EA acceleration (EAA) in comparison to healthy controls. Genome-wide methylation patterns were measured using the Illumina Infinum Methylation Epic BeadChip in whole blood from 97 EUPD patients and 32 healthy controls. The control group was significantly older (p < 0.0001) and reported lesser exposure to violent behavior in both youth and adulthood (p < 0.0001). Groups were otherwise comparable regarding gender, BMI, or tobacco usage (p > 0.05). EA estimator DNAmGrimAge exceeded chronological age by 8.8 and 2.3 years in the EUPD and control group, respectively. Similarly, EAA marker AgeAccelGrim was substantially higher in EUPD subjects when compared to controls, in both univariate and multivariate analyzes (p < 0.00001). Tobacco usage conferred substantial within-group effects on the EA-chronological age difference, i.e., 10.74 years (SD = 4.19) compared to 6.00 years (SD = 3.10) in the non-user EUPD group (p < 0.00001). Notably, past alcohol and substance abuse, use of psychotropic medications, global assessment of functioning, self-reported exposure to violent behavior in youth and adulthood, later completed suicide (N = 8) and age at first suicide attempt did not predict EAA in the EUPD group (p > 0.05). These results underscore the importance of addressing medical health conditions along with low-cost preventative interventions aimed at improving somatic health outcomes in EUPD, such as efforts to support cessation of tobacco use. The independency of GrimAge to other EA algorithms in this group of severely impaired EUPD patients, suggest it may have unique characteristics to evaluate risk of adverse health outcomes in context of psychiatric disorders.", "doi": "10.1038/s41398-023-02369-7", "pmid": "36813766", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI SNP genotyping": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41398-023-02369-7"}, {"db": "pmc", "key": "PMC9946998"}], "notes": [], "created": "2023-02-24T13:14:04.756Z", "modified": "2023-02-24T13:14:04.784Z"}, {"entity": "publication", "iuid": "fb41fa7668a64161a4558d8647c73b7e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/fb41fa7668a64161a4558d8647c73b7e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/fb41fa7668a64161a4558d8647c73b7e"}}, "title": "Targeting the gut-lung axis by synbiotic feeding to infants in a randomized controlled trial.", "authors": [{"family": "Sj\u00f6din", "given": "Kotryna Simonyt\u00e9", "initials": "KS", "orcid": "0000-0002-1323-9913", "researcher": {"href": "https://publications.scilifelab.se/researcher/f00fe6a2da9b447f949b5b2f26bda908.json"}}, {"family": "Sj\u00f6din", "given": "Andreas", "initials": "A", "orcid": "0000-0001-5350-4219", "researcher": {"href": "https://publications.scilifelab.se/researcher/6398d7c06a414ea6bcaf2579a8587452.json"}}, {"family": "Ruszczy\u0144ski", "given": "Marek", "initials": "M"}, {"family": "Kristensen", "given": "Mette Bach", "initials": "MB"}, {"family": "Hernell", "given": "Olle", "initials": "O"}, {"family": "Szajewska", "given": "Hania", "initials": "H"}, {"family": "West", "given": "Christina E", "initials": "CE", "orcid": "0000-0001-9599-2580", "researcher": {"href": "https://publications.scilifelab.se/researcher/be2972e4afa744e5aa0525a4c9d89348.json"}}], "type": "randomized controlled trial", "published": "2023-02-20", "journal": {"title": "BMC Biol.", "issn": "1741-7007", "issn-l": "1741-7007", "volume": "21", "issue": "1", "pages": "38"}, "abstract": "Formula-fed infants are at increased risk of infections. Due to the cross-talk between the mucosal systems of the gastrointestinal and respiratory tracts, adding synbiotics (prebiotics and probiotics) to infant formula may prevent infections even at distant sites. Infants that were born full term and weaned from breast milk were randomized to prebiotic formula (fructo- and galactooligosaccharides) or the same prebiotic formula with Lactobacillus paracasei ssp. paracasei F19 (synbiotics) from 1 to 6 months of age. The objective was to examine the synbiotic effects on gut microbiota development.\r\n\r\nFecal samples collected at ages 1, 4, 6, and 12 months were analyzed using 16S rRNA gene sequencing and a combination of untargeted gas chromatography-mass spectrometry/liquid chromatography-mass spectrometry. These analyses revealed that the synbiotic group had a lower abundance of Klebsiella, a higher abundance of Bifidobacterium breve compared to the prebiotic group, and increases in the anti-microbial metabolite d-3-phenyllactic acid. We also analyzed the fecal metagenome and antibiotic resistome in the 11 infants that had been diagnosed with lower respiratory tract infection (cases) and 11 matched controls using deep metagenomic sequencing. Cases with lower respiratory tract infection had a higher abundance of Klebsiella species and antimicrobial resistance genes related to Klebsiella pneumoniae, compared to controls. The results obtained using 16S rRNA gene amplicon and metagenomic sequencing were confirmed in silico by successful recovery of the metagenome-assembled genomes of the bacteria of interest.\r\n\r\nThis study demonstrates the additional benefit of feeding specific synbiotics to formula-fed infants over prebiotics only. Synbiotic feeding led to the underrepresentation of Klebsiella, enrichment of bifidobacteria, and increases in microbial degradation metabolites implicated in immune signaling and in the gut-lung and gut-skin axes. Our findings support future clinical evaluation of synbiotic formula in the prevention of infections and associated antibiotic treatment as a primary outcome when breastfeeding is not feasible.\r\n\r\nClinicalTrials.gov NCT01625273 . Retrospectively registered on 21 June 2012.", "doi": "10.1186/s12915-023-01531-3", "pmid": "36803508", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Swedish Metabolomics Centre": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9940374"}, {"db": "pii", "key": "10.1186/s12915-023-01531-3"}, {"db": "ClinicalTrials.gov", "key": "NCT01625273"}], "notes": [], "created": "2023-08-30T07:07:12.511Z", "modified": "2025-10-17T13:03:14.225Z"}, {"entity": "publication", "iuid": "f3bbf73bbbd4488dbd6ed6b3b52fd575", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f3bbf73bbbd4488dbd6ed6b3b52fd575.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f3bbf73bbbd4488dbd6ed6b3b52fd575"}}, "title": "Endosperm cellularization failure induces a dehydration-stress response leading to embryo arrest.", "authors": [{"family": "Xu", "given": "Wenjia", "initials": "W", "orcid": "0000-0003-1945-4451", "researcher": {"href": "https://publications.scilifelab.se/researcher/20c6bb89f2a047328e12ef6f6f36fc91.json"}}, {"family": "Sato", "given": "Hikaru", "initials": "H", "orcid": "0000-0001-7628-0414", "researcher": {"href": "https://publications.scilifelab.se/researcher/910d1533dd744edcbb4950dfc7c7f7c6.json"}}, {"family": "Bente", "given": "Heinrich", "initials": "H", "orcid": "0000-0001-9229-5149", "researcher": {"href": "https://publications.scilifelab.se/researcher/cf580937ed9c45a5b736c95699ccd8eb.json"}}, {"family": "Santos-Gonz\u00e1lez", "given": "Juan", "initials": "J", "orcid": "0000-0002-8712-9776", "researcher": {"href": "https://publications.scilifelab.se/researcher/d26cc8b837e64875aa2226cb9a8b8da3.json"}}, {"family": "K\u00f6hler", "given": "Claudia", "initials": "C", "orcid": "0000-0002-2619-4857", "researcher": {"href": "https://publications.scilifelab.se/researcher/accd3f9307614c8ab67154dd5e50cdac.json"}}], "type": "journal article", "published": "2023-02-20", "journal": {"title": "Plant Cell", "issn": "1532-298X", "volume": "35", "issue": "2", "pages": "874-888", "issn-l": "1040-4651"}, "abstract": "The endosperm is a nutritive tissue supporting embryo growth in flowering plants. Most commonly, the endosperm initially develops as a coenocyte (multinucleate cell) and then cellularizes. This process of cellularization is frequently disrupted in hybrid seeds generated by crosses between different flowering plant species or plants that differ in ploidy, resulting in embryo arrest and seed lethality. The reason for embryo arrest upon cellularization failure remains unclear. In this study, we show that triploid Arabidopsis thaliana embryos surrounded by uncellularized endosperm mount an osmotic stress response that is connected to increased levels of abscisic acid (ABA) and enhanced ABA responses. Impairing ABA biosynthesis and signaling aggravated triploid seed abortion, while increasing endogenous ABA levels as well as the exogenous application of ABA-induced endosperm cellularization and suppressed embryo growth arrest. Taking these results together, we propose that endosperm cellularization is required to establish dehydration tolerance in the developing embryo, ensuring its survival during seed maturation.", "doi": "10.1093/plcell/koac337", "pmid": "36427255", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Swedish Metabolomics Centre": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9940880"}, {"db": "pii", "key": "6847301"}], "notes": [], "created": "2022-11-29T09:51:04.203Z", "modified": "2025-10-17T13:03:14.237Z"}, {"entity": "publication", "iuid": "0a59c27f5dc3494c8e620e4f3637a7a0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0a59c27f5dc3494c8e620e4f3637a7a0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0a59c27f5dc3494c8e620e4f3637a7a0"}}, "title": "Associations of DNA Methylation With Behavioral Problems, Gray Matter Volumes, and Negative Life Events Across Adolescence: Evidence From the Longitudinal IMAGEN Study.", "authors": [{"family": "Sun", "given": "Yan", "initials": "Y"}, {"family": "Jia", "given": "Tianye", "initials": "T"}, {"family": "Barker", "given": "Edward D", "initials": "ED"}, {"family": "Chen", "given": "Di", "initials": "D"}, {"family": "Zhang", "given": "Zuo", "initials": "Z"}, {"family": "Xu", "given": "Jiayuan", "initials": "J"}, {"family": "Chang", "given": "Suhua", "initials": "S"}, {"family": "Zhou", "given": "Guangdong", "initials": "G"}, {"family": "Liu", "given": "Yun", "initials": "Y"}, {"family": "Tay", "given": "Nicole", "initials": "N"}, {"family": "Luo", "given": "Qiang", "initials": "Q"}, {"family": "Chang", "given": "Xiao", "initials": "X"}, {"family": "Banaschewski", "given": "Tobias", "initials": "T"}, {"family": "Bokde", "given": "Arun L W", "initials": "ALW"}, {"family": "Flor", "given": "Herta", "initials": "H"}, {"family": "Grigis", "given": "Antoine", "initials": "A"}, {"family": "Garavan", "given": "Hugh", "initials": "H"}, {"family": "Heinz", "given": "Andreas", "initials": "A"}, {"family": "Martinot", "given": "Jean-Luc", "initials": "JL"}, {"family": "Paill\u00e8re Martinot", "given": "Marie-Laure", "initials": "ML"}, {"family": "Artiges", "given": "Eric", "initials": "E"}, {"family": "Nees", "given": "Frauke", "initials": "F"}, {"family": "Orfanos", "given": "Dimitri Papadopoulos", "initials": "DP"}, {"family": "Paus", "given": "Tom\u00e1\u0161", "initials": "T"}, {"family": "Poustka", "given": "Luise", "initials": "L"}, {"family": "Hohmann", "given": "Sarah", "initials": "S"}, {"family": "Millenet", "given": "Sabina", "initials": "S"}, {"family": "Fr\u00f6hner", "given": "Juliane H", "initials": "JH"}, {"family": "Smolka", "given": "Michael N", "initials": "MN"}, {"family": "Walter", "given": "Henrik", "initials": "H"}, {"family": "Whelan", "given": "Robert", "initials": "R"}, {"family": "Lu", "given": "Lin", "initials": "L"}, {"family": "Shi", "given": "Jie", "initials": "J"}, {"family": "Schumann", "given": "Gunter", "initials": "G"}, {"family": "Desrivi\u00e8res", "given": "Sylvane", "initials": "S"}], "type": "journal article", "published": "2023-02-15", "journal": {"title": "Biol. Psychiatry", "issn": "1873-2402", "volume": "93", "issue": "4", "pages": "342-351", "issn-l": "0006-3223"}, "abstract": "Negative life events (NLEs) increase the risk for externalizing behaviors (EBs) and internalizing behaviors (IBs) in adolescence and adult psychopathology. DNA methylation associated with behavioral problems may reflect this risk and long-lasting effects of NLEs.\n\nTo identify consistent associations between blood DNA methylation and EBs or IBs across adolescence, we conducted longitudinal epigenome-wide association studies (EWASs) using data from the IMAGEN cohort, collected at ages 14 and 19 years (n = 506). Significant findings were validated in a separate subsample (n = 823). Methylation risk scores were generated by 10-fold cross-validation and further tested for their associations with gray matter volumes and NLEs.\n\nNo significant findings were obtained for the IB-EWAS. The EB-EWAS identified a genome-wide significant locus in a gene linked to attention-deficit/hyperactivity disorder (ADHD) (IQSEC1, cg01460382; p = 1.26 \u00d7 10-8). Other most significant CpG sites were near ADHD-related genes and enriched for genes regulating tumor necrosis factor and interferon-\u03b3 signaling, highlighting the relevance of EB-EWAS findings for ADHD. Analyses with the EB methylation risk scores suggested that it partly reflected comorbidity with IBs in late adolescence. Specific to EBs, EB methylation risk scores correlated with smaller gray matter volumes in medial orbitofrontal and anterior/middle cingulate cortices, brain regions known to associate with ADHD and conduct problems. Longitudinal mediation analyses indicated that EB-related DNA methylation were more likely the outcomes of problematic behaviors accentuated by NLEs, and less likely the epigenetic bases of such behaviors.\n\nOur findings suggest that novel epigenetic mechanisms through which NLEs exert short and longer-term effects on behavior may contribute to ADHD.", "doi": "10.1016/j.biopsych.2022.06.012", "pmid": "36241462", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI SNP genotyping": "Service"}, "xrefs": [{"db": "pii", "key": "S0006-3223(22)01356-7"}], "notes": [], "created": "2023-02-24T13:14:06.009Z", "modified": "2023-02-24T13:14:06.023Z"}, {"entity": "publication", "iuid": "d03cd66d9f694b8da2a36e70178b23f2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d03cd66d9f694b8da2a36e70178b23f2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d03cd66d9f694b8da2a36e70178b23f2"}}, "title": "Bacteroidetes to Firmicutes: captivity changes the gut microbiota composition and diversity in a social subterranean rodent.", "authors": [{"family": "Bensch", "given": "Hanna M", "initials": "HM", "orcid": "0000-0002-8449-9843", "researcher": {"href": "https://publications.scilifelab.se/researcher/9a204f1b0fe34b8999893abe65fb3e8c.json"}}, {"family": "Tolf", "given": "Conny", "initials": "C"}, {"family": "Waldenstr\u00f6m", "given": "Jonas", "initials": "J", "orcid": "0000-0002-1152-4235", "researcher": {"href": "https://publications.scilifelab.se/researcher/53013aa313214e26abdb18ea0199371f.json"}}, {"family": "Lundin", "given": "Daniel", "initials": "D", "orcid": "0000-0002-8779-6464", "researcher": {"href": "https://publications.scilifelab.se/researcher/227cc90e084348a193fee05eb23a6bf3.json"}}, {"family": "Z\u00f6ttl", "given": "Markus", "initials": "M", "orcid": "0000-0002-5582-2306", "researcher": {"href": "https://publications.scilifelab.se/researcher/e262a41c07044bd88a4bd6f1dcc2f1eb.json"}}], "type": "journal article", "published": "2023-02-10", "journal": {"title": "Anim Microbiome", "issn": "2524-4671", "volume": "5", "issue": "1", "pages": "9", "issn-l": null}, "abstract": "In mammals, the gut microbiota has important effects on the health of their hosts. Recent research highlights that animal populations that live in captivity often differ in microbiota diversity and composition from wild populations. However, the changes that may occur when animals move to captivity remain difficult to predict and factors generating such differences are poorly understood. Here we compare the bacterial gut microbiota of wild and captive Damaraland mole-rats (Fukomys damarensis) originating from a population in the southern Kalahari Desert to characterise the changes of the gut microbiota that occur from one generation to the next generation in a long-lived, social rodent species.\n\nWe found a clear divergence in the composition of the gut microbiota of captive and wild Damaraland mole-rats. Although the dominating higher-rank bacterial taxa were the same in the two groups, captive animals had an increased ratio of relative abundance of Firmicutes to Bacteroidetes compared to wild animals. The Amplicon Sequence Variants (ASVs) that were strongly associated with wild animals were commonly members of the same bacterial families as those strongly associated with captive animals. Captive animals had much higher ASV richness compared to wild-caught animals, explained by an increased richness within the Firmicutes.\n\nWe found that the gut microbiota of captive hosts differs substantially from the gut microbiota composition of wild hosts. The largest differences between the two groups were found in shifts in relative abundances and diversity of Firmicutes and Bacteroidetes.", "doi": "10.1186/s42523-023-00231-1", "pmid": "36765400", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9912604"}, {"db": "pii", "key": "10.1186/s42523-023-00231-1"}], "notes": [], "created": "2023-11-29T11:42:36.598Z", "modified": "2023-11-29T11:42:36.636Z"}, {"entity": "publication", "iuid": "6679c4b418fa47b3a6bf6e9d7539b0f1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6679c4b418fa47b3a6bf6e9d7539b0f1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6679c4b418fa47b3a6bf6e9d7539b0f1"}}, "title": "Inversions maintain differences between migratory phenotypes of a songbird.", "authors": [{"family": "Lundberg", "given": "Max", "initials": "M", "orcid": "0000-0002-1895-3622", "researcher": {"href": "https://publications.scilifelab.se/researcher/5b6a6dafa8fe4371ab26ed02ca5a550c.json"}}, {"family": "Mackintosh", "given": "Alexander", "initials": "A"}, {"family": "Petri", "given": "Anna", "initials": "A"}, {"family": "Bensch", "given": "Staffan", "initials": "S", "orcid": "0000-0002-0082-0899", "researcher": {"href": "https://publications.scilifelab.se/researcher/b925a620a68049928c3dc0cbc87948ba.json"}}], "type": "journal article", "published": "2023-01-27", "journal": {"title": "Nat Commun", "issn": "2041-1723", "issn-l": "2041-1723", "volume": "14", "issue": "1", "pages": "452"}, "abstract": "Structural rearrangements have been shown to be important in local adaptation and speciation, but have been difficult to reliably identify and characterize in non-model species. Here we combine long reads, linked reads and optical mapping to characterize three divergent chromosome regions in the willow warbler Phylloscopus trochilus, of which two are associated with differences in migration and one with an environmental gradient. We show that there are inversions (0.4-13 Mb) in each of the regions and that the divergence times between inverted and non-inverted haplotypes are similar across the regions (~1.2 Myrs), which is compatible with a scenario where inversions arose in either of two allopatric populations that subsequently hybridized. The improved genomes allow us to detect additional functional differences in the divergent regions, providing candidate genes for migration and adaptations to environmental gradients.", "doi": "10.1038/s41467-023-36167-y", "pmid": "36707538", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Uppsala (Uppsala Genome Center)": "Collaborative", "NGI Short read": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Other": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9883250"}, {"db": "pii", "key": "10.1038/s41467-023-36167-y"}], "notes": [], "created": "2023-03-06T13:47:37.052Z", "modified": "2024-01-16T13:48:34.085Z"}, {"entity": "publication", "iuid": "8d88408f966c47f889a1837ae4c1b936", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8d88408f966c47f889a1837ae4c1b936.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8d88408f966c47f889a1837ae4c1b936"}}, "title": "Highly differentiated loci resolve phylogenetic relationships in the Bean Goose complex.", "authors": [{"family": "Ottenburghs", "given": "Jente", "initials": "J"}, {"family": "Honka", "given": "Johanna", "initials": "J"}, {"family": "Heikkinen", "given": "Marja E", "initials": "ME"}, {"family": "Madsen", "given": "Jesper", "initials": "J"}, {"family": "M\u00fcskens", "given": "Gerhard J D M", "initials": "GJDM"}, {"family": "Ellegren", "given": "Hans", "initials": "H"}], "type": "journal article", "published": "2023-01-19", "journal": {"title": "BMC Ecol Evol", "issn": "2730-7182", "volume": "23", "issue": "1", "pages": "2", "issn-l": null}, "abstract": "Reconstructing phylogenetic relationships with genomic data remains a challenging endeavor. Numerous phylogenomic studies have reported incongruent gene trees when analyzing different genomic regions, complicating the search for a 'true' species tree. Some authors have argued that genomic regions of increased divergence (i.e. differentiation islands) reflect the species tree, although other studies have shown that these regions might produce misleading topologies due to species-specific selective sweeps or ancient introgression events. In this study, we tested the extent to which highly differentiated loci can resolve phylogenetic relationships in the Bean Goose complex, a group of goose taxa that includes the Taiga Bean Goose (Anser fabalis), the Tundra Bean Goose (Anser serrirostris) and the Pink-footed Goose (Anser brachyrhynchus).\n\nFirst, we show that a random selection of genomic loci-which mainly samples the undifferentiated regions of the genome-results in an unresolved species complex with a monophyletic A. brachyrhynchus embedded within a paraphyletic cluster of A. fabalis and A. serrirostris. Next, phylogenetic analyses of differentiation islands converged upon a topology of three monophyletic clades in which A. brachyrhynchus is sister to A. fabalis, and A. serrirostris is sister to the clade uniting these two species. Close inspection of the locus trees within the differentiated regions revealed that this topology was consistently supported over other phylogenetic arrangements. As it seems unlikely that selection or introgression events have impacted all differentiation islands in the same way, we are convinced that this topology reflects the 'true' species tree. Additional analyses, based on D-statistics, revealed extensive introgression between A. fabalis and A. serrirostris, which partly explains the failure to resolve the species complex with a random selection of genomic loci. Recent introgression between these taxa has probably erased the phylogenetic branching pattern across a large section of the genome, whereas differentiation islands were unaffected by the homogenizing gene flow and maintained the phylogenetic patterns that reflect the species tree.\n\nThe evolution of the Bean Goose complex can be depicted as a simple bifurcating tree, but this would ignore the impact of introgressive hybridization. Hence, we advocate that the evolutionary relationships between these taxa are best represented as a phylogenetic network.", "doi": "10.1186/s12862-023-02103-3", "pmid": "36658479", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9854053"}, {"db": "pii", "key": "10.1186/s12862-023-02103-3"}], "notes": [], "created": "2023-11-30T13:15:16.114Z", "modified": "2024-01-16T13:48:34.115Z"}, {"entity": "publication", "iuid": "8fdf3ddb19384b72b7184506e4a87f19", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8fdf3ddb19384b72b7184506e4a87f19.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8fdf3ddb19384b72b7184506e4a87f19"}}, "title": "Microbial communities mediating net methylmercury formation along a trophic gradient in a peatland chronosequence.", "authors": [{"family": "Wang", "given": "Baolin", "initials": "B"}, {"family": "Hu", "given": "Haiyan", "initials": "H"}, {"family": "Bishop", "given": "Kevin", "initials": "K"}, {"family": "Buck", "given": "Moritz", "initials": "M"}, {"family": "Bj\u00f6rn", "given": "Erik", "initials": "E"}, {"family": "Skyllberg", "given": "Ulf", "initials": "U"}, {"family": "Nilsson", "given": "Mats B", "initials": "MB"}, {"family": "Bertilsson", "given": "Stefan", "initials": "S"}, {"family": "Bravo", "given": "Andrea G", "initials": "AG"}], "type": "journal article", "published": "2023-01-15", "journal": {"title": "J Hazard Mater", "issn": "1873-3336", "volume": "442", "pages": "130057", "issn-l": null}, "abstract": "Peatlands are generally important sources of methylmercury (MeHg) to adjacent aquatic ecosystems, increasing the risk of human and wildlife exposure to this highly toxic compound. While microorganisms play important roles in mercury (Hg) geochemical cycles where they directly and indirectly affect MeHg formation in peatlands, potential linkages between net MeHg formation and microbial communities involving these microorganisms remain unclear. To address this gap, microbial community composition and specific marker gene transcripts were investigated along a trophic gradient in a geographically constrained peatland chronosequence. Our results showed a clear spatial pattern in microbial community composition along the gradient that was highly driven by peat soil properties and significantly associated with net MeHg formation as approximated by MeHg concentration and %MeHg of total Hg concentration. Known fermentative, syntrophic, methanogenic and iron-reducing metabolic guilds had the strong positive correlations to net MeHg formation, while methanotrophic and methylotrophic microorganisms were negatively correlated. Our results indicated that sulfate reducers did not have a key role in net MeHg formation. Microbial activity as interpreted from 16S rRNA sequences was significantly correlated with MeHg and %MeHg. Our findings shed new light on the role of microbial community in net MeHg formation of peatlands that undergo ontogenetic change.", "doi": "10.1016/j.jhazmat.2022.130057", "pmid": "36179622", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "S0304-3894(22)01851-9"}], "notes": [], "created": "2022-11-29T12:19:05.196Z", "modified": "2024-01-16T13:48:34.134Z"}, {"entity": "publication", "iuid": "cb8bdac206dc430f8174e8cbcd6281cf", "links": {"self": {"href": "https://publications.scilifelab.se/publication/cb8bdac206dc430f8174e8cbcd6281cf.json"}, "display": {"href": "https://publications.scilifelab.se/publication/cb8bdac206dc430f8174e8cbcd6281cf"}}, "title": "PIK3CA is recurrently mutated in canine mammary tumors, similarly to in human mammary neoplasia.", "authors": [{"family": "Arendt", "given": "Maja Louise", "initials": "ML"}, {"family": "Sakthikumar", "given": "Sharadha", "initials": "S"}, {"family": "Melin", "given": "Malin", "initials": "M"}, {"family": "Elvers", "given": "Ingegerd", "initials": "I"}, {"family": "Rivera", "given": "Patricio", "initials": "P"}, {"family": "Larsen", "given": "Majbritt", "initials": "M"}, {"family": "Saellstr\u00f6m", "given": "Sara", "initials": "S"}, {"family": "Lingaas", "given": "Frode", "initials": "F"}, {"family": "R\u00f6nnberg", "given": "Henrik", "initials": "H"}, {"family": "Lindblad-Toh", "given": "Kerstin", "initials": "K"}], "type": "journal article", "published": "2023-01-12", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "13", "issue": "1", "pages": "632", "issn-l": "2045-2322"}, "abstract": "Biological features of neoplastic disease affecting mammary gland tissue are shared between canines and humans. Research performed in either species has translational value and early phase clinical trials performed in canines with spontaneous disease could be informative for human trials. The purpose of this study was to investigate the somatic genetic aberrations occurring in canine mammary neoplasia by exome capture and next generation sequencing. Based on 55 tumor-normal pairs we identified the PIK3CA gene as the most commonly mutated gene in canine mammary tumors, with 25% of samples carrying mutations in this gene. A recurrent missense mutation was identified, p.H1047R, which is homologous to the human PIK3CA hotspot mutation found in different types of breast neoplasia. Mutations homologous to other known human mutation hotspots such as the PIK3CA p.E545K and the KRAS p.G12V/D were also identified. We identified copy number aberrations affecting important tumor suppressor and oncogenic pathways including deletions affecting the PTEN tumor suppressor gene. We suggest that activation of the KRAS or PIK3CA oncogenes or loss of the PTEN suppressor gene may be important for mammary tumor development in dogs. This data endorses the conservation of cancer across species and the validity of studying cancer in non-human species.", "doi": "10.1038/s41598-023-27664-7", "pmid": "36635367", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9837039"}, {"db": "pii", "key": "10.1038/s41598-023-27664-7"}], "notes": [], "created": "2023-11-29T11:40:33.492Z", "modified": "2024-01-16T13:48:34.144Z"}, {"entity": "publication", "iuid": "dbd47bdc131a45f6866e697cbdbc8196", "links": {"self": {"href": "https://publications.scilifelab.se/publication/dbd47bdc131a45f6866e697cbdbc8196.json"}, "display": {"href": "https://publications.scilifelab.se/publication/dbd47bdc131a45f6866e697cbdbc8196"}}, "title": "Longitudinal single-cell analysis of SARS-CoV-2-reactive B cells uncovers persistence of early-formed, antigen-specific clones.", "authors": [{"family": "Scharf", "given": "Lydia", "initials": "L"}, {"family": "Axelsson", "given": "Hannes", "initials": "H"}, {"family": "Emmanouilidi", "given": "Aikaterini", "initials": "A"}, {"family": "Mathew", "given": "Nimitha R", "initials": "NR"}, {"family": "Sheward", "given": "Daniel J", "initials": "DJ"}, {"family": "Leach", "given": "Susannah", "initials": "S"}, {"family": "Isakson", "given": "Pauline", "initials": "P"}, {"family": "Smirnov", "given": "Ilya V", "initials": "IV"}, {"family": "Marklund", "given": "Emelie", "initials": "E"}, {"family": "Miron", "given": "Nicolae", "initials": "N"}, {"family": "Andersson", "given": "Lars-Magnus", "initials": "LM"}, {"family": "Gissl\u00e9n", "given": "Magnus", "initials": "M"}, {"family": "Murrell", "given": "Ben", "initials": "B"}, {"family": "Lundgren", "given": "Anna", "initials": "A"}, {"family": "Bemark", "given": "Mats", "initials": "M"}, {"family": "Angeletti", "given": "Davide", "initials": "D"}], "type": "journal article", "published": "2023-01-10", "journal": {"title": "JCI Insight", "issn": "2379-3708", "volume": "8", "issue": "1", "issn-l": "2379-3708"}, "abstract": "Understanding persistence and evolution of B cell clones after COVID-19 infection and vaccination is crucial for predicting responses against emerging viral variants and optimizing vaccines. Here, we collected longitudinal samples from patients with severe COVID-19 every third to seventh day during hospitalization and every third month after recovery. We profiled their antigen-specific immune cell dynamics by combining single-cell RNA-Seq, Cellular Indexing of Transcriptomes and Epitopes by Sequencing (CITE-Seq), and B cell receptor-Seq (BCR-Seq) with oligo-tagged antigen baits. While the proportion of Spike receptor binding domain-specific memory B cells (MBC) increased from 3 months after infection, the other Spike- and Nucleocapsid-specific B cells remained constant. All patients showed ongoing class switching and sustained affinity maturation of antigen-specific cells, and affinity maturation was not significantly increased early after vaccine. B cell analysis revealed a polyclonal response with limited clonal expansion; nevertheless, some clones detected during hospitalization, as plasmablasts, persisted for up to 1 year, as MBC. Monoclonal antibodies derived from persistent B cell families increased their binding and neutralization breadth and started recognizing viral variants by 3 months after infection. Overall, our findings provide important insights into the clonal evolution and dynamics of antigen-specific B cell responses in longitudinally sampled patients infected with COVID-19.", "doi": "10.1172/jci.insight.165299", "pmid": "36445762", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9870078"}, {"db": "pii", "key": "165299"}], "notes": [], "created": "2023-11-29T11:33:16.662Z", "modified": "2023-11-29T11:33:16.666Z"}, {"entity": "publication", "iuid": "02fa1bf524494d89adbe4ed1bcb16013", "links": {"self": {"href": "https://publications.scilifelab.se/publication/02fa1bf524494d89adbe4ed1bcb16013.json"}, "display": {"href": "https://publications.scilifelab.se/publication/02fa1bf524494d89adbe4ed1bcb16013"}}, "title": "Methylation in MAD1L1 is associated with the severity of suicide attempt and phenotypes of depression.", "authors": [{"family": "Sokolov", "given": "Aleksandr V", "initials": "AV"}, {"family": "Manu", "given": "Diana-Maria", "initials": "DM"}, {"family": "Nordberg", "given": "Didi O T", "initials": "DOT"}, {"family": "Bostr\u00f6m", "given": "Adrian D E", "initials": "ADE"}, {"family": "Jokinen", "given": "Jussi", "initials": "J"}, {"family": "Schi\u00f6th", "given": "Helgi B", "initials": "HB"}], "type": "journal article", "published": "2023-01-04", "journal": {"title": "Clin Epigenetics", "issn": "1868-7083", "volume": "15", "issue": "1", "pages": "1", "issn-l": "1868-7075"}, "abstract": "Depression is a multifactorial disorder representing a significant public health burden. Previous studies have linked multiple single nucleotide polymorphisms with depressive phenotypes and suicidal behavior. MAD1L1 is a mitosis metaphase checkpoint protein that has been linked to depression in GWAS. Using a longitudinal EWAS approach in an adolescent cohort at two time points (n = 216 and n = 154), we identified differentially methylated sites that were associated with depression-related genetic variants in MAD1L1. Three methylation loci (cg02825527, cg18302629, and cg19624444) were consistently hypomethylated in the minor allele carriers, being cross-dependent on several SNPs. We further investigated whether DNA methylation at these CpGs is associated with depressive psychiatric phenotypes in independent cohorts. The first site (cg02825527) was hypomethylated in blood (exp(\u03b2) = 84.521, p value ~ 0.003) in participants with severe suicide attempts (n = 88). The same locus showed increased methylation in glial cells (exp(\u03b2) = 0.041, p value ~ 0.004) in the validation cohort, involving 29 depressed patients and 29 controls, and showed a trend for association with suicide (n = 40, p value ~ 0.089) and trend for association with depression treatment (n = 377, p value ~ 0.075). The second CpG (cg18302629) was significantly hypomethylated in depressed participants (exp(\u03b2) = 56.374, p value ~ 0.023) in glial cells, but did not show associations in the discovery cohorts. The last methylation site (cg19624444) was hypomethylated in the whole blood of severe suicide attempters; however, this association was at the borderline for statistical significance (p value ~ 0.061). This locus, however, showed a strong association with depression treatment in the validation cohort (exp(\u03b2) = 2.237, p value ~ 0.003) with 377 participants. The direction of associations between psychiatric phenotypes appeared to be different in the whole blood in comparison with brain samples for cg02825527 and cg19624444. The association analysis between methylation at cg18302629 and cg19624444 and MAD1L1 transcript levels in CD14+ cells shows a potential link between methylation at these CpGs and MAD1L1 expression. This study suggests evidence that methylation at MAD1L1 is important for psychiatric health as supported by several independent cohorts.", "doi": "10.1186/s13148-022-01394-5", "pmid": "36600305", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI SNP genotyping": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9811786"}, {"db": "pii", "key": "10.1186/s13148-022-01394-5"}], "notes": [], "created": "2023-02-24T13:14:08.673Z", "modified": "2023-02-24T13:14:08.688Z"}, {"entity": "publication", "iuid": "18d1940c083c4e4780bea26c0c4df967", "links": {"self": {"href": "https://publications.scilifelab.se/publication/18d1940c083c4e4780bea26c0c4df967.json"}, "display": {"href": "https://publications.scilifelab.se/publication/18d1940c083c4e4780bea26c0c4df967"}}, "title": "Experimental Life History Evolution Results in Sex-specific Evolution of Gene Expression in Seed Beetles.", "authors": [{"family": "Immonen", "given": "Elina", "initials": "E", "orcid": "0000-0003-1121-6950", "researcher": {"href": "https://publications.scilifelab.se/researcher/f6c9af5588c64dfdacba192b65524d43.json"}}, {"family": "Sayadi", "given": "Ahmed", "initials": "A"}, {"family": "Stojkovi\u0107", "given": "Biljana", "initials": "B"}, {"family": "Savkovi\u0107", "given": "Uro\u0161", "initials": "U"}, {"family": "\u0110or\u0111evi\u0107", "given": "Mirko", "initials": "M"}, {"family": "Liljestrand-R\u00f6nn", "given": "Johanna", "initials": "J"}, {"family": "Wiberg", "given": "R Axel W", "initials": "RAW"}, {"family": "Arnqvist", "given": "G\u00f6ran", "initials": "G", "orcid": "0000-0002-3501-3376", "researcher": {"href": "https://publications.scilifelab.se/researcher/a2e926bfdd22419eb57d2c375041150f.json"}}], "type": "journal article", "published": "2023-01-04", "journal": {"title": "Genome Biol Evol", "issn": "1759-6653", "issn-l": "1759-6653", "volume": "15", "issue": "1", "pages": null}, "abstract": "The patterns of reproductive timing and senescence vary within and across species owing to differences in reproductive strategies, but our understanding of the molecular underpinnings of such variation is incomplete. This is perhaps particularly true for sex differences. We investigated the evolution of sex-specific gene expression associated with life history divergence in replicated populations of the seed beetle Acanthoscelides obtectus, experimentally evolving under (E)arly or (L)ate life reproduction for >200 generations which has resulted in strongly divergent life histories. We detected 1,646 genes that were differentially expressed in E and L lines, consistent with a highly polygenic basis of life history evolution. Only 30% of differentially expressed genes were similarly affected in males and females. The evolution of long life was associated with significantly reduced sex differences in expression, especially in non-reproductive tissues. The expression differences were overall more pronounced in females, in accordance with their greater phenotypic divergence in lifespan. Functional enrichment analysis revealed differences between E and L beetles in gene categories previously implicated in aging, such as mitochondrial function and defense response. The results show that divergent life history evolution can be associated with profound changes in gene expression that alter the transcriptome in a sex-specific way, highlighting the importance of understanding the mechanisms of aging in each sex.", "doi": "10.1093/gbe/evac177", "pmid": "36542472", "labels": {"Bioinformatics Support and Infrastructure": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support for Computational Resources": "Service", "NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9830990"}, {"db": "pii", "key": "6948356"}], "notes": [], "created": "2023-12-01T12:26:26.019Z", "modified": "2024-07-01T06:04:47.982Z"}, {"entity": "publication", "iuid": "570bc081259441e1810c050f69061aa3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/570bc081259441e1810c050f69061aa3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/570bc081259441e1810c050f69061aa3"}}, "title": "The path to immortalization of cells starts by managing stress through gene duplications.", "authors": [{"family": "Lewerentz", "given": "Jacob", "initials": "J"}, {"family": "Johansson", "given": "Anna-Mia", "initials": "AM"}, {"family": "Stenberg", "given": "Per", "initials": "P"}], "type": "journal article", "published": "2023-01-01", "journal": {"title": "Exp. Cell Res.", "issn": "1090-2422", "volume": "422", "issue": "1", "pages": "113431", "issn-l": "0014-4827"}, "abstract": "The genomes of immortalized cell lines (and cancer cells) are characterized by multiple types of aberrations, ranging from single nucleotide polymorphisms (SNPs) to structural rearrangements that have accumulated over time. Consequently, it is difficult to estimate the relative impact of different aberrations, the order of events, and which gene functions were under selective pressure at the early stage towards cellular immortalization. Here, we have established novel cell cultures derived from Drosophila melanogaster embryos that were sampled at multiple time points over a one-year period. Using short-read DNA sequencing, we show that copy-number gain in preferentially stress-related genes were acquired in a dominant fraction of cells in 300-days old cultures. Furthermore, transposable elements were active in cells of all cultures. Only a few (<1%) SNPs could be followed over time, and these showed no trend to increase or decrease. We conclude that the early cellular responses of a novel culture comprise sequence duplication and transposable element activity. During immortalization, positive selection first occurs on genes that are related to stress response before shifting to genes that are related to growth.", "doi": "10.1016/j.yexcr.2022.113431", "pmid": "36423660", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "S0014-4827(22)00424-4"}], "notes": [], "created": "2022-11-29T09:11:25.498Z", "modified": "2024-01-16T13:48:34.230Z"}, {"entity": "publication", "iuid": "5eb9ce6d678b47a8a7e86b5fe0b1e75c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5eb9ce6d678b47a8a7e86b5fe0b1e75c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5eb9ce6d678b47a8a7e86b5fe0b1e75c"}}, "title": "Rare tandem repeat expansions associate with genes involved in synaptic and neuronal signaling functions in schizophrenia.", "authors": [{"family": "Wen", "given": "Jia", "initials": "J"}, {"family": "Trost", "given": "Brett", "initials": "B", "orcid": "0000-0003-4863-7273", "researcher": {"href": "https://publications.scilifelab.se/researcher/f5d8ce778d624eef846a7b72bdf00f52.json"}}, {"family": "Engchuan", "given": "Worrawat", "initials": "W"}, {"family": "Halvorsen", "given": "Matthew", "initials": "M"}, {"family": "Pallotto", "given": "Linda M", "initials": "LM"}, {"family": "Mitina", "given": "Aleksandra", "initials": "A"}, {"family": "Ancalade", "given": "NaEshia", "initials": "N"}, {"family": "Farrell", "given": "Martilias", "initials": "M", "orcid": "0000-0002-9520-6209", "researcher": {"href": "https://publications.scilifelab.se/researcher/20be04f56c474537ad8fa07cb17241cf.json"}}, {"family": "Backstrom", "given": "Ian", "initials": "I", "orcid": "0000-0003-2203-540X", "researcher": {"href": "https://publications.scilifelab.se/researcher/d8473bd9fd724354a100af414ad1126e.json"}}, {"family": "Guo", "given": "Keyi", "initials": "K"}, {"family": "Pellecchia", "given": "Giovanna", "initials": "G", "orcid": "0000-0003-4747-3473", "researcher": {"href": "https://publications.scilifelab.se/researcher/c9f06138fd254a6fa35e81614a9d9ae9.json"}}, {"family": "Thiruvahindrapuram", "given": "Bhooma", "initials": "B", "orcid": "0000-0003-1128-008X", "researcher": {"href": "https://publications.scilifelab.se/researcher/f13d26ba0fac47d4a966f4189af223ec.json"}}, {"family": "Giusti-Rodriguez", "given": "Paola", "initials": "P"}, {"family": "Rosen", "given": "Jonathan David", "initials": "JD"}, {"family": "Li", "given": "Yun", "initials": "Y"}, {"family": "Won", "given": "Hyejung", "initials": "H", "orcid": "0000-0003-3651-0566", "researcher": {"href": "https://publications.scilifelab.se/researcher/ec02856f79674901b278a7c04b7ed8d8.json"}}, {"family": "Magnusson", "given": "Patrik K E", "initials": "PKE", "orcid": "0000-0002-7315-7899", "researcher": {"href": "https://publications.scilifelab.se/researcher/b277b6387de142bbab91fad82d9eff09.json"}}, {"family": "Gyllensten", "given": "Ulf", "initials": "U"}, {"family": "Bassett", "given": "Anne S", "initials": "AS", "orcid": "0000-0002-0681-7279", "researcher": {"href": "https://publications.scilifelab.se/researcher/4884004ffeb34bcfbe80536ae35ba668.json"}}, {"family": "Hultman", "given": "Christina M", "initials": "CM"}, {"family": "Sullivan", "given": "Patrick F", "initials": "PF"}, {"family": "Yuen", "given": "Ryan K C", "initials": "RKC", "orcid": "0000-0001-7273-4968", "researcher": {"href": "https://publications.scilifelab.se/researcher/a867c10748aa4c6ab8191fbfbe5757c9.json"}}, {"family": "Szatkiewicz", "given": "Jin P", "initials": "JP", "orcid": "0000-0002-4898-7401", "researcher": {"href": "https://publications.scilifelab.se/researcher/eb39edd3c6c14938a47f1e22ecfea080.json"}}], "type": "journal article", "published": "2023-01-00", "journal": {"title": "Mol. Psychiatry", "issn": "1476-5578", "issn-l": "1359-4184", "volume": "28", "issue": "1", "pages": "475-482"}, "abstract": "Tandem repeat expansions (TREs) are associated with over 60 monogenic disorders and have recently been implicated in complex disorders such as cancer and autism spectrum disorder. The role of TREs in schizophrenia is now emerging. In this study, we have performed a genome-wide investigation of TREs in schizophrenia. Using genome sequence data from 1154 Swedish schizophrenia cases and 934 ancestry-matched population controls, we have detected genome-wide rare (<0.1% population frequency) TREs that have motifs with a length of 2-20 base pairs. We find that the proportion of individuals carrying rare TREs is significantly higher in the schizophrenia group. There is a significantly higher burden of rare TREs in schizophrenia cases than in controls in genic regions, particularly in postsynaptic genes, in genes overlapping brain expression quantitative trait loci, and in brain-expressed genes that are differentially expressed between schizophrenia cases and controls. We demonstrate that TRE-associated genes are more constrained and primarily impact synaptic and neuronal signaling functions. These results have been replicated in an independent Canadian sample that consisted of 252 schizophrenia cases of European ancestry and 222 ancestry-matched controls. Our results support the involvement of rare TREs in schizophrenia etiology.", "doi": "10.1038/s41380-022-01857-4", "pmid": "36380236", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9812781"}, {"db": "pii", "key": "10.1038/s41380-022-01857-4"}], "notes": [], "created": "2022-11-29T12:28:58.891Z", "modified": "2023-10-16T12:47:55.341Z"}, {"entity": "publication", "iuid": "04040a914b004690821288e088f5fc28", "links": {"self": {"href": "https://publications.scilifelab.se/publication/04040a914b004690821288e088f5fc28.json"}, "display": {"href": "https://publications.scilifelab.se/publication/04040a914b004690821288e088f5fc28"}}, "title": "Bayesian mixed model analysis uncovered 21 risk loci for chronic kidney disease in boxer dogs.", "authors": [{"family": "Lingaas", "given": "Frode", "initials": "F"}, {"family": "Tengvall", "given": "Katarina", "initials": "K"}, {"family": "Jansen", "given": "Johan H\u00f8gset", "initials": "JH"}, {"family": "Pelander", "given": "Lena", "initials": "L", "orcid": "0000-0001-9865-312X", "researcher": {"href": "https://publications.scilifelab.se/researcher/8be30ac7ae7c4dc29a715bd3dbe73f65.json"}}, {"family": "Hurst", "given": "Maria H", "initials": "MH"}, {"family": "Meuwissen", "given": "Theo", "initials": "T"}, {"family": "Karlsson", "given": "\u00c5sa", "initials": "\u00c5"}, {"family": "Meadows", "given": "Jennifer R S", "initials": "JRS"}, {"family": "Sundstr\u00f6m", "given": "Elisabeth", "initials": "E"}, {"family": "Thoresen", "given": "Stein Istre", "initials": "SI"}, {"family": "Arnet", "given": "Ellen Fr\u00f8ysadal", "initials": "EF"}, {"family": "Guttersrud", "given": "Ole Albert", "initials": "OA"}, {"family": "Kierczak", "given": "Marcin", "initials": "M"}, {"family": "Hyt\u00f6nen", "given": "Marjo K", "initials": "MK", "orcid": "0000-0003-1976-5874", "researcher": {"href": "https://publications.scilifelab.se/researcher/89e3788ab09f415f918f0bf9ed441fac.json"}}, {"family": "Lohi", "given": "Hannes", "initials": "H"}, {"family": "Hedhammar", "given": "\u00c5ke", "initials": "\u00c5"}, {"family": "Lindblad-Toh", "given": "Kerstin", "initials": "K"}, {"family": "Wang", "given": "Chao", "initials": "C", "orcid": "0000-0003-3936-4023", "researcher": {"href": "https://publications.scilifelab.se/researcher/202a8fd115e14824809a362a7cfc5a41.json"}}], "type": "journal article", "published": "2023-01-00", "journal": {"title": "PLoS Genet.", "issn": "1553-7404", "issn-l": "1553-7390", "volume": "19", "issue": "1", "pages": "e1010599"}, "abstract": "Chronic kidney disease (CKD) affects 10% of the human population, with only a small fraction genetically defined. CKD is also common in dogs and has been diagnosed in nearly all breeds, but its genetic basis remains unclear. Here, we performed a Bayesian mixed model genome-wide association analysis for canine CKD in a boxer population of 117 canine cases and 137 controls, and identified 21 genetic regions associated with the disease. At the top markers from each CKD region, the cases carried an average of 20.2 risk alleles, significantly higher than controls (15.6 risk alleles). An ANOVA test showed that the 21 CKD regions together explained 57% of CKD phenotypic variation in the population. Based on whole genome sequencing data of 20 boxers, we identified 5,206 variants in LD with the top 50 BayesR markers. Following comparative analysis with human regulatory data, 17 putative regulatory variants were identified and tested with electrophoretic mobility shift assays. In total four variants, three intronic variants from the MAGI2 and GALNT18 genes, and one variant in an intergenic region on chr28, showed alternative binding ability for the risk and protective alleles in kidney cell lines. Many genes from the 21 CKD regions, RELN, MAGI2, FGFR2 and others, have been implicated in human kidney development or disease. The results from this study provide new information that may enlighten the etiology of CKD in both dogs and humans.", "doi": "10.1371/journal.pgen.1010599", "pmid": "36693108", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI SNP genotyping": "Service", "Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC9897549"}, {"db": "pii", "key": "PGENETICS-D-22-01022"}], "notes": [], "created": "2023-02-24T13:14:07.307Z", "modified": "2024-01-16T13:48:34.288Z"}, {"entity": "publication", "iuid": "143d5dc074ac4e879e945f5b9bad3e15", "links": {"self": {"href": "https://publications.scilifelab.se/publication/143d5dc074ac4e879e945f5b9bad3e15.json"}, "display": {"href": "https://publications.scilifelab.se/publication/143d5dc074ac4e879e945f5b9bad3e15"}}, "title": "Implicating genes, pleiotropy, and sexual dimorphism at blood lipid loci through multi-ancestry meta-analysis", "authors": [{"family": "Kanoni", "given": "Stavroula", "initials": "S"}, {"family": "Graham", "given": "Sarah E", "initials": "SE"}, {"family": "Wang", "given": "Yuxuan", "initials": "Y"}, {"family": "Surakka", "given": "Ida", "initials": "I"}, {"family": "Ramdas", "given": "Shweta", "initials": "S"}, {"family": "Zhu", "given": "Xiang", "initials": "X"}, {"family": "Clarke", "given": "Shoa L", "initials": "SL"}, {"family": "Bhatti", "given": "Konain Fatima", "initials": "KF"}, {"family": "Vedantam", "given": "Sailaja", "initials": "S"}, {"family": "Winkler", "given": "Thomas W", "initials": "TW"}, {"family": "Locke", "given": "Adam E", "initials": "AE"}, {"family": "Marouli", "given": "Eirini", "initials": "E"}, {"family": "Zajac", "given": "Greg J M", "initials": "GJM"}, {"family": "Wu", "given": "Kuan Han H", "initials": "KHH"}, {"family": "Ntalla", "given": "Ioanna", "initials": "I"}, {"family": "Hui", "given": "Qin", "initials": "Q"}, {"family": "Klarin", "given": "Derek", "initials": "D"}, {"family": "Hilliard", "given": "Austin T", "initials": "AT"}, {"family": "Wang", "given": "Zeyuan", "initials": "Z"}, {"family": "Xue", "given": "Chao", "initials": "C"}, {"family": "Thorleifsson", "given": "Gudmar", "initials": "G"}, {"family": "Helgadottir", "given": "Anna", "initials": "A"}, {"family": "Gudbjartsson", "given": "Daniel F", "initials": "DF"}, {"family": "Holm", "given": "Hilma", "initials": "H"}, {"family": "Olafsson", "given": "Isleifur", "initials": "I"}, {"family": "Hwang", "given": "Mi Yeong", "initials": "MY"}, {"family": "Han", "given": "Sohee", "initials": "S"}, {"family": "Akiyama", "given": "Masato", "initials": "M"}, {"family": "Sakaue", "given": "Saori", "initials": "S"}, {"family": "Terao", "given": "Chikashi", "initials": "C"}, {"family": "Kanai", "given": "Masahiro", "initials": "M"}, {"family": "Zhou", "given": "Wei", "initials": "W"}, {"family": "Brumpton", "given": "Ben M", "initials": "BM"}, {"family": "Rasheed", "given": "Humaira", "initials": "H"}, {"family": "Havulinna", "given": "Aki S", "initials": "AS"}, {"family": "Veturi", "given": "Yogasudha", "initials": "Y"}, {"family": "Pacheco", "given": "Jennifer Allen", "initials": "JA"}, {"family": "Rosenthal", "given": "Elisabeth A", "initials": "EA"}, {"family": "Lingren", "given": "Todd", "initials": "T"}, {"family": "Feng", "given": "QiPing", "initials": "Q"}, {"family": "Kullo", "given": "Iftikhar J", "initials": "IJ"}, {"family": "Narita", "given": "Akira", "initials": "A"}, {"family": "Takayama", "given": "Jun", "initials": "J"}, {"family": "Martin", "given": "Hilary C", "initials": "HC"}, {"family": "Hunt", "given": "Karen A", "initials": "KA"}, {"family": "Trivedi", "given": "Bhavi", "initials": "B"}, {"family": "Haessler", "given": "Jeffrey", "initials": "J"}, {"family": "Giulianini", "given": "Franco", "initials": "F"}, {"family": "Bradford", "given": "Yuki", "initials": "Y"}, {"family": "Miller", "given": "Jason E", "initials": "JE"}, {"family": "Campbell", "given": "Archie", "initials": "A"}, {"family": "Lin", "given": "Kuang", "initials": "K"}, {"family": "Millwood", "given": "Iona Y", "initials": "IY"}, {"family": "Rasheed", "given": "Asif", "initials": "A"}, {"family": "Hindy", "given": "George", "initials": "G"}, {"family": "Faul", "given": "Jessica D", "initials": "JD"}, {"family": "Zhao", "given": "Wei", "initials": "W"}, {"family": "Weir", "given": "David R", "initials": "DR"}, {"family": "Turman", "given": "Constance", "initials": "C"}, {"family": "Huang", "given": "Hongyan", "initials": "H"}, {"family": "Graff", "given": "Mariaelisa", "initials": "M"}, {"family": "Choudhury", "given": "Ananyo", "initials": "A"}, {"family": "Sengupta", "given": "Dhriti", "initials": "D"}, {"family": "Mahajan", "given": "Anubha", "initials": "A"}, {"family": "Brown", "given": "Michael R", "initials": "MR"}, {"family": "Zhang", "given": "Weihua", "initials": "W"}, {"family": "Yu", "given": "Ketian", "initials": "K"}, {"family": "Schmidt", "given": "Ellen M", "initials": "EM"}, {"family": "Pandit", "given": "Anita", "initials": "A"}, {"family": "Gustafsson", "given": "Stefan", "initials": "S"}, {"family": "Yin", "given": "Xianyong", "initials": "X"}, {"family": "Luan", "given": "Jian\u2019an", "initials": "J"}, {"family": "Zhao", "given": "Jing Hua", "initials": "JH"}, {"family": "Matsuda", "given": "Fumihiko", "initials": "F"}, {"family": "Jang", "given": "Hye Mi", "initials": "HM"}, {"family": "Yoon", "given": "Kyungheon", "initials": "K"}, {"family": "Medina-Gomez", "given": "Carolina", "initials": "C"}, {"family": "Pitsillides", "given": "Achilleas", "initials": "A"}, {"family": "Hottenga", "given": "Jouke Jan", "initials": "JJ"}, {"family": "Wood", "given": "Andrew R", "initials": "AR"}, {"family": "Ji", "given": "Yingji", "initials": "Y"}, {"family": "Gao", "given": "Zishan", "initials": "Z"}, {"family": "Haworth", "given": "Simon", "initials": "S"}, {"family": "Yousri", "given": "Noha A", "initials": "NA"}, {"family": "Mitchell", "given": "Ruth E", "initials": "RE"}, {"family": "Chai", "given": "Jin Fang", "initials": "JF"}, {"family": "Aadahl", "given": "Mette", "initials": "M"}, {"family": "Bjerregaard", "given": "Anne A", "initials": "AA"}, {"family": "Yao", "given": "Jie", "initials": "J"}, {"family": "Manichaikul", "given": "Ani", "initials": "A"}, {"family": "Hwu", "given": "Chii Min", "initials": "CM"}, {"family": "Hung", "given": "Yi Jen", "initials": "YJ"}, {"family": "Warren", "given": "Helen R", "initials": "HR"}, {"family": "Ramirez", "given": "Julia", "initials": "J"}, {"family": "Bork-Jensen", "given": "Jette", "initials": "J"}, {"family": "K\u00e5rhus", "given": "Line L", "initials": "LL"}, {"family": "Goel", "given": "Anuj", "initials": "A"}, {"family": "Sabater-Lleal", "given": "Maria", "initials": "M"}, {"family": "Noordam", "given": "Raymond", "initials": "R"}, {"family": "Mauro", "given": "Pala", "initials": "P"}, {"family": "Matteo", "given": "Floris", "initials": "F"}, {"family": "McDaid", "given": "Aaron F", "initials": "AF"}, {"family": "Marques-Vidal", "given": "Pedro", "initials": "P"}, {"family": "Wielscher", "given": "Matthias", "initials": "M"}, {"family": "Trompet", "given": "Stella", "initials": "S"}, {"family": "Sattar", "given": "Naveed", "initials": "N"}, {"family": "M\u00f8llehave", "given": "Line T", "initials": "LT"}, {"family": "Munz", "given": "Matthias", "initials": "M"}, {"family": "Zeng", "given": "Lingyao", "initials": "L"}, {"family": "Huang", "given": "Jianfeng", "initials": "J"}, {"family": "Yang", "given": "Bin", "initials": "B"}, {"family": "Poveda", "given": "Alaitz", "initials": "A"}, {"family": "Kurbasic", "given": "Azra", "initials": "A"}, {"family": "Lamina", "given": "Claudia", "initials": "C"}, {"family": "Forer", "given": "Lukas", "initials": "L"}, {"family": "Scholz", "given": "Markus", "initials": "M"}, {"family": "Galesloot", "given": "Tessel E", "initials": "TE"}, {"family": "Bradfield", "given": "Jonathan P", "initials": "JP"}, {"family": "Ruotsalainen", "given": "Sanni E", "initials": "SE"}, {"family": "Daw", "given": "EWarwick", "initials": "E"}, {"family": "Zmuda", "given": "Joseph M", "initials": "JM"}, {"family": "Mitchell", "given": "Jonathan S", "initials": "JS"}, {"family": "Fuchsberger", "given": "Christian", "initials": "C"}, {"family": "Christensen", "given": "Henry", "initials": "H"}, {"family": "Brody", "given": "Jennifer A", "initials": "JA"}, {"family": "Vazquez-Moreno", "given": "Miguel", "initials": "M"}, {"family": "Feitosa", "given": "Mary F", "initials": "MF"}, {"family": "Wojczynski", "given": "Mary K", "initials": "MK"}, {"family": "Wang", "given": "Zhe", "initials": "Z"}, {"family": "Preuss", "given": "Michael H", "initials": "MH"}, {"family": "Mangino", "given": "Massimo", "initials": "M"}, {"family": "Christofidou", "given": "Paraskevi", "initials": "P"}, {"family": "Verweij", "given": "Niek", "initials": "N"}, {"family": "Benjamins", "given": "Jan W", "initials": "JW"}, {"family": "Engmann", "given": "Jorgen", "initials": "J"}, {"family": "Tsao", "given": "Noah L", "initials": "NL"}, {"family": "Verma", "given": "Anurag", "initials": "A"}, {"family": "Slieker", "given": "Roderick C", "initials": "RC"}, {"family": "Lo", "given": "Ken Sin", "initials": "KS"}, {"family": "Zilhao", "given": "Nuno R", "initials": "NR"}, {"family": "Le", "given": "Phuong", "initials": "P"}, {"family": "Kleber", "given": "Marcus E", "initials": "ME"}, {"family": "Delgado", "given": "Graciela E", "initials": "GE"}, {"family": "Huo", "given": "Shaofeng", "initials": "S"}, {"family": "Ikeda", "given": "Daisuke D", "initials": "DD"}, {"family": "Iha", "given": "Hiroyuki", "initials": "H"}, {"family": "Yang", "given": "Jian", "initials": "J"}, {"family": "Liu", 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{"family": "Buring", "given": "Julie E", "initials": "JE"}, {"family": "Ridker", "given": "Paul M", "initials": "PM"}, {"family": "Chasman", "given": "Daniel I", "initials": "DI"}, {"family": "Kooperberg", "given": "Charles", "initials": "C"}, {"family": "Tamiya", "given": "Gen", "initials": "G"}, {"family": "Yamamoto", "given": "Masayuki", "initials": "M"}, {"family": "van Heel", "given": "David A", "initials": "DA"}, {"family": "Trembath", "given": "Richard C", "initials": "RC"}, {"family": "Wei", "given": "Wei Qi", "initials": "WQ"}, {"family": "Jarvik", "given": "Gail P", "initials": "GP"}, {"family": "Namjou", "given": "Bahram", "initials": "B"}, {"family": "Hayes", "given": "M Geoffrey", "initials": "MG"}, {"family": "Ritchie", "given": "Marylyn D", "initials": "MD"}, {"family": "Jousilahti", "given": "Pekka", "initials": "P"}, {"family": "Salomaa", "given": "Veikko", "initials": "V"}, {"family": "Hveem", "given": "Kristian", "initials": "K"}, {"family": "\u00c5svold", "given": "Bj\u00f8rn Olav", "initials": "BO"}, {"family": "Kubo", "given": "Michiaki", "initials": "M"}, {"family": "Kamatani", "given": "Yoichiro", "initials": "Y"}, {"family": "Okada", "given": "Yukinori", "initials": "Y"}, {"family": "Murakami", "given": "Yoshinori", "initials": "Y"}, {"family": "Kim", "given": "Bong Jo", "initials": "BJ"}, {"family": "Thorsteinsdottir", "given": "Unnur", "initials": "U"}, {"family": "Stefansson", "given": "Kari", "initials": "K"}, {"family": "Zhang", "given": "Jifeng", "initials": "J"}, {"family": "Chen", "given": "YEugene", "initials": "Y"}, {"family": "Ho", "given": "Yuk Lam", "initials": "YL"}, {"family": "Lynch", "given": "Julie A", "initials": "JA"}, {"family": "Rader", "given": "Daniel J", "initials": "DJ"}, {"family": "Tsao", "given": "Philip S", "initials": "PS"}, {"family": "Chang", "given": "Kyong Mi", "initials": "KM"}, {"family": "Cho", "given": "Kelly", "initials": "K"}, {"family": "O\u2019Donnell", "given": "Christopher J", "initials": "CJ"}, {"family": "Gaziano", "given": "John M", "initials": "JM"}, {"family": "Wilson", "given": "Peter W F", "initials": "PWF"}, {"family": "Frayling", "given": "Timothy M", "initials": "TM"}, {"family": "Hirschhorn", "given": "Joel N", "initials": "JN"}, {"family": "Kathiresan", "given": "Sekar", "initials": "S"}, {"family": "Mohlke", "given": "Karen L", "initials": "KL"}, {"family": "Sun", "given": "Yan V", "initials": "YV"}, {"family": "Morris", "given": "Andrew P", "initials": "AP"}, {"family": "Boehnke", "given": "Michael", "initials": "M"}, {"family": "Brown", "given": "Christopher D", "initials": "CD"}, {"family": "Natarajan", "given": "Pradeep", "initials": "P"}, {"family": "Deloukas", "given": "Panos", "initials": "P"}, {"family": "Willer", "given": "Cristen J", "initials": "CJ"}, {"family": "Assimes", "given": "Themistocles L", "initials": "TL"}, {"family": "Peloso", "given": "Gina M", "initials": "GM", "orcid": "0000-0002-5355-8636", "researcher": {"href": "https://publications.scilifelab.se/researcher/3a0c07ebec3741efa6ef71d416e7c66a.json"}}], "type": "journal-article", "published": "2022-12-27", "journal": {"title": "Genome Biol.", "issn": "1474-760X", "volume": "23", "issue": "1", "pages": "268", "issn-l": "1474-7596"}, "abstract": "Genetic variants within nearly 1000 loci are known to contribute to modulation of blood lipid levels. However, the biological pathways underlying these associations are frequently unknown, limiting understanding of these findings and hindering downstream translational efforts such as drug target discovery.\n\nTo expand our understanding of the underlying biological pathways and mechanisms controlling blood lipid levels, we leverage a large multi-ancestry meta-analysis (N = 1,654,960) of blood lipids to prioritize putative causal genes for 2286 lipid associations using six gene prediction approaches. Using phenome-wide association (PheWAS) scans, we identify relationships of genetically predicted lipid levels to other diseases and conditions. We confirm known pleiotropic associations with cardiovascular phenotypes and determine novel associations, notably with cholelithiasis risk. We perform sex-stratified GWAS meta-analysis of lipid levels and show that 3-5% of autosomal lipid-associated loci demonstrate sex-biased effects. Finally, we report 21 novel lipid loci identified on the X chromosome. Many of the sex-biased autosomal and X chromosome lipid loci show pleiotropic associations with sex hormones, emphasizing the role of hormone regulation in lipid metabolism.\n\nTaken together, our findings provide insights into the biological mechanisms through which associated variants lead to altered lipid levels and potentially cardiovascular disease risk.", "doi": "10.1186/s13059-022-02837-1", "pmid": "36575460", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI SNP genotyping": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9793579"}, {"db": "pii", "key": "10.1186/s13059-022-02837-1"}], "notes": [], "created": "2023-02-24T13:14:10.096Z", "modified": "2023-06-19T08:56:05.544Z"}, {"entity": "publication", "iuid": "044cd2cc0a644d81948691614fa8c89b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/044cd2cc0a644d81948691614fa8c89b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/044cd2cc0a644d81948691614fa8c89b"}}, "title": "Leukocyte DNA methylation in Alzheimer\u00b4s disease associated genes: replication of findings from neuronal cells.", "authors": [{"family": "Karlsson", "given": "Ida K", "initials": "IK", "orcid": "0000-0003-3605-7829", "researcher": {"href": "https://publications.scilifelab.se/researcher/b2c87ada82ae43df9753a891305ddb40.json"}}, {"family": "Ploner", "given": "Alexander", "initials": "A"}, {"family": "Wang", "given": "Yunzhang", "initials": "Y"}, {"family": "Gatz", "given": "Margaret", "initials": "M"}, {"family": "Pedersen", "given": "Nancy L", "initials": "NL"}, {"family": "H\u00e4gg", "given": "Sara", "initials": "S"}], "type": "journal article", "published": "2022-12-26", "journal": {"title": "Epigenetics", "issn": "1559-2308", "pages": "1-5", "issn-l": "1559-2294"}, "abstract": "Differences in gene-wide DNA methylation of the Alzheimer's disease (AD)-associated genes BIN1, HLA-DRB5, SORL1, SLC24A4, and ABCA7 are reported to be associated with AD in post-mortem brain samples. We investigated whether the same associations could be found in leukocytes collected pre-mortem. Using cohort data of 544 Swedish twins (204 dementia diagnoses), we replicated the findings in HLA-DRB5 and SLC24A4 at P < 0.05. However, co-twin control analyses indicated that the associations were partly explained by familial confounding. Thus, DNA methylation differences in HLA-DRB5 and SLC24A4 are present in both neuronal cells and leukocytes, and not fully explained familial factors.", "doi": "10.1080/15592294.2022.2158285", "pmid": "36573011", "labels": {"NGI SNP genotyping": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [], "notes": [], "created": "2023-01-07T19:43:44.639Z", "modified": "2023-01-19T07:58:14.561Z"}, {"entity": "publication", "iuid": "7d5d646edfce4e7ca163863ea1e99260", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7d5d646edfce4e7ca163863ea1e99260.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7d5d646edfce4e7ca163863ea1e99260"}}, "title": "Investigation of the Virome and Characterization of Issyk-Kul Virus from Swedish Myotis brandtii Bats.", "authors": [{"family": "Cholleti", "given": "Harindranath", "initials": "H"}, {"family": "de Jong", "given": "Johnny", "initials": "J"}, {"family": "Blomstr\u00f6m", "given": "Anne-Lie", "initials": "AL"}, {"family": "Berg", "given": "Mikael", "initials": "M", "orcid": "0000-0001-5779-3345", "researcher": {"href": "https://publications.scilifelab.se/researcher/bf3060c6eae54268b8e5dee8cf0b7a19.json"}}], "type": "journal article", "published": "2022-12-21", "journal": {"title": "Pathogens", "issn": "2076-0817", "volume": "12", "issue": "1", "issn-l": null}, "abstract": "Bats are reservoirs for many different viruses, including some that can be transmitted to and cause disease in humans and/or animals. However, less is known about the bat-borne viruses circulating in Northern European countries such as in Sweden. In this study, saliva from Myotis brandtii bats, collected from south-central Sweden, was analyzed for viruses. The metagenomic analysis identified viral sequences belonging to different viral families, including, e.g., Nairoviridae, Retroviridae, Poxviridae, Herpesviridae and Siphoviridae. Interestingly, through the data analysis, the near-complete genome of Issyk-Kul virus (ISKV), a zoonotic virus within the Nairoviridae family, was obtained, showing 95-99% protein sequence identity to previously described ISKVs. This virus is believed to infect humans via an intermediate tick host or through contact with bat excrete. ISKV has previously been found in bats in Europe, but not previously in the Nordic region. In addition, near full-length genomes of two novel viruses belonging to Picornavirales order and Tymoviridae family were characterized. Taken together, our study has not only identified novel viruses, but also the presence of a zoonotic virus not previously known to circulate in this region. Thus, the results from these types of studies can help us to better understand the diversity of viruses circulating in bat populations, as well as identify viruses with zoonotic potential that could possibly be transmitted to humans.", "doi": "10.3390/pathogens12010012", "pmid": "36678360", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pii", "key": "pathogens12010012"}], "notes": [], "created": "2023-01-23T07:18:22.877Z", "modified": "2023-01-23T07:18:22.969Z"}, {"entity": "publication", "iuid": "1176beb197da4692837d803afde65d55", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1176beb197da4692837d803afde65d55.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1176beb197da4692837d803afde65d55"}}, "title": "Gene Networks and Pathways Involved in LPS-Induced Proliferative Response of Bovine Endometrial Epithelial Cells.", "authors": [{"family": "Najafi", "given": "Mojtaba", "initials": "M", "orcid": "0000-0002-5463-8873", "researcher": {"href": "https://publications.scilifelab.se/researcher/3411ca5b1bb944e88880f0a3d99c547f.json"}}, {"family": "Guo", "given": "Yongzhi", "initials": "Y"}, {"family": "Andersson", "given": "G\u00f6ran", "initials": "G", "orcid": "0000-0001-5131-3144", "researcher": {"href": "https://publications.scilifelab.se/researcher/39ce81c314db47c8ad63c3ed38dffcb3.json"}}, {"family": "Humblot", "given": "Patrice", "initials": "P"}, {"family": "Bongcam-Rudloff", "given": "Erik", "initials": "E", "orcid": "0000-0002-1947-8288", "researcher": {"href": "https://publications.scilifelab.se/researcher/6970ca57259d498588ecf9e1ad28a9b0.json"}}], "type": "journal article", "published": "2022-12-12", "journal": {"title": "Genes", "issn": "2073-4425", "volume": "13", "issue": "12", "issn-l": "2073-4425"}, "abstract": "Lipopolysaccharide (LPS) is a component of the outer membrane of Gram-negative bacteria involved in the pathogenic processes leading to mastitis and metritis in animals such as dairy cattle. LPS causes cell proliferation associated with endometrium inflammation. Former in vitro studies have demonstrated that LPS induces an intense stimulation of the proliferation of a pure population of bovine endometrial epithelial cells. In a follow-up transcriptomic study based on RNA-sequencing data obtained after 24 h exposure of primary bovine endometrial epithelial cells to 0, 2, and 8 \u03bcg/mL LPS, 752 and 727 differentially expressed genes (DEGs) were detected between the controls and LPS-treated samples that encode proteins known to be associated with either proliferation or apoptosis, respectively. The present bioinformatic analysis was performed to decipher the gene networks involved to obtain a deeper understanding of the mechanisms underlying the proliferative and apoptosis processes. Our findings have revealed 116 putative transcription factors (TFs) and the most significant number of interactions between these TFs and DEGs belong to NFK\u03b21, TP53, STAT1, and HIF1A. Moreover, our results provide novel insights into the early signaling and metabolic pathways in bovine endometrial epithelial cells associated with the innate immune response and cell proliferation to Escherichia coli-LPS infection. The results further indicated that LPS challenge elicited a strong transcriptomic response, leading to potent activation of pro-inflammatory pathways that are associated with a marked endometrial cancer, Toll-like receptor, NFK\u03b2, AKT, apoptosis, and MAPK signaling pathways. This effect may provide a mechanistic explanation for the relationship between LPS and cell proliferation.", "doi": "10.3390/genes13122342", "pmid": "36553609", "labels": {"NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9778113"}, {"db": "pii", "key": "genes13122342"}], "notes": [], "created": "2022-12-27T07:30:58.773Z", "modified": "2022-12-27T07:30:58.916Z"}, {"entity": "publication", "iuid": "48bff1064bfd4dcd87dde962700ef0f6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/48bff1064bfd4dcd87dde962700ef0f6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/48bff1064bfd4dcd87dde962700ef0f6"}}, "title": "Genetics of tibia bone properties of crossbred commercial laying hens in different housing systems.", "authors": [{"family": "Johnsson", "given": "Martin", "initials": "M", "orcid": "0000-0003-1262-4585", "researcher": {"href": "https://publications.scilifelab.se/researcher/02b768197c08422aaad526f35c526eaf.json"}}, {"family": "Wall", "given": "Helena", "initials": "H"}, {"family": "Lopes Pinto", "given": "Fernando A", "initials": "FA"}, {"family": "Fleming", "given": "Robert H", "initials": "RH"}, {"family": "McCormack", "given": "Heather A", "initials": "HA"}, {"family": "Benavides-Reyes", "given": "Cristina", "initials": "C"}, {"family": "Dominguez-Gasca", "given": "Nazaret", "initials": "N"}, {"family": "Sanchez-Rodriguez", "given": "Estefania", "initials": "E"}, {"family": "Dunn", "given": "Ian C", "initials": "IC"}, {"family": "Rodriguez-Navarro", "given": "Alejandro B", "initials": "AB"}, {"family": "Kindmark", "given": "Andreas", "initials": "A"}, {"family": "de Koning", "given": "Dirk-Jan", "initials": "DJ", "orcid": "0000-0001-6343-8155", "researcher": {"href": "https://publications.scilifelab.se/researcher/c4447969cae94642b161f87e8fd1db95.json"}}], "type": "journal article", "published": "2022-12-01", "journal": {"title": "G3 (Bethesda)", "issn": "2160-1836", "issn-l": "2160-1836"}, "abstract": "Osteoporosis and bone fractures are a severe problem for the welfare of laying hens, with genetics and environment, such as housing system, each making substantial contributions to bone strength. In this work, we performed genetic analyses of bone strength, bone mineral density and bone composition, as well as body weight, in 860 commercial crossbred laying hens from two different companies, kept in either furnished cages or floor pens. We compared bone traits between housing systems and crossbreds, and performed a genome-wide association study of bone properties and body weight. As expected, the two housing systems produced a large difference in bone strength, with layers housed in floor pens having stronger bones. These differences were accompanied by differences in bone geometry, mineralisation and chemical composition. Genome-scans either combining or independently analysing the two housing systems revealed no genome-wide significant loci for bone breaking strength. We detected three loci for body weight that were shared between the housing systems on chromosomes 4, 6 and 27 (either genome-wide significant or suggestive) and these coincide with associations for bone length. In summary, we found substantial differences in bone strength, content and composition between hens kept in floor pens and furnished cages that could be attributed to greater physical activity in pen housing. We found little evidence for large-effect loci for bone strength in commercial crossbred hens, consistent with a highly polygenic architecture for bone strength in the production environment.\u200b The lack of consistent genetic associations between housing systems in combination with the differences in bone phenotypes could be due to gene-by-environment interactions with housing system or a lack of power to detect shared associations for bone strength.", "doi": "10.1093/g3journal/jkac302", "pmid": "36453438", "labels": {"National Genomics Infrastructure": "Service", "NGI SNP genotyping": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "6855652"}], "notes": [], "created": "2022-12-23T11:26:46.441Z", "modified": "2022-12-23T11:26:46.478Z"}, {"entity": "publication", "iuid": "5c8d3a6fb3974c9188bf3477d7615c70", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5c8d3a6fb3974c9188bf3477d7615c70.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5c8d3a6fb3974c9188bf3477d7615c70"}}, "title": "Genome-wide association and Mendelian randomization study of fibroblast growth factor 21 reveals causal associations with hyperlipidemia and possibly NASH.", "authors": [{"family": "Larsson", "given": "Susanna C", "initials": "SC"}, {"family": "Micha\u00eblsson", "given": "Karl", "initials": "K"}, {"family": "Mola-Caminal", "given": "Marina", "initials": "M"}, {"family": "H\u00f6ijer", "given": "Jonas", "initials": "J"}, {"family": "Mantzoros", "given": "Christos S", "initials": "CS"}], "type": "journal article", "published": "2022-12-00", "journal": {"title": "Metabolism", "issn": "1532-8600", "volume": "137", "pages": "155329", "issn-l": "0026-0495"}, "abstract": "Fibroblast growth factor 21 (FGF21) is a hepatokine that produces metabolic benefits, such as improvements of lipid profile. We performed a genome-wide association study (GWAS) to identify genetic variants associated with circulating FGF21 and investigated the causal effects of FGF21 on pertinent outcomes using Mendelian randomization (MR).\n\nWe conducted a GWAS testing \u223c7.8 million DNA sequence variants with circulating FGF21 in a discovery cohort of 6259 Swedish adults with replication in 4483 Swedish women. We then performed two-sample MR analyses of genetically predicted circulating FGF21 in relation to alcohol and nutrient intake, cardiovascular and metabolic biomarkers and diseases, and liver function biomarkers using publicly available GWAS summary statistics data.\n\nOur GWAS identified multiple single-nucleotide polymorphisms with genome-wide significant associations (P < 5 \u00d7 10-8) with circulating FGF21 on chromosomes 2 and 19 in or near the GCKR and FGF21 genes, respectively. The strongest signal at the FGF21 locus (rs2548957, \u03b2 = 0.181, P < 2.18 \u00d7 10-42) displayed in two-sample MR analyses robust associations with lower alcohol intake, lower circulating low-density lipoprotein cholesterol, apolipoprotein B, C-reactive protein, gamma-glutamyl transferase, and galectin-3 concentrations, and higher circulating insulin-like growth factor-I and alkaline phosphatase concentrations after correcting for multiple testing (P < 0.0018) whereas associations with fat mass, type 2 diabetes, and cardiovascular disease were largely null.\n\nWe identified robust associations of certain genetic variants in or near the GCKR and FGF21 genes with circulating FGF21 concentrations. Furthermore, our results support a strong causal effect of FGF21 on improved lipid profile, reduced alcohol consumption and C-reactive protein concentrations, and liver function biomarkers including fibrosis. We found largely null or weak positive associations with fat mass, diabetes, and cardiovascular disease as well as higher insulin-like growth factor-I concentrations, which could indicate a compensatory increase to regulate the above FGF21 resistant states in humans.", "doi": "10.1016/j.metabol.2022.155329", "pmid": "36208799", "labels": {"National Genomics Infrastructure": "Service", "NGI SNP genotyping": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Affinity Proteomics Uppsala": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "S0026-0495(22)00207-4"}], "notes": [], "created": "2022-11-09T14:36:35.965Z", "modified": "2024-01-16T13:48:34.388Z"}, {"entity": "publication", "iuid": "9004dc1628114cde8ae8db0a3a963600", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9004dc1628114cde8ae8db0a3a963600.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9004dc1628114cde8ae8db0a3a963600"}}, "title": "Cone-setting in spruce is regulated by conserved elements of the age-dependent flowering pathway.", "authors": [{"family": "Akhter", "given": "Shirin", "initials": "S", "orcid": "0000-0003-4238-3110", "researcher": {"href": "https://publications.scilifelab.se/researcher/bbaba07c47b04b56bd303e120dd944b4.json"}}, {"family": "Westrin", "given": "Karl Johan", "initials": "KJ", "orcid": "0000-0002-6937-9245", "researcher": {"href": "https://publications.scilifelab.se/researcher/033a4b9be9db4317b11a1d31e5c9986b.json"}}, {"family": "Zivi", "given": "Nathan", "initials": "N"}, {"family": "Nordal", "given": "Veronika", "initials": "V"}, {"family": "Kretzschmar", "given": "Warren W", "initials": "WW", "orcid": "0000-0002-2575-0807", "researcher": {"href": "https://publications.scilifelab.se/researcher/a67389ef276a47cfacec7cbe50da37a7.json"}}, {"family": "Delhomme", "given": "Nicolas", "initials": "N", "orcid": "0000-0002-3053-0796", "researcher": {"href": "https://publications.scilifelab.se/researcher/107fbbd40f1444fb838ad4c0365738fa.json"}}, {"family": "Street", "given": "Nathaniel R", "initials": "NR", "orcid": "0000-0001-6031-005X", "researcher": {"href": "https://publications.scilifelab.se/researcher/cb9ceb237a724046a1454179a32de1b0.json"}}, {"family": "Nilsson", "given": "Ove", "initials": "O", "orcid": "0000-0002-1033-1909", "researcher": {"href": "https://publications.scilifelab.se/researcher/729146afe5e24eb0a6f107db10e95e01.json"}}, {"family": "Emanuelsson", "given": "Olof", "initials": "O", "orcid": "0000-0002-8879-9245", "researcher": {"href": "https://publications.scilifelab.se/researcher/0e9c21102e97491bb88a25db8ae1b8d8.json"}}, {"family": "Sundstr\u00f6m", "given": "Jens F", "initials": "JF", "orcid": "0000-0003-2848-5284", "researcher": {"href": "https://publications.scilifelab.se/researcher/be85f558ad8a4f57b3b366812f1b5faa.json"}}], "type": "journal article", "published": "2022-12-00", "journal": {"title": "New Phytol.", "issn": "1469-8137", "issn-l": "0028-646X", "volume": "236", "issue": "5", "pages": "1951-1963"}, "abstract": "Reproductive phase change is well characterized in angiosperm model species, but less studied in gymnosperms. We utilize the early cone-setting acrocona mutant to study reproductive phase change in the conifer Picea abies (Norway spruce), a gymnosperm. The acrocona mutant frequently initiates cone-like structures, called transition shoots, in positions where wild-type P. abies always produces vegetative shoots. We collect acrocona and wild-type samples, and RNA-sequence their messenger RNA (mRNA) and microRNA (miRNA) fractions. We establish gene expression patterns and then use allele-specific transcript assembly to identify mutations in acrocona. We genotype a segregating population of inbred acrocona trees. A member of the SQUAMOSA BINDING PROTEIN-LIKE (SPL) gene family, PaSPL1, is active in reproductive meristems, whereas two putative negative regulators of PaSPL1, miRNA156 and the conifer specific miRNA529, are upregulated in vegetative and transition shoot meristems. We identify a mutation in a putative miRNA156/529 binding site of the acrocona PaSPL1 allele and show that the mutation renders the acrocona allele tolerant to these miRNAs. We show co-segregation between the early cone-setting phenotype and trees homozygous for the acrocona mutation. In conclusion, we demonstrate evolutionary conservation of the age-dependent flowering pathway and involvement of this pathway in regulating reproductive phase change in the conifer P. abies.", "doi": "10.1111/nph.18449", "pmid": "36076311", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9825996"}, {"db": "RefSeq", "key": "AF064080"}], "notes": [], "created": "2022-11-09T15:42:14.878Z", "modified": "2024-01-16T13:48:34.395Z"}, {"entity": "publication", "iuid": "afd4af822f044a1c82fffcedc63262ed", "links": {"self": {"href": "https://publications.scilifelab.se/publication/afd4af822f044a1c82fffcedc63262ed.json"}, "display": {"href": "https://publications.scilifelab.se/publication/afd4af822f044a1c82fffcedc63262ed"}}, "title": "Dynamic patterns of blood lipids and DNA methylation in response to statin therapy.", "authors": [{"family": "Qin", "given": "Xueying", "initials": "X"}, {"family": "Wang", "given": "Yunzhang", "initials": "Y"}, {"family": "Pedersen", "given": "Nancy L", "initials": "NL"}, {"family": "Tang", "given": "Bowen", "initials": "B"}, {"family": "H\u00e4gg", "given": "Sara", "initials": "S"}], "type": "journal article", "published": "2022-11-28", "journal": {"title": "Clin Epigenetics", "issn": "1868-7083", "volume": "14", "issue": "1", "pages": "153", "issn-l": "1868-7075"}, "abstract": "Statins are lipid-lowering drugs and starting treatment has been associated with DNA methylation changes at genes related to lipid metabolism. However, the longitudinal pattern of how statins affect DNA methylation in relation to lipid levels has not been well investigated.\n\nWe conducted an epigenetic association study in a longitudinal Swedish twin sample in previously reported lipid-related CpGs (cg10177197, cg17901584 and cg27243685). First, we applied a mixed-effect model to assess the association between blood lipids (total cholesterol (TC), low-density lipoprotein cholesterol (LDL), high-density lipoprotein cholesterol (HDL), total triglyceride (TG)) and DNA methylation. Then, we performed a piecewise latent linear-linear growth curve model (LGCM) to explore the long-term changing pattern of lipids and methylation in response to statin treatment. Finally, we used a bivariate autoregressive latent trajectory model with structured residuals (ALT-SR) to analyze the cross-lagged effects in different lipid-CpG pairs in statin users and non-users.\n\nWe replicated the associations between TC, LDL, HDL and DNA methylation level in cg17901584 and cg27243685 (P values ranged from 4.70E-12 to 1.84E-04). From the piecewise LGCM, we showed that TC and LDL significantly decreased in statin users before treatment started and then remained stable. For non-statin users, we only found a slightly significant decreasing trend for TC and TG. We observed a similar dynamic pattern for methylation levels at cg27243685 and cg17901584. Before statin initiation, cg27243685 showed a significantly increasing trend and cg17901584 a decreasing trend, but post-treatment, there were no additional changes. From the ALT-SR model, we found TG levels to be significantly associated with the DNA methylation level of cg27243685 at the next measurement in statin users (estimate = 0.383, 95% CI: 0.173, 0.594, P value < 0.001).\n\nLongitudinal blood lipid and DNA methylation levels change after statin treatment initiation, where the latter is mostly a response to alterations in lipid levels and not vice versa.", "doi": "10.1186/s13148-022-01375-8", "pmid": "36443870", "labels": {"National Genomics Infrastructure": "Service", "NGI SNP genotyping": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9706978"}, {"db": "pii", "key": "10.1186/s13148-022-01375-8"}], "notes": [], "created": "2022-12-23T11:26:51.795Z", "modified": "2022-12-23T11:26:51.810Z"}, {"entity": "publication", "iuid": "ff8dc12cb1284e6b88f4db7e43d66c19", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ff8dc12cb1284e6b88f4db7e43d66c19.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ff8dc12cb1284e6b88f4db7e43d66c19"}}, "title": "Anti-citrullinated protein antibody specificities and pulmonary fibrosis in relation to genetic loci in early rheumatoid arthritis.", "authors": [{"family": "Brink", "given": "Mikael", "initials": "M", "orcid": "0000-0001-7675-3488", "researcher": {"href": "https://publications.scilifelab.se/researcher/ecbce4cc891249c5b96f71b6586aa777.json"}}, {"family": "Ljung", "given": "Lotta", "initials": "L", "orcid": "0000-0001-8999-0925", "researcher": {"href": "https://publications.scilifelab.se/researcher/ad0a3f26e6a64fa9b42d4c4dbcd9a2f6.json"}}, {"family": "Hansson", "given": "Monika", "initials": "M"}, {"family": "R\u00f6nnelid", "given": "Johan", "initials": "J", "orcid": "0000-0003-1186-3226", "researcher": {"href": "https://publications.scilifelab.se/researcher/25d1ba81c51a4bca974e84c9ea117cbe.json"}}, {"family": "Holmdahl", "given": "Rickard", "initials": "R", "orcid": "0000-0002-4969-2576", "researcher": {"href": "https://publications.scilifelab.se/researcher/49e60d22dd1a4dd1a4ca5a50d9fc4fc7.json"}}, {"family": "Skriner", "given": "Karl", "initials": "K", "orcid": "0000-0002-5415-270X", "researcher": {"href": "https://publications.scilifelab.se/researcher/649a490bd59b4775997cce2cd5f60bed.json"}}, {"family": "Serre", "given": "Guy", "initials": "G"}, {"family": "Klareskog", "given": "Lars", "initials": "L"}, {"family": "Rantap\u00e4\u00e4-Dahlqvist", "given": "Solbritt", "initials": "S", "orcid": "0000-0001-8259-3863", "researcher": {"href": "https://publications.scilifelab.se/researcher/dfca4bfdcf3946fda64397d3b7debc59.json"}}], "type": "journal article", "published": "2022-11-28", "journal": {"title": "Rheumatology (Oxford)", "issn": "1462-0332", "volume": "61", "issue": "12", "pages": "4985-4990", "issn-l": "1462-0324"}, "abstract": "Pulmonary manifestations in RA are common comorbidities, but the underlying mechanisms are largely unknown. The added value of a multiplex of ACPA and genetic risk markers was evaluated for the development of pulmonary fibrosis (PF) in an inception cohort.\n\nA total of 1184 patients with early RA were consecutively included and followed prospectively from the index date until death or 31 December 2016. The presence of 21 ACPA fine specificities was analysed using a custom-made microarray chip (Thermo Fisher Scientific, Uppsala, Sweden). Three SNPs, previously found related to PF were evaluated, rs2609255 (FAM13A), rs111521887 (TOLLIP) and rs35705950 (MUC5B). ACPA and genetic data were available for 841 RA patients, of whom 50 developed radiologically defined PF.\n\nIn unadjusted analyses, 11 ACPA specificities were associated with PF development. In multiple variable analyses, six ACPA specificities were associated with increased risk of PF: vimentin (Vim)60-75, fibrinogen (Fib)\u03b262-78 (72), Fib\u03b1621-635, Bla26, collagen (C)II359-369 and F4-CIT-R (P < 0.01 to P < 0.05). The number of ACPA specificities was also related to PF development (P < 0.05 crude and adjusted models). In multiple variable models respectively adjusted for each of the SNPs, the number of ACPA specificities (P < 0.05 in all models), anti-Vim60-75 (P < 0.05, in all models), anti-Fib\u03b262-78 (72) (P < 0.001 to P < 0.05), anti-CII359-369 (P < 0.05 in all models) and anti-F4-CIT-R AQ4 (P < 0.01 to P < 0.05), anti-Fib\u03b1621-635 (P < 0.05 in one) and anti-Bla26 (P < 0.05 in two) were significantly associated with PF development.\n\nThe development of PF in an inception cohort of RA patients was associated with both presence of certain ACPA and the number of ACPA specificities and risk genes.", "doi": "10.1093/rheumatology/keac280", "pmid": "35532073", "labels": {"National Genomics Infrastructure": "Service", "NGI SNP genotyping": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "6582550"}], "notes": [], "created": "2022-05-23T13:59:39.107Z", "modified": "2024-01-16T13:48:34.409Z"}, {"entity": "publication", "iuid": "af709cc9882b4b46851b735254ff5af0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/af709cc9882b4b46851b735254ff5af0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/af709cc9882b4b46851b735254ff5af0"}}, "title": "Stage-specific transposon activity in the life cycle of the fairy-ring mushroom <i>Marasmius oreades<\/i>.", "authors": [{"family": "Hiltunen", "given": "Markus", "initials": "M", "orcid": "0000-0002-8880-872X", "researcher": {"href": "https://publications.scilifelab.se/researcher/77b54361528b4c7c8f5122d91d58b36d.json"}}, {"family": "Ament-Vel\u00e1squez", "given": "Sandra Lorena", "initials": "SL", "orcid": "0000-0003-3371-9292", "researcher": {"href": "https://publications.scilifelab.se/researcher/9d54ef94f91c4c1c85d5dc3a846023e5.json"}}, {"family": "Ryberg", "given": "Martin", "initials": "M", "orcid": "0000-0002-6795-4349", "researcher": {"href": "https://publications.scilifelab.se/researcher/c0a8578a1ace4105be91ec8116c84365.json"}}, {"family": "Johannesson", "given": "Hanna", "initials": "H", "orcid": "0000-0001-6359-9856", "researcher": {"href": "https://publications.scilifelab.se/researcher/36e8fe278e01470e8cddaaccc5dad596.json"}}], "type": "journal article", "published": "2022-11-16", "journal": {"title": "Proc. Natl. Acad. Sci. U.S.A.", "issn": "1091-6490", "issn-l": "0027-8424", "volume": "119", "issue": "46", "pages": "e2208575119"}, "abstract": "Genetic variability can be generated by different mechanisms, and across the life cycle. Many basidiomycete fungi have an extended somatic stage, during which each cell carries two genetically distinct haploid nuclei (dikaryosis), resulting from fusion of two compatible monokaryotic individuals. Recent findings have revealed remarkable genome stability at the nucleotide level during dikaryotic growth in these organisms, but whether this pattern extends to mutations affecting large genomic regions remains unknown. Furthermore, despite high genome integrity during dikaryosis, basidiomycete populations are not devoid of genetic diversity, begging the question of when this diversity is introduced. Here, we used a <i>Marasmius oreades<\/i> fairy ring to investigate the rise of large-scale variants during mono- and dikaryosis. By separating the two nuclear genotypes from four fruiting bodies and generating complete genome assemblies, we gained access to investigate genomic changes of any size. We found that during dikaryotic growth in nature the genome stayed intact, but after separating the nucleotypes into monokaryons, a considerable amount of structural variation started to accumulate, driven to large extent by transposons. Transposon insertions were also found in monokaryotic single-meiospore isolates. Hence, we show that genome integrity in basidiomycetes can be interrupted during monokaryosis, leading to genomic rearrangements and increased activity of transposable elements. We suggest that genetic diversification is disproportionate between life cycle stages in mushroom-forming fungi, so that the short-lived monokaryotic growth stage is more prone to genetic changes than the dikaryotic stage.", "doi": "10.1073/pnas.2208575119", "pmid": "36343254", "labels": {"NGI Uppsala (Uppsala Genome Center)": "Service", "NGI Long read": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9674265"}], "notes": [], "created": "2022-11-21T09:59:53.450Z", "modified": "2024-01-16T13:48:34.455Z"}, {"entity": "publication", "iuid": "93dff8562c4a43bf9052f0be7d1f2716", "links": {"self": {"href": "https://publications.scilifelab.se/publication/93dff8562c4a43bf9052f0be7d1f2716.json"}, "display": {"href": "https://publications.scilifelab.se/publication/93dff8562c4a43bf9052f0be7d1f2716"}}, "title": "Meta-analysis of genome-wide association studies of hoarding symptoms in 27,537 individuals.", "authors": [{"family": "Strom", "given": "Nora I", "initials": "NI", "orcid": "0000-0002-5261-8852", "researcher": {"href": "https://publications.scilifelab.se/researcher/bcd18b76d8d948dfb5529a2be294ecab.json"}}, {"family": "Smit", "given": "Dirk J A", "initials": "DJA", "orcid": "0000-0001-8301-8860", "researcher": {"href": "https://publications.scilifelab.se/researcher/fe64f7980537495aba79c0eca978e95d.json"}}, {"family": "Silzer", "given": "Talisa", "initials": "T"}, {"family": "Iyegbe", "given": "Conrad", "initials": "C"}, {"family": "Burton", "given": "Christie L", "initials": "CL", "orcid": "0000-0002-8955-6528", "researcher": {"href": "https://publications.scilifelab.se/researcher/4607f407ac9d4213a81b4a77b4cce4ad.json"}}, {"family": "Pool", "given": "Ren\u00e9", "initials": "R", "orcid": "0000-0001-5579-0933", "researcher": {"href": "https://publications.scilifelab.se/researcher/fc33e91c50654a6a88a44db4b6755f73.json"}}, {"family": "Lemire", "given": "Mathieu", "initials": "M"}, {"family": "Crowley", "given": "James J", "initials": "JJ", "orcid": "0000-0001-9051-1557", "researcher": {"href": "https://publications.scilifelab.se/researcher/14ecad66262b47dcadebcc8c7e759024.json"}}, {"family": "Hottenga", "given": "Jouke-Jan", "initials": "JJ", "orcid": "0000-0002-5668-2368", "researcher": {"href": "https://publications.scilifelab.se/researcher/75553b594b1f4255833de730f7f7d170.json"}}, {"family": "Ivanov", "given": "Volen Z", "initials": "VZ"}, {"family": "Larsson", "given": "Henrik", "initials": "H", "orcid": "0000-0002-6851-3297", "researcher": {"href": "https://publications.scilifelab.se/researcher/21f2cca2f6b74c5393c0fc33bcf15ee6.json"}}, {"family": "Lichtenstein", "given": "Paul", "initials": "P", "orcid": "0000-0003-3037-5287", "researcher": {"href": "https://publications.scilifelab.se/researcher/4db67c51837b4cdfa18cacbc3fca1173.json"}}, {"family": "Magnusson", "given": "Patrik", "initials": "P", "orcid": "0000-0002-7315-7899", "researcher": {"href": "https://publications.scilifelab.se/researcher/b277b6387de142bbab91fad82d9eff09.json"}}, {"family": "R\u00fcck", "given": "Christian", "initials": "C", "orcid": "0000-0002-8742-0168", "researcher": {"href": "https://publications.scilifelab.se/researcher/496a782babf3403ba32f805f360d246f.json"}}, {"family": "Schachar", "given": "Russell J", "initials": "RJ"}, {"family": "Wu", "given": "Hei Man", "initials": "HM", "orcid": "0000-0003-1559-7586", "researcher": {"href": "https://publications.scilifelab.se/researcher/1578fafcb32642609d408fcff09cd91e.json"}}, {"family": "Meier", "given": "Sandra M", "initials": "SM"}, {"family": "Crosbie", "given": "Jennifer", "initials": "J"}, {"family": "Arnold", "given": "Paul D", "initials": "PD", "orcid": "0000-0003-2496-4624", "researcher": {"href": "https://publications.scilifelab.se/researcher/c21fa35b3bf246ab8a96866510fc069b.json"}}, {"family": "Mattheisen", "given": "Manuel", "initials": "M", "orcid": "0000-0002-8442-493X", "researcher": {"href": "https://publications.scilifelab.se/researcher/c38fef539c2c4cebb81eff917aa3d4ef.json"}}, {"family": "Boomsma", "given": "Dorret I", "initials": "DI", "orcid": "0000-0002-7099-7972", "researcher": {"href": "https://publications.scilifelab.se/researcher/4b66ab2525fd4a468e7a4ad14c955cb4.json"}}, {"family": "Mataix-Cols", "given": "David", "initials": "D", "orcid": "0000-0002-4545-0924", "researcher": {"href": "https://publications.scilifelab.se/researcher/9954431e50b749aeb6957835ae1632f3.json"}}, {"family": "Cath", "given": "Danielle", "initials": "D"}], "type": "meta-analysis", "published": "2022-11-15", "journal": {"title": "Transl Psychiatry", "issn": "2158-3188", "volume": "12", "issue": "1", "pages": "479", "issn-l": "2158-3188"}, "abstract": "Hoarding Disorder (HD) is a mental disorder characterized by persistent difficulties discarding or parting with possessions, often resulting in cluttered living spaces, distress, and impairment. Its etiology is largely unknown, but twin studies suggest that it is moderately heritable. In this study, we pooled phenotypic and genomic data from seven international cohorts (N = 27,537 individuals) and conducted a genome wide association study (GWAS) meta-analysis of parent- or self-reported hoarding symptoms (HS). We followed up the results with gene-based and gene-set analyses, as well as leave-one-out HS polygenic risk score (PRS) analyses. To examine a possible genetic association between hoarding symptoms and other phenotypes we conducted cross-trait PRS analyses. Though we did not report any genome-wide significant SNPs, we report heritability estimates for the twin-cohorts between 26-48%, and a SNP-heritability of 11% for an unrelated sub-cohort. Cross-trait PRS analyses showed that the genetic risk for schizophrenia and autism spectrum disorder were significantly associated with hoarding symptoms. We also found suggestive evidence for an association with educational attainment. There were no significant associations with other phenotypes previously linked to HD, such as obsessive-compulsive disorder, depression, anxiety, or attention-deficit hyperactivity disorder. To conclude, we found that HS are heritable, confirming and extending previous twin studies but we had limited power to detect any genome-wide significant loci. Much larger samples will be needed to further extend these findings and reach a \"gene discovery zone\". To move the field forward, future research should not only include genetic analyses of quantitative hoarding traits in larger samples, but also in samples of individuals meeting strict diagnostic criteria for HD, and more ethnically diverse samples.", "doi": "10.1038/s41398-022-02248-7", "pmid": "36379924", "labels": {"National Genomics Infrastructure": "Service", "NGI SNP genotyping": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9666541"}, {"db": "pii", "key": "10.1038/s41398-022-02248-7"}], "notes": [], "created": "2022-12-23T11:26:48.889Z", "modified": "2024-01-16T13:48:34.470Z"}, {"entity": "publication", "iuid": "176af94247064339a6083776c29a51fb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/176af94247064339a6083776c29a51fb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/176af94247064339a6083776c29a51fb"}}, "title": "Genetic regulation of serum IgA levels and susceptibility to common immune, infectious, kidney, and cardio-metabolic traits.", "authors": [{"family": "Liu", "given": "Lili", "initials": "L", "orcid": "0000-0002-2622-9669", "researcher": {"href": "https://publications.scilifelab.se/researcher/763a2755eb5540a2a92d6dc59754fb97.json"}}, {"family": "Khan", "given": "Atlas", "initials": "A", "orcid": "0000-0002-6651-2725", "researcher": {"href": "https://publications.scilifelab.se/researcher/5058de1650d3456993dcf3ab02a8f9bb.json"}}, {"family": "Sanchez-Rodriguez", "given": "Elena", "initials": "E", "orcid": "0000-0002-7041-5485", "researcher": {"href": "https://publications.scilifelab.se/researcher/d2ee1321f3514835b7e48e794edf9283.json"}}, {"family": "Zanoni", "given": "Francesca", "initials": "F"}, {"family": "Li", "given": "Yifu", "initials": "Y"}, {"family": "Steers", "given": "Nicholas", "initials": "N"}, {"family": "Balderes", "given": "Olivia", "initials": "O"}, {"family": "Zhang", "given": "Junying", "initials": "J", "orcid": "0000-0003-4996-8699", "researcher": {"href": "https://publications.scilifelab.se/researcher/31ced250baba47f5ae40d6b0730ac75b.json"}}, {"family": "Krithivasan", "given": "Priya", "initials": "P"}, {"family": "LeDesma", "given": "Robert A", "initials": "RA"}, {"family": "Fischman", "given": "Clara", "initials": "C"}, {"family": "Hebbring", "given": "Scott J", "initials": "SJ"}, {"family": "Harley", "given": "John B", "initials": "JB"}, {"family": "Moncrieffe", "given": "Halima", "initials": "H", "orcid": "0000-0001-9744-4879", "researcher": {"href": "https://publications.scilifelab.se/researcher/97d79764251c4ac790c01b7cbcc7fe86.json"}}, {"family": "Kottyan", "given": "Leah C", "initials": "LC", "orcid": "0000-0003-3979-2220", "researcher": {"href": "https://publications.scilifelab.se/researcher/661ee875ca2445cb96d30e95bb8a7728.json"}}, {"family": "Namjou-Khales", "given": "Bahram", "initials": "B", "orcid": "0000-0003-4452-7878", "researcher": {"href": "https://publications.scilifelab.se/researcher/5e21a127ed014c01bce3c1136648307c.json"}}, {"family": "Walunas", "given": "Theresa L", "initials": "TL", "orcid": "0000-0002-7653-3650", "researcher": {"href": "https://publications.scilifelab.se/researcher/e41f13951de944f6a5d1537cb4fb1de6.json"}}, {"family": "Knevel", "given": "Rachel", "initials": "R"}, {"family": "Raychaudhuri", "given": "Soumya", "initials": "S"}, {"family": "Karlson", "given": "Elizabeth W", "initials": "EW"}, {"family": "Denny", "given": "Joshua C", "initials": "JC"}, {"family": "Stanaway", "given": "Ian B", "initials": "IB", "orcid": "0000-0002-0783-0918", "researcher": {"href": "https://publications.scilifelab.se/researcher/390eac8ddd9b4d308f347311f45d63d9.json"}}, {"family": "Crosslin", "given": "David", "initials": "D"}, {"family": "Rauen", "given": "Thomas", "initials": "T"}, {"family": "Floege", "given": "J\u00fcrgen", "initials": "J"}, {"family": "Eitner", "given": "Frank", "initials": "F"}, {"family": "Moldoveanu", "given": "Zina", "initials": "Z"}, {"family": "Reily", "given": "Colin", "initials": "C"}, {"family": "Knoppova", "given": "Barbora", "initials": "B", "orcid": "0000-0003-2997-4952", "researcher": {"href": "https://publications.scilifelab.se/researcher/c1ae8af419664853903c2af954425155.json"}}, {"family": "Hall", "given": "Stacy", "initials": "S"}, {"family": "Sheff", "given": "Justin T", "initials": "JT"}, {"family": "Julian", "given": "Bruce A", "initials": "BA"}, {"family": "Wyatt", "given": "Robert J", "initials": "RJ"}, {"family": "Suzuki", "given": "Hitoshi", "initials": "H", "orcid": "0000-0002-1901-2111", "researcher": {"href": "https://publications.scilifelab.se/researcher/e033cc3f91d14466895f025044a1ec2e.json"}}, {"family": "Xie", "given": "Jingyuan", "initials": "J"}, {"family": "Chen", "given": "Nan", "initials": "N"}, {"family": "Zhou", "given": "Xujie", "initials": "X", "orcid": "0000-0002-7215-707X", "researcher": {"href": "https://publications.scilifelab.se/researcher/04c7801d74fb4056ad7a48824413bbce.json"}}, {"family": "Zhang", "given": "Hong", "initials": "H"}, {"family": "Hammarstr\u00f6m", "given": "Lennart", "initials": "L"}, {"family": "Viktorin", "given": "Alexander", "initials": "A", "orcid": "0000-0003-2141-2816", "researcher": {"href": "https://publications.scilifelab.se/researcher/0f02b9aad56348c28f639bf231748096.json"}}, {"family": "Magnusson", "given": "Patrik K E", "initials": "PKE", "orcid": "0000-0002-7315-7899", "researcher": {"href": "https://publications.scilifelab.se/researcher/b277b6387de142bbab91fad82d9eff09.json"}}, {"family": "Shang", "given": "Ning", "initials": "N", "orcid": "0000-0001-7040-5204", "researcher": {"href": "https://publications.scilifelab.se/researcher/c5c4b535488448c9a911ce8db475f830.json"}}, {"family": "Hripcsak", "given": "George", "initials": "G"}, {"family": "Weng", "given": "Chunhua", "initials": "C", "orcid": "0000-0002-9624-0214", "researcher": {"href": "https://publications.scilifelab.se/researcher/8ea1b4a4132242e3abac469d5f85d58c.json"}}, {"family": "Rundek", "given": "Tatjana", "initials": "T", "orcid": "0000-0002-7115-9815", "researcher": {"href": "https://publications.scilifelab.se/researcher/34ebc54256244a76a59f4eef9540522c.json"}}, {"family": "Elkind", "given": "Mitchell S V", "initials": "MSV", "orcid": "0000-0003-2562-1156", "researcher": {"href": "https://publications.scilifelab.se/researcher/64f1771d64184c9db275c6308ea92c67.json"}}, {"family": "Oelsner", "given": "Elizabeth C", "initials": "EC", "orcid": "0000-0002-7481-9671", "researcher": {"href": "https://publications.scilifelab.se/researcher/afb61a7c022d4d24890446aa80c447b3.json"}}, {"family": "Barr", "given": "R Graham", "initials": "RG"}, {"family": "Ionita-Laza", "given": "Iuliana", "initials": "I"}, {"family": "Novak", "given": "Jan", "initials": "J", "orcid": "0000-0002-9211-6670", "researcher": {"href": "https://publications.scilifelab.se/researcher/e44350372d7947c9b2e4c9d2c9baab4f.json"}}, {"family": "Gharavi", "given": "Ali G", "initials": "AG", "orcid": "0000-0003-2801-233X", "researcher": {"href": "https://publications.scilifelab.se/researcher/8fe768273c7343098d829bcd64038707.json"}}, {"family": "Kiryluk", "given": "Krzysztof", "initials": "K", "orcid": "0000-0002-5047-6715", "researcher": {"href": "https://publications.scilifelab.se/researcher/b6e7b5668c0141728599d5ebb68c8929.json"}}], "type": "journal article", "published": "2022-11-11", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "13", "issue": "1", "pages": "6859", "issn-l": "2041-1723"}, "abstract": "Immunoglobulin A (IgA) mediates mucosal responses to food antigens and the intestinal microbiome and is involved in susceptibility to mucosal pathogens, celiac disease, inflammatory bowel disease, and IgA nephropathy. We performed a genome-wide association study of serum IgA levels in 41,263 individuals of diverse ancestries and identified 20 genome-wide significant loci, including 9 known and 11 novel loci. Co-localization analyses with expression QTLs prioritized candidate genes for 14 of 20 significant loci. Most loci encoded genes that produced immune defects and IgA abnormalities when genetically manipulated in mice. We also observed positive genetic correlations of serum IgA levels with IgA nephropathy, type 2 diabetes, and body mass index, and negative correlations with celiac disease, inflammatory bowel disease, and several infections. Mendelian randomization supported elevated serum IgA as a causal factor in IgA nephropathy. African ancestry was consistently associated with higher serum IgA levels and greater frequency of IgA-increasing alleles compared to other ancestries. Our findings provide novel insights into the genetic regulation of IgA levels and its potential role in human disease.", "doi": "10.1038/s41467-022-34456-6", "pmid": "36369178", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI SNP genotyping": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9651905"}, {"db": "pii", "key": "10.1038/s41467-022-34456-6"}], "notes": [], "created": "2023-02-24T13:14:55.508Z", "modified": "2023-06-19T13:19:40.686Z"}, {"entity": "publication", "iuid": "c6cb0a80038d48c69c3e38c25d0ed018", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c6cb0a80038d48c69c3e38c25d0ed018.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c6cb0a80038d48c69c3e38c25d0ed018"}}, "title": "Whole genome analyses based on single, field collected spores of the arbuscular mycorrhizal fungus Funneliformis geosporum.", "authors": [{"family": "Sahraei", "given": "Shadi Eshghi", "initials": "SE", "orcid": "0000-0003-4741-5871", "researcher": {"href": "https://publications.scilifelab.se/researcher/98f7d11029704e33b61a8c27daa54378.json"}}, {"family": "S\u00e1nchez-Garc\u00eda", "given": "Marisol", "initials": "M", "orcid": "0000-0002-0635-6281", "researcher": {"href": "https://publications.scilifelab.se/researcher/5ccb3584fa144e178750ff2fc4666cfe.json"}}, {"family": "Montoliu-Nerin", "given": "Merce", "initials": "M", "orcid": "0000-0002-5200-0411", "researcher": {"href": "https://publications.scilifelab.se/researcher/7f89e94a04c6429db7e706b4d8d6626a.json"}}, {"family": "Manyara", "given": "David", "initials": "D", "orcid": "0000-0002-8370-2651", "researcher": {"href": "https://publications.scilifelab.se/researcher/2132548af20445b2b0561fa38b8f8b89.json"}}, {"family": "Bergin", "given": "Claudia", "initials": "C", "orcid": "0000-0001-7960-1789", "researcher": {"href": "https://publications.scilifelab.se/researcher/fdd58ab07d964bcfb865ce67f7826816.json"}}, {"family": "Rosendahl", "given": "S\u00f8ren", "initials": "S", "orcid": "0000-0001-5202-6585", "researcher": {"href": "https://publications.scilifelab.se/researcher/111116b3b09343f783385c30207fd9b3.json"}}, {"family": "Rosling", "given": "Anna", "initials": "A", "orcid": "0000-0002-7003-5941", "researcher": {"href": "https://publications.scilifelab.se/researcher/c4c4bbb9e6c343808e8fa9345b7c05b2.json"}}], "type": "journal article", "published": "2022-11-00", "journal": {"title": "Mycorrhiza", "issn": "1432-1890", "issn-l": "0940-6360", "volume": "32", "issue": "5-6", "pages": "361-371"}, "abstract": "Arbuscular mycorrhizal (AM) fungi are ubiquitous mutualistic symbionts of most terrestrial plants and many complete their lifecycles underground. Whole genome analysis of AM fungi has long been restricted to species and strains that can be maintained under controlled conditions that facilitate collection of biological samples. There is some evidence suggesting that AM fungi can adapt to culture resulting in phenotypic and possibly also genotypic changes in the fungi. In this study, we used field isolated spores of AM fungi and identified them as Funneliformis geosporum based on morphology and phylogenetic analyses. We separately assembled the genomes of two representative spores using DNA sequences of 19 and 22 individually amplified nuclei. The genomes were compared with previously published data from other members of Glomeraceae including two strains of F. mosseae. No significant differences were observed among the species in terms of gene content, while the single nucleotide polymorphism density was higher in the strains of F. geosporum than in the strains of F. mosseae. In this study, we demonstrate that it is possible to sequence and assemble genomes from AM fungal spores sampled in the field, which opens up the possibility to include uncultured AM fungi in phylogenomic and comparative genomic analysis and to study genomic variation in natural populations of these important plant symbionts.", "doi": "10.1007/s00572-022-01091-4", "pmid": "36161535", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Microbial Single Cell Genomics": "Service", "Bioinformatics Support and Infrastructure": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9560946"}, {"db": "pii", "key": "10.1007/s00572-022-01091-4"}], "notes": [], "created": "2022-11-29T12:15:19.004Z", "modified": "2024-01-16T13:48:34.535Z"}, {"entity": "publication", "iuid": "799166a7e02e4d8baee46b54d0b639e9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/799166a7e02e4d8baee46b54d0b639e9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/799166a7e02e4d8baee46b54d0b639e9"}}, "title": "Strong Association of Combined Genetic Deficiencies in the Classical Complement Pathway With Risk of Systemic Lupus Erythematosus and Primary Sj\u00f6gren's Syndrome.", "authors": [{"family": "Lundtoft", "given": "Christian", "initials": "C"}, {"family": "Sj\u00f6wall", "given": "Christopher", "initials": "C"}, {"family": "Rantap\u00e4\u00e4-Dahlqvist", "given": "Solbritt", "initials": "S"}, {"family": "Bengtsson", "given": "Anders A", "initials": "AA"}, {"family": "J\u00f6nsen", "given": "Andreas", "initials": "A"}, {"family": "Pucholt", "given": "Pascal", "initials": "P"}, {"family": "Wu", "given": "Yee Ling", "initials": "YL"}, {"family": "Lundstr\u00f6m", "given": "Emeli", "initials": "E"}, {"family": "Eloranta", "given": "Maija-Leena", "initials": "ML"}, {"family": "Gunnarsson", "given": "Iva", "initials": "I"}, {"family": "Baecklund", "given": "Eva", "initials": "E"}, {"family": "Jonsson", "given": "Roland", "initials": "R"}, {"family": "Hammenfors", "given": "Daniel", "initials": "D"}, {"family": "Forsblad-d'Elia", "given": "Helena", "initials": "H"}, {"family": "Eriksson", "given": "Per", "initials": "P"}, {"family": "Mandl", "given": "Thomas", "initials": "T"}, {"family": "Bucher", "given": "Sara", "initials": "S"}, {"family": "Norheim", "given": "Katrine B", "initials": "KB"}, {"family": "Auglaend Johnsen", "given": "Svein Joar", "initials": "SJ"}, {"family": "Omdal", "given": "Roald", "initials": "R"}, {"family": "Kvarnstr\u00f6m", "given": "Marika", "initials": "M"}, {"family": "Wahren-Herlenius", "given": "Marie", "initials": "M"}, {"family": "Truedsson", "given": "Lennart", "initials": "L"}, {"family": "Nilsson", "given": "Bo", "initials": "B"}, {"family": "Kozyrev", "given": "Sergey V", "initials": "SV"}, {"family": "Bianchi", "given": "Matteo", "initials": "M"}, {"family": "Lindblad-Toh", "given": "Kerstin", "initials": "K"}, {"family": "DISSECT consortium, the ImmunoArray consortium", "given": "", "initials": ""}, {"family": "Yu", "given": "Chack-Yung", "initials": "CY"}, {"family": "Nordmark", "given": "Gunnel", "initials": "G"}, {"family": "Sandling", "given": "Johanna K", "initials": "JK"}, {"family": "Svenungsson", "given": "Elisabet", "initials": "E"}, {"family": "Leonard", "given": "Dag", "initials": "D"}, {"family": "R\u00f6nnblom", "given": "Lars", "initials": "L"}], "type": "journal article", "published": "2022-11-00", "journal": {"title": "Arthritis & rheumatology (Hoboken, N.J.)", "issn": "2326-5205", "issn-l": "2326-5191", "volume": "74", "issue": "11", "pages": "1842-1850"}, "abstract": "Complete genetic deficiency of the complement component C2 is a strong risk factor for monogenic systemic lupus erythematosus (SLE), but whether heterozygous C2 deficiency adds to the risk of SLE or primary Sj\u00f6gren's syndrome (SS) has not been studied systematically. This study was undertaken to investigate potential associations of heterozygous C2 deficiency and C4 copy number variation with clinical manifestations in patients with SLE and patients with primary SS.\n\nThe presence of the common 28-bp C2 deletion rs9332736 and C4 copy number variation was examined in Scandinavian patients who had received a diagnosis of SLE (n = 958) or primary SS (n = 911) and in 2,262 healthy controls through the use of DNA sequencing. The concentration of complement proteins in plasma and classical complement function were analyzed in a subgroup of SLE patients.\n\nHeterozygous C2 deficiency-when present in combination with a low C4A copy number-substantially increased the risk of SLE (odds ratio [OR] 10.2 [95% confidence interval (95% CI) 3.5-37.0]) and the risk of primary SS (OR 13.0 [95% CI 4.5-48.4]) when compared to individuals with 2 C4A copies and normal C2. For patients heterozygous for rs9332736 with 1 C4A copy, the median age at diagnosis was 7 years earlier in patients with SLE and 12 years earlier in patients with primary SS when compared to patients with normal C2. Reduced C2 levels in plasma (P = 2 \u00d7 10-9 ) and impaired function of the classical complement pathway (P = 0.03) were detected in SLE patients with heterozygous C2 deficiency. Finally, in a primary SS patient homozygous for C2 deficiency, we observed low levels of anti-Scl-70, which suggests a risk of developing systemic sclerosis or potential overlap between primary SS and other systemic autoimmune diseases.\n\nWe demonstrate that a genetic pattern involving partial deficiencies of C2 and C4A in the classical complement pathway is a strong risk factor for SLE and for primary SS. Our results emphasize the central role of the complement system in the pathogenesis of both SLE and primary SS.", "doi": "10.1002/art.42270", "pmid": "35729719", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Short read": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9828039"}], "notes": [], "created": "2022-11-02T11:56:01.128Z", "modified": "2024-01-16T13:48:34.645Z"}, {"entity": "publication", "iuid": "a85b4e387fa944659cfb0c8c1c5b47ad", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a85b4e387fa944659cfb0c8c1c5b47ad.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a85b4e387fa944659cfb0c8c1c5b47ad"}}, "title": "Stroke genetics informs drug discovery and risk prediction across ancestries.", "authors": [{"family": "Mishra", "given": "Aniket", "initials": "A", "orcid": "0000-0002-8141-1543", "researcher": {"href": "https://publications.scilifelab.se/researcher/5e95668f120440e5bb3ea9554377aa69.json"}}, {"family": "Malik", "given": "Rainer", "initials": "R"}, {"family": "Hachiya", "given": "Tsuyoshi", "initials": "T", "orcid": "0000-0002-5274-3266", "researcher": {"href": "https://publications.scilifelab.se/researcher/052c404d92294a5794513bbd8bf9ad44.json"}}, {"family": "J\u00fcrgenson", "given": "Tuuli", "initials": "T"}, {"family": "Namba", "given": "Shinichi", "initials": "S", "orcid": "0000-0002-7486-3146", "researcher": {"href": "https://publications.scilifelab.se/researcher/2e3a77716d0947eca303cb3a836e7606.json"}}, {"family": "Posner", "given": "Daniel C", "initials": "DC", "orcid": "0000-0002-3056-6924", "researcher": {"href": "https://publications.scilifelab.se/researcher/4b23b7f5718543519b63b5f5241270b1.json"}}, {"family": "Kamanu", "given": "Frederick K", "initials": "FK", "orcid": "0000-0001-7208-1047", "researcher": {"href": 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"initials": "H", "orcid": "0000-0003-3687-2508", "researcher": {"href": "https://publications.scilifelab.se/researcher/ab5c4744d60d4290a3a8a6b80c107f42.json"}}, {"family": "Wassertheil-Smoller", "given": "Sylvia", "initials": "S", "orcid": "0000-0002-5447-4653", "researcher": {"href": "https://publications.scilifelab.se/researcher/d091e3704a9948209449f28c974181a8.json"}}, {"family": "Christensen", "given": "Kaare", "initials": "K", "orcid": "0000-0002-5429-5292", "researcher": {"href": "https://publications.scilifelab.se/researcher/e79ea43d09544efc95351b52ac682910.json"}}, {"family": "Ikram", "given": "Mohammad A", "initials": "MA", "orcid": "0000-0003-0372-8585", "researcher": {"href": "https://publications.scilifelab.se/researcher/2ec81571f4a94af682b4e23526f87385.json"}}, {"family": "Rundek", "given": "Tatjana", "initials": "T", "orcid": "0000-0002-7115-9815", "researcher": {"href": "https://publications.scilifelab.se/researcher/34ebc54256244a76a59f4eef9540522c.json"}}, {"family": "Worrall", "given": "Bradford B", "initials": "BB", "orcid": "0000-0001-9386-4091", "researcher": {"href": "https://publications.scilifelab.se/researcher/159cc0760bf542129d186e25dfde87bc.json"}}, {"family": "Lathrop", "given": "G Mark", "initials": "GM"}, {"family": "Riaz", "given": "Moeen", "initials": "M"}, {"family": "Simonsick", "given": "Eleanor M", "initials": "EM"}, {"family": "K\u00f5rv", "given": "Janika", "initials": "J", "orcid": "0000-0002-6074-0727", "researcher": {"href": "https://publications.scilifelab.se/researcher/c9943be062e54db085c24868a871404f.json"}}, {"family": "Fran\u00e7a", "given": "Paulo H C", "initials": "PHC", "orcid": "0000-0002-1750-9132", "researcher": {"href": "https://publications.scilifelab.se/researcher/0d3c1d16b0e54523b12c12e52f245fda.json"}}, {"family": "Zand", "given": "Ramin", "initials": "R"}, {"family": "Prasad", "given": "Kameshwar", "initials": "K"}, {"family": "Frikke-Schmidt", "given": "Ruth", "initials": "R", "orcid": "0000-0003-4084-5027", "researcher": {"href": "https://publications.scilifelab.se/researcher/740b72fe0c02411094886de5b2e705ec.json"}}, {"family": "de Leeuw", "given": "Frank-Erik", "initials": "FE"}, {"family": "Liman", "given": "Thomas", "initials": "T"}, {"family": "Haeusler", "given": "Karl Georg", "initials": "KG", "orcid": "0000-0002-6389-5054", "researcher": {"href": "https://publications.scilifelab.se/researcher/63ced1b703e342acb1bf978473feeb61.json"}}, {"family": "Ruigrok", "given": "Ynte M", "initials": "YM"}, {"family": "Heuschmann", "given": "Peter Ulrich", "initials": "PU", "orcid": "0000-0002-2681-3515", "researcher": {"href": "https://publications.scilifelab.se/researcher/3f07487486974308b2b315200c2a8ee8.json"}}, {"family": "Longstreth", "given": "W T", "initials": "WT"}, {"family": "Jung", "given": "Keum Ji", "initials": "KJ"}, {"family": "Bastarache", "given": "Lisa", "initials": "L"}, {"family": "Par\u00e9", "given": "Guillaume", "initials": "G", "orcid": "0000-0002-6795-4760", "researcher": {"href": "https://publications.scilifelab.se/researcher/4e23d12d8f5340a79e86a293593c9598.json"}}, {"family": "Damrauer", "given": "Scott M", "initials": "SM"}, {"family": "Chasman", "given": "Daniel I", "initials": "DI", "orcid": "0000-0003-3357-0862", "researcher": {"href": "https://publications.scilifelab.se/researcher/1c06690291064fe58836958edbcaafbc.json"}}, {"family": "Rotter", "given": "Jerome I", "initials": "JI"}, {"family": "Anderson", "given": "Christopher D", "initials": "CD"}, {"family": "Zwart", "given": "John-Anker", "initials": "JA", "orcid": "0000-0001-5721-0154", "researcher": {"href": "https://publications.scilifelab.se/researcher/d6ba64e625064349b7405b23439e1bfe.json"}}, {"family": "Niiranen", "given": "Teemu J", "initials": "TJ", "orcid": "0000-0002-7394-7487", "researcher": {"href": "https://publications.scilifelab.se/researcher/d52ad3773441442fbad63cbe33959735.json"}}, {"family": "Fornage", "given": "Myriam", "initials": "M", "orcid": "0000-0003-0677-8158", "researcher": {"href": "https://publications.scilifelab.se/researcher/b5de431c325e40f4adfe13c06cf1e0b9.json"}}, {"family": "Liaw", "given": "Yung-Po", "initials": "YP"}, {"family": "Seshadri", "given": "Sudha", "initials": "S", "orcid": "0000-0001-6135-2622", "researcher": {"href": "https://publications.scilifelab.se/researcher/429e370668ec47ce9945bc5262dccbb3.json"}}, {"family": "Fern\u00e1ndez-Cadenas", "given": "Israel", "initials": "I"}, {"family": "Walters", "given": "Robin G", "initials": "RG", "orcid": "0000-0002-9179-0321", "researcher": {"href": "https://publications.scilifelab.se/researcher/f36254611faa44b782b76da870e89bd3.json"}}, {"family": "Ruff", "given": "Christian T", "initials": "CT"}, {"family": "Owolabi", "given": "Mayowa O", "initials": "MO", "orcid": "0000-0003-1146-3070", "researcher": {"href": "https://publications.scilifelab.se/researcher/9ad3b2f403a34896a655f9c318af4c17.json"}}, {"family": "Huffman", "given": "Jennifer E", "initials": "JE", "orcid": "0000-0002-9672-2491", "researcher": {"href": "https://publications.scilifelab.se/researcher/cfa4efb5afae47528265d8be0d5e67fd.json"}}, {"family": "Milani", "given": "Lili", "initials": "L", "orcid": "0000-0002-5323-3102", "researcher": {"href": "https://publications.scilifelab.se/researcher/dec8d00c4b9d43458c5c895b164695d5.json"}}, {"family": "Kamatani", "given": "Yoichiro", "initials": "Y"}, {"family": "Dichgans", "given": "Martin", "initials": "M", "orcid": "0000-0002-0654-387X", "researcher": {"href": "https://publications.scilifelab.se/researcher/f41f224e973440f6a78a49b54ca35e3a.json"}}, {"family": "Debette", "given": "Stephanie", "initials": "S"}], "type": "journal article", "published": "2022-11-00", "journal": {"title": "Nature", "issn": "1476-4687", "volume": "611", "issue": "7934", "pages": "115-123", "issn-l": "0028-0836"}, "abstract": "Previous genome-wide association studies (GWASs) of stroke - the second leading cause of death worldwide - were conducted predominantly in populations of European ancestry1,2. Here, in cross-ancestry GWAS meta-analyses of 110,182 patients who have had a stroke (five ancestries, 33% non-European) and 1,503,898 control individuals, we identify association signals for stroke and its subtypes at 89 (61 new) independent loci: 60 in primary inverse-variance-weighted analyses and 29 in secondary meta-regression and multitrait analyses. On the basis of internal cross-ancestry validation and an independent follow-up in 89,084 additional cases of stroke (30% non-European) and 1,013,843 control individuals, 87% of the primary stroke risk loci and 60% of the secondary stroke risk loci were replicated (P < 0.05). Effect sizes were highly correlated across ancestries. Cross-ancestry fine-mapping, in silico mutagenesis analysis3, and transcriptome-wide and proteome-wide association analyses revealed putative causal genes (such as SH3PXD2A and FURIN) and variants (such as at GRK5 and NOS3). Using a three-pronged approach4, we provide genetic evidence for putative drug effects, highlighting F11, KLKB1, PROC, GP1BA, LAMC2 and VCAM1 as possible targets, with drugs already under investigation for stroke for F11 and PROC. A polygenic score integrating cross-ancestry and ancestry-specific stroke GWASs with vascular-risk factor GWASs (integrative polygenic scores) strongly predicted ischaemic stroke in populations of European, East Asian and African ancestry5. Stroke genetic risk scores were predictive of ischaemic stroke independent of clinical risk factors in 52,600 clinical-trial participants with cardiometabolic disease. Our results provide insights to inform biology, reveal potential drug targets and derive genetic risk prediction tools across ancestries.", "doi": "10.1038/s41586-022-05165-3", "pmid": "36180795", "labels": {"National Genomics Infrastructure": "Service", "NGI SNP genotyping": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41586-022-05165-3"}, {"db": "pmc", "key": "PMC9524349"}], "notes": [], "created": "2022-11-09T14:36:41.202Z", "modified": "2022-11-09T14:37:47.411Z"}, {"entity": "publication", "iuid": "12159c4661c1445a9deed2ed84fce70f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/12159c4661c1445a9deed2ed84fce70f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/12159c4661c1445a9deed2ed84fce70f"}}, "title": "Mer-tyrosine kinase: a novel susceptibility gene for SLE related end-stage renal disease.", "authors": [{"family": "Yavuz", "given": "Sule", "initials": "S"}, {"family": "Pucholt", "given": "Pascal", "initials": "P", "orcid": "0000-0003-3342-1373", "researcher": {"href": "https://publications.scilifelab.se/researcher/61a214ff2d494b568cb6da944e858acf.json"}}, {"family": "Sandling", "given": "Johanna K", "initials": "JK", "orcid": "0000-0003-1382-2321", "researcher": {"href": "https://publications.scilifelab.se/researcher/9c7bae5a05ac47eeac96547ca7336767.json"}}, {"family": "Bianchi", "given": "Matteo", "initials": "M"}, {"family": "Leonard", "given": "Dag", "initials": "D", "orcid": "0000-0002-6275-7282", "researcher": {"href": "https://publications.scilifelab.se/researcher/42ed25c2f495484db4757f4fef51abae.json"}}, {"family": "Bolin", "given": "Karin", "initials": "K"}, {"family": "Imgenberg-Kreuz", "given": "Juliana", "initials": "J"}, {"family": "Eloranta", "given": "Maija-Leena", "initials": "ML"}, {"family": "Kozyrev", "given": "Sergey V", "initials": "SV", "orcid": "0000-0001-6209-4100", "researcher": {"href": "https://publications.scilifelab.se/researcher/b6be89ad73a14d66a3b9439efc9c4099.json"}}, {"family": "Lanata", "given": "Cristina M", "initials": "CM"}, {"family": "J\u00f6nsen", "given": "Andreas", "initials": "A"}, {"family": "Bengtsson", "given": "Anders A", "initials": "AA"}, {"family": "Sj\u00f6wall", "given": "Christopher", "initials": "C", "orcid": "0000-0003-0900-2048", "researcher": {"href": "https://publications.scilifelab.se/researcher/fe4dd47b8ca1436e8a26fdea33f5e7f6.json"}}, {"family": "Svenungsson", "given": "Elisabet", "initials": "E", "orcid": "0000-0003-3396-3244", "researcher": {"href": "https://publications.scilifelab.se/researcher/0ab5989c3c604a96bf42b1b6f90434a0.json"}}, {"family": "Gunnarsson", "given": "Iva", "initials": "I"}, {"family": "Rantap\u00e4\u00e4-Dahlqvist", "given": "Solbritt", "initials": "S"}, {"family": "ImmunoArray Development Consortium", "given": "", "initials": ""}, {"family": "DISSECT Consortium", "given": "", "initials": ""}, {"family": "Nititham", "given": "Joanne", "initials": "J"}, {"family": "Criswell", "given": "Lindsey A", "initials": "LA"}, {"family": "Lindblad-Toh", "given": "Kerstin", "initials": "K"}, {"family": "R\u00f6nnblom", "given": "Lars", "initials": "L", "orcid": "0000-0001-9403-6503", "researcher": {"href": "https://publications.scilifelab.se/researcher/053ed3b657124a1bab3a78dc685556e6.json"}}], "type": "meta-analysis", "published": "2022-11-00", "journal": {"title": "Lupus Sci Med", "issn": "2053-8790", "volume": "9", "issue": "1", "issn-l": "2053-8790"}, "abstract": "Lupus nephritis (LN) is a common and severe manifestation of SLE. The genetic risk for nephritis and progression to end-stage renal disease (ESRD) in patients with LN remains unclear. Herein, we aimed to identify novel genetic associations with LN, focusing on subphenotypes and ESRD.\n\nWe analysed genomic data on 958 patients with SLE (discovery cohort: LN=338) with targeted sequencing data from 1832 immunological pathway genes. We used an independent multiethnic cohort comprising 1226 patients with SLE (LN=603) as a replication dataset. Detailed functional annotation and functional epigenomic enrichment analyses were applied to predict functional effects of the candidate variants.\n\nA genetic variant (rs56097910) within the MERTK gene was associated with ESRD in both cohorts, meta-analysis OR=5.4 (2.8 to 10.6); p=1.0\u00d710-6. We observed decreased methylation levels in peripheral blood cells from SLE patients with ESRD, compared with patients without renal SLE (p=2.7\u00d710-4), at one CpG site (cg16333401) in close vicinity to the transcription start site of MERTK and located in a DNAse hypersensitivity region in T and B cells. Rs56097910 is linked to altered MERTK expression in kidney tissue in public eQTL databases. Two loci were replicated for association with proliferative LN: PRDM1 (rs6924535, pmeta=1.6\u00d710-5, OR=0.58) and APOA1BP (NAXE) (rs942960, pmeta=1.2\u00d710-5, OR=2.64).\n\nWe identified a novel genetic risk locus, MERTK, associated with SLE-ESRD using the data from two large SLE cohorts. Through DNA methylation analysis and functional annotation, we showed that the risk could be mediated through regulation of gene expression. Our results suggest that variants in the MERTK gene are important for the risk of developing SLE-ESRD and suggest a role for PRDM1 and APOA1BP in proliferative LN.", "doi": "10.1136/lupus-2022-000752", "pmid": "36332927", "labels": {"NGI Short read": "Service", "NGI SNP genotyping": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9639142"}, {"db": "pii", "key": "9/1/e000752"}], "notes": [], "created": "2022-11-29T12:21:01.345Z", "modified": "2024-01-16T13:48:34.678Z"}, {"entity": "publication", "iuid": "d9be4ec5baae47499d9976f9b113a4d0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d9be4ec5baae47499d9976f9b113a4d0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d9be4ec5baae47499d9976f9b113a4d0"}}, "title": "Exome-wide association study to identify rare variants influencing COVID-19 outcomes: Results from the Host Genetics Initiative.", "authors": [{"family": "Butler-Laporte", "given": "Guillaume", "initials": "G", "orcid": "0000-0001-5388-0396", "researcher": {"href": "https://publications.scilifelab.se/researcher/1c165ac40c3c409b93acbb13ac63579a.json"}}, {"family": "Povysil", "given": "Gundula", "initials": "G", "orcid": "0000-0003-4625-5909", "researcher": {"href": "https://publications.scilifelab.se/researcher/78129fef5aad4ba8ad154d9a4908974f.json"}}, {"family": "Kosmicki", "given": "Jack A", "initials": "JA", "orcid": "0000-0003-1252-6192", "researcher": {"href": "https://publications.scilifelab.se/researcher/21b8896b49bd48a6b9b21b84a76cda41.json"}}, {"family": "Cirulli", "given": "Elizabeth T", "initials": "ET", "orcid": "0000-0001-7808-2809", "researcher": {"href": "https://publications.scilifelab.se/researcher/566755e2fb34412c93b01245e512f9fd.json"}}, {"family": "Drivas", "given": "Theodore", "initials": "T", "orcid": "0000-0002-8717-0111", "researcher": {"href": "https://publications.scilifelab.se/researcher/0adcb730c0f644ceb712e774801cb74a.json"}}, {"family": "Furini", "given": "Simone", "initials": "S"}, {"family": "Saad", "given": "Chadi", "initials": "C", "orcid": "0000-0001-6963-9126", "researcher": {"href": "https://publications.scilifelab.se/researcher/ac0b588b98a7496aa8a422ce08dd89c9.json"}}, {"family": "Schmidt", "given": "Axel", "initials": "A", "orcid": "0000-0002-1185-3012", "researcher": {"href": "https://publications.scilifelab.se/researcher/3708b225fbae4c239bdc3bea34beff17.json"}}, {"family": "Olszewski", "given": "Pawel", "initials": "P", "orcid": "0000-0003-1010-8843", "researcher": {"href": "https://publications.scilifelab.se/researcher/175cf3dd63e54f7c919ed3b1de3d4b11.json"}}, {"family": "Korotko", "given": "Urszula", "initials": "U", "orcid": "0000-0002-1779-8368", "researcher": {"href": "https://publications.scilifelab.se/researcher/9960078bdffa4561a9111e37390c44eb.json"}}, {"family": "Quinodoz", "given": "Mathieu", "initials": "M", "orcid": "0000-0002-9841-4433", "researcher": {"href": "https://publications.scilifelab.se/researcher/140e63b09c3340a0ae6aeb8124ea15b1.json"}}, {"family": "\u00c7elik", "given": "Elifnaz", "initials": "E", "orcid": "0000-0002-0324-5228", "researcher": {"href": "https://publications.scilifelab.se/researcher/68a15c971dbe44bda2ee9381196c6f23.json"}}, {"family": "Kundu", "given": "Kousik", "initials": "K", "orcid": "0000-0002-1019-8351", "researcher": {"href": "https://publications.scilifelab.se/researcher/55dbffb9b2234f8db2b17025bd053aa7.json"}}, {"family": "Walter", "given": "Klaudia", "initials": "K", "orcid": "0000-0003-4448-0301", "researcher": {"href": "https://publications.scilifelab.se/researcher/bd5029beabb34e18869a535f9578bbd6.json"}}, {"family": "Jung", "given": "Junghyun", "initials": "J"}, {"family": "Stockwell", "given": "Amy D", "initials": "AD"}, {"family": "Sloofman", "given": "Laura G", "initials": "LG", "orcid": 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"https://publications.scilifelab.se/researcher/b6e7b5668c0141728599d5ebb68c8929.json"}}, {"family": "Renieri", "given": "Alessandra", "initials": "A", "orcid": "0000-0002-0846-9220", "researcher": {"href": "https://publications.scilifelab.se/researcher/3dbf990f1e0c4fd99e45c945915f25b0.json"}}, {"family": "Ferreira", "given": "Manuel A R", "initials": "MAR", "orcid": "0000-0001-9059-1825", "researcher": {"href": "https://publications.scilifelab.se/researcher/d27aef5015494b018b22352125c0225d.json"}}, {"family": "Richards", "given": "J Brent", "initials": "JB", "orcid": "0000-0002-3746-9086", "researcher": {"href": "https://publications.scilifelab.se/researcher/c2c20c901fd041c194dae79b29b94ec2.json"}}], "type": "journal article", "published": "2022-11-00", "journal": {"title": "PLoS Genet.", "issn": "1553-7404", "issn-l": "1553-7390", "volume": "18", "issue": "11", "pages": "e1010367"}, "abstract": "Host genetics is a key determinant of COVID-19 outcomes. Previously, the COVID-19 Host Genetics Initiative genome-wide association study used common variants to identify multiple loci associated with COVID-19 outcomes. However, variants with the largest impact on COVID-19 outcomes are expected to be rare in the population. Hence, studying rare variants may provide additional insights into disease susceptibility and pathogenesis, thereby informing therapeutics development. Here, we combined whole-exome and whole-genome sequencing from 21 cohorts across 12 countries and performed rare variant exome-wide burden analyses for COVID-19 outcomes. In an analysis of 5,085 severe disease cases and 571,737 controls, we observed that carrying a rare deleterious variant in the SARS-CoV-2 sensor toll-like receptor TLR7 (on chromosome X) was associated with a 5.3-fold increase in severe disease (95% CI: 2.75-10.05, p = 5.41x10-7). This association was consistent across sexes. These results further support TLR7 as a genetic determinant of severe disease and suggest that larger studies on rare variants influencing COVID-19 outcomes could provide additional insights.", "doi": "10.1371/journal.pgen.1010367", "pmid": "36327219", "labels": {"NGI Short read": "Collaborative", "NGI Uppsala (SNP&SEQ Technology Platform)": "Collaborative", "National Genomics Infrastructure": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC9632827"}, {"db": "pii", "key": "PGENETICS-D-22-00434"}], "notes": [], "created": "2022-11-29T14:02:16.675Z", "modified": "2023-06-16T12:55:14.973Z"}, {"entity": "publication", "iuid": "87091aedf5f94a5c86600d25244ac164", "links": {"self": {"href": "https://publications.scilifelab.se/publication/87091aedf5f94a5c86600d25244ac164.json"}, "display": {"href": "https://publications.scilifelab.se/publication/87091aedf5f94a5c86600d25244ac164"}}, "title": "ZEB2 haploinsufficient Mowat-Wilson syndrome induced pluripotent stem cells show disrupted GABAergic transcriptional regulation and function.", "authors": [{"family": "Schuster", "given": "Jens", "initials": "J"}, {"family": "Klar", "given": "Joakim", "initials": "J"}, {"family": "Khalfallah", "given": "Ayda", "initials": "A"}, {"family": "Laan", "given": "Loora", "initials": "L"}, {"family": "Hoeber", "given": "Jan", "initials": "J"}, {"family": "Fatima", "given": "Ambrin", "initials": "A"}, {"family": "Sequeira", "given": "Velin Marita", "initials": "VM"}, {"family": "Jin", "given": "Zhe", "initials": "Z"}, {"family": "Korol", "given": "Sergiy V", "initials": "SV"}, {"family": "Huss", "given": "Mikael", "initials": "M"}, {"family": "Nordgren", "given": "Ann", "initials": "A"}, {"family": "Anderlid", "given": "Britt Marie", "initials": "BM"}, {"family": "Gallant", "given": "Caroline", "initials": "C"}, {"family": "Birnir", "given": "Bryndis", "initials": "B"}, {"family": "Dahl", "given": "Niklas", "initials": "N"}], "type": "journal article", "published": "2022-10-24", "journal": {"title": "Front Mol Neurosci", "issn": "1662-5099", "volume": "15", "pages": "988993", "issn-l": null}, "abstract": "Mowat-Wilson syndrome (MWS) is a severe neurodevelopmental disorder caused by heterozygous variants in the gene encoding transcription factor ZEB2. Affected individuals present with structural brain abnormalities, speech delay and epilepsy. In mice, conditional loss of Zeb2 causes hippocampal degeneration, altered migration and differentiation of GABAergic interneurons, a heterogeneous population of mainly inhibitory neurons of importance for maintaining normal excitability. To get insights into GABAergic development and function in MWS we investigated ZEB2 haploinsufficient induced pluripotent stem cells (iPSC) of MWS subjects together with iPSC of healthy donors. Analysis of RNA-sequencing data at two time points of GABAergic development revealed an attenuated interneuronal identity in MWS subject derived iPSC with enrichment of differentially expressed genes required for transcriptional regulation, cell fate transition and forebrain patterning. The ZEB2 haploinsufficient neural stem cells (NSCs) showed downregulation of genes required for ventral telencephalon specification, such as FOXG1, accompanied by an impaired migratory capacity. Further differentiation into GABAergic interneuronal cells uncovered upregulation of transcription factors promoting pallial and excitatory neurons whereas cortical markers were downregulated. The differentially expressed genes formed a neural protein-protein network with extensive connections to well-established epilepsy genes. Analysis of electrophysiological properties in ZEB2 haploinsufficient GABAergic cells revealed overt perturbations manifested as impaired firing of repeated action potentials. Our iPSC model of ZEB2 haploinsufficient GABAergic development thus uncovers a dysregulated gene network leading to immature interneurons with mixed identity and altered electrophysiological properties, suggesting mechanisms contributing to the neuropathogenesis and seizures in MWS.", "doi": "10.3389/fnmol.2022.988993", "pmid": "36353360", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC9637781"}], "notes": [], "created": "2022-11-29T12:21:58.551Z", "modified": "2024-01-16T13:48:34.689Z"}, {"entity": "publication", "iuid": "cf165c58527e41439582a10d2cc5f063", "links": {"self": {"href": "https://publications.scilifelab.se/publication/cf165c58527e41439582a10d2cc5f063.json"}, "display": {"href": "https://publications.scilifelab.se/publication/cf165c58527e41439582a10d2cc5f063"}}, "title": "Genomic analyses of the Linum distyly supergene reveal convergent evolution at the molecular level.", "authors": [{"family": "Guti\u00e9rrez-Valencia", "given": "Juanita", "initials": "J"}, {"family": "Fracassetti", "given": "Marco", "initials": "M"}, {"family": "Berdan", "given": "Emma L", "initials": "EL"}, {"family": "Bunikis", "given": "Ignas", "initials": "I"}, {"family": "Soler", "given": "Lucile", "initials": "L"}, {"family": "Dainat", "given": "Jacques", "initials": "J"}, {"family": "Kutschera", "given": "Verena E", "initials": "VE"}, {"family": "Losvik", "given": "Aleksandra", "initials": "A"}, {"family": "D\u00e9samor\u00e9", "given": "Aur\u00e9lie", "initials": "A"}, {"family": "Hughes", "given": "P William", "initials": "PW"}, {"family": "Foroozani", "given": "Alireza", "initials": "A"}, {"family": "Laenen", "given": "Benjamin", "initials": "B"}, {"family": "Pesquet", "given": "Edouard", "initials": "E"}, {"family": "Abdelaziz", "given": "Mohamed", "initials": "M"}, {"family": "Pettersson", "given": "Olga Vinnere", "initials": "OV"}, {"family": "Nystedt", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Brennan", "given": "Adrian C", "initials": "AC"}, {"family": "Arroyo", "given": "Juan", "initials": "J"}, {"family": "Slotte", "given": "Tanja", "initials": "T"}], "type": "journal article", "published": "2022-10-24", "journal": {"title": "Curr. Biol.", "issn": "1879-0445", "issn-l": "0960-9822", "volume": "32", "issue": "20", "pages": "4360-4371.e6"}, "abstract": "Supergenes govern multi-trait-balanced polymorphisms in a wide range of systems; however, our understanding of their origins and evolution remains incomplete. The reciprocal placement of stigmas and anthers in pin and thrum floral morphs of distylous species constitutes an iconic example of a balanced polymorphism governed by a supergene, the distyly S-locus. Recent studies have shown that the Primula and Turnera distyly supergenes are both hemizygous in thrums, but it remains unknown whether hemizygosity is pervasive among distyly S-loci. As hemizygosity has major consequences for supergene evolution and loss, clarifying whether this genetic architecture is shared among distylous species is critical. Here, we have characterized the genetic architecture and evolution of the distyly supergene in Linum by generating a chromosome-level genome assembly of Linum tenue, followed by the identification of the S-locus using population genomic data. We show that hemizygosity and thrum-specific expression of S-linked genes, including a pistil-expressed candidate gene for style length, are major features of the Linum S-locus. Structural variation is likely instrumental for recombination suppression, and although the non-recombining dominant haplotype has accumulated transposable elements, S-linked genes are not under relaxed purifying selection. Our findings reveal remarkable convergence in the genetic architecture and evolution of independently derived distyly supergenes, provide a counterexample to classic inversion-based supergenes, and shed new light on the origin and maintenance of an iconic floral polymorphism.", "doi": "10.1016/j.cub.2022.08.042", "pmid": "36087578", "labels": {"Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "NGI Uppsala (Uppsala Genome Center)": "Collaborative", "NGI Long read": "Collaborative", "National Genomics Infrastructure": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "S0960-9822(22)01364-1"}], "notes": [], "created": "2022-09-22T18:45:15.012Z", "modified": "2024-01-16T13:48:34.696Z"}, {"entity": "publication", "iuid": "3606ec85387645718697cbbf8d7cb694", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3606ec85387645718697cbbf8d7cb694.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3606ec85387645718697cbbf8d7cb694"}}, "title": "Glucocorticoids and glucolipotoxicity alter the DNA methylome and function of human EndoC-\u03b2H1 cells.", "authors": [{"family": "Dos Santos", "given": "Cristiane", "initials": "C"}, {"family": "Karagiannopoulos", "given": "Alexandros", "initials": "A"}, {"family": "Rafacho", "given": "Alex", "initials": "A"}, {"family": "Perfilyev", "given": "Alexander", "initials": "A"}, {"family": "Eliasson", "given": "Lena", "initials": "L"}, {"family": "Ling", "given": "Charlotte", "initials": "C"}, {"family": "Bacos", "given": "Karl", "initials": "K"}], "type": "journal article", "published": "2022-10-15", "journal": {"title": "Life Sciences", "issn": "1879-0631", "volume": "307", "pages": "120854", "issn-l": "0024-3205"}, "abstract": "Synthetic glucocorticoids, including dexamethasone (DEX), are clinically prescribed due to their immunoregulatory properties. In excess they can perturb glucose homeostasis, with individuals predisposed to glucose intolerance more sensitive to these negative effects. While DEX is known to negatively impact \u03b2-cell function, it is unclear how. Hence, our aim was to investigate the effect of DEX on \u03b2-cell function, both alone and in combination with a diabetogenic milieu in the form of elevated glucose and palmitate.\n\nHuman pancreatic EndoC-\u03b2H1 cells were cultured in the presence of high glucose and palmitate (glucolipotoxicity) and/or a pharmacological concentration of DEX, before functional and molecular analyses.\n\nEither treatment alone resulted in reduced insulin content and secretion, while the combination of DEX and glucolipotoxicity promoted a strong synergistic effect. These effects were associated with reduced insulin biosynthesis, likely due to downregulation of PDX1, MAFA, and the proinsulin converting enzymes, as well as reduced ATP response upon glucose stimulation. Genome-wide DNA methylation analysis found changes on PDE4D, MBNL1 and TMEM178B, all implicated in \u03b2-cell function, after all three treatments. DEX alone caused very strong demethylation of the glucocorticoid-regulated gene ZBTB16, also known to influence the \u03b2-cell, while the combined treatment caused altered methylation of many known \u03b2-cell regulators and diabetes candidate genes.\n\nDEX treatment and glucolipotoxic conditions separately alter the \u03b2-cell epigenome and function. The combination of both treatments exacerbates these changes, showing that caution is needed when prescribing potent glucocorticoids in patients with dysregulated metabolism.", "doi": "10.1016/j.lfs.2022.120854", "pmid": "35917939", "labels": {"National Genomics Infrastructure": "Service", "NGI SNP genotyping": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "S0024-3205(22)00554-9"}], "notes": [], "created": "2022-11-09T14:36:33.674Z", "modified": "2022-11-09T14:37:40.354Z"}, {"entity": "publication", "iuid": "52583936c1024a468226e9c12527aaaa", "links": {"self": {"href": "https://publications.scilifelab.se/publication/52583936c1024a468226e9c12527aaaa.json"}, "display": {"href": "https://publications.scilifelab.se/publication/52583936c1024a468226e9c12527aaaa"}}, "title": "Comparative genome analysis of mycobacteria focusing on tRNA and non-coding RNA.", "authors": [{"family": "Behra", "given": "Phani Rama Krishna", "initials": "PRK"}, {"family": "Pettersson", "given": "B M Fredrik", "initials": "BMF"}, {"family": "Ramesh", "given": "Malavika", "initials": "M"}, {"family": "Das", "given": "Sarbashis", "initials": "S"}, {"family": "Dasgupta", "given": "Santanu", "initials": "S"}, {"family": "Kirsebom", "given": "Leif A", "initials": "LA"}], "type": "journal article", "published": "2022-10-15", "journal": {"title": "BMC Genomics", "issn": "1471-2164", "issn-l": "1471-2164", "volume": "23", "issue": "1", "pages": "704"}, "abstract": "The Mycobacterium genus encompasses at least 192 named species, many of which cause severe diseases such as tuberculosis. Non-tuberculosis mycobacteria (NTM) can also infect humans and animals. Some are of emerging concern because they show high resistance to commonly used antibiotics while others are used and evaluated in bioremediation or included in anticancer vaccines.\r\n\r\nWe provide the genome sequences for 114 mycobacterial type strains and together with 130 available mycobacterial genomes we generated a phylogenetic tree based on 387 core genes and supported by average nucleotide identity (ANI) data. The 244 genome sequences cover most of the species constituting the Mycobacterium genus. The genome sizes ranged from 3.2 to 8.1 Mb with an average of 5.7 Mb, and we identified 14 new plasmids. Moreover, mycobacterial genomes consisted of phage-like sequences ranging between 0 and 4.64% dependent on mycobacteria while the number of IS elements varied between 1 and 290. Our data also revealed that, depending on the mycobacteria, the number of tRNA and non-coding (nc) RNA genes differ and that their positions on the chromosome varied. We identified a conserved core set of 12 ncRNAs, 43 tRNAs and 18 aminoacyl-tRNA synthetases among mycobacteria.\r\n\r\nPhages, IS elements, tRNA and ncRNAs appear to have contributed to the evolution of the Mycobacterium genus where several tRNA and ncRNA genes have been horizontally transferred. On the basis of our phylogenetic analysis, we identified several isolates of unnamed species as new mycobacterial species or strains of known mycobacteria. The predicted number of coding sequences correlates with genome size while the number of tRNA, rRNA and ncRNA genes does not. Together these findings expand our insight into the evolution of the Mycobacterium genus and as such they establish a platform to understand mycobacterial pathogenicity, their evolution, antibiotic resistance/tolerance as well as the function and evolution of ncRNA among mycobacteria.", "doi": "10.1186/s12864-022-08927-5", "pmid": "36243697", "labels": {"NGI Uppsala (Uppsala Genome Center)": "Service", "NGI Long read": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1186/s12864-022-08927-5"}, {"db": "pmc", "key": "PMC9569102"}], "notes": [], "created": "2022-11-21T10:04:26.689Z", "modified": "2024-01-16T13:48:34.732Z"}, {"entity": "publication", "iuid": "4c6123a4087b412baae9242b060eeb12", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4c6123a4087b412baae9242b060eeb12.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4c6123a4087b412baae9242b060eeb12"}}, "title": "Tackling the translational challenges of multi-omics research in the realm of European personalised medicine: A workshop report.", "authors": [{"family": "Oldoni", "given": "Emanuela", "initials": "E"}, {"family": "Saunders", "given": "Gary", "initials": "G"}, {"family": "Bietrix", "given": "Florence", "initials": "F"}, {"family": "Garcia Bermejo", "given": "Maria Laura", "initials": "ML"}, {"family": "Niehues", "given": "Anna", "initials": "A"}, {"family": "'t Hoen", "given": "Peter A C", "initials": "PAC"}, {"family": "Nordlund", "given": "Jessica", "initials": "J"}, {"family": "Hajduch", "given": "Marian", "initials": "M"}, {"family": "Scherer", "given": "Andreas", "initials": "A"}, {"family": "Kivinen", "given": "Katja", "initials": "K"}, {"family": "Pitk\u00e4nen", "given": "Esa", "initials": "E"}, {"family": "M\u00e4kela", "given": "Tomi Pekka", "initials": "TP"}, {"family": "Gut", "given": "Ivo", "initials": "I"}, {"family": "Scollen", "given": "Serena", "initials": "S"}, {"family": "Kozera", "given": "\u0141ukasz", "initials": "\u0141"}, {"family": "Esteller", "given": "Manel", "initials": "M"}, {"family": "Shi", "given": "Leming", "initials": "L"}, {"family": "Ussi", "given": "Anton", "initials": "A"}, {"family": "Andreu", "given": "Antonio L", "initials": "AL"}, {"family": "van Gool", "given": "Alain J", "initials": "AJ"}], "type": "journal article", "published": "2022-10-13", "journal": {"title": "Front Mol Biosci", "issn": "2296-889X", "issn-l": "2296-889X", "volume": "9", "issue": null, "pages": "974799"}, "abstract": "Personalised medicine (PM) presents a great opportunity to improve the future of individualised healthcare. Recent advances in -omics technologies have led to unprecedented efforts characterising the biology and molecular mechanisms that underlie the development and progression of a wide array of complex human diseases, supporting further development of PM. This article reflects the outcome of the 2021 EATRIS-Plus Multi-omics Stakeholder Group workshop organised to 1) outline a global overview of common promises and challenges that key European stakeholders are facing in the field of multi-omics research, 2) assess the potential of new technologies, such as artificial intelligence (AI), and 3) establish an initial dialogue between key initiatives in this space. Our focus is on the alignment of agendas of European initiatives in multi-omics research and the centrality of patients in designing solutions that have the potential to advance PM in long-term healthcare strategies.", "doi": "10.3389/fmolb.2022.974799", "pmid": "36310597", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Collaborative", "National Genomics Infrastructure": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC9608444"}, {"db": "pii", "key": "974799"}], "notes": [], "created": "2022-11-29T14:00:58.731Z", "modified": "2022-11-29T14:01:15.351Z"}, {"entity": "publication", "iuid": "c27764ed4c514f2592c156cc59d23608", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c27764ed4c514f2592c156cc59d23608.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c27764ed4c514f2592c156cc59d23608"}}, "title": "Spatiotemporal variations in retrovirus-host interactions among Darwin's finches.", "authors": [{"family": "Hill", "given": "Jason", "initials": "J", "orcid": "0000-0002-0151-8931", "researcher": {"href": "https://publications.scilifelab.se/researcher/a2cb6f3cce5f4919959e18074d51256d.json"}}, {"family": "Lillie", "given": "Mette", "initials": "M", "orcid": "0000-0001-8714-0812", "researcher": {"href": "https://publications.scilifelab.se/researcher/3ce02b2116c0417e8a4dcd578f45983b.json"}}, {"family": "Pettersson", "given": "Mats E", "initials": "ME", "orcid": "0000-0002-7372-9076", "researcher": {"href": "https://publications.scilifelab.se/researcher/27011c7fbb8a44dda536a4fc876675b0.json"}}, {"family": "Rubin", "given": "Carl-Johan", "initials": "C"}, {"family": "Grant", "given": "B Rosemary", "initials": "BR"}, {"family": "Grant", "given": "Peter R", "initials": "PR"}, {"family": "Andersson", "given": "Leif", "initials": "L", "orcid": "0000-0002-4085-6968", "researcher": {"href": "https://publications.scilifelab.se/researcher/bd3343c12f994b1fabcae23027d3a76d.json"}}, {"family": "Jern", "given": "Patric", "initials": "P", "orcid": "0000-0003-3393-5825", "researcher": {"href": "https://publications.scilifelab.se/researcher/8baed28572fd470ba1e7b18fccd2e275.json"}}], "type": "journal article", "published": "2022-10-13", "journal": {"title": "Nat Commun", "issn": "2041-1723", "issn-l": "2041-1723", "volume": "13", "issue": "1", "pages": "6033"}, "abstract": "Endogenous retroviruses (ERVs) are inherited remnants of retroviruses that colonized host germline over millions of years, providing a sampling of retroviral diversity across time. Here, we utilize the strength of Darwin's finches, a system synonymous with evolutionary studies, for investigating ERV history, revealing recent retrovirus-host interactions in natural populations. By mapping ERV variation across all species of Darwin's finches and comparing with outgroup species, we highlight geographical and historical patterns of retrovirus-host occurrence, utilizing the system for evaluating the extent and timing of retroviral activity in hosts undergoing adaptive radiation and colonization of new environments. We find shared ERVs among all samples indicating retrovirus-host associations pre-dating host speciation, as well as considerable ERV variation across populations of the entire Darwin's finches' radiation. Unexpected ERV variation in finch species on different islands suggests historical changes in gene flow and selection. Non-random distribution of ERVs along and between chromosomes, and across finch species, suggests association between ERV accumulation and the rapid speciation of Darwin's finches.", "doi": "10.1038/s41467-022-33723-w", "pmid": "36229469", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-022-33723-w"}, {"db": "pmc", "key": "PMC9562234"}], "notes": [], "created": "2022-11-09T16:00:11.231Z", "modified": "2024-01-16T13:48:34.742Z"}, {"entity": "publication", "iuid": "af444c3012184e0887f12a8f83b56952", "links": {"self": {"href": "https://publications.scilifelab.se/publication/af444c3012184e0887f12a8f83b56952.json"}, "display": {"href": "https://publications.scilifelab.se/publication/af444c3012184e0887f12a8f83b56952"}}, "title": "Dormant SOX9-positive cells facilitate MYC-driven recurrence of medulloblastoma.", "authors": [{"family": "Borgenvik", "given": "Anna", "initials": "A", "orcid": "0000-0003-4696-7703", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a6b1da64eeb459092d6f32823d474ba.json"}}, {"family": "Holmberg", "given": "Karl O", "initials": "KO", "orcid": "0000-0002-4402-0586", "researcher": {"href": "https://publications.scilifelab.se/researcher/1b44ff77230e492bb0630372281a432c.json"}}, {"family": "Bolin", "given": "Sara", "initials": "S", "orcid": "0000-0003-2835-1518", "researcher": {"href": "https://publications.scilifelab.se/researcher/8d4cf00b336942638b1b06bb8a3e95f8.json"}}, {"family": "Zhao", "given": "Miao", "initials": "M", "orcid": "0000-0002-4895-1177", "researcher": {"href": "https://publications.scilifelab.se/researcher/b9c4e2515b414dee94aaeca71569699b.json"}}, {"family": "Savov", "given": "Vasil", "initials": "V", "orcid": "0000-0003-2347-1975", "researcher": {"href": "https://publications.scilifelab.se/researcher/326ce1c1944c4217bcdf25520774d403.json"}}, {"family": "Ros\u00e9n", "given": "Gabriela", "initials": "G", "orcid": "0000-0002-7762-1468", "researcher": {"href": "https://publications.scilifelab.se/researcher/6f652227f9c147f082404e42d4b06e76.json"}}, {"family": "Hutter", "given": "Sonja", "initials": "S", "orcid": "0000-0003-3340-9315", "researcher": {"href": "https://publications.scilifelab.se/researcher/b75be5efd15d4575a6d8b70a3d08ee7d.json"}}, {"family": "Garancher", "given": "Alexandra", "initials": "A", "orcid": "0000-0001-5779-2860", "researcher": {"href": "https://publications.scilifelab.se/researcher/80409227c84144c2b287efe12d6adbeb.json"}}, {"family": "Suryo Rahmanto", "given": "Aldwin", "initials": "A", "orcid": "0000-0002-4593-286X", "researcher": {"href": "https://publications.scilifelab.se/researcher/f6e9bc6bf4684bb2bd6a299cd475d4fa.json"}}, {"family": "Bergstr\u00f6m", "given": "Tobias", "initials": "T", "orcid": "0000-0002-4557-2390", "researcher": {"href": "https://publications.scilifelab.se/researcher/170dee5895114905a47f673c23bc27c5.json"}}, {"family": "Olsen", "given": "Thale Kristin", "initials": "TK", "orcid": "0000-0003-4655-7384", "researcher": {"href": "https://publications.scilifelab.se/researcher/fa772bafc60a42f7a4e24b724b9dd529.json"}}, {"family": "Mainwaring", "given": "Oliver J", "initials": "OJ", "orcid": "0000-0002-7973-9849", "researcher": {"href": "https://publications.scilifelab.se/researcher/494a0479041f41149902feb34f668043.json"}}, {"family": "Sattanino", "given": "Damiana", "initials": "D", "orcid": "0000-0002-2747-4842", "researcher": {"href": "https://publications.scilifelab.se/researcher/f76c1d5a46fa446b928e1bacb1e2f81b.json"}}, {"family": "Verbaan", "given": "Annemieke D", "initials": "AD", "orcid": "0000-0001-6793-0577", "researcher": {"href": "https://publications.scilifelab.se/researcher/38f656179a264c8baf3f7515fc642ee0.json"}}, {"family": "Rusert", "given": "Jessica M", "initials": "JM", "orcid": "0000-0003-0751-2693", "researcher": {"href": "https://publications.scilifelab.se/researcher/68b9b78643ed4cf686a48177971def24.json"}}, {"family": "Sundstrom", "given": "Anders", "initials": "A", "orcid": "0000-0003-3942-6271", "researcher": {"href": "https://publications.scilifelab.se/researcher/4cf009de33e547aa9f850ac18c2a0c32.json"}}, {"family": "Ballester Bravo", "given": "Mar", "initials": "M", "orcid": "0000-0002-1371-6679", "researcher": {"href": "https://publications.scilifelab.se/researcher/a54bfd8cca5d472f9917bcb7d75f98fd.json"}}, {"family": "Dang", "given": "Yonglong", "initials": "Y", "orcid": "0000-0001-9705-5507", "researcher": {"href": "https://publications.scilifelab.se/researcher/be8f706e753a4d10ba4ee5f3aef6fc6b.json"}}, {"family": "Wenz", "given": "Amelie S", "initials": "AS", "orcid": "0000-0003-1929-382X", "researcher": {"href": "https://publications.scilifelab.se/researcher/113e59df51d0438c90dfef742c67fead.json"}}, {"family": "Richardson", "given": "Stacey", "initials": "S", "orcid": "0000-0003-1841-6330", "researcher": {"href": "https://publications.scilifelab.se/researcher/89ecfd4f24154b6eb4ac6befcc72ae35.json"}}, {"family": "Fotaki", "given": "Grammatiki", "initials": "G", "orcid": "0000-0002-1343-1921", "researcher": {"href": "https://publications.scilifelab.se/researcher/65f67224986646d3a74b6733253ec0a1.json"}}, {"family": "Hill", "given": "Rebecca M", "initials": "RM", "orcid": "0000-0001-8405-2219", "researcher": {"href": "https://publications.scilifelab.se/researcher/59da56669a874fa5af8c3009595c1190.json"}}, {"family": "Dubuc", "given": "Adrian M", "initials": "AM", "orcid": "0000-0002-3447-6715", "researcher": {"href": "https://publications.scilifelab.se/researcher/4df0a67f53ac4fb3b62bc35e06bb6d7c.json"}}, {"family": "Kalushkova", "given": "Antonia", "initials": "A", "orcid": "0000-0003-4535-506X", "researcher": {"href": "https://publications.scilifelab.se/researcher/df89c7522b7b4af3b3cef8555380fe8c.json"}}, {"family": "Remke", "given": "Marc", "initials": "M", "orcid": "0000-0002-9404-9993", "researcher": {"href": "https://publications.scilifelab.se/researcher/8de3293b14654714a490ad3c1ebacdb9.json"}}, {"family": "Cancer", "given": "Matko", "initials": "M", "orcid": "0000-0001-5825-5151", "researcher": {"href": "https://publications.scilifelab.se/researcher/9a428908f080488a990cef0ce873e17d.json"}}, {"family": "Jernberg-Wiklund", "given": "Helena", "initials": "H", "orcid": "0000-0002-9319-7986", "researcher": {"href": "https://publications.scilifelab.se/researcher/dc67ebc79ba54e0aa635f58641533f0e.json"}}, {"family": "Giraud", "given": "G\u00e9raldine", "initials": "G", "orcid": "0000-0002-2771-9889", "researcher": {"href": "https://publications.scilifelab.se/researcher/802841f141834cf28283e925f9e08b54.json"}}, {"family": "Chen", "given": "Xingqi", "initials": "X", "orcid": "0000-0002-5657-2839", "researcher": {"href": "https://publications.scilifelab.se/researcher/ef7ddc09e57745909175e41ac2d1b647.json"}}, {"family": "Taylor", "given": "Michael D", "initials": "MD", "orcid": "0000-0001-7009-3466", "researcher": {"href": "https://publications.scilifelab.se/researcher/9ed8b81b674444bdb45e080ec459252f.json"}}, {"family": "Sangfelt", "given": "Olle", "initials": "O", "orcid": "0000-0002-0316-0195", "researcher": {"href": "https://publications.scilifelab.se/researcher/2cd4756206314abf9e23caca719b70ec.json"}}, {"family": "Clifford", "given": "Steven C", "initials": "SC", "orcid": "0000-0003-4893-2184", "researcher": {"href": "https://publications.scilifelab.se/researcher/ed4d6271609e412a9c57bc3206b17c1f.json"}}, {"family": "Schuller", "given": "Ulrich", "initials": "U", "orcid": "0000-0002-8731-1121", "researcher": {"href": "https://publications.scilifelab.se/researcher/e8e5ba2ee7244467b78a810618ee055d.json"}}, {"family": "Wechsler-Reya", "given": "Robert J", "initials": "RJ", "orcid": "0000-0002-7463-8352", "researcher": {"href": "https://publications.scilifelab.se/researcher/25ca624b1ebd4fae9533cb83e8df3804.json"}}, {"family": "Weishaupt", "given": "Holger", "initials": "H", "orcid": "0000-0002-0364-2709", "researcher": {"href": "https://publications.scilifelab.se/researcher/5f48d0ba4ee14f1eb17f1597d3aa70e5.json"}}, {"family": "Swartling", "given": "Fredrik J", "initials": "FJ", "orcid": "0000-0002-8460-4367", "researcher": {"href": "https://publications.scilifelab.se/researcher/69679cebbc90496f9c5b32f56d966654.json"}}], "type": "journal article", "published": "2022-10-11", "journal": {"title": "Cancer Res.", "issn": "1538-7445", "issn-l": "0008-5472", "volume": null, "issue": null, "pages": null}, "abstract": "Relapse is the leading cause of death in patients with medulloblastoma, the most common malignant pediatric brain tumor. A better understanding of the mechanisms underlying recurrence could lead to more effective therapies for targeting tumor relapses. Here, we observed that SOX9, a transcription factor and stem cell/glial fate marker, is limited to rare, quiescent cells in high-risk medulloblastoma with MYC amplification. In paired primary-recurrent patient samples, SOX9-positive cells accumulated in medulloblastoma relapses. SOX9 expression anti-correlated with MYC expression in murine and human medulloblastoma cells. However, SOX9-positive cells were plastic and could give rise to a MYC high state. To follow relapse at the single-cell level, an inducible dual Tet model of medulloblastoma was developed, in which MYC expression was redirected in vivo from treatment-sensitive bulk cells to dormant SOX9-positive cells using doxycycline treatment. SOX9 was essential for relapse initiation and depended on suppression of MYC activity to promote therapy resistance, epithelial-mesenchymal transition, and immune escape. p53 and DNA repair pathways were downregulated in recurrent tumors, while MGMT was upregulated. Recurrent tumor cells were found to be sensitive to treatment with an MGMT inhibitor and doxorubicin. These findings suggest that recurrence-specific targeting coupled with DNA repair inhibition comprises a potential therapeutic strategy in patients affected by medulloblastoma relapse.", "doi": "10.1158/0008-5472.CAN-22-2108", "pmid": "36219398", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "NGI Single cell": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "709709"}], "notes": [], "created": "2022-11-29T09:32:14.890Z", "modified": "2024-01-16T13:48:34.774Z"}, {"entity": "publication", "iuid": "02ca612014284b319f023360ee4fefe4", "links": {"self": {"href": "https://publications.scilifelab.se/publication/02ca612014284b319f023360ee4fefe4.json"}, "display": {"href": "https://publications.scilifelab.se/publication/02ca612014284b319f023360ee4fefe4"}}, "title": "Absence of oxygen effect on microbial structure and methane production during drying and rewetting events.", "authors": [{"family": "Liu", "given": "Tong", "initials": "T"}, {"family": "Li", "given": "Xiaoxiao", "initials": "X"}, {"family": "Yekta", "given": "Sepehr Shakeri", "initials": "SS"}, {"family": "Bj\u00f6rn", "given": "Annika", "initials": "A"}, {"family": "Mu", "given": "Bo-Zhong", "initials": "BZ"}, {"family": "Masuda", "given": "Laura Shizue Moriga", "initials": "LSM"}, {"family": "Schn\u00fcrer", "given": "Anna", "initials": "A"}, {"family": "Enrich-Prast", "given": "Alex", "initials": "A"}], "type": "journal article", "published": "2022-10-04", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "12", "issue": "1", "pages": "16570", "issn-l": "2045-2322"}, "abstract": "Natural environments with frequent drainage experience drying and rewetting events that impose fluctuations in water availability and oxygen exposure. These relatively dramatic cycles profoundly impact microbial activity in the environment and subsequent emissions of methane and carbon dioxide. In this study, we mimicked drying and rewetting events by submitting methanogenic communities from strictly anaerobic environments (anaerobic digestors) with different phylogenetic structures to consecutive desiccation events under aerobic (air) and anaerobic (nitrogen) conditions followed by rewetting. We showed that methane production quickly recovered after each rewetting, and surprisingly, no significant difference was observed between the effects of the aerobic or anaerobic desiccation events. There was a slight change in the microbial community structure and a decrease in methane production rates after consecutive drying and rewetting, which can be attributed to a depletion of the pool of available organic matter or the inhibition of the methanogenic communities. These observations indicate that in comparison to the drying and rewetting events or oxygen exposure, the initial phylogenetic structure and the organic matter quantity and quality exhibited a stronger influence on the methanogenic communities and overall microbial community responses. These results change the current paradigm of the sensitivity of strict anaerobic microorganisms to oxygen exposure.", "doi": "10.1038/s41598-022-20448-5", "pmid": "36195651", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9532411"}, {"db": "pii", "key": "10.1038/s41598-022-20448-5"}], "notes": [], "created": "2022-11-29T09:55:59.009Z", "modified": "2022-11-29T09:55:59.014Z"}, {"entity": "publication", "iuid": "2f52edf26b6d4e70b518038783cd933a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2f52edf26b6d4e70b518038783cd933a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2f52edf26b6d4e70b518038783cd933a"}}, "title": "Genome-wide association study of liver enzyme elevation in an extended cohort of rheumatoid arthritis patients starting low-dose methotrexate.", "authors": [{"family": "Cavalli", "given": "Marco", "initials": "M", "orcid": "0000-0003-1143-1431", "researcher": {"href": "https://publications.scilifelab.se/researcher/e35211c06385459baee12101121d2a15.json"}}, {"family": "Eriksson", "given": "Niclas", "initials": "N", "orcid": "0000-0002-2152-4343", "researcher": {"href": "https://publications.scilifelab.se/researcher/64611a83caba46d597f45371b77de26b.json"}}, {"family": "Sundbaum", "given": "Johanna Karlsson", "initials": "JK", "orcid": "0000-0001-5313-7981", "researcher": {"href": "https://publications.scilifelab.se/researcher/aae0af5ecb664750a7fe9f482181e571.json"}}, {"family": "Wallenberg", "given": "Matilda", "initials": "M"}, {"family": "Kohnke", "given": "Hugo", "initials": "H"}, {"family": "Baecklund", "given": "Eva", "initials": "E"}, {"family": "Hallberg", "given": "P\u00e4r", "initials": "P", "orcid": "0000-0003-3465-3280", "researcher": {"href": "https://publications.scilifelab.se/researcher/968cb3fe072d4ed09739e8be6668d168.json"}}, {"family": "Wadelius", "given": "Mia", "initials": "M", "orcid": "0000-0002-6368-2622", "researcher": {"href": "https://publications.scilifelab.se/researcher/ec07b9869a1f4b77b734c5dc567dc630.json"}}], "type": "journal article", "published": "2022-10-00", "journal": {"title": "Pharmacogenomics", "issn": "1744-8042", "volume": "23", "issue": "15", "pages": "813-820", "issn-l": "1462-2416"}, "abstract": "Aim: A follow-up genome-wide association study (GWAS) in an extended cohort of rheumatoid arthritis (RA) patients starting low-dose methotrexate (MTX) treatment was performed to identify further genetic variants associated with alanine aminotransferase (ALT) elevation. Patients & methods: A GWAS was performed on 346 RA patients. Two outcomes within the first 6 months of MTX treatment were assessed: ALT >1.5-times the upper level of normal (ULN) and maximum level of ALT. Results: SPATA9 (rs72783407) was significantly associated with maximum level of ALT (p = 2.58 \u00d7 10-8) and PLCG2 (rs60427389) was tentatively associated with ALT >1.5 \u00d7 ULN. Conclusion: Associations with SNPs in genes related to male fertility (SPATA9) and inflammatory processes (PLCG2) were identified.", "doi": "10.2217/pgs-2022-0074", "pmid": "36070248", "labels": {"National Genomics Infrastructure": "Service", "NGI SNP genotyping": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2022-09-19T11:57:03.359Z", "modified": "2024-01-16T13:48:34.919Z"}, {"entity": "publication", "iuid": "363812b85aa2484ca8e3b4177158469e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/363812b85aa2484ca8e3b4177158469e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/363812b85aa2484ca8e3b4177158469e"}}, "title": "A saturated map of common genetic variants associated with human height.", "authors": [{"family": "Yengo", "given": "Lo\u00efc", "initials": "L", "orcid": "0000-0002-4272-9305", "researcher": {"href": "https://publications.scilifelab.se/researcher/8f357358f7564da39cd810b8bff6c2b8.json"}}, {"family": "Vedantam", "given": "Sailaja", "initials": "S"}, {"family": "Marouli", "given": "Eirini", "initials": "E"}, {"family": "Sidorenko", "given": "Julia", "initials": "J"}, {"family": "Bartell", "given": "Eric", "initials": "E"}, {"family": "Sakaue", "given": "Saori", "initials": "S"}, {"family": "Graff", "given": "Marielisa", "initials": "M"}, {"family": "Eliasen", "given": "Anders U", "initials": "AU"}, {"family": "Jiang", "given": "Yunxuan", "initials": "Y"}, {"family": "Raghavan", "given": "Sridharan", "initials": "S"}, {"family": "Miao", "given": "Jenkai", "initials": "J"}, {"family": "Arias", "given": "Joshua D", "initials": "JD"}, {"family": "Graham", "given": "Sarah E", "initials": "SE"}, {"family": "Mukamel", "given": "Ronen E", "initials": "RE"}, {"family": "Spracklen", "given": "Cassandra N", "initials": "CN"}, {"family": "Yin", "given": "Xianyong", "initials": "X"}, {"family": "Chen", "given": "Shyh-Huei", "initials": "SH"}, {"family": "Ferreira", "given": "Teresa", "initials": "T"}, {"family": "Highland", "given": "Heather H", "initials": "HH"}, {"family": "Ji", "given": "Yingjie", "initials": "Y"}, {"family": "Karaderi", "given": "Tugce", "initials": "T"}, {"family": "Lin", "given": "Kuang", "initials": "K"}, {"family": "L\u00fcll", "given": "Kreete", "initials": "K"}, {"family": "Malden", "given": "Deborah E", "initials": "DE"}, {"family": "Medina-Gomez", "given": "Carolina", "initials": "C"}, {"family": "Machado", "given": "Moara", "initials": "M"}, {"family": "Moore", "given": "Amy", "initials": "A"}, {"family": "R\u00fceger", "given": "Sina", "initials": "S"}, {"family": "Sim", "given": "Xueling", "initials": "X"}, {"family": "Vrieze", "given": "Scott", "initials": "S"}, {"family": "Ahluwalia", "given": "Tarunveer S", "initials": "TS"}, {"family": "Akiyama", "given": "Masato", "initials": "M"}, {"family": "Allison", "given": "Matthew A", "initials": "MA"}, {"family": "Alvarez", "given": "Marcus", "initials": "M"}, {"family": "Andersen", "given": "Mette K", "initials": "MK"}, {"family": "Ani", "given": "Alireza", "initials": "A"}, {"family": "Appadurai", "given": "Vivek", "initials": "V"}, {"family": "Arbeeva", "given": "Liubov", "initials": "L"}, {"family": "Bhaskar", "given": "Seema", "initials": "S"}, {"family": "Bielak", "given": "Lawrence F", "initials": "LF"}, {"family": "Bollepalli", "given": "Sailalitha", "initials": "S"}, {"family": "Bonnycastle", "given": "Lori L", "initials": "LL"}, {"family": "Bork-Jensen", "given": "Jette", "initials": "J"}, {"family": "Bradfield", "given": "Jonathan P", "initials": "JP"}, {"family": "Bradford", "given": "Yuki", "initials": "Y"}, {"family": "Braund", "given": "Peter S", "initials": "PS"}, {"family": "Brody", "given": "Jennifer A", "initials": "JA"}, {"family": "Burgdorf", "given": "Kristoffer S", "initials": "KS"}, {"family": "Cade", "given": "Brian E", "initials": "BE"}, 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"initials": "XO"}, {"family": "Simonsick", "given": "Eleanor M", "initials": "EM"}, {"family": "Sims", "given": "Mario", "initials": "M"}, {"family": "Singh", "given": "Jai Rup", "initials": "JR"}, {"family": "Singleton", "given": "Andrew B", "initials": "AB"}, {"family": "Sinner", "given": "Moritz F", "initials": "MF"}, {"family": "Smith", "given": "J Gustav", "initials": "JG"}, {"family": "Snieder", "given": "Harold", "initials": "H"}, {"family": "Spector", "given": "Tim D", "initials": "TD"}, {"family": "Stampfer", "given": "Meir J", "initials": "MJ"}, {"family": "Stark", "given": "Klaus J", "initials": "KJ"}, {"family": "Strachan", "given": "David P", "initials": "DP"}, {"family": "'t Hart", "given": "Leen M", "initials": "LM", "orcid": "0000-0003-4401-2938", "researcher": {"href": "https://publications.scilifelab.se/researcher/3cb1193c2ad3419899ec86d9d95bf25d.json"}}, {"family": "Tabara", "given": "Yasuharu", "initials": "Y"}, {"family": "Tang", "given": "Hua", "initials": "H"}, {"family": "Tardif", "given": "Jean-Claude", "initials": "JC"}, {"family": "Thanaraj", "given": "Thangavel A", "initials": "TA"}, {"family": "Timpson", "given": "Nicholas J", "initials": "NJ"}, {"family": "T\u00f6njes", "given": "Anke", "initials": "A"}, {"family": "Tremblay", "given": "Angelo", "initials": "A"}, {"family": "Tuomi", "given": "Tiinamaija", "initials": "T"}, {"family": "Tuomilehto", "given": "Jaakko", "initials": "J"}, {"family": "Tusi\u00e9-Luna", "given": "Maria-Teresa", "initials": "MT"}, {"family": "Uitterlinden", "given": "Andre G", "initials": "AG"}, {"family": "van Dam", "given": "Rob M", "initials": "RM"}, {"family": "van der Harst", "given": "Pim", "initials": "P"}, {"family": "Van der Velde", "given": "Nathalie", "initials": "N"}, {"family": "van Duijn", "given": "Cornelia M", "initials": "CM"}, {"family": "van Schoor", "given": "Natasja M", "initials": "NM"}, {"family": "Vitart", "given": "Veronique", "initials": "V"}, {"family": "V\u00f6lker", "given": "Uwe", 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{"family": "Woo", "given": "Jeong-Taek", "initials": "JT"}, {"family": "Wright", "given": "Alan F", "initials": "AF"}, {"family": "Wu", "given": "Jer-Yuarn", "initials": "JY"}, {"family": "Xu", "given": "Huichun", "initials": "H"}, {"family": "Yajnik", "given": "Chittaranjan S", "initials": "CS"}, {"family": "Yokota", "given": "Mitsuhiro", "initials": "M"}, {"family": "Yuan", "given": "Jian-Min", "initials": "JM"}, {"family": "Zeggini", "given": "Eleftheria", "initials": "E"}, {"family": "Zemel", "given": "Babette S", "initials": "BS"}, {"family": "Zheng", "given": "Wei", "initials": "W"}, {"family": "Zhu", "given": "Xiaofeng", "initials": "X"}, {"family": "Zmuda", "given": "Joseph M", "initials": "JM"}, {"family": "Zonderman", "given": "Alan B", "initials": "AB"}, {"family": "Zwart", "given": "John-Anker", "initials": "JA"}, {"family": "23andMe Research Team", "given": "", "initials": ""}, {"family": "VA Million Veteran Program", "given": "", "initials": ""}, {"family": "DiscovEHR (DiscovEHR and MyCode Community Health Initiative)", "given": "", "initials": ""}, {"family": "eMERGE (Electronic Medical Records and Genomics Network)", "given": "", "initials": ""}, {"family": "Lifelines Cohort Study", "given": "", "initials": ""}, {"family": "PRACTICAL Consortium", "given": "", "initials": ""}, {"family": "Understanding Society Scientific Group", "given": "", "initials": ""}, {"family": "Chasman", "given": "Daniel I", "initials": "DI"}, {"family": "Cho", "given": "Yoon Shin", "initials": "YS"}, {"family": "Heid", "given": "Iris M", "initials": "IM"}, {"family": "McCarthy", "given": "Mark I", "initials": "MI"}, {"family": "Ng", "given": "Maggie C Y", "initials": "MCY"}, {"family": "O'Donnell", "given": "Christopher J", "initials": "CJ"}, {"family": "Rivadeneira", "given": "Fernando", "initials": "F"}, {"family": "Thorsteinsdottir", "given": "Unnur", "initials": "U"}, {"family": "Sun", "given": "Yan V", "initials": "YV"}, {"family": "Tai", "given": "E Shyong", "initials": "ES"}, {"family": "Boehnke", "given": "Michael", "initials": "M"}, {"family": "Deloukas", "given": "Panos", "initials": "P"}, {"family": "Justice", "given": "Anne E", "initials": "AE"}, {"family": "Lindgren", "given": "Cecilia M", "initials": "CM"}, {"family": "Loos", "given": "Ruth J F", "initials": "RJF"}, {"family": "Mohlke", "given": "Karen L", "initials": "KL"}, {"family": "North", "given": "Kari E", "initials": "KE"}, {"family": "Stefansson", "given": "Kari", "initials": "K"}, {"family": "Walters", "given": "Robin G", "initials": "RG"}, {"family": "Winkler", "given": "Thomas W", "initials": "TW"}, {"family": "Young", "given": "Kristin L", "initials": "KL"}, {"family": "Loh", "given": "Po-Ru", "initials": "PR"}, {"family": "Yang", "given": "Jian", "initials": "J"}, {"family": "Esko", "given": "T\u00f5nu", "initials": "T"}, {"family": "Assimes", "given": "Themistocles L", "initials": "TL"}, {"family": "Auton", "given": "Adam", "initials": "A"}, {"family": "Abecasis", "given": "Goncalo R", "initials": "GR"}, {"family": "Willer", "given": "Cristen J", "initials": "CJ"}, {"family": "Locke", "given": "Adam E", "initials": "AE"}, {"family": "Berndt", "given": "Sonja I", "initials": "SI"}, {"family": "Lettre", "given": "Guillaume", "initials": "G"}, {"family": "Frayling", "given": "Timothy M", "initials": "TM"}, {"family": "Okada", "given": "Yukinori", "initials": "Y"}, {"family": "Wood", "given": "Andrew R", "initials": "AR"}, {"family": "Visscher", "given": "Peter M", "initials": "PM"}, {"family": "Hirschhorn", "given": "Joel N", "initials": "JN"}], "type": "journal article", "published": "2022-10-00", "journal": {"title": "Nature", "issn": "1476-4687", "volume": "610", "issue": "7933", "pages": "704-712", "issn-l": "0028-0836"}, "abstract": "Common single-nucleotide polymorphisms (SNPs) are predicted to collectively explain 40-50% of phenotypic variation in human height, but identifying the specific variants and associated regions requires huge sample sizes1. Here, using data from a genome-wide association study of 5.4 million individuals of diverse ancestries, we show that 12,111 independent SNPs that are significantly associated with height account for nearly all of the common SNP-based heritability. These SNPs are clustered within 7,209 non-overlapping genomic segments with a mean size of around 90 kb, covering about 21% of the genome. The density of independent associations varies across the genome and the regions of increased density are enriched for biologically relevant genes. In out-of-sample estimation and prediction, the 12,111 SNPs (or all SNPs in the HapMap 3 panel2) account for 40% (45%) of phenotypic variance in populations of European ancestry but only around 10-20% (14-24%) in populations of other ancestries. Effect sizes, associated regions and gene prioritization are similar across ancestries, indicating that reduced prediction accuracy is likely to be explained by linkage disequilibrium and differences in allele frequency within associated regions. Finally, we show that the relevant biological pathways are detectable with smaller sample sizes than are needed to implicate causal genes and variants. Overall, this study provides a comprehensive map of specific genomic regions that contain the vast majority of common height-associated variants. Although this map is saturated for populations of European ancestry, further research is needed to achieve equivalent saturation in other ancestries.", "doi": "10.1038/s41586-022-05275-y", "pmid": "36224396", "labels": {"National Genomics Infrastructure": "Service", "NGI SNP genotyping": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9605867"}, {"db": "pii", "key": "10.1038/s41586-022-05275-y"}], "notes": [], "created": "2022-11-09T14:36:38.607Z", "modified": "2023-06-19T12:30:42.324Z"}, {"entity": "publication", "iuid": "b5b41e59d80945f0b7a009d2dd268562", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b5b41e59d80945f0b7a009d2dd268562.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b5b41e59d80945f0b7a009d2dd268562"}}, "title": "A possible genomic footprint of polygenic adaptation on population divergence in seed beetles?", "authors": [{"family": "Arnqvist", "given": "G\u00f6ran", "initials": "G", "orcid": "0000-0002-3501-3376", "researcher": {"href": "https://publications.scilifelab.se/researcher/a2e926bfdd22419eb57d2c375041150f.json"}}, {"family": "Sayadi", "given": "Ahmed", "initials": "A"}], "type": "journal article", "published": "2022-10-00", "journal": {"title": "Ecol Evol", "issn": "2045-7758", "volume": "12", "issue": "10", "pages": "e9440", "issn-l": "2045-7758"}, "abstract": "Efforts to unravel the genomic basis of incipient speciation are hampered by a mismatch between our toolkit and our understanding of the ecology and genetics of adaptation. While the former is focused on detecting selective sweeps involving few independently acting or linked speciation genes, the latter states that divergence typically occurs in polygenic traits under stabilizing selection. Here, we ask whether a role of stabilizing selection on polygenic traits in population divergence may be unveiled by using a phenotypically informed integrative approach, based on genome-wide variation segregating in divergent populations. We compare three divergent populations of seed beetles (Callosobruchus maculatus) where previous work has demonstrated a prominent role for stabilizing selection on, and population divergence in, key life history traits that reflect rate-dependent metabolic processes. We derive and assess predictions regarding the expected pattern of covariation between genetic variation segregating within populations and genetic differentiation between populations. Population differentiation was considerable (mean F ST = 0.23-0.26) and was primarily built by genes showing high selective constraints and an imbalance in inferred selection in different populations (positive Tajima's D NS in one and negative in one), and this set of genes was enriched with genes with a metabolic function. Repeatability of relative population differentiation was low at the level of individual genes but higher at the level of broad functional classes, again spotlighting metabolic genes. Absolute differentiation (d XY) showed a very different general pattern at this scale of divergence, more consistent with an important role for genetic drift. Although our exploration is consistent with stabilizing selection on polygenic metabolic phenotypes as an important engine of genome-wide relative population divergence and incipient speciation in our study system, we note that it is exceedingly difficult to firmly exclude other scenarios.", "doi": "10.1002/ece3.9440", "pmid": "36311399", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9608792"}, {"db": "pii", "key": "ECE39440"}], "notes": [], "created": "2022-11-29T09:34:26.276Z", "modified": "2022-11-29T09:34:26.313Z"}, {"entity": "publication", "iuid": "13e8aeb7d3f94c85981ecd78c1ad217a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/13e8aeb7d3f94c85981ecd78c1ad217a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/13e8aeb7d3f94c85981ecd78c1ad217a"}}, "title": "Loss of SNAI1 induces cellular plasticity in invasive triple-negative breast cancer cells.", "authors": [{"family": "Tsirigoti", "given": "Chrysoula", "initials": "C"}, {"family": "Ali", "given": "Mohamad Moustafa", "initials": "MM", "orcid": "0000-0002-4902-0550", "researcher": {"href": "https://publications.scilifelab.se/researcher/780c944670ff4d7489410895569ac257.json"}}, {"family": "Maturi", "given": "Varun", "initials": "V", "orcid": "0000-0003-1177-0839", "researcher": {"href": "https://publications.scilifelab.se/researcher/0bd84539b66b4e79964ec0330f1aefd7.json"}}, {"family": "Heldin", "given": "Carl-Henrik", "initials": "CH", "orcid": "0000-0002-9508-896X", "researcher": {"href": "https://publications.scilifelab.se/researcher/f705f7c509904a1db721ace2267ca48f.json"}}, {"family": "Moustakas", "given": "Aristidis", "initials": "A", "orcid": "0000-0001-9131-3827", "researcher": {"href": "https://publications.scilifelab.se/researcher/6c1626d991f3485e81232db174537e6d.json"}}], "type": "journal article", "published": "2022-09-28", "journal": {"title": "Cell Death Dis", "issn": "2041-4889", "volume": "13", "issue": "9", "pages": "832", "issn-l": "2041-4889"}, "abstract": "The transcription factor SNAI1 mediates epithelial-mesenchymal transition, fibroblast activation and controls inter-tissue migration. High SNAI1 expression characterizes metastatic triple-negative breast carcinomas, and its knockout by CRISPR/Cas9 uncovered an epithelio-mesenchymal phenotype accompanied by reduced signaling by the cytokine TGF\u03b2. The SNAI1 knockout cells exhibited plasticity in differentiation, drifting towards the luminal phenotype, gained stemness potential and could differentiate into acinar mammospheres in 3D culture. Loss of SNAI1 de-repressed the transcription factor FOXA1, a pioneering factor of mammary luminal progenitors. FOXA1 induced a specific gene program, including the androgen receptor (AR). Inhibiting AR via a specific antagonist regenerated the basal phenotype and blocked acinar differentiation. Thus, loss of SNAI1 in the context of triple-negative breast carcinoma cells promotes an intermediary luminal progenitor phenotype that gains differentiation plasticity based on the dual transcriptional action of FOXA1 and AR. This function of SNAI1 provides means to separate cell invasiveness from progenitor cell de-differentiation as independent cellular programs.", "doi": "10.1038/s41419-022-05280-z", "pmid": "36171192", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9519755"}, {"db": "pii", "key": "10.1038/s41419-022-05280-z"}], "notes": [], "created": "2022-11-29T09:54:47.071Z", "modified": "2024-01-16T13:48:34.962Z"}, {"entity": "publication", "iuid": "af3c88c82b9847cf8eb6003405006660", "links": {"self": {"href": "https://publications.scilifelab.se/publication/af3c88c82b9847cf8eb6003405006660.json"}, "display": {"href": "https://publications.scilifelab.se/publication/af3c88c82b9847cf8eb6003405006660"}}, "title": "A novel neo-sex chromosome in Sylvietta brachyura (Macrosphenidae) adds to the extraordinary avian sex chromosome diversity among Sylvioidea songbirds.", "authors": [{"family": "Sigeman", "given": "Hanna", "initials": "H", "orcid": "0000-0002-1457-4174", "researcher": {"href": "https://publications.scilifelab.se/researcher/f75fea472d1d495a92228c50bd63891e.json"}}, {"family": "Zhang", "given": "Hongkai", "initials": "H", "orcid": "0000-0001-7371-9612", "researcher": {"href": "https://publications.scilifelab.se/researcher/33b4db2c681b400c9106f8d27b6fb714.json"}}, {"family": "Ali Abed", "given": "Salwan", "initials": "S", "orcid": "0000-0001-7347-3843", "researcher": {"href": "https://publications.scilifelab.se/researcher/df39e4e79acb469aa3d842fbb764b888.json"}}, {"family": "Hansson", "given": "Bengt", "initials": "B", "orcid": "0000-0001-6694-8169", "researcher": {"href": "https://publications.scilifelab.se/researcher/01f0144e207c41dcbc4d5aec68690e4b.json"}}], "type": "journal article", "published": "2022-09-26", "journal": {"title": "J. Evol. Biol.", "issn": "1420-9101", "issn-l": "1010-061X"}, "abstract": "We report the discovery of a novel neo-sex chromosome in an African warbler, Sylvietta brachyura (northern crombec; Macrosphenidae). This species is part of the Sylvioidea superfamily, where four separate autosome-sex chromosome translocation events have previously been discovered via comparative genomics of 11 of the 22 families in this clade. Our discovery here resulted from analyses of genomic data of single species-representatives from three additional Sylvioidea families (Macrosphenidae, Pycnonotidae and Leiothrichidae). In all three species, we confirmed the translocation of a part of chromosome 4A to the sex chromosomes, which originated basally in Sylvioidea. In S. brachyura, we found that a part of chromosome 8 has been translocated to the sex chromosomes, forming a unique neo-sex chromosome in this lineage. Furthermore, the non-recombining part of 4A in S. brachyura is smaller than in other Sylvioidea species, which suggests that recombination continued along this region after the fusion event in the Sylvioidea ancestor. These findings reveal additional sex chromosome diversity among the Sylvioidea, where five separate translocation events are now confirmed.", "doi": "10.1111/jeb.14096", "pmid": "36156325", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "RefSeq", "key": "GCF_003957565.1"}], "notes": [], "created": "2022-11-29T09:53:49.879Z", "modified": "2024-01-16T13:48:34.983Z"}, {"entity": "publication", "iuid": "dc75e1039071444c97665eeac886fd6a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/dc75e1039071444c97665eeac886fd6a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/dc75e1039071444c97665eeac886fd6a"}}, "title": "Expression Levels of hgcAB Genes and Mercury Availability Jointly Explain Methylmercury Formation in Stratified Brackish Waters.", "authors": [{"family": "Capo", "given": "Eric", "initials": "E", "orcid": "0000-0001-9143-7061", "researcher": {"href": "https://publications.scilifelab.se/researcher/a4017e9c8167487b882ee2d045d96494.json"}}, {"family": "Feng", "given": "Caiyan", "initials": "C"}, {"family": "Bravo", "given": "Andrea G", "initials": "AG"}, {"family": "Bertilsson", "given": "Stefan", "initials": "S"}, {"family": "Soerensen", "given": "Anne L", "initials": "AL", "orcid": "0000-0002-8490-8600", "researcher": {"href": "https://publications.scilifelab.se/researcher/80c5602b03254dd6a9bee71d0429b678.json"}}, {"family": "Pinhassi", "given": "Jarone", "initials": "J"}, {"family": "Buck", "given": "Moritz", "initials": "M"}, {"family": "Karlsson", "given": "Camilla", "initials": "C"}, {"family": "Hawkes", "given": "Jeffrey", "initials": "J", "orcid": "0000-0003-0664-2242", "researcher": {"href": "https://publications.scilifelab.se/researcher/cf1580e588fb405b95b1690038d93914.json"}}, {"family": "Bj\u00f6rn", "given": "Erik", "initials": "E", "orcid": "0000-0001-9570-8738", "researcher": {"href": "https://publications.scilifelab.se/researcher/d52d4c83dda84cea9e018199a8cfc304.json"}}], "type": "journal article", "published": "2022-09-20", "journal": {"title": "Environ. Sci. Technol.", "issn": "1520-5851", "issn-l": "0013-936X", "volume": "56", "issue": "18", "pages": "13119-13130"}, "abstract": "Neurotoxic methylmercury (MeHg) is formed by microbial methylation of inorganic divalent Hg (HgII) and constitutes severe environmental and human health risks. The methylation is enabled by hgcA and hgcB genes, but it is not known if the associated molecular-level processes are rate-limiting or enable accurate prediction of MeHg formation in nature. In this study, we investigated the relationships between hgc genes and MeHg across redox-stratified water columns in the brackish Baltic Sea. We showed, for the first time, that hgc transcript abundance and the concentration of dissolved HgII-sulfide species were strong predictors of both the HgII methylation rate and MeHg concentration, implying their roles as principal joint drivers of MeHg formation in these systems. Additionally, we characterized the metabolic capacities of hgc+ microorganisms by reconstructing their genomes from metagenomes (i.e., hgc+ MAGs), which highlighted the versatility of putative HgII methylators in the water column of the Baltic Sea. In establishing relationships between hgc transcripts and the HgII methylation rate, we advance the fundamental understanding of mechanistic principles governing MeHg formation in nature and enable refined predictions of MeHg levels in coastal seas in response to the accelerating spread of oxygen-deficient zones.", "doi": "10.1021/acs.est.2c03784", "pmid": "36069707", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9494745"}], "notes": [], "created": "2022-11-29T09:47:11.811Z", "modified": "2023-10-04T10:56:50.418Z"}, {"entity": "publication", "iuid": "fee6a328f53e4013a6ce31dfa9144540", "links": {"self": {"href": "https://publications.scilifelab.se/publication/fee6a328f53e4013a6ce31dfa9144540.json"}, "display": {"href": "https://publications.scilifelab.se/publication/fee6a328f53e4013a6ce31dfa9144540"}}, "title": "Congenital tremor and splay leg in piglets - insights into the virome, local cytokine response, and histology.", "authors": [{"family": "Stenberg", "given": "Hedvig", "initials": "H"}, {"family": "Hellman", "given": "Stina", "initials": "S"}, {"family": "Lindstr\u00f6m", "given": "Lisa", "initials": "L"}, {"family": "Jacobson", "given": "Magdalena", "initials": "M"}, {"family": "Fossum", "given": "Caroline", "initials": "C"}, {"family": "Hayer", "given": "Juliette", "initials": "J"}, {"family": "Malmberg", "given": "Maja", "initials": "M"}], "type": "journal article", "published": "2022-09-16", "journal": {"title": "BMC Vet Res", "issn": "1746-6148", "issn-l": null, "volume": "18", "issue": "1", "pages": "348"}, "abstract": "Atypical porcine pestivirus (APPV) is a neurotropic virus associated with congenital tremor type A-II. A few experimental studies also indicate an association between APPV and splay leg. The overarching aim of the present study was to provide insights into the virome, local cytokine response, and histology of the CNS in piglets with signs of congenital tremor or splay leg.\r\n\r\nCharacterization of the cytokine profile and virome of the brain in piglets with signs of congenital tremor revealed an APPV-associated upregulation of Stimulator of interferon genes (STING). The upregulation of STING was associated with an increased expression of the gene encoding IFN-\u03b1 but no differential expression was recorded for the genes encoding CXCL8, IFN-\u03b2, IFN-\u03b3, IL-1\u03b2, IL-6, or IL-10. No viral agents or cytokine upregulation could be detected in the spinal cord of piglets with signs of splay leg or in the brain of piglets without an APPV-infection. The histopathological examination showed no lesions in the CNS that could be attributed to the APPV-infection, as no difference between sick and healthy piglets could be seen.\r\n\r\nThe results from this study provide evidence of an APPV-induced antiviral cytokine response but found no lesions related to the infection nor any support for a common causative agent.", "doi": "10.1186/s12917-022-03443-w", "pmid": "36109741", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Short read": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support and Infrastructure": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1186/s12917-022-03443-w"}, {"db": "pmc", "key": "PMC9479355"}], "notes": [], "created": "2022-09-23T08:16:31.989Z", "modified": "2024-01-16T13:48:35.004Z"}, {"entity": "publication", "iuid": "5da648ba2e464fc99db858358c6e79e7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5da648ba2e464fc99db858358c6e79e7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5da648ba2e464fc99db858358c6e79e7"}}, "title": "Genomic evidence that a sexually selected trait captures genome-wide variation and facilitates the purging of genetic load.", "authors": [{"family": "Parrett", "given": "Jonathan M", "initials": "JM", "orcid": "0000-0001-9141-1371", "researcher": {"href": "https://publications.scilifelab.se/researcher/74066c0ef87340f6b9f8479fd6fafdb1.json"}}, {"family": "Chmielewski", "given": "Sebastian", "initials": "S", "orcid": "0000-0002-0719-4499", "researcher": {"href": "https://publications.scilifelab.se/researcher/0d42c65e47fc4ffd844b997ed143960f.json"}}, {"family": "Aydogdu", "given": "Eylem", "initials": "E"}, {"family": "\u0141ukasiewicz", "given": "Aleksandra", "initials": "A", "orcid": "0000-0001-8038-8700", "researcher": {"href": "https://publications.scilifelab.se/researcher/6e82002ce08541e187e286c0ab0d82c4.json"}}, {"family": "Rombauts", "given": "Stephane", "initials": "S", "orcid": "0000-0002-3985-4981", "researcher": {"href": "https://publications.scilifelab.se/researcher/78f2ecf95c174f0e927996e186c21f48.json"}}, {"family": "Szubert-Kruszy\u0144ska", "given": "Agnieszka", "initials": "A"}, {"family": "Babik", "given": "Wies\u0142aw", "initials": "W", "orcid": "0000-0002-1698-6615", "researcher": {"href": "https://publications.scilifelab.se/researcher/b0314840d7fd469bbef8d1cbf05a830f.json"}}, {"family": "Konczal", "given": "Mateusz", "initials": "M", "orcid": "0000-0002-7691-8075", "researcher": {"href": "https://publications.scilifelab.se/researcher/cbd64205c1674cd5999b83f2e1032d95.json"}}, {"family": "Radwan", "given": "Jacek", "initials": "J", "orcid": "0000-0001-8503-5701", "researcher": {"href": "https://publications.scilifelab.se/researcher/3b62da0fe50f4c0e80bca59e881ed63c.json"}}], "type": "journal article", "published": "2022-09-00", "journal": {"title": "Nat Ecol Evol", "issn": "2397-334X", "volume": "6", "issue": "9", "pages": "1330-1342", "issn-l": "2397-334X"}, "abstract": "The evolution of costly traits such as deer antlers and peacock trains, which drove the formation of Darwinian sexual selection theory, has been suggested to both reflect and affect patterns of genetic variance across the genome, but direct tests are missing. Here, we used an evolve and resequence approach to reveal patterns of genome-wide diversity associated with the expression of a sexually selected weapon that is dimorphic among males of the bulb mite, Rhizoglyphus robini. Populations selected for the weapon showed reduced genome-wide diversity compared to populations selected against the weapon, particularly in terms of the number of segregating non-synonymous positions, indicating enhanced purifying selection. This increased purifying selection reduced inbreeding depression, but outbred female fitness did not improve, possibly because any benefits were offset by increased sexual antagonism. Most single nucleotide polymorphisms (SNPs) that consistently diverged in response to selection were initially rare and overrepresented in exons, and enriched in regions under balancing or relaxed selection, suggesting they are probably moderately deleterious variants. These diverged SNPs were scattered across the genome, further demonstrating that selection for or against the weapon and the associated changes to the mating system can both capture and influence genome-wide variation.", "doi": "10.1038/s41559-022-01816-w", "pmid": "35851852", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41559-022-01816-w"}, {"db": "Dryad", "key": "10.5061/dryad.ncjsxksxg"}], "notes": [], "created": "2022-11-29T09:21:13.426Z", "modified": "2022-11-29T09:21:13.647Z"}, {"entity": "publication", "iuid": "75a1fcfdbb4d43ac9dab3cba90b8ece5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/75a1fcfdbb4d43ac9dab3cba90b8ece5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/75a1fcfdbb4d43ac9dab3cba90b8ece5"}}, "title": "Genomic and gene expression associations to morphology of a sexual ornament in the chicken.", "authors": [{"family": "Bakovic", "given": "Vid", "initials": "V", "orcid": "0000-0001-9506-5816", "researcher": {"href": "https://publications.scilifelab.se/researcher/613026a563c543c794e0094c0239920b.json"}}, {"family": "H\u00f6glund", "given": "Andrey", "initials": "A"}, {"family": "Martin Cerezo", "given": "Maria Luisa", "initials": "ML", "orcid": "0000-0003-3952-2853", "researcher": {"href": "https://publications.scilifelab.se/researcher/53e025902fc04455ad70a33ba146c003.json"}}, {"family": "Henriksen", "given": "Rie", "initials": "R"}, {"family": "Wright", "given": "Dominic", "initials": "D", "orcid": "0000-0003-2329-2635", "researcher": {"href": "https://publications.scilifelab.se/researcher/6447b896ea3b453ab10136b5f44ae241.json"}}], "type": "journal article", "published": "2022-08-25", "journal": {"title": "G3 (Bethesda)", "issn": "2160-1836", "issn-l": "2160-1836", "volume": "12", "issue": "9", "pages": "jkac174"}, "abstract": "How sexual selection affects the genome ultimately relies on the strength and type of selection, and the genetic architecture of the involved traits. While associating genotype with phenotype often utilizes standard trait morphology, trait representations in morphospace using geometric morphometric approaches receive less focus in this regard. Here, we identify genetic associations to a sexual ornament, the comb, in the chicken system (Gallus gallus). Our approach combined genome-wide genotype and gene expression data (>30k genes) with different aspects of comb morphology in an advanced intercross line (F8) generated by crossing a wild-type Red Junglefowl with a domestic breed of chicken (White Leghorn). In total, 10 quantitative trait loci were found associated to various aspects of comb shape and size, while 1,184 expression QTL were found associated to gene expression patterns, among which 98 had overlapping confidence intervals with those of quantitative trait loci. Our results highlight both known genomic regions confirming previous records of a large effect quantitative trait loci associated to comb size, and novel quantitative trait loci associated to comb shape. Genes were considered candidates affecting comb morphology if they were found within both confidence intervals of the underlying quantitative trait loci and eQTL. Overlaps between quantitative trait loci and genome-wide selective sweeps identified in a previous study revealed that only loci associated to comb size may be experiencing on-going selection under domestication.", "doi": "10.1093/g3journal/jkac174", "pmid": "35801935", "labels": {"NGI SNP genotyping": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "6633936"}, {"db": "pmc", "key": "PMC9434260"}], "notes": [], "created": "2022-08-16T13:29:35.931Z", "modified": "2024-01-16T13:48:35.097Z"}, {"entity": "publication", "iuid": "84870ae38812488595d58a590c3f912d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/84870ae38812488595d58a590c3f912d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/84870ae38812488595d58a590c3f912d"}}, "title": "Seasonal dynamics in picocyanobacterial abundance and clade composition at coastal and offshore stations in the Baltic Sea.", "authors": [{"family": "Zufia", "given": "Javier Alegria", "initials": "JA"}, {"family": "Legrand", "given": "Catherine", "initials": "C"}, {"family": "Farnelid", "given": "Hanna", "initials": "H"}], "type": "journal article", "published": "2022-08-22", "journal": {"title": "Sci Rep", "issn": "2045-2322", "issn-l": "2045-2322", "volume": "12", "issue": "1", "pages": "14330"}, "abstract": "Picocyanobacteria (< 2 \u00b5m in diameter) are significant contributors to total phytoplankton biomass. Due to the high diversity within this group, their seasonal dynamics and relationship with environmental parameters, especially in brackish waters, are largely unknown. In this study, the abundance and community composition of phycoerythrin rich picocyanobacteria (PE-SYN) and phycocyanin rich picocyanobacteria (PC-SYN) were monitored at a coastal (K-station) and at an offshore station (LMO; ~ 10 km from land) in the Baltic Sea over three years (2018-2020). Cell abundances of picocyanobacteria correlated positively to temperature and negatively to nitrate (NO3) concentration. While PE-SYN abundance correlated to the presence of nitrogen fixers, PC-SYN abundance was linked to stratification/shallow waters. The picocyanobacterial targeted amplicon sequencing revealed an unprecedented diversity of 2169 picocyanobacterial amplicons sequence variants (ASVs). A unique assemblage of distinct picocyanobacterial clades across seasons was identified. Clade A/B dominated the picocyanobacterial community, except during summer when low NO3, high phosphate (PO4) concentrations and warm temperatures promoted S5.2 dominance. This study, providing multiyear data, links picocyanobacterial populations to environmental parameters. The difference in the response of the two functional groups and clades underscore the need for further high-resolution studies to understand their role in the ecosystem.", "doi": "10.1038/s41598-022-18454-8", "pmid": "35995823", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9395346"}, {"db": "pii", "key": "10.1038/s41598-022-18454-8"}], "notes": [], "created": "2022-11-29T09:33:46.926Z", "modified": "2024-01-16T13:48:35.127Z"}, {"entity": "publication", "iuid": "c8fc3fc8849a44069ad6865663765a11", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c8fc3fc8849a44069ad6865663765a11.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c8fc3fc8849a44069ad6865663765a11"}}, "title": "Characterization of hemocytes and hematopoietic cells of a freshwater crayfish based on single-cell transcriptome analysis.", "authors": [{"family": "S\u00f6derh\u00e4ll", "given": "Irene", "initials": "I"}, {"family": "Fasterius", "given": "Erik", "initials": "E"}, {"family": "Ekblom", "given": "Charlotta", "initials": "C"}, {"family": "S\u00f6derh\u00e4ll", "given": "Kenneth", "initials": "K"}], "type": "journal article", "published": "2022-08-19", "journal": {"title": "iScience", "issn": "2589-0042", "issn-l": "2589-0042", "volume": "25", "issue": "8", "pages": "104850"}, "abstract": "Crustaceans constitute a species-rich and ecologically important animal group, and their circulating blood cells (hemocytes) are of critical importance in immunity as key players in pathogen recognition, phagocytosis, melanization, and antimicrobial defense. To gain a better understanding of the immune responses to different pathogens, it is crucial that we identify different hemocyte subpopulations with different functions and gain a better understanding of how these cells are formed. Here, we performed single-cell RNA sequencing of isolated hematopoietic tissue (HPT) cells and hemocytes from the crayfish Pacifastacus leniusculus to identify hitherto undescribed hemocyte types in the circulation and show that the circulating cells are more diversified than previously recognized. In addition, we discovered cell populations in the HPT with clear precursor characteristics as well as cells involved in iron homeostasis, representing a previously undiscovered cell type. These findings may improve our understanding of hematopoietic stem cell regulation in crustaceans and other animals.", "doi": "10.1016/j.isci.2022.104850", "pmid": "35996577", "labels": {"Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "NGI Single cell": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC9391574"}, {"db": "pii", "key": "S2589-0042(22)01122-1"}], "notes": [], "created": "2022-08-22T07:54:42.628Z", "modified": "2024-01-16T13:48:35.160Z"}, {"entity": "publication", "iuid": "fa2c051345524172bdb5e411f318fc00", "links": {"self": {"href": "https://publications.scilifelab.se/publication/fa2c051345524172bdb5e411f318fc00.json"}, "display": {"href": "https://publications.scilifelab.se/publication/fa2c051345524172bdb5e411f318fc00"}}, "title": "Ecosystem size-induced environmental fluctuations affect the temporal dynamics of community assembly mechanisms.", "authors": [{"family": "Bier", "given": "Raven L", "initials": "RL"}, {"family": "Vass", "given": "M\u00e1t\u00e9", "initials": "M", "orcid": "0000-0003-0718-7659", "researcher": {"href": "https://publications.scilifelab.se/researcher/6fed30af96e540269edcb565cb34bc39.json"}}, {"family": "Sz\u00e9kely", "given": "Anna J", "initials": "AJ", "orcid": "0000-0001-8063-7156", "researcher": {"href": "https://publications.scilifelab.se/researcher/c9b2d69cfd6a4f41a978b38ddf66c8d5.json"}}, {"family": "Langenheder", "given": "Silke", "initials": "S", "orcid": "0000-0002-5245-9935", "researcher": {"href": "https://publications.scilifelab.se/researcher/efa9e8f2174a4c7cb903b0f9b895a183.json"}}], "type": "journal article", "published": "2022-08-18", "journal": {"title": "ISME J", "issn": "1751-7370", "issn-l": "1751-7362", "volume": "16", "issue": "12", "pages": "2635-2643"}, "abstract": "Understanding processes that determine community membership and abundance is important for many fields from theoretical community ecology to conservation. However, spatial community studies are often conducted only at a single timepoint despite the known influence of temporal variability on community assembly processes. Here we used a spatiotemporal study to determine how environmental fluctuation differences induced by mesocosm volumes (larger volumes were more stable) influence assembly processes of aquatic bacterial metacommunities along a press disturbance gradient. By combining path analysis and network approaches, we found mesocosm size categories had distinct relative influences of assembly process and environmental factors that determined spatiotemporal bacterial community composition, including dispersal and species sorting by conductivity. These processes depended on, but were not affected proportionately by, mesocosm size. Low fluctuation, large mesocosms primarily developed through the interplay of species sorting that became more important over time and transient priority effects as evidenced by more time-delayed associations. High fluctuation, small mesocosms had regular disruptions to species sorting and greater importance of ecological drift and dispersal limitation indicated by lower richness and higher taxa replacement. Together, these results emphasize that environmental fluctuations influence ecosystems over time and its impacts are modified by biotic properties intrinsic to ecosystem size.", "doi": "10.1038/s41396-022-01286-9", "pmid": "35982230", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41396-022-01286-9"}], "notes": [], "created": "2022-11-09T15:56:21.456Z", "modified": "2024-01-16T13:48:35.168Z"}, {"entity": "publication", "iuid": "26915f1cd4ba474aac0a8a591527744e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/26915f1cd4ba474aac0a8a591527744e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/26915f1cd4ba474aac0a8a591527744e"}}, "title": "Isolated Grauer's gorilla populations differ in diet and gut microbiome.", "authors": [{"family": "Michel", "given": "Alice", "initials": "A", "orcid": "0000-0002-0273-4097", "researcher": {"href": "https://publications.scilifelab.se/researcher/5300682d3a4e486d9403e970ca82f8e7.json"}}, {"family": "Minocher", "given": "Riana", "initials": "R"}, {"family": "Niehoff", "given": "Peter-Philip", "initials": "PP"}, {"family": "Li", "given": "Yuhong", "initials": "Y"}, {"family": "Nota", "given": "Kevin", "initials": "K"}, {"family": "Gadhvi", "given": "Maya A", "initials": "MA"}, {"family": "Su", "given": "Jiancheng", "initials": "J"}, {"family": "Iyer", "given": "Neetha", "initials": "N"}, {"family": "Porter", "given": "Amy", "initials": "A"}, {"family": "Ngobobo-As-Ibungu", "given": "Urbain", "initials": "U"}, {"family": "Binyinyi", "given": "Escobar", "initials": "E"}, {"family": "Nishuli Pekeyake", "given": "Radar", "initials": "R"}, {"family": "Parducci", "given": "Laura", "initials": "L"}, {"family": "Caillaud", "given": "Damien", "initials": "D"}, {"family": "Guschanski", "given": "Katerina", "initials": "K", "orcid": "0000-0002-8493-5457", "researcher": {"href": "https://publications.scilifelab.se/researcher/84b8b0757f02429b9bd419acb42ab6a3.json"}}], "type": "journal article", "published": "2022-08-17", "journal": {"title": "Mol. Ecol.", "issn": "1365-294X", "issn-l": "0962-1083"}, "abstract": "The animal gut microbiome has been implicated in a number of key biological processes, ranging from digestion to behaviour, and has also been suggested to facilitate local adaptation. Yet studies in wild animals rarely compare multiple populations that differ ecologically, which is the level at which local adaptation may occur. Further, few studies simultaneously characterize diet and gut microbiome from the same sample, despite their probable interdependence. Here, we investigate the interplay between diet and gut microbiome in three geographically isolated populations of the critically endangered Grauer's gorilla (Gorilla beringei graueri), which we show to be genetically differentiated. We find population- and social group-specific dietary and gut microbial profiles and covariation between diet and gut microbiome, despite the presence of core microbial taxa. There was no detectable effect of age, and only marginal effects of sex and genetic relatedness on the microbiome. Diet differed considerably across populations, with the high-altitude population consuming a lower diversity of plants compared to low-altitude populations, consistent with plant availability constraining dietary choices. The observed pattern of covariation between diet and gut microbiome is probably a result of long-term social and environmental factors. Our study suggests that the gut microbiome is sufficiently plastic to support flexible food selection and hence contribute to local adaptation.", "doi": "10.1111/mec.16663", "pmid": "35976262", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2022-11-29T09:59:56.243Z", "modified": "2024-01-16T13:48:35.191Z"}, {"entity": "publication", "iuid": "83170949a3664c28be863b7ae471fc06", "links": {"self": {"href": "https://publications.scilifelab.se/publication/83170949a3664c28be863b7ae471fc06.json"}, "display": {"href": "https://publications.scilifelab.se/publication/83170949a3664c28be863b7ae471fc06"}}, "title": "Nuclear-specific gene expression in heterokaryons of the filamentous ascomycete Neurospora tetrasperma.", "authors": [{"family": "Meunier", "given": "C\u00e9cile", "initials": "C"}, {"family": "Darolti", "given": "Iulia", "initials": "I"}, {"family": "Reimeg\u00e5rd", "given": "Johan", "initials": "J"}, {"family": "Mank", "given": "Judith E", "initials": "JE", "orcid": "0000-0002-2450-513X", "researcher": {"href": "https://publications.scilifelab.se/researcher/42f3e1ac3beb4d9cb0c6687ec7d94c68.json"}}, {"family": "Johannesson", "given": "Hanna", "initials": "H", "orcid": "0000-0001-6359-9856", "researcher": {"href": "https://publications.scilifelab.se/researcher/36e8fe278e01470e8cddaaccc5dad596.json"}}], "type": "journal article", "published": "2022-08-10", "journal": {"title": "Proc. Biol. Sci.", "issn": "1471-2954", "issn-l": "0962-8452", "volume": "289", "issue": "1980", "pages": "20220971"}, "abstract": "Heterokaryosis is a system in which genetically distinct nuclei coexist within the same cytoplasm. While heterokaryosis dominates the life cycle of many fungal species, the transcriptomic changes associated with the transition from homokaryosis to heterokaryosis is not well understood. Here, we analyse gene expression profiles of homokaryons and heterokaryons from three phylogenetically and reproductively isolated lineages of the filamentous ascomycete Neurospora tetrasperma. We show that heterokaryons are transcriptionally distinct from homokaryons in the sexual stage of development, but not in the vegetative stage, suggesting that the phenotypic switch to fertility in heterokaryons is associated with major changes in gene expression. Heterokaryon expression is predominantly defined by additive effects of its two nuclear components. Furthermore, allele-specific expression analysis of heterokaryons with varying nuclear ratios show patterns of expression ratios strongly dependent on nuclear ratios in the vegetative stage. By contrast, in the sexual stage, strong deviations of expression ratios indicate a co-regulation of nuclear gene expression in all three lineages. Taken together, our results show two levels of expression control: additive effects suggest a nuclear level of expression, whereas co-regulation of gene expression indicate a heterokaryon level of control.", "doi": "10.1098/rspb.2022.0971", "pmid": "35946150", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC9363985"}], "notes": [], "created": "2022-08-12T11:13:21.820Z", "modified": "2024-01-16T13:48:35.404Z"}, {"entity": "publication", "iuid": "4a28dd5860e7477c82ea19ebbdb98820", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4a28dd5860e7477c82ea19ebbdb98820.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4a28dd5860e7477c82ea19ebbdb98820"}}, "title": "Identification and functional characterization of a novel susceptibility locus for small vessel vasculitis with MPO-ANCA.", "authors": [{"family": "Dahlqvist", "given": "Johanna", "initials": "J", "orcid": "0000-0002-6283-644X", "researcher": {"href": "https://publications.scilifelab.se/researcher/8fb2ab2d83b6437f9918f330e5fb81b2.json"}}, {"family": "Ekman", "given": "Diana", "initials": "D"}, {"family": "Sennblad", "given": "Bengt", "initials": "B"}, {"family": "Kozyrev", "given": "Sergey V", "initials": "SV"}, {"family": "Nordin", "given": "Jessika", "initials": "J"}, {"family": "Karlsson", "given": "\u00c5sa", "initials": "\u00c5"}, {"family": "Meadows", "given": "Jennifer R S", "initials": "JRS"}, {"family": "Hellbacher", "given": "Erik", "initials": "E"}, {"family": "Rantap\u00e4\u00e4-Dahlqvist", "given": "Solbritt", "initials": "S", "orcid": "0000-0001-8259-3863", "researcher": {"href": "https://publications.scilifelab.se/researcher/dfca4bfdcf3946fda64397d3b7debc59.json"}}, {"family": "Berglin", "given": "Ewa", "initials": "E"}, {"family": "Stegmayr", "given": "Bernd", "initials": "B"}, {"family": "Baslund", "given": "Bo", "initials": "B"}, {"family": "Palm", "given": "\u00d8yvind", "initials": "\u00d8"}, {"family": "Haukeland", "given": "Hilde", "initials": "H"}, {"family": "Gunnarsson", "given": "Iva", "initials": "I"}, {"family": "Bruchfeld", "given": "Annette", "initials": "A", "orcid": "0000-0002-9752-9941", "researcher": {"href": "https://publications.scilifelab.se/researcher/dc6ee3e8a4124c5f8d6506ab762949ae.json"}}, {"family": "Segelmark", "given": "M\u00e5rten", "initials": "M"}, {"family": "Ohlsson", "given": "Sophie", "initials": "S"}, {"family": "Mohammad", "given": "Aladdin J", "initials": "AJ", "orcid": "0000-0002-7169-6936", "researcher": {"href": "https://publications.scilifelab.se/researcher/d7010c3f5b91415dbc26c87d6a923f68.json"}}, {"family": "Sv\u00e4rd", "given": "Anna", "initials": "A"}, {"family": "Pullerits", "given": "Rille", "initials": "R"}, {"family": "Herlitz", "given": "Hans", "initials": "H"}, {"family": "S\u00f6derbergh", "given": "Annika", "initials": "A"}, {"family": "Rosengren Pielberg", "given": "Gerli", "initials": "G"}, {"family": "Hultin Rosenberg", "given": "Lina", "initials": "L"}, {"family": "Bianchi", "given": "Matteo", "initials": "M"}, {"family": "Mur\u00e9n", "given": "Eva", "initials": "E"}, {"family": "Omdal", "given": "Roald", "initials": "R"}, {"family": "Jonsson", "given": "Roland", "initials": "R"}, {"family": "Eloranta", "given": "Maija-Leena", "initials": "ML"}, {"family": "R\u00f6nnblom", "given": "Lars", "initials": "L"}, {"family": "S\u00f6derkvist", "given": "Peter", "initials": "P"}, {"family": "Knight", "given": "Ann", "initials": "A"}, {"family": "Eriksson", "given": "Per", "initials": "P"}, {"family": "Lindblad-Toh", "given": "Kerstin", "initials": "K"}], "type": "journal article", "published": "2022-08-03", "journal": {"title": "Rheumatology (Oxford)", "issn": "1462-0332", "volume": "61", "issue": "8", "pages": "3461-3470", "issn-l": "1462-0324"}, "abstract": "To identify and characterize genetic loci associated with the risk of developing ANCA-associated vasculitides (AAV).\n\nGenetic association analyses were performed after Illumina sequencing of 1853 genes and subsequent replication with genotyping of selected single nucleotide polymorphisms in a total cohort of 1110 Scandinavian cases with granulomatosis with polyangiitis or microscopic polyangiitis, and 1589 controls. A novel AAV-associated single nucleotide polymorphism was analysed for allele-specific effects on gene expression using luciferase reporter assay.\n\nPR3-ANCA+ AAV was significantly associated with two independent loci in the HLA-DPB1/HLA-DPA1 region [rs1042335, P = 6.3 \u00d7 10-61, odds ratio (OR) 0.10; rs9277341, P = 1.5 \u00d7 10-44, OR 0.22] and with rs28929474 in the SERPINA1 gene (P = 2.7 \u00d7 10-10, OR 2.9). MPO-ANCA+ AAV was significantly associated with the HLA-DQB1/HLA-DQA2 locus (rs9274619, P = 5.4 \u00d7 10-25, OR 3.7) and with a rare variant in the BACH2 gene (rs78275221, P = 7.9 \u00d7 10-7, OR 3.0), the latter a novel susceptibility locus for MPO-ANCA+ granulomatosis with polyangiitis/microscopic polyangiitis. The rs78275221-A risk allele reduced luciferase gene expression in endothelial cells, specifically, as compared with the non-risk allele.\n\nWe identified a novel susceptibility locus for MPO-ANCA+ AAV and propose that the associated variant is of mechanistic importance, exerting a regulatory function on gene expression in specific cell types.", "doi": "10.1093/rheumatology/keab912", "pmid": "34888651", "labels": {"Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "NGI SNP genotyping": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC9348767"}, {"db": "pii", "key": "6458341"}], "notes": [], "created": "2021-12-16T12:04:03.431Z", "modified": "2024-01-16T13:48:35.466Z"}, {"entity": "publication", "iuid": "925dfb57c60840669f1589754cd95335", "links": {"self": {"href": "https://publications.scilifelab.se/publication/925dfb57c60840669f1589754cd95335.json"}, "display": {"href": "https://publications.scilifelab.se/publication/925dfb57c60840669f1589754cd95335"}}, "title": "A relationship between phages and organic carbon in wastewater treatment plant effluents.", "authors": [{"family": "Modin", "given": "Oskar", "initials": "O"}, {"family": "Fuad", "given": "Nafis", "initials": "N"}, {"family": "Abadikhah", "given": "Marie", "initials": "M"}, {"family": "I'Ons", "given": "David", "initials": "D"}, {"family": "Ossiansson", "given": "Elin", "initials": "E"}, {"family": "Gustavsson", "given": "David J I", "initials": "DJI"}, {"family": "Edefell", "given": "Ellen", "initials": "E"}, {"family": "Suarez", "given": "Carolina", "initials": "C"}, {"family": "Persson", "given": "Frank", "initials": "F"}, {"family": "Wil\u00e9n", "given": "Britt-Marie", "initials": "BM"}], "type": "journal article", "published": "2022-08-01", "journal": {"title": "Water Res X", "issn": "2589-9147", "volume": "16", "pages": "100146", "issn-l": null}, "abstract": "With stringent effluent requirements and the implementation of new processes for micropollutant removal, it is increasingly important for wastewater treatment plants (WWTPs) to understand the factors affecting effluent quality. Phages (viruses infecting prokaryotes) are abundant in the biological treatment processes. They can contribute to organic carbon in the treated effluent both because they are organic in nature and occur in the effluent and because they cause lysis of microorganisms. Today very little is known about the effects of phages on effluent quality. The goal of this study was, therefore, to determine the relationship between phages and organic carbon in WWTP effluents. We also examined the diversity, taxonomy, and host-association of DNA phages using metagenomics. Effluent samples were collected from four WWTPs treating municipal wastewater. Significant differences in both organic carbon and virus-like particle concentrations were observed between the plants and there was a linear relationship between the two parameters. The phage communities were diverse with many members being taxonomically unclassified. Putative hosts were dominated by bacteria known to be abundant in activated sludge systems such as Comamonadaceae. The composition of phages differed between the WWTPs, suggesting that local conditions shape the communities. Overall, our findings suggest that the abundance and composition of phages are related to effluent quality. Thus, there is a need for further research clarifying the association between phage dynamics and WWTP function.", "doi": "10.1016/j.wroa.2022.100146", "pmid": "35761925", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9233278"}, {"db": "pii", "key": "S2589-9147(22)00016-0"}], "notes": [], "created": "2022-11-29T09:36:29.491Z", "modified": "2024-01-16T13:48:35.500Z"}, {"entity": "publication", "iuid": "034f6544dc3b4fbfb4aa2a0f67d8bcc3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/034f6544dc3b4fbfb4aa2a0f67d8bcc3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/034f6544dc3b4fbfb4aa2a0f67d8bcc3"}}, "title": "Human adaptation to arsenic in Bolivians living in the Andes.", "authors": [{"family": "De Loma", "given": "Jessica", "initials": "J"}, {"family": "Vicente", "given": "M\u00e1rio", "initials": "M"}, {"family": "Tirado", "given": "Noemi", "initials": "N"}, {"family": "Ascui", "given": "Franz", "initials": "F"}, {"family": "Vahter", "given": "Marie", "initials": "M"}, {"family": "Gardon", "given": "Jacques", "initials": "J"}, {"family": "Schlebusch", "given": "Carina M", "initials": "CM"}, {"family": "Broberg", "given": "Karin", "initials": "K"}], "type": "journal article", "published": "2022-08-00", "journal": {"title": "Chemosphere", "issn": "1879-1298", "volume": "301", "pages": "134764", "issn-l": "0045-6535"}, "abstract": "Humans living in the Andes Mountains have been historically exposed to arsenic from natural sources, including drinking water. Enzymatic methylation of arsenic allows it to be excreted more efficiently by the human body. Adaptation to high-arsenic environments via enhanced methylation and excretion of arsenic was first reported in indigenous women in the Argentinean Andes, but whether adaptation to arsenic is a general phenomenon across native populations from the Andes Mountains remains unclear. Therefore, we evaluated whether adaptation to arsenic has occurred in the Bolivian Andes by studying indigenous groups who belong to the Aymara-Quechua and Uru ethnicities and have lived in the Bolivian Andes for generations. Our population genetics methods, including genome-wide selection scans based on linkage disequilibrium patterns and allele frequency differences, in combination with targeted and whole-genome sequencing and genotype-phenotype association analyses, detected signatures of positive selection near the gene encoding arsenite methyltransferase (AS3MT), the main arsenic methylating enzyme. This was among the strongest selection signals (top 0.5% signals via locus-specific branch length and extended haplotype homozygosity tests) at a genome-wide level in the Bolivian study groups. We found a large haplotype block of 676 kb in the AS3MT region and identified candidate functional variants for further analysis. Moreover, our analyses revealed associations between AS3MT variants and the fraction of mono-methylated arsenic in urine and showed that the Bolivian study groups had the highest frequency of alleles associated with more efficient arsenic metabolism reported so far. Our data support the idea that arsenic exposure has been a driver for human adaptation to tolerate arsenic through more efficient arsenic detoxification in different Andean populations.", "doi": "10.1016/j.chemosphere.2022.134764", "pmid": "35490756", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support and Infrastructure": "Service", "NGI Long read": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pii", "key": "S0045-6535(22)01257-7"}], "notes": [], "created": "2022-06-14T13:16:20.200Z", "modified": "2024-01-16T13:48:35.529Z"}, {"entity": "publication", "iuid": "9711136f1e1945caad4b5ed63968451c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9711136f1e1945caad4b5ed63968451c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9711136f1e1945caad4b5ed63968451c"}}, "title": "Complement C4 Copy Number Variation is Linked to SSA/Ro and SSB/La Autoantibodies in Systemic Inflammatory Autoimmune Diseases.", "authors": [{"family": "Lundtoft", "given": "Christian", "initials": "C"}, {"family": "Pucholt", "given": "Pascal", "initials": "P"}, {"family": "Martin", "given": "Myriam", "initials": "M"}, {"family": "Bianchi", "given": "Matteo", "initials": "M"}, {"family": "Lundstr\u00f6m", "given": "Emeli", "initials": "E"}, {"family": "Eloranta", "given": "Maija-Leena", "initials": "ML"}, {"family": "Sandling", "given": "Johanna K", "initials": "JK"}, {"family": "Sj\u00f6wall", "given": "Christopher", "initials": "C"}, {"family": "J\u00f6nsen", "given": "Andreas", "initials": "A"}, {"family": "Gunnarsson", "given": "Iva", "initials": "I"}, {"family": "Rantap\u00e4\u00e4-Dahlqvist", "given": "Solbritt", "initials": "S"}, {"family": "Bengtsson", "given": "Anders A", "initials": "AA"}, {"family": "Leonard", "given": "Dag", "initials": "D"}, {"family": "Baecklund", "given": "Eva", "initials": "E"}, {"family": "Jonsson", "given": "Roland", "initials": "R"}, {"family": "Hammenfors", "given": "Daniel", "initials": "D"}, {"family": "Forsblad-d'Elia", "given": "Helena", "initials": "H"}, {"family": "Eriksson", "given": "Per", "initials": "P"}, {"family": "Mandl", "given": "Thomas", "initials": "T"}, {"family": "Magnusson Bucher", "given": "Sara", "initials": "S"}, {"family": "Norheim", "given": "Katrine B", "initials": "KB"}, {"family": "Auglaend Johnsen", "given": "Svein Joar", "initials": "SJ"}, {"family": "Omdal", "given": "Roald", "initials": "R"}, {"family": "Kvarnstr\u00f6m", "given": "Marika", "initials": "M"}, {"family": "Wahren-Herlenius", "given": "Marie", "initials": "M"}, {"family": "Notarnicola", "given": "Antonella", "initials": "A"}, {"family": "Andersson", "given": "Helena", "initials": "H"}, {"family": "Molberg", "given": "\u00d8yvind", "initials": "\u00d8"}, {"family": "Diederichsen", "given": "Louise Pyndt", "initials": "LP"}, {"family": "Alml\u00f6f", "given": "Jonas", "initials": "J"}, {"family": "Syv\u00e4nen", "given": "Ann-Christine", "initials": "AC"}, {"family": "Kozyrev", "given": "Sergey V", "initials": "SV"}, {"family": "Lindblad-Toh", "given": "Kerstin", "initials": "K"}, {"family": "DISSECT Consortium", "given": "", "initials": ""}, {"family": "ImmunoArray Development Consortium", "given": "", "initials": ""}, {"family": "Nilsson", "given": "Bo", "initials": "B"}, {"family": "Blom", "given": "Anna M", "initials": "AM"}, {"family": "Lundberg", "given": "Ingrid E", "initials": "IE"}, {"family": "Nordmark", "given": "Gunnel", "initials": "G"}, {"family": "Diaz-Gallo", "given": "Lina Marcela", "initials": "LM"}, {"family": "Svenungsson", "given": "Elisabet", "initials": "E"}, {"family": "R\u00f6nnblom", "given": "Lars", "initials": "L"}], "type": "journal article", "published": "2022-08-00", "journal": {"title": "Arthritis & rheumatology (Hoboken, N.J.)", "issn": "2326-5205", "volume": "74", "issue": "8", "pages": "1440-1450", "issn-l": "2326-5191"}, "abstract": "Copy number variation of the C4 complement components, C4A and C4B, has been associated with systemic inflammatory autoimmune diseases. This study was undertaken to investigate whether C4 copy number variation is connected to the autoimmune repertoire in systemic lupus erythematosus (SLE), primary Sj\u00f6gren's syndrome (SS), or myositis.\n\nUsing targeted DNA sequencing, we determined the copy number and genetic variants of C4 in 2,290 well-characterized Scandinavian patients with SLE, primary SS, or myositis and 1,251 healthy controls.\n\nA prominent relationship was observed between C4A copy number and the presence of SSA/SSB autoantibodies, which was shared between the 3 diseases. The strongest association was detected in patients with autoantibodies against both SSA and SSB and 0 C4A copies when compared to healthy controls (odds ratio [OR] 18.0 [95% confidence interval (95% CI) 10.2-33.3]), whereas a weaker association was seen in patients without SSA/SSB autoantibodies (OR 3.1 [95% CI 1.7-5.5]). The copy number of C4 correlated positively with C4 plasma levels. Further, a common loss-of-function variant in C4A leading to reduced plasma C4 was more prevalent in SLE patients with a low copy number of C4A. Functionally, we showed that absence of C4A reduced the individuals' capacity to deposit C4b on immune complexes.\n\nWe show that a low C4A copy number is more strongly associated with the autoantibody repertoire than with the clinically defined disease entities. These findings may have implications for understanding the etiopathogenetic mechanisms of systemic inflammatory autoimmune diseases and for patient stratification when taking the genetic profile into account.", "doi": "10.1002/art.42122", "pmid": "35315244", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Short read": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9543510"}], "notes": [], "created": "2022-09-06T15:12:48.456Z", "modified": "2024-01-16T13:48:35.558Z"}, {"entity": "publication", "iuid": "9c68253c983c4dd8b33da093c868b3ba", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9c68253c983c4dd8b33da093c868b3ba.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9c68253c983c4dd8b33da093c868b3ba"}}, "title": "A polygenic architecture with habitat-dependent effects underlies ecological differentiation in Silene.", "authors": [{"family": "Gramlich", "given": "Susanne", "initials": "S", "orcid": "0000-0003-1224-0514", "researcher": {"href": "https://publications.scilifelab.se/researcher/49a7319974c04884b77987640ab92994.json"}}, {"family": "Liu", "given": "Xiaodong", "initials": "X", "orcid": "0000-0001-8839-2659", "researcher": {"href": "https://publications.scilifelab.se/researcher/fabce70bd90a4bfe8923d6167e236cff.json"}}, {"family": "Favre", "given": "Adrien", "initials": "A", "orcid": "0000-0001-6132-2992", "researcher": {"href": "https://publications.scilifelab.se/researcher/c6992fd6e45a41ffb6fe4aa2a11e812a.json"}}, {"family": "Buerkle", "given": "C Alex", "initials": "CA", "orcid": "0000-0003-4222-8858", "researcher": {"href": "https://publications.scilifelab.se/researcher/3f8582095a674055b811170719618d0b.json"}}, {"family": "Karrenberg", "given": "Sophie", "initials": "S", "orcid": "0000-0002-7146-588X", "researcher": {"href": "https://publications.scilifelab.se/researcher/3a982636b44f4b93b7ec0bd64e5d6bfb.json"}}], "type": "journal article", "published": "2022-08-00", "journal": {"title": "New Phytol.", "issn": "1469-8137", "issn-l": "0028-646X", "volume": "235", "issue": "4", "pages": "1641-1652"}, "abstract": "Ecological differentiation can drive speciation but it is unclear how the genetic architecture of habitat-dependent fitness contributes to lineage divergence. We investigated the genetic architecture of cumulative flowering, a fitness component, in second-generation hybrids between Silene dioica and Silene latifolia transplanted into the natural habitat of each species. We used reduced-representation sequencing and Bayesian sparse linear mixed models (BSLMMs) to analyze the genetic control of cumulative flowering in each habitat. Our results point to a polygenic architecture of cumulative flowering. Allelic effects were mostly beneficial or deleterious in one habitat and neutral in the other. Positive-effect alleles often were derived from the native species, whereas negative-effect alleles, at other loci, tended to originate from the non-native species. We conclude that ecological differentiation is governed and maintained by many loci with small, habitat-dependent effects consistent with conditional neutrality. This pattern may result from differences in selection targets in the two habitats and from environmentally dependent deleterious load. Our results further suggest that selection for native alleles and against non-native alleles acts as a barrier to gene flow between species.", "doi": "10.1111/nph.18260", "pmid": "35586969", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9544174"}, {"db": "Dryad", "key": "10.5061/dryad.4tmpg4fcn"}], "notes": [], "created": "2022-11-09T15:42:31.295Z", "modified": "2024-01-16T13:48:35.574Z"}, {"entity": "publication", "iuid": "45a51eb4bc4745719bd5194ba4e25e02", "links": {"self": {"href": "https://publications.scilifelab.se/publication/45a51eb4bc4745719bd5194ba4e25e02.json"}, "display": {"href": "https://publications.scilifelab.se/publication/45a51eb4bc4745719bd5194ba4e25e02"}}, "title": "A multi-layer functional genomic analysis to understand noncoding genetic variation in lipids", "authors": [{"family": "Ramdas", "given": "Shweta", "initials": "S", "orcid": "0000-0001-8888-4661", "researcher": {"href": "https://publications.scilifelab.se/researcher/95d26310e5ad4ec1b0ea9d64260c7e93.json"}}, {"family": "Judd", "given": "Jonathan", "initials": "J"}, {"family": "Graham", "given": "Sarah E", "initials": "SE"}, {"family": "Kanoni", "given": "Stavroula", "initials": "S"}, {"family": "Wang", "given": "Yuxuan", "initials": "Y"}, {"family": "Surakka", "given": "Ida", "initials": "I"}, {"family": "Wenz", "given": "Brandon", "initials": "B"}, {"family": "Clarke", "given": "Shoa L", "initials": "SL"}, {"family": "Chesi", "given": "Alessandra", "initials": "A"}, {"family": "Wells", "given": "Andrew", "initials": "A"}, {"family": "Bhatti", "given": "Konain Fatima", "initials": "KF"}, {"family": "Vedantam", "given": "Sailaja", "initials": "S"}, {"family": "Winkler", "given": "Thomas W", "initials": "TW"}, {"family": "Locke", "given": "Adam E", "initials": "AE"}, {"family": "Marouli", "given": "Eirini", "initials": "E"}, {"family": "Zajac", "given": "Greg J M", "initials": "GJM"}, {"family": "Wu", "given": "Kuan Han H", "initials": "KHH"}, {"family": "Ntalla", "given": "Ioanna", "initials": "I"}, {"family": "Hui", "given": "Qin", "initials": "Q"}, {"family": "Klarin", "given": "Derek", "initials": "D"}, {"family": "Hilliard", "given": "Austin T", "initials": "AT"}, {"family": "Wang", "given": "Zeyuan", "initials": "Z"}, {"family": "Xue", "given": "Chao", "initials": "C"}, {"family": "Thorleifsson", "given": "Gudmar", "initials": "G"}, {"family": "Helgadottir", "given": "Anna", "initials": "A"}, {"family": "Gudbjartsson", "given": "Daniel F", "initials": "DF"}, {"family": "Holm", "given": "Hilma", "initials": "H"}, {"family": "Olafsson", "given": "Isleifur", "initials": "I"}, {"family": "Hwang", "given": "Mi Yeong", "initials": "MY"}, {"family": "Han", "given": "Sohee", "initials": "S"}, {"family": "Akiyama", "given": "Masato", "initials": "M"}, {"family": "Sakaue", "given": "Saori", "initials": "S"}, {"family": "Terao", "given": "Chikashi", "initials": "C"}, {"family": "Kanai", "given": "Masahiro", "initials": "M"}, {"family": "Zhou", "given": "Wei", "initials": "W"}, {"family": "Brumpton", "given": "Ben M", "initials": "BM"}, {"family": "Rasheed", "given": "Humaira", "initials": "H"}, {"family": "Havulinna", "given": "Aki S", "initials": "AS"}, {"family": "Veturi", "given": "Yogasudha", "initials": "Y"}, {"family": "Pacheco", "given": "Jennifer Allen", "initials": "JA"}, {"family": "Rosenthal", "given": "Elisabeth A", "initials": "EA"}, {"family": "Lingren", "given": "Todd", "initials": "T"}, {"family": "Feng", "given": "QiPing", "initials": "Q"}, {"family": "Kullo", "given": "Iftikhar J", "initials": "IJ"}, {"family": "Narita", "given": "Akira", "initials": "A"}, {"family": "Takayama", "given": "Jun", "initials": "J"}, {"family": "Martin", "given": "Hilary C", "initials": "HC"}, {"family": "Hunt", "given": "Karen A", "initials": "KA"}, {"family": "Trivedi", "given": "Bhavi", "initials": "B"}, {"family": "Haessler", "given": "Jeffrey", "initials": "J"}, {"family": "Giulianini", "given": "Franco", "initials": "F"}, {"family": "Bradford", "given": "Yuki", "initials": "Y"}, {"family": "Miller", "given": "Jason E", "initials": "JE"}, {"family": "Campbell", "given": "Archie", "initials": "A"}, {"family": "Lin", "given": "Kuang", "initials": "K"}, {"family": "Millwood", "given": "Iona Y", "initials": "IY"}, {"family": "Rasheed", "given": "Asif", "initials": "A"}, {"family": "Hindy", "given": "George", "initials": "G"}, {"family": "Faul", "given": "Jessica D", "initials": "JD"}, {"family": "Zhao", "given": "Wei", "initials": "W"}, {"family": "Weir", "given": "David R", "initials": "DR"}, {"family": "Turman", "given": "Constance", "initials": "C"}, {"family": "Huang", "given": "Hongyan", "initials": "H"}, {"family": "Graff", "given": "Mariaelisa", "initials": "M"}, {"family": "Choudhury", "given": "Ananyo", "initials": "A"}, {"family": "Sengupta", "given": "Dhriti", "initials": "D"}, {"family": "Mahajan", "given": "Anubha", "initials": "A"}, {"family": "Brown", "given": "Michael R", "initials": "MR"}, {"family": "Zhang", "given": "Weihua", "initials": "W"}, {"family": "Yu", "given": "Ketian", "initials": "K"}, {"family": "Schmidt", "given": "Ellen M", "initials": "EM"}, {"family": "Pandit", "given": "Anita", "initials": "A"}, {"family": "Gustafsson", "given": "Stefan", "initials": "S"}, {"family": "Yin", "given": "Xianyong", "initials": "X"}, {"family": "Luan", "given": "Jian\u2019an", "initials": "J"}, {"family": "Zhao", "given": "Jing Hua", "initials": "JH"}, {"family": "Matsuda", "given": "Fumihiko", "initials": "F"}, {"family": "Jang", "given": "Hye Mi", "initials": "HM"}, {"family": "Yoon", "given": "Kyungheon", "initials": "K"}, {"family": "Medina-Gomez", "given": "Carolina", "initials": "C"}, {"family": "Pitsillides", "given": "Achilleas", "initials": "A"}, {"family": "Hottenga", "given": "Jouke Jan", "initials": "JJ"}, {"family": "Wood", "given": "Andrew R", "initials": "AR"}, {"family": "Ji", "given": "Yingji", "initials": "Y"}, {"family": "Gao", "given": "Zishan", "initials": "Z"}, {"family": "Haworth", "given": "Simon", "initials": "S"}, {"family": "Mitchell", "given": "Ruth E", "initials": "RE"}, {"family": "Chai", "given": "Jin Fang", "initials": "JF"}, {"family": "Aadahl", "given": "Mette", "initials": "M"}, {"family": "Bjerregaard", "given": "Anne A", "initials": "AA"}, {"family": "Yao", "given": "Jie", "initials": "J"}, {"family": "Manichaikul", "given": "Ani", "initials": "A"}, {"family": "Lee", "given": "Wen Jane", "initials": "WJ"}, {"family": "Hsiung", "given": "Chao Agnes", "initials": "CA"}, {"family": "Warren", "given": "Helen R", "initials": "HR"}, {"family": "Ramirez", "given": "Julia", "initials": "J"}, {"family": "Bork-Jensen", "given": "Jette", "initials": "J"}, {"family": "K\u00e5rhus", "given": "Line L", "initials": "LL"}, {"family": "Goel", "given": "Anuj", "initials": "A"}, {"family": "Sabater-Lleal", "given": "Maria", "initials": "M"}, {"family": "Noordam", "given": "Raymond", "initials": "R"}, {"family": "Mauro", "given": "Pala", "initials": "P"}, {"family": "Matteo", "given": "Floris", "initials": "F"}, {"family": "McDaid", "given": "Aaron F", "initials": "AF"}, {"family": "Marques-Vidal", "given": "Pedro", "initials": "P"}, {"family": "Wielscher", "given": "Matthias", "initials": "M"}, {"family": "Trompet", "given": "Stella", "initials": "S"}, {"family": "Sattar", "given": "Naveed", "initials": "N"}, {"family": "M\u00f8llehave", "given": "Line T", "initials": "LT"}, {"family": "Munz", "given": "Matthias", "initials": "M"}, {"family": "Zeng", "given": "Lingyao", "initials": "L"}, {"family": "Huang", "given": "Jianfeng", "initials": "J"}, {"family": "Yang", "given": "Bin", "initials": "B"}, {"family": "Poveda", "given": "Alaitz", "initials": "A"}, {"family": "Kurbasic", "given": "Azra", "initials": "A"}, {"family": "Sch\u00f6nherr", "given": "Sebastian", "initials": "S"}, {"family": "Forer", "given": "Lukas", "initials": "L"}, {"family": "Scholz", "given": "Markus", "initials": "M"}, {"family": "Galesloot", "given": "Tessel E", "initials": "TE"}, {"family": "Bradfield", "given": "Jonathan P", "initials": "JP"}, {"family": "Ruotsalainen", "given": "Sanni E", "initials": "SE"}, {"family": "Daw", "given": "E Warwick", "initials": "EW"}, {"family": "Zmuda", "given": "Joseph M", "initials": "JM"}, {"family": "Mitchell", "given": "Jonathan S", "initials": "JS"}, {"family": "Fuchsberger", "given": "Christian", "initials": "C"}, {"family": "Christensen", "given": "Henry", "initials": "H"}, {"family": "Brody", "given": "Jennifer A", "initials": "JA"}, {"family": "Le", "given": "Phuong", "initials": "P"}, {"family": "Feitosa", "given": "Mary F", "initials": "MF"}, {"family": "Wojczynski", "given": "Mary K", "initials": "MK"}, {"family": "Hemerich", "given": "Daiane", "initials": "D"}, {"family": "Preuss", "given": "Michael", "initials": "M"}, {"family": "Mangino", "given": "Massimo", "initials": "M"}, {"family": "Christofidou", "given": "Paraskevi", "initials": "P"}, {"family": "Verweij", "given": "Niek", "initials": "N"}, {"family": "Benjamins", "given": "Jan W", "initials": "JW"}, {"family": "Engmann", "given": "Jorgen", "initials": "J"}, {"family": "Noah", "given": "Tsao L", "initials": "TL"}, {"family": "Verma", "given": "Anurag", "initials": "A"}, {"family": "Slieker", "given": "Roderick C", "initials": "RC"}, {"family": "Lo", "given": "Ken Sin", "initials": "KS"}, {"family": "Zilhao", "given": "Nuno R", "initials": "NR"}, {"family": "Kleber", "given": "Marcus E", "initials": "ME"}, {"family": "Delgado", "given": "Graciela E", "initials": "GE"}, {"family": "Huo", "given": "Shaofeng", "initials": "S"}, {"family": "Ikeda", "given": "Daisuke D", "initials": "DD"}, {"family": "Iha", "given": "Hiroyuki", "initials": "H"}, {"family": "Yang", "given": "Jian", "initials": "J"}, {"family": "Liu", "given": "Jun", "initials": "J"}, {"family": "Demirkan", "given": "Ay\u015fe", "initials": "A"}, {"family": "Leonard", "given": "Hampton L", "initials": "HL"}, {"family": "Marten", "given": "Jonathan", "initials": "J"}, {"family": "Emmel", "given": "Carina", "initials": "C"}, {"family": "Schmidt", "given": "B\u00f6rge", "initials": "B"}, {"family": "Smyth", "given": "Laura J", "initials": "LJ"}, {"family": "Ca\u00f1adas-Garre", "given": "Marisa", "initials": "M"}, {"family": "Wang", "given": "Chaolong", "initials": "C"}, {"family": "Nakatochi", "given": "Masahiro", "initials": "M"}, {"family": "Wong", "given": "Andrew", "initials": "A"}, {"family": "Hutri-K\u00e4h\u00f6nen", "given": "Nina", "initials": "N"}, {"family": "Sim", "given": "Xueling", "initials": "X"}, {"family": "Xia", "given": "Rui", "initials": "R"}, {"family": "Huerta-Chagoya", "given": "Alicia", "initials": "A"}, {"family": "Fernandez-Lopez", "given": "Juan Carlos", "initials": "JC"}, {"family": "Lyssenko", 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"initials": "Y"}, {"family": "Murakami", "given": "Yoshinori", "initials": "Y"}, {"family": "Kim", "given": "Bong Jo", "initials": "BJ"}, {"family": "Thorsteinsdottir", "given": "Unnur", "initials": "U"}, {"family": "Stefansson", "given": "Kari", "initials": "K"}, {"family": "Zhang", "given": "Jifeng", "initials": "J"}, {"family": "Chen", "given": "Y Eugene", "initials": "YE"}, {"family": "Ho", "given": "Yuk Lam", "initials": "YL"}, {"family": "Lynch", "given": "Julie A", "initials": "JA"}, {"family": "Tsao", "given": "Philip S", "initials": "PS"}, {"family": "Chang", "given": "Kyong Mi", "initials": "KM"}, {"family": "Cho", "given": "Kelly", "initials": "K"}, {"family": "O'Donnell", "given": "Christopher J", "initials": "CJ"}, {"family": "Gaziano", "given": "John M", "initials": "JM"}, {"family": "Wilson", "given": "Peter", "initials": "P"}, {"family": "Mohlke", "given": "Karen L", "initials": "KL"}, {"family": "Frayling", "given": "Timothy M", "initials": "TM"}, {"family": "Hirschhorn", "given": "Joel N", "initials": "JN"}, {"family": "Kathiresan", "given": "Sekar", "initials": "S"}, {"family": "Boehnke", "given": "Michael", "initials": "M"}, {"family": "Struan Grant", "given": "", "initials": ""}, {"family": "Natarajan", "given": "Pradeep", "initials": "P"}, {"family": "Sun", "given": "Yan V", "initials": "YV"}, {"family": "Morris", "given": "Andrew P", "initials": "AP"}, {"family": "Deloukas", "given": "Panos", "initials": "P"}, {"family": "Peloso", "given": "Gina", "initials": "G"}, {"family": "Assimes", "given": "Themistocles L", "initials": "TL"}, {"family": "Willer", "given": "Cristen J", "initials": "CJ"}, {"family": "Zhu", "given": "Xiang", "initials": "X", "orcid": "0000-0003-1134-6413", "researcher": {"href": "https://publications.scilifelab.se/researcher/e0f3c87254544315866874830d160110.json"}}, {"family": "Brown", "given": "Christopher D", "initials": "CD"}], "type": "journal-article", "published": "2022-08-00", "journal": {"title": "The American Journal of Human Genetics", "issn": "0002-9297", "volume": "109", "issue": "8", "pages": "1366-1387", "issn-l": "0002-9297"}, "abstract": "A major challenge of genome-wide association studies (GWASs) is to translate phenotypic associations into biological insights. Here, we integrate a large GWAS on blood lipids involving 1.6 million individuals from five ancestries with a wide array of functional genomic datasets to discover regulatory mechanisms underlying lipid associations. We first prioritize lipid-associated genes with expression quantitative trait locus (eQTL) colocalizations and then add chromatin interaction data to narrow the search for functional genes. Polygenic enrichment analysis across 697 annotations from a host of tissues and cell types confirms the central role of the liver in lipid levels and highlights the selective enrichment of adipose-specific chromatin marks in high-density lipoprotein cholesterol and triglycerides. Overlapping transcription factor (TF) binding sites with lipid-associated loci identifies TFs relevant in lipid biology. In addition, we present an integrative framework to prioritize causal variants at GWAS loci, producing a comprehensive list of candidate causal genes and variants with multiple layers of functional evidence. We highlight two of the prioritized genes, CREBRF and RRBP1, which show convergent evidence across functional datasets supporting their roles in lipid biology.", "doi": "10.1016/j.ajhg.2022.06.012", "pmid": "35931049", "labels": {"NGI SNP genotyping": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9388392"}, {"db": "pii", "key": "S0002-9297(22)00265-8"}], "notes": [], "created": "2022-08-16T13:29:30.128Z", "modified": "2023-06-19T08:56:55.259Z"}, {"entity": "publication", "iuid": "425bcad722be4cf8b20047dcd31f3141", "links": {"self": {"href": "https://publications.scilifelab.se/publication/425bcad722be4cf8b20047dcd31f3141.json"}, "display": {"href": "https://publications.scilifelab.se/publication/425bcad722be4cf8b20047dcd31f3141"}}, "title": "Characterization of Pipistrellus pygmaeus Bat Virome from Sweden.", "authors": [{"family": "Cholleti", "given": "Harindranath", "initials": "H"}, {"family": "de Jong", "given": "Johnny", "initials": "J"}, {"family": "Blomstr\u00f6m", "given": "Anne-Lie", "initials": "AL"}, {"family": "Berg", "given": "Mikael", "initials": "M"}], "type": "journal article", "published": "2022-07-28", "journal": {"title": "Viruses", "issn": "1999-4915", "volume": "14", "issue": "8", "issn-l": "1999-4915"}, "abstract": "Increasing amounts of data indicate that bats harbor a higher viral diversity relative to other mammalian orders, and they have been recognized as potential reservoirs for pathogenic viruses, such as the Hendra, Nipah, Marburg, and SARS-CoV viruses. Here, we present the first viral metagenomic analysis of Pipistrellus pygmaeus from Uppsala, Sweden. Total RNA was extracted from the saliva and feces of individual bats and analyzed using Illumina sequencing. The results identified sequences related to 51 different viral families, including vertebrate, invertebrate, and plant viruses. These viral families include Coronaviridae, Picornaviridae, Dicistroviridae, Astroviridae, Hepeviridae, Reoviridae, Botourmiaviridae, Lispviridae, Totiviridae, Botoumiaviridae, Parvoviridae, Retroviridae, Adenoviridae, and Partitiviridae, as well as different unclassified viruses. We further characterized three near full-length genome sequences of bat coronaviruses. A phylogenetic analysis showed that these belonged to alphacoronaviruses with the closest similarity (78-99% at the protein level) to Danish and Finnish bat coronaviruses detected in Pipistrellus and Myotis bats. In addition, the full-length and the near full-length genomes of picornavirus were characterized. These showed the closest similarity (88-94% at the protein level) to bat picornaviruses identified in Chinese bats. Altogether, the results of this study show that Swedish Pipistrellus bats harbor a great diversity of viruses, some of which are closely related to mammalian viruses. This study expands our knowledge on the bat population virome and improves our understanding of the evolution and transmission of viruses among bats and to other species.", "doi": "10.3390/v14081654", "pmid": "36016275", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Short read": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9415950"}, {"db": "pii", "key": "v14081654"}], "notes": [], "created": "2022-09-06T05:44:09.655Z", "modified": "2024-01-16T13:48:35.624Z"}, {"entity": "publication", "iuid": "796f460ce9794c089a8bdd175c3a9b65", "links": {"self": {"href": "https://publications.scilifelab.se/publication/796f460ce9794c089a8bdd175c3a9b65.json"}, "display": {"href": "https://publications.scilifelab.se/publication/796f460ce9794c089a8bdd175c3a9b65"}}, "title": "Restricted X chromosome introgression and support for Haldane's rule in hybridizing damselflies.", "authors": [{"family": "Swaegers", "given": "Janne", "initials": "J", "orcid": "0000-0003-1952-3170", "researcher": {"href": "https://publications.scilifelab.se/researcher/0cb5191ea7e94e8696e42fc15e854ce8.json"}}, {"family": "S\u00e1nchez-Guill\u00e9n", "given": "Rosa Ana", "initials": "RA", "orcid": "0000-0001-6024-8321", "researcher": {"href": "https://publications.scilifelab.se/researcher/c03f95fe4ced4dd690950ab8bb656710.json"}}, {"family": "Chauhan", "given": "Pallavi", "initials": "P", "orcid": "0000-0002-5160-6673", "researcher": {"href": "https://publications.scilifelab.se/researcher/c2ca3733447d4e38ae5cce50d1b4d165.json"}}, {"family": "Wellenreuther", "given": "Maren", "initials": "M", "orcid": "0000-0002-2764-8291", "researcher": {"href": "https://publications.scilifelab.se/researcher/82e9b593bf0f4535a7b9231608b1e27d.json"}}, {"family": "Hansson", "given": "Bengt", "initials": "B", "orcid": "0000-0001-6694-8169", "researcher": {"href": "https://publications.scilifelab.se/researcher/01f0144e207c41dcbc4d5aec68690e4b.json"}}], "type": "journal article", "published": "2022-07-27", "journal": {"title": "Proc. Biol. Sci.", "issn": "1471-2954", "issn-l": "0962-8452", "volume": "289", "issue": "1979", "pages": "20220968"}, "abstract": "Contemporary hybrid zones act as natural laboratories for the investigation of species boundaries and may shed light on the little understood roles of sex chromosomes in species divergence. Sex chromosomes are considered to function as a hotspot of genetic divergence between species; indicated by less genomic introgression compared to autosomes during hybridization. Moreover, they are thought to contribute to Haldane's rule, which states that hybrids of the heterogametic sex are more likely to be inviable or sterile. To test these hypotheses, we used contemporary hybrid zones of Ischnura elegans, a damselfly species that has been expanding its range into the northern and western regions of Spain, leading to chronic hybridization with its sister species Ischnura graellsii. We analysed genome-wide SNPs in the Spanish I. elegans and I. graellsii hybrid zone and found (i) that the X chromosome shows less genomic introgression compared to autosomes, and (ii) that males are underrepresented among admixed individuals, as predicted by Haldane's rule. This is the first study in Odonata that suggests a role of the X chromosome in reproductive isolation. Moreover, our data add to the few studies on species with X0 sex determination system and contradict the hypothesis that the absence of a Y chromosome causes exceptions to Haldane's rule.", "doi": "10.1098/rspb.2022.0968", "pmid": "35855603", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9297008"}, {"db": "Dryad", "key": "10.5061/dryad.gqnk98sp8"}], "notes": [], "created": "2022-11-09T15:50:07.860Z", "modified": "2024-01-16T13:48:35.646Z"}, {"entity": "publication", "iuid": "72892165f88842119e37a0f4bdf0fbd2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/72892165f88842119e37a0f4bdf0fbd2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/72892165f88842119e37a0f4bdf0fbd2"}}, "title": "Genome-wide association study identifies Sj\u00f6gren's risk loci with functional implications in immune and glandular cells.", "authors": [{"family": "Khatri", "given": "Bhuwan", "initials": "B", "orcid": "0000-0001-5456-2963", "researcher": {"href": "https://publications.scilifelab.se/researcher/babac1d62a5c4e929151c502d43362aa.json"}}, {"family": "Tessneer", "given": "Kandice L", "initials": "KL"}, {"family": "Rasmussen", "given": "Astrid", "initials": "A"}, {"family": "Aghakhanian", "given": "Farhang", "initials": "F"}, {"family": "Reksten", "given": "Tove Ragna", "initials": "TR", "orcid": "0000-0001-8704-4943", "researcher": {"href": "https://publications.scilifelab.se/researcher/2097777ee53f41339a0e5b407aac739b.json"}}, {"family": "Adler", "given": "Adam", "initials": "A"}, {"family": "Alevizos", "given": "Ilias", "initials": "I"}, {"family": "Anaya", "given": "Juan-Manuel", "initials": "JM", "orcid": "0000-0002-6444-1249", "researcher": {"href": "https://publications.scilifelab.se/researcher/00723e72bf0e4333a503614c07dc718e.json"}}, {"family": "Aqrawi", "given": "Lara A", "initials": "LA"}, {"family": "Baecklund", "given": "Eva", "initials": "E"}, {"family": "Brun", "given": "Johan G", "initials": "JG"}, {"family": "Bucher", "given": "Sara Magnusson", "initials": "SM"}, {"family": "Eloranta", "given": "Maija-Leena", "initials": "ML"}, {"family": "Engelke", "given": "Fiona", "initials": "F", "orcid": "0000-0002-5673-1705", "researcher": {"href": "https://publications.scilifelab.se/researcher/77af0d191e65475fb24a088ad1ea8cae.json"}}, {"family": "Forsblad-d'Elia", "given": "Helena", "initials": "H"}, {"family": "Glenn", "given": "Stuart B", "initials": "SB"}, {"family": "Hammenfors", "given": "Daniel", "initials": "D"}, {"family": "Imgenberg-Kreuz", "given": "Juliana", "initials": "J"}, {"family": "Jensen", "given": "Janicke Liaaen", "initials": "JL", "orcid": "0000-0003-4276-9611", "researcher": {"href": "https://publications.scilifelab.se/researcher/773434ab6d4845d187376dd8cc972d8b.json"}}, {"family": "Johnsen", "given": "Svein Joar Augl\u00e6nd", "initials": "SJA", "orcid": "0000-0002-1591-9250", "researcher": {"href": "https://publications.scilifelab.se/researcher/1fcaa1c5f1164f9d87e856a6eafb9e2c.json"}}, {"family": "Jonsson", "given": "Malin V", "initials": "MV", "orcid": "0000-0001-5655-5513", "researcher": {"href": "https://publications.scilifelab.se/researcher/11e3b5d3254449b69d2fca5fc5f5738a.json"}}, {"family": "Kvarnstr\u00f6m", "given": "Marika", "initials": "M", "orcid": "0000-0002-4948-8380", "researcher": {"href": "https://publications.scilifelab.se/researcher/24d1313454704814b6f591a63dc5d5cb.json"}}, {"family": "Kelly", "given": "Jennifer A", "initials": "JA"}, {"family": "Li", "given": "He", "initials": "H"}, {"family": "Mandl", "given": "Thomas", "initials": "T", "orcid": "0000-0002-7143-7088", "researcher": {"href": "https://publications.scilifelab.se/researcher/b72a91b349c148c9b9b59028d079217d.json"}}, {"family": "Mart\u00edn", "given": "Javier", "initials": "J"}, {"family": "Nocturne", "given": "Ga\u00e9tane", "initials": "G", "orcid": "0000-0001-6809-0733", "researcher": {"href": "https://publications.scilifelab.se/researcher/74e763eb9c864a6a84259f807a381725.json"}}, {"family": "Norheim", "given": "Katrine Br\u00e6kke", "initials": "KB"}, {"family": "Palm", "given": "\u00d8yvind", "initials": "\u00d8"}, {"family": "Skarstein", "given": "Kathrine", "initials": "K"}, {"family": "Stolarczyk", "given": "Anna M", "initials": "AM"}, {"family": "Taylor", "given": "Kimberly E", "initials": "KE"}, {"family": "Teruel", "given": "Maria", "initials": "M", "orcid": "0000-0002-5315-2660", "researcher": {"href": "https://publications.scilifelab.se/researcher/025b474fb4a34fe68e52ebf2455d1cf0.json"}}, {"family": "Theander", "given": "Elke", "initials": "E"}, {"family": "Venuturupalli", "given": "Swamy", "initials": "S"}, {"family": "Wallace", "given": "Daniel J", "initials": "DJ"}, {"family": "Grundahl", "given": "Kiely M", "initials": "KM"}, {"family": "Hefner", "given": "Kimberly S", "initials": "KS"}, {"family": "Radfar", "given": "Lida", "initials": "L"}, {"family": "Lewis", "given": "David M", "initials": "DM"}, {"family": "Stone", "given": "Donald U", "initials": "DU"}, {"family": "Kaufman", "given": "C Erick", "initials": "CE"}, {"family": "Brennan", "given": "Michael T", "initials": "MT"}, {"family": "Guthridge", "given": "Joel M", "initials": "JM"}, {"family": "James", "given": "Judith A", "initials": "JA", "orcid": "0000-0002-9574-7355", "researcher": {"href": "https://publications.scilifelab.se/researcher/0ac95ea8fa4f43939f8e4a94bc422ffd.json"}}, {"family": "Scofield", "given": "R Hal", "initials": "RH"}, {"family": "Gaffney", "given": "Patrick M", "initials": "PM"}, {"family": "Criswell", "given": "Lindsey A", "initials": "LA", "orcid": "0000-0002-0761-7543", "researcher": {"href": "https://publications.scilifelab.se/researcher/e36beb11c7a7495290765a85d81928fd.json"}}, {"family": "Jonsson", "given": "Roland", "initials": "R"}, {"family": "Eriksson", "given": "Per", "initials": "P"}, {"family": "Bowman", "given": "Simon J", "initials": "SJ"}, {"family": "Omdal", "given": "Roald", "initials": "R"}, {"family": "R\u00f6nnblom", "given": "Lars", "initials": "L", "orcid": "0000-0001-9403-6503", "researcher": {"href": "https://publications.scilifelab.se/researcher/053ed3b657124a1bab3a78dc685556e6.json"}}, {"family": "Warner", "given": "Blake", "initials": "B", "orcid": "0000-0002-4961-018X", "researcher": {"href": "https://publications.scilifelab.se/researcher/1a00e0cef8794b4e8d13cb963539e1fe.json"}}, {"family": "Rischmueller", "given": "Maureen", "initials": "M"}, {"family": "Witte", "given": "Torsten", "initials": "T"}, {"family": "Farris", "given": "A Darise", "initials": "AD"}, {"family": "Mariette", "given": "Xavier", "initials": "X", "orcid": "0000-0002-4244-5417", "researcher": {"href": "https://publications.scilifelab.se/researcher/13855fe7b68b4235a48a8dda9a0d5fd6.json"}}, {"family": "Alarcon-Riquelme", "given": "Marta E", "initials": "ME", "orcid": "0000-0002-7632-4154", "researcher": {"href": "https://publications.scilifelab.se/researcher/61acb7fc644c42d9ba02804f58b1eeee.json"}}, {"family": "PRECISESADS Clinical Consortium", "given": "", "initials": ""}, {"family": "Shiboski", "given": "Caroline H", "initials": "CH"}, {"family": "Sj\u00f6gren\u2019s International Collaborative Clinical Alliance (SICCA)", "given": "", "initials": ""}, {"family": "Wahren-Herlenius", "given": "Marie", "initials": "M", "orcid": "0000-0002-0915-7245", "researcher": {"href": "https://publications.scilifelab.se/researcher/a8451e7f5e6e4e4da0bace3dfafaeb38.json"}}, {"family": "Ng", "given": "Wan-Fai", "initials": "WF"}, {"family": "UK Primary Sj\u00f6gren\u2019s Syndrome Registry", "given": "", "initials": ""}, {"family": "Sivils", "given": "Kathy L", "initials": "KL"}, {"family": "Adrianto", "given": "Indra", "initials": "I", "orcid": "0000-0002-9973-3057", "researcher": {"href": "https://publications.scilifelab.se/researcher/4d109293e1044471b8cefff69b1b3f67.json"}}, {"family": "Nordmark", "given": "Gunnel", "initials": "G", "orcid": "0000-0002-3829-7431", "researcher": {"href": "https://publications.scilifelab.se/researcher/188fda53498740dbb007441cc94bb1ad.json"}}, {"family": "Lessard", "given": "Christopher J", "initials": "CJ", "orcid": "0000-0003-2440-3843", "researcher": {"href": "https://publications.scilifelab.se/researcher/c476c83630ad4fe6acbd1930cfedffa8.json"}}], "type": "journal article", "published": "2022-07-27", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "13", "issue": "1", "pages": "4287", "issn-l": "2041-1723"}, "abstract": "Sj\u00f6gren's disease is a complex autoimmune disease with twelve established susceptibility loci. This genome-wide association study (GWAS) identifies ten novel genome-wide significant (GWS) regions in Sj\u00f6gren's cases of European ancestry: CD247, NAB1, PTTG1-MIR146A, PRDM1-ATG5, TNFAIP3, XKR6, MAPT-CRHR1, RPTOR-CHMP6-BAIAP6, TYK2, SYNGR1. Polygenic risk scores yield predictability (AUROC = 0.71) and relative risk of 12.08. Interrogation of bioinformatics databases refine the associations, define local regulatory networks of GWS SNPs from the 95% credible set, and expand the implicated gene list to >40. Many GWS SNPs are eQTLs for genes within topologically associated domains in immune cells and/or eQTLs in the main target tissue, salivary glands.", "doi": "10.1038/s41467-022-30773-y", "pmid": "35896530", "labels": {"NGI SNP genotyping": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-022-30773-y"}, {"db": "pmc", "key": "PMC9329286"}], "notes": [], "created": "2022-08-16T13:29:32.951Z", "modified": "2022-08-16T13:29:33.688Z"}, {"entity": "publication", "iuid": "45433b3cce4846679af7f62c08acb69b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/45433b3cce4846679af7f62c08acb69b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/45433b3cce4846679af7f62c08acb69b"}}, "title": "Lipoxins reduce obesity-induced adipose tissue inflammation in 3D-cultured human adipocytes and explant cultures.", "authors": [{"family": "Sot\u00e1k", "given": "Mat\u00fa\u0161", "initials": "M"}, {"family": "Rajan", "given": "Meenu Rohini", "initials": "MR"}, {"family": "Clark", "given": "Madison", "initials": "M"}, {"family": "Harms", "given": "Matthew", "initials": "M"}, {"family": "Rani", "given": "Alankrita", "initials": "A"}, {"family": "Kraft", "given": "Jamie D", "initials": "JD"}, {"family": "Tandio", "given": "David", "initials": "D"}, {"family": "Shen", "given": "Tong", "initials": "T"}, {"family": "Borkowski", "given": "Kamil", "initials": "K"}, {"family": "Fiehn", "given": "Oliver", "initials": "O"}, {"family": "Newman", "given": "John W", "initials": "JW"}, {"family": "Quiding-J\u00e4rbrink", "given": "Marianne", "initials": "M"}, {"family": "Bi\u00f6rserud", "given": "Christina", "initials": "C"}, {"family": "Apelgren", "given": "Peter", "initials": "P"}, {"family": "Staalesen", "given": "Trude", "initials": "T"}, {"family": "Hagberg", "given": "Carolina E", "initials": "CE"}, {"family": "Boucher", "given": "Jeremie", "initials": "J"}, {"family": "Wallenius", "given": "Ville", "initials": "V"}, {"family": "Lange", "given": "Stephan", "initials": "S"}, {"family": "B\u00f6rgeson", "given": "Emma", "initials": "E"}], "type": "journal article", "published": "2022-07-15", "journal": {"title": "iScience", "issn": "2589-0042", "volume": "25", "issue": "7", "pages": "104602", "issn-l": "2589-0042"}, "abstract": "Adipose tissue inflammation drives obesity-related cardiometabolic diseases. Enhancing endogenous resolution mechanisms through administration of lipoxin A4, a specialized pro-resolving lipid mediator, was shown to reduce adipose inflammation and subsequently protects against obesity-induced systemic disease in mice. Here, we demonstrate that lipoxins reduce inflammation in 3D-cultured human adipocytes and adipose tissue explants from obese patients. Approximately 50% of patients responded particularly well to lipoxins by reducing inflammatory cytokines and promoting an anti-inflammatory M2 macrophage phenotype. Responding patients were characterized by elevated systemic levels of C-reactive protein, which causes inflammation in cultured human adipocytes. Responders appeared more prone to producing anti-inflammatory oxylipins and displayed elevated prostaglandin D2 levels, which has been interlinked with transcription of lipoxin-generating enzymes. Using explant cultures, this study provides the first proof-of-concept evidence supporting the therapeutic potential of lipoxins in reducing human adipose tissue inflammation. Our data further indicate that lipoxin treatment may require a tailored personalized-medicine approach.", "doi": "10.1016/j.isci.2022.104602", "pmid": "35789845", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9249816"}, {"db": "pii", "key": "S2589-0042(22)00874-4"}], "notes": [], "created": "2022-11-29T09:47:56.917Z", "modified": "2022-11-29T09:47:56.920Z"}, {"entity": "publication", "iuid": "c2eb6231b5e54b648bdaf3fb9a000dba", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c2eb6231b5e54b648bdaf3fb9a000dba.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c2eb6231b5e54b648bdaf3fb9a000dba"}}, "title": "Equilibrated evolution of the mixed auto-/allopolyploid haplotype-resolved genome of the invasive hexaploid Prussian carp.", "authors": [{"family": "Kuhl", "given": "Heiner", "initials": "H", "orcid": "0000-0001-7623-9227", "researcher": {"href": "https://publications.scilifelab.se/researcher/c3326add41974413be16c8a2bed157f8.json"}}, {"family": "Du", "given": "Kang", "initials": "K", "orcid": "0000-0002-1497-8945", "researcher": {"href": "https://publications.scilifelab.se/researcher/7eda8755c14042289ac7196edeffca01.json"}}, {"family": "Schartl", "given": "Manfred", "initials": "M", "orcid": "0000-0001-9882-5948", "researcher": {"href": "https://publications.scilifelab.se/researcher/5f97783b5013409ebc1a6bd2df5ca92c.json"}}, {"family": "Kalous", "given": "Luk\u00e1\u0161", "initials": "L", "orcid": "0000-0001-5518-1505", "researcher": {"href": "https://publications.scilifelab.se/researcher/c086140440e54f3793c444182f695216.json"}}, {"family": "St\u00f6ck", "given": "Matthias", "initials": "M", "orcid": "0000-0003-4888-8371", "researcher": {"href": "https://publications.scilifelab.se/researcher/83a4dc450751436d9b552ce68da65fd9.json"}}, {"family": "Lamatsch", "given": "Dunja K", "initials": "DK", "orcid": "0000-0002-6023-4381", "researcher": {"href": "https://publications.scilifelab.se/researcher/68f2363dc6d8417b88455ec1aadec818.json"}}], "type": "journal article", "published": "2022-07-14", "journal": {"title": "Nat Commun", "issn": "2041-1723", "issn-l": "2041-1723", "volume": "13", "issue": "1", "pages": "4092"}, "abstract": "Understanding genome evolution of polyploids requires dissection of their often highly similar subgenomes and haplotypes. Polyploid animal genome assemblies so far restricted homologous chromosomes to a 'collapsed' representation. Here, we sequenced the genome of the asexual Prussian carp, which is a close relative of the goldfish, and present a haplotype-resolved chromosome-scale assembly of a hexaploid animal. Genome-wide comparisons of the 150 chromosomes with those of two ancestral diploid cyprinids and the allotetraploid goldfish and common carp revealed the genomic structure, phylogeny and genome duplication history of its genome. It consists of 25 syntenic, homeologous chromosome groups and evolved by a recent autoploid addition to an allotetraploid ancestor. We show that de-polyploidization of the alloploid subgenomes on the individual gene level occurred in an equilibrated fashion. Analysis of the highly conserved actinopterygian gene set uncovered a subgenome dominance in duplicate gene loss of one ancestral chromosome set.", "doi": "10.1038/s41467-022-31515-w", "pmid": "35835759", "labels": {"NGI Uppsala (Uppsala Genome Center)": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Short read": "Service", "NGI Other": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9283417"}, {"db": "pii", "key": "10.1038/s41467-022-31515-w"}], "notes": [], "created": "2022-08-19T08:38:44.948Z", "modified": "2024-01-16T13:48:35.681Z"}, {"entity": "publication", "iuid": "64ad69b112e8486882a7f3720623a583", "links": {"self": {"href": "https://publications.scilifelab.se/publication/64ad69b112e8486882a7f3720623a583.json"}, "display": {"href": "https://publications.scilifelab.se/publication/64ad69b112e8486882a7f3720623a583"}}, "title": "Single-cell transcriptional pharmacodynamics of trifluridine in a tumor-immune model.", "authors": [{"family": "Selvin", "given": "Tove", "initials": "T"}, {"family": "Fasterius", "given": "Erik", "initials": "E"}, {"family": "Jarvius", "given": "Malin", "initials": "M"}, {"family": "Frykn\u00e4s", "given": "M\u00e5rten", "initials": "M"}, {"family": "Larsson", "given": "Rolf", "initials": "R"}, {"family": "Andersson", "given": "Claes R", "initials": "CR"}], "type": "journal article", "published": "2022-07-13", "journal": {"title": "Sci Rep", "issn": "2045-2322", "issn-l": "2045-2322", "volume": "12", "issue": "1", "pages": "11960"}, "abstract": "Understanding the immunological effects of chemotherapy is of great importance, especially now that we have entered an era where ever-increasing pre-clinical and clinical efforts are put into combining chemotherapy and immunotherapy to combat cancer. Single-cell RNA sequencing (scRNA-seq) has proved to be a powerful technique with a broad range of applications, studies evaluating drug effects in co-cultures of tumor and immune cells are however scarce. We treated a co-culture comprised of human colorectal cancer (CRC) cells and peripheral blood mononuclear cells (PBMCs) with the nucleoside analogue trifluridine (FTD) and used scRNA-seq to analyze posttreatment gene expression profiles in thousands of individual cancer and immune cells concurrently. ScRNA-seq recapitulated major mechanisms of action previously described for FTD and provided new insight into possible treatment-induced effects on T-cell mediated antitumor responses.", "doi": "10.1038/s41598-022-16077-7", "pmid": "35831404", "labels": {"Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "NGI Single cell": "Service", "NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC9279337"}, {"db": "pii", "key": "10.1038/s41598-022-16077-7"}], "notes": [], "created": "2022-08-22T07:53:44.772Z", "modified": "2024-01-16T13:48:35.689Z"}, {"entity": "publication", "iuid": "6ac7c7975ef94079a12757f6846f20a6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6ac7c7975ef94079a12757f6846f20a6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6ac7c7975ef94079a12757f6846f20a6"}}, "title": "Co-Occurrence of Francisella, Spotted Fever Group Rickettsia, and Midichloria in Avian-Associated Hyalomma rufipes", "authors": [{"family": "Hoffman", "given": "Tove", "initials": "T", "orcid": "0000-0003-2239-9078", "researcher": {"href": "https://publications.scilifelab.se/researcher/b8baafa073c34cfcbdfb513392373b3f.json"}}, {"family": "Sj\u00f6din", "given": "Andreas", "initials": "A", "orcid": "0000-0001-5350-4219", "researcher": {"href": "https://publications.scilifelab.se/researcher/6398d7c06a414ea6bcaf2579a8587452.json"}}, {"family": "\u00d6hrman", "given": "Caroline", "initials": "C", "orcid": "0000-0001-8489-757X", "researcher": {"href": "https://publications.scilifelab.se/researcher/804b654aa0be4d7a9ecdf113487fe443.json"}}, {"family": "Karlsson", "given": "Linda", "initials": "L"}, {"family": "McDonough", "given": "Ryelan Francis", "initials": "RF"}, {"family": "Sahl", "given": "Jason W", "initials": "JW"}, {"family": "Birdsell", "given": "Dawn", "initials": "D"}, {"family": "Wagner", "given": "David M", "initials": "DM", "orcid": "0000-0003-2684-6007", "researcher": {"href": "https://publications.scilifelab.se/researcher/04dbf7488dc54ca3b7031571b9acc982.json"}}, {"family": "Carra", "given": "Laura G", "initials": "LG"}, {"family": "Wilhelmsson", "given": "Peter", "initials": "P"}, {"family": "Pettersson", "given": "John H O", "initials": "JHO"}, {"family": "Barboutis", "given": "Christos", "initials": "C", "orcid": "0000-0002-5644-4327", "researcher": {"href": "https://publications.scilifelab.se/researcher/9c4a150259c44fe1a79914c1c0605130.json"}}, {"family": "Figuerola", "given": "Jordi", "initials": "J", "orcid": "0000-0002-4664-9011", "researcher": {"href": "https://publications.scilifelab.se/researcher/3832a2f08cec48848cf289134a105840.json"}}, {"family": "Onrubia", "given": "Alejandro", "initials": "A", "orcid": "0000-0001-8860-3524", "researcher": {"href": "https://publications.scilifelab.se/researcher/c73213860576464fafb5b1565d7299cc.json"}}, {"family": "Kiat", "given": "Yosef", "initials": "Y", "orcid": "0000-0002-3485-3517", "researcher": {"href": "https://publications.scilifelab.se/researcher/40519e89d3e44b47bf402078e687a45a.json"}}, {"family": "Piacentini", "given": "Dario", "initials": "D"}, {"family": "Jaenson", "given": "Thomas G T", "initials": "TGT"}, {"family": "Lindgren", "given": "Per Eric", "initials": "PE", "orcid": "0000-0003-2767-3638", "researcher": {"href": "https://publications.scilifelab.se/researcher/a4a6e70c9c514a48a40c3edf446ab5ce.json"}}, {"family": "Moutailler", "given": "Sara", "initials": "S", "orcid": "0000-0003-3010-6968", "researcher": {"href": "https://publications.scilifelab.se/researcher/b332d118556846808a1df98dbd5da020.json"}}, {"family": "Fransson", "given": "Thord", "initials": "T", "orcid": "0000-0002-9721-7024", "researcher": {"href": "https://publications.scilifelab.se/researcher/d17e09b5057d47eb87174f839d16c257.json"}}, {"family": "Forsman", "given": "Mats", "initials": "M", "orcid": "0000-0002-4466-5325", "researcher": {"href": "https://publications.scilifelab.se/researcher/b52b5a759a3e452b80728241c50c76dd.json"}}, {"family": "Nilsson", "given": "Kenneth", "initials": "K"}, {"family": "Lundkvist", "given": "\u00c5ke", "initials": "\u00c5", "orcid": "0000-0001-8608-6551", "researcher": {"href": "https://publications.scilifelab.se/researcher/f3c4bcad692e48dfb25a551f014d8482.json"}}, {"family": "Olsen", "given": "Bj\u00f6rn", "initials": "B"}], "type": "journal-article", "published": "2022-07-11", "journal": {"title": "Microorganisms", "issn": "2076-2607", "issn-l": "2076-2607", "volume": "10", "issue": "7", "pages": "1393"}, "abstract": "The migratory behavior of wild birds contributes to the geographical spread of ticks and their microorganisms. In this study, we aimed to investigate the dispersal and co-occurrence of Francisella and spotted fever group Rickettsia (SFGR) in ticks infesting birds migrating northward in the African-Western Palaearctic region (AWPR). Birds were trapped with mist nests across the Mediterranean basin during the 2014 and 2015 spring migration. In total, 575 ticks were collected from 244 birds. We screened the ticks for the species Francisella tularensis, the genus Francisella, and SFGR by microfluidic real-time PCR. Confirmatory analyses and metagenomic sequencing were performed on tick samples that putatively tested positive for F. tularensis during initial screenings. Hyalomma rufipes was the most common tick species and had a high prevalence of Francisella, including co-occurrence of Francisella and SFGR. Metagenomic analysis of total DNA extracted from two H. rufipes confirmed the presence of Francisella, Rickettsia, and Midichloria. Average nucleotide identity and phylogenetic inference indicated the highest identity of the metagenome-assembled genomes to a Francisella-like endosymbiont (FLE), Rickettsia aeschlimannii, and Midichloria mitochondrii. The results of this study suggest that (i) FLE- and SFGR-containing ticks are dispersed by northbound migratory birds in the AWPR, (ii) H. rufipes likely is not involved in transmission of F. tularensis in the AWPR, and (iii) a dual endosymbiosis of FLEs and Midichloria may support some of the nutritional requirements of H. rufipes.", "doi": "10.3390/microorganisms10071393", "pmid": "35889112", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9323704"}, {"db": "pii", "key": "microorganisms10071393"}], "notes": [], "created": "2022-11-09T15:44:20.894Z", "modified": "2024-01-16T13:48:35.835Z"}, {"entity": "publication", "iuid": "42b992446dbf48e7aa157bc279607840", "links": {"self": {"href": "https://publications.scilifelab.se/publication/42b992446dbf48e7aa157bc279607840.json"}, "display": {"href": "https://publications.scilifelab.se/publication/42b992446dbf48e7aa157bc279607840"}}, "title": "Microplastic exposure across trophic levels: effects on the host-microbiota of freshwater organisms.", "authors": [{"family": "Varg", "given": "Javier Edo", "initials": "JE", "orcid": "0000-0002-7895-4563", "researcher": {"href": "https://publications.scilifelab.se/researcher/72cb1019516e49f7b8f39b18924babc2.json"}}, {"family": "Outomuro", "given": "David", "initials": "D"}, {"family": "Kunce", "given": "Warren", "initials": "W"}, {"family": "Kuehrer", "given": "Lukas", "initials": "L"}, {"family": "Svanb\u00e4ck", "given": "Richard", "initials": "R"}, {"family": "Johansson", "given": "Frank", "initials": "F"}], "type": "journal article", "published": "2022-07-06", "journal": {"title": "Environ Microbiome", "issn": "2524-6372", "volume": "17", "issue": "1", "pages": "36", "issn-l": null}, "abstract": "Microplastics are a pervasive pollutant widespread in the sea and freshwater from anthropogenic sources, and together with the presence of pesticides, they can have physical and chemical effects on aquatic organisms and on their microbiota. Few studies have explored the combined effects of microplastics and pesticides on the host-microbiome, and more importantly, the effects across multiple trophic levels. In this work, we studied the effects of exposure to microplastics and the pesticide deltamethrin on the diversity and abundance of the host-microbiome across a three-level food chain: daphnids-damselfly-dragonflies. Daphnids were the only organism exposed to 1 \u00b5m microplastic beads, and they were fed to damselfly larvae. Those damselfly larvae were exposed to deltamethrin and then fed to the dragonfly larvae. The microbiotas of the daphnids, damselflies, and dragonflies were analyzed.\n\nExposure to microplastics and deltamethrin had a direct effect on the microbiome of the species exposed to these pollutants. An indirect effect was also found since exposure to the pollutants at lower trophic levels showed carry over effects on the diversity and abundance of the microbiome on higher trophic levels, even though the organisms at these levels where not directly exposed to the pollutants. Moreover, the exposure to deltamethrin on the damselflies negatively affected their survival rate in the presence of the dragonfly predator, but no such effects were found on damselflies fed with daphnids that had been exposed to microplastics.\n\nOur study highlights the importance of evaluating ecotoxicological effects at the community level. Importantly, the indirect exposure to microplastics and pesticides through diet can potentially have bottom-up effects on the trophic webs.", "doi": "10.1186/s40793-022-00429-x", "pmid": "35794681", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9258161"}, {"db": "pii", "key": "10.1186/s40793-022-00429-x"}], "notes": [], "created": "2022-11-29T09:37:16.537Z", "modified": "2022-11-29T09:37:16.572Z"}, {"entity": "publication", "iuid": "6f309d38fa3443c59966f673a7b43fdb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6f309d38fa3443c59966f673a7b43fdb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6f309d38fa3443c59966f673a7b43fdb"}}, "title": "Practical application of a Bayesian network approach to poultry epigenetics and stress.", "authors": [{"family": "Videla Rodriguez", "given": "Emiliano A", "initials": "EA"}, {"family": "P\u00e9rtille", "given": "F\u00e1bio", "initials": "F"}, {"family": "Guerrero-Bosagna", "given": "Carlos", "initials": "C"}, {"family": "Mitchell", "given": "John B O", "initials": "JBO"}, {"family": "Jensen", "given": "Per", "initials": "P"}, {"family": "Smith", "given": "V Anne", "initials": "VA"}], "type": "journal article", "published": "2022-07-01", "journal": {"title": "BMC Bioinformatics", "issn": "1471-2105", "volume": "23", "issue": "1", "pages": "261", "issn-l": "1471-2105"}, "abstract": "Relationships among genetic or epigenetic features can be explored by learning probabilistic networks and unravelling the dependencies among a set of given genetic/epigenetic features. Bayesian networks (BNs) consist of nodes that represent the variables and arcs that represent the probabilistic relationships between the variables. However, practical guidance on how to make choices among the wide array of possibilities in Bayesian network analysis is limited. Our study aimed to apply a BN approach, while clearly laying out our analysis choices as an example for future researchers, in order to provide further insights into the relationships among epigenetic features and a stressful condition in chickens (Gallus gallus).\n\nChickens raised under control conditions (n = 22) and chickens exposed to a social isolation protocol (n = 24) were used to identify differentially methylated regions (DMRs). A total of 60 DMRs were selected by a threshold, after bioinformatic pre-processing and analysis. The treatment was included as a binary variable (control = 0; stress = 1). Thereafter, a BN approach was applied: initially, a pre-filtering test was used for identifying pairs of features that must not be included in the process of learning the structure of the network; then, the average probability values for each arc of being part of the network were calculated; and finally, the arcs that were part of the consensus network were selected. The structure of the BN consisted of 47 out of 61 features (60 DMRs and the stressful condition), displaying 43 functional relationships. The stress condition was connected to two DMRs, one of them playing a role in tight and adhesive intracellular junctions in organs such as ovary, intestine, and brain.\n\nWe clearly explain our steps in making each analysis choice, from discrete BN models to final generation of a consensus network from multiple model averaging searches. The epigenetic BN unravelled functional relationships among the DMRs, as well as epigenetic features in close association with the stressful condition the chickens were exposed to. The DMRs interacting with the stress condition could be further explored in future studies as possible biomarkers of stress in poultry species.", "doi": "10.1186/s12859-022-04800-0", "pmid": "35778683", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9250184"}, {"db": "pii", "key": "10.1186/s12859-022-04800-0"}], "notes": [], "created": "2022-11-29T09:52:41.045Z", "modified": "2024-01-16T13:48:35.948Z"}, {"entity": "publication", "iuid": "903a0d4b47c0422abb32f266006c4d51", "links": {"self": {"href": "https://publications.scilifelab.se/publication/903a0d4b47c0422abb32f266006c4d51.json"}, "display": {"href": "https://publications.scilifelab.se/publication/903a0d4b47c0422abb32f266006c4d51"}}, "title": "Allorecognition genes drive reproductive isolation in Podospora anserina.", "authors": [{"family": "Ament-Vel\u00e1squez", "given": "S Lorena", "initials": "SL", "orcid": "0000-0003-3371-9292", "researcher": {"href": "https://publications.scilifelab.se/researcher/9d54ef94f91c4c1c85d5dc3a846023e5.json"}}, {"family": "Vogan", "given": "Aaron A", "initials": "AA", "orcid": "0000-0003-2013-7445", "researcher": {"href": "https://publications.scilifelab.se/researcher/71c6d460e3b44712a1a9dc19066211a4.json"}}, {"family": "Granger-Farbos", "given": "Alexandra", "initials": "A"}, {"family": "Bastiaans", "given": "Eric", "initials": "E", "orcid": "0000-0003-1502-0947", "researcher": {"href": "https://publications.scilifelab.se/researcher/870bd6035e54489187ef1d5131d14108.json"}}, {"family": "Martinossi-Allibert", "given": "Ivain", "initials": "I"}, {"family": "Saupe", "given": "Sven J", "initials": "SJ"}, {"family": "de Groot", "given": "Suzette", "initials": "S"}, {"family": "Lascoux", "given": "Martin", "initials": "M", "orcid": "0000-0003-1699-9042", "researcher": {"href": "https://publications.scilifelab.se/researcher/4ad3fadfb69448f397ad3bf55b2d2cb3.json"}}, {"family": "Debets", "given": "Alfons J M", "initials": "AJM", "orcid": "0000-0002-1799-4617", "researcher": {"href": "https://publications.scilifelab.se/researcher/b95b282c02d44a1a9f4d3d2aa7578b8a.json"}}, {"family": "Clav\u00e9", "given": "Corinne", "initials": "C"}, {"family": "Johannesson", "given": "Hanna", "initials": "H", "orcid": "0000-0001-6359-9856", "researcher": {"href": "https://publications.scilifelab.se/researcher/36e8fe278e01470e8cddaaccc5dad596.json"}}], "type": "journal article", "published": "2022-07-00", "journal": {"title": "Nat Ecol Evol", "issn": "2397-334X", "issn-l": "2397-334X", "volume": "6", "issue": "7", "pages": "910-923"}, "abstract": "Allorecognition, the capacity to discriminate self from conspecific non-self, is a ubiquitous organismal feature typically governed by genes evolving under balancing selection. Here, we show that in the fungus Podospora anserina, allorecognition loci controlling vegetative incompatibility (het genes), define two reproductively isolated groups through pleiotropic effects on sexual compatibility. These two groups emerge from the antagonistic interactions of the unlinked loci het-r (encoding a NOD-like receptor) and het-v (encoding a methyltransferase and an MLKL/HeLo domain protein). Using a combination of genetic and ecological data, supported by simulations, we provide a concrete and molecularly defined example whereby the origin and coexistence of reproductively isolated groups in sympatry is driven by pleiotropic genes under balancing selection.", "doi": "10.1038/s41559-022-01734-x", "pmid": "35551248", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41559-022-01734-x"}, {"db": "pmc", "key": "PMC9262711"}], "notes": [], "created": "2022-11-09T15:43:47.396Z", "modified": "2024-01-16T13:48:36.025Z"}, {"entity": "publication", "iuid": "63c5e806be664ee6b43ccdf91e815ab6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/63c5e806be664ee6b43ccdf91e815ab6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/63c5e806be664ee6b43ccdf91e815ab6"}}, "title": "High prevalence of somatic PIK3CA and TP53 pathogenic variants in the normal mammary gland tissue of sporadic breast cancer patients revealed by duplex sequencing.", "authors": [{"family": "Kostecka", "given": "Anna", "initials": "A", "orcid": "0000-0001-5705-0795", "researcher": {"href": "https://publications.scilifelab.se/researcher/74d8ad89e47c48d4b2266f6e0f1e4c5c.json"}}, {"family": "Nowikiewicz", "given": "Tomasz", "initials": "T"}, {"family": "Olszewski", "given": "Pawe\u0142", "initials": "P"}, {"family": "Koczkowska", "given": "Magdalena", "initials": "M"}, {"family": "Horbacz", "given": "Monika", "initials": "M", "orcid": "0000-0003-1644-2957", "researcher": {"href": "https://publications.scilifelab.se/researcher/76c7f6d571214ca9a6940293c3dbc6c1.json"}}, {"family": "Heinzl", "given": "Monika", "initials": "M"}, {"family": "Andreou", "given": "Maria", "initials": "M", "orcid": "0000-0002-2197-597X", "researcher": {"href": "https://publications.scilifelab.se/researcher/620718a324c741c5848719b18c953746.json"}}, {"family": "Salazar", "given": "Renato", "initials": "R", "orcid": "0000-0001-8436-9304", "researcher": {"href": "https://publications.scilifelab.se/researcher/ba0e45cecf6044b8a0519456de70d17d.json"}}, {"family": "Mair", "given": "Theresa", "initials": "T"}, {"family": "Madanecki", "given": "Piotr", "initials": "P"}, {"family": "Gucwa", "given": "Magdalena", "initials": "M"}, {"family": "Davies", "given": "Hanna", "initials": "H"}, {"family": "Skokowski", "given": "Jaros\u0142aw", "initials": "J", "orcid": "0000-0002-3079-3502", "researcher": {"href": "https://publications.scilifelab.se/researcher/105710cc7a9240a99ed6be5e665243be.json"}}, {"family": "Buckley", "given": "Patrick G", "initials": "PG"}, {"family": "P\u0119ksa", "given": "Rafa\u0142", "initials": "R"}, {"family": "\u015arutek", "given": "Ewa", "initials": "E"}, {"family": "Szylberg", "given": "\u0141ukasz", "initials": "\u0141"}, {"family": "Hartman", "given": "Johan", "initials": "J", "orcid": "0000-0002-6500-8527", "researcher": {"href": "https://publications.scilifelab.se/researcher/da7cefda6e00463d8ba95fc63eeb8f0a.json"}}, {"family": "Jankowski", "given": "Micha\u0142", "initials": "M"}, {"family": "Zegarski", "given": "Wojciech", "initials": "W"}, {"family": "Tiemann-Boege", "given": "Irene", "initials": "I"}, {"family": "Dumanski", "given": "Jan P", "initials": "JP"}, {"family": "Piotrowski", "given": "Arkadiusz", "initials": "A", "orcid": "0000-0002-0823-0607", "researcher": {"href": "https://publications.scilifelab.se/researcher/5263e32c89e24ed796cb04f68be36b99.json"}}], "type": "journal article", "published": "2022-06-29", "journal": {"title": "NPJ Breast Cancer", "issn": "2374-4677", "volume": "8", "issue": "1", "pages": "76", "issn-l": null}, "abstract": "The mammary gland undergoes hormonally stimulated cycles of proliferation, lactation, and involution. We hypothesized that these factors increase the mutational burden in glandular tissue and may explain high cancer incidence rate in the general population, and recurrent disease. Hence, we investigated the DNA sequence variants in the normal mammary gland, tumor, and peripheral blood from 52 reportedly sporadic breast cancer patients. Targeted resequencing of 542 cancer-associated genes revealed subclonal somatic pathogenic variants of: PIK3CA, TP53, AKT1, MAP3K1, CDH1, RB1, NCOR1, MED12, CBFB, TBX3, and TSHR in the normal mammary gland at considerable allelic frequencies (9 \u00d7 10-2- 5.2 \u00d7 10-1), indicating clonal expansion. Further evaluation of the frequently damaged PIK3CA and TP53 genes by ultra-sensitive duplex sequencing demonstrated a diversified picture of multiple low-level subclonal (in 10-2-10-4 alleles) hotspot pathogenic variants. Our results raise a question about the oncogenic potential in non-tumorous mammary gland tissue of breast-conserving surgery patients.", "doi": "10.1038/s41523-022-00443-9", "pmid": "35768433", "labels": {"NGI SNP genotyping": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41523-022-00443-9"}, {"db": "pmc", "key": "PMC9243094"}], "notes": [], "created": "2022-08-16T13:29:38.239Z", "modified": "2022-08-16T13:29:38.504Z"}, {"entity": "publication", "iuid": "060874a4da484eb1bb146a7d3c2a60be", "links": {"self": {"href": "https://publications.scilifelab.se/publication/060874a4da484eb1bb146a7d3c2a60be.json"}, "display": {"href": "https://publications.scilifelab.se/publication/060874a4da484eb1bb146a7d3c2a60be"}}, "title": "MYCN induces cell-specific tumorigenic growth in RB1-proficient human retinal organoid and chicken retina models of retinoblastoma.", "authors": [{"family": "Blixt", "given": "Maria K E", "initials": "MKE"}, {"family": "Hellsand", "given": "Minas", "initials": "M", "orcid": "0000-0002-1459-0377", "researcher": {"href": "https://publications.scilifelab.se/researcher/caa1e2f60d8c4fcd97c54b23246f55f2.json"}}, {"family": "Konjusha", "given": "Dardan", "initials": "D", "orcid": "0000-0002-6959-8376", "researcher": {"href": "https://publications.scilifelab.se/researcher/dfa3697dd35c422a993a87be8d50c40b.json"}}, {"family": "Zhang", "given": "Hanzhao", "initials": "H"}, {"family": "Stenfelt", "given": "Sonya", "initials": "S"}, {"family": "\u00c5kesson", "given": "Mikael", "initials": "M"}, {"family": "Rafati", "given": "Nima", "initials": "N", "orcid": "0000-0002-3687-9745", "researcher": {"href": "https://publications.scilifelab.se/researcher/8b5c32bab72f430a80485c0312ca0e21.json"}}, {"family": "Tararuk", "given": "Tatsiana", "initials": "T"}, {"family": "St\u00e5lhammar", "given": "Gustav", "initials": "G"}, {"family": "All-Eriksson", "given": "Charlotta", "initials": "C"}, {"family": "Ring", "given": "Henrik", "initials": "H"}, {"family": "Hallb\u00f6\u00f6k", "given": "Finn", "initials": "F", "orcid": "0000-0001-7552-187X", "researcher": {"href": "https://publications.scilifelab.se/researcher/6fd6bad55b67431c82e2e54e5b007917.json"}}], "type": "journal article", "published": "2022-06-21", "journal": {"title": "Oncogenesis", "issn": "2157-9024", "issn-l": null, "volume": "11", "issue": "1", "pages": "34"}, "abstract": "Retinoblastoma is a rare, intraocular paediatric cancer that originates in the neural retina and is most frequently caused by bi-allelic loss of RB1 gene function. Other oncogenic mutations, such as amplification and increased expression of the MYCN gene, have been found even with proficient RB1 function. In this study, we investigated whether MYCN over-expression can drive carcinogenesis independently of RB1 loss-of-function mutations. The aim was to elucidate the events that result in carcinogenesis and identify the cancer cell-of-origin. We used the chicken retina, a well-established model for studying retinal neurogenesis, and established human embryonic stem cell-derived retinal organoids as model systems. We over-expressed MYCN by electroporation of piggyBac genome-integrating expression vectors. We found that over-expression of MYCN induced tumorigenic growth with high frequency in RB1-proficient chicken retinas and human organoids. In both systems, the tumorigenic cells expressed markers for undifferentiated cone photoreceptor/horizontal cell progenitors. The over-expression resulted in metastatic retinoblastoma within 7-9 weeks in chicken. Cells expressing MYCN could be grown in vitro and, when orthotopically injected, formed tumours that infiltrated the sclera and optic nerve and expressed markers for cone progenitors. Investigation of the tumour cell phenotype determined that the potential for neoplastic growth was embryonic stage-dependent and featured a cell-specific resistance to apoptosis in the cone/horizontal cell lineage, but not in ganglion or amacrine cells. We conclude that MYCN over-expression is sufficient to drive tumorigenesis and that a cell-specific resistance to apoptosis in the cone/horizontal cell lineage mediates the cancer phenotype.", "doi": "10.1038/s41389-022-00409-3", "pmid": "35729105", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC9213451"}, {"db": "pii", "key": "10.1038/s41389-022-00409-3"}], "notes": [], "created": "2022-11-09T15:38:35.302Z", "modified": "2024-01-16T13:48:36.126Z"}, {"entity": "publication", "iuid": "02116106bceb47e79fce7b41053a01d8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/02116106bceb47e79fce7b41053a01d8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/02116106bceb47e79fce7b41053a01d8"}}, "title": "Genetic loci and prioritization of genes for kidney function decline derived from a meta-analysis of 62 longitudinal genome-wide association studies.", "authors": [{"family": "Gorski", "given": "Mathias", "initials": "M"}, {"family": "Rasheed", "given": "Humaira", "initials": "H"}, {"family": "Teumer", "given": "Alexander", "initials": "A"}, {"family": "Thomas", "given": "Laurent F", "initials": "LF"}, {"family": "Graham", "given": "Sarah E", "initials": "SE"}, {"family": "Sveinbjornsson", "given": "Gardar", "initials": "G"}, {"family": "Winkler", "given": "Thomas W", "initials": "TW"}, {"family": "G\u00fcnther", "given": "Felix", "initials": "F"}, {"family": "Stark", "given": "Klaus J", "initials": "KJ"}, {"family": "Chai", "given": "Jin-Fang", "initials": "JF"}, {"family": "Tayo", "given": "Bamidele O", "initials": "BO"}, {"family": "Wuttke", "given": "Matthias", "initials": "M"}, {"family": "Li", "given": "Yong", "initials": "Y"}, {"family": "Tin", "given": "Adrienne", "initials": "A"}, {"family": "Ahluwalia", "given": "Tarunveer S", "initials": "TS"}, {"family": "\u00c4rnl\u00f6v", "given": "Johan", "initials": "J"}, {"family": "\u00c5svold", "given": "Bj\u00f8rn Olav", "initials": "BO"}, {"family": "Bakker", "given": "Stephan J L", "initials": "SJL"}, {"family": "Banas", "given": "Bernhard", "initials": "B"}, {"family": "Bansal", "given": "Nisha", "initials": "N"}, {"family": "Biggs", "given": "Mary L", "initials": "ML"}, {"family": "Biino", "given": "Ginevra", "initials": "G"}, {"family": "B\u00f6hnke", "given": "Michael", "initials": "M"}, {"family": "Boerwinkle", "given": "Eric", "initials": "E"}, {"family": "Bottinger", "given": "Erwin P", "initials": "EP"}, {"family": "Brenner", "given": "Hermann", "initials": "H"}, {"family": "Brumpton", "given": "Ben", "initials": "B"}, {"family": "Carroll", "given": "Robert J", "initials": "RJ"}, {"family": "Chaker", "given": "Layal", "initials": "L"}, {"family": "Chalmers", "given": "John", "initials": "J"}, {"family": "Chee", "given": "Miao-Li", "initials": "ML"}, {"family": "Chee", "given": "Miao-Ling", "initials": "ML"}, {"family": "Cheng", "given": "Ching-Yu", "initials": "CY"}, {"family": "Chu", "given": "Audrey Y", "initials": "AY"}, {"family": "Ciullo", "given": "Marina", "initials": "M"}, {"family": "Cocca", "given": "Massimiliano", "initials": "M"}, {"family": "Cook", "given": "James P", "initials": "JP"}, {"family": "Coresh", "given": "Josef", "initials": "J"}, {"family": "Cusi", "given": "Daniele", "initials": "D"}, {"family": "de Borst", "given": "Martin H", "initials": "MH"}, {"family": "Degenhardt", "given": "Frauke", "initials": "F"}, {"family": "Eckardt", "given": "Kai-Uwe", "initials": "KU"}, {"family": "Endlich", "given": "Karlhans", "initials": "K"}, {"family": "Evans", "given": "Michele K", "initials": "MK"}, {"family": "Feitosa", "given": "Mary F", "initials": "MF"}, {"family": "Franke", "given": "Andre", "initials": "A"}, {"family": "Freitag-Wolf", "given": "Sandra", "initials": "S"}, {"family": "Fuchsberger", "given": "Christian", "initials": "C"}, {"family": "Gampawar", "given": "Piyush", "initials": "P"}, {"family": "Gansevoort", "given": "Ron T", "initials": "RT"}, {"family": "Ghanbari", "given": "Mohsen", "initials": "M"}, {"family": "Ghasemi", "given": "Sahar", "initials": "S"}, {"family": "Giedraitis", "given": "Vilmantas", "initials": "V"}, {"family": "Gieger", "given": "Christian", "initials": "C"}, {"family": "Gudbjartsson", "given": "Daniel F", "initials": "DF"}, {"family": "Hallan", "given": "Stein", "initials": "S"}, {"family": "Hamet", "given": "Pavel", "initials": "P"}, {"family": "Hishida", "given": "Asahi", "initials": "A"}, {"family": "Ho", "given": "Kevin", "initials": "K"}, {"family": "Hofer", "given": "Edith", "initials": "E"}, {"family": "Holleczek", "given": "Bernd", "initials": "B"}, {"family": "Holm", "given": "Hilma", "initials": "H"}, {"family": "Hoppmann", "given": "Anselm", "initials": "A"}, {"family": "Horn", "given": "Katrin", "initials": "K"}, {"family": "Hutri-K\u00e4h\u00f6nen", "given": "Nina", "initials": "N"}, {"family": "Hveem", "given": "Kristian", "initials": "K"}, {"family": "Hwang", "given": "Shih-Jen", "initials": "SJ"}, {"family": "Ikram", "given": "M Arfan", "initials": "MA"}, {"family": "Josyula", "given": "Navya Shilpa", "initials": "NS"}, {"family": "Jung", "given": "Bettina", "initials": "B"}, {"family": "K\u00e4h\u00f6nen", "given": "Mika", "initials": "M"}, {"family": "Karabegovi\u0107", "given": "Irma", "initials": "I"}, {"family": "Khor", "given": "Chiea-Chuen", "initials": "CC"}, {"family": "Koenig", "given": "Wolfgang", "initials": "W"}, {"family": "Kramer", "given": "Holly", "initials": "H"}, {"family": "Kr\u00e4mer", "given": "Bernhard K", "initials": "BK"}, {"family": "K\u00fchnel", "given": "Brigitte", "initials": "B"}, {"family": "Kuusisto", "given": "Johanna", "initials": "J"}, {"family": "Laakso", "given": "Markku", "initials": "M"}, {"family": "Lange", "given": "Leslie A", "initials": "LA"}, {"family": "Lehtim\u00e4ki", "given": "Terho", "initials": "T"}, {"family": "Li", "given": "Man", "initials": "M"}, {"family": "Lieb", "given": "Wolfgang", "initials": "W"}, {"family": "Lifelines Cohort Study", "given": "", "initials": ""}, {"family": "Lind", "given": "Lars", "initials": "L"}, {"family": "Lindgren", "given": "Cecilia M", "initials": "CM"}, {"family": "Loos", "given": "Ruth J F", "initials": "RJF"}, {"family": "Lukas", "given": "Mary Ann", "initials": "MA"}, {"family": "Lyytik\u00e4inen", "given": "Leo-Pekka", "initials": "LP"}, {"family": "Mahajan", "given": "Anubha", "initials": "A"}, {"family": "Matias-Garcia", "given": "Pamela R", "initials": "PR"}, {"family": "Meisinger", "given": "Christa", "initials": "C"}, {"family": "Meitinger", "given": "Thomas", "initials": "T"}, {"family": "Melander", "given": "Olle", "initials": "O"}, {"family": "Milaneschi", "given": "Yuri", "initials": "Y"}, {"family": "Mishra", "given": "Pashupati P", "initials": "PP"}, {"family": "Mononen", "given": "Nina", "initials": "N"}, {"family": "Morris", "given": "Andrew P", "initials": "AP"}, {"family": "Mychaleckyj", "given": "Josyf C", "initials": "JC"}, {"family": "Nadkarni", "given": "Girish N", "initials": "GN"}, {"family": "Naito", "given": "Mariko", "initials": "M"}, {"family": "Nakatochi", "given": "Masahiro", "initials": "M"}, {"family": "Nalls", "given": "Mike A", "initials": "MA"}, {"family": "Nauck", "given": "Matthias", "initials": "M"}, {"family": "Nikus", "given": "Kjell", "initials": "K"}, {"family": "Ning", "given": "Boting", "initials": "B"}, {"family": "Nolte", "given": "Ilja M", "initials": "IM"}, {"family": "Nutile", "given": "Teresa", "initials": "T"}, {"family": "O'Donoghue", "given": "Michelle L", "initials": "ML"}, {"family": "O'Connell", "given": "Jeffrey", "initials": "J"}, {"family": "Olafsson", "given": "Isleifur", "initials": "I"}, {"family": "Orho-Melander", "given": "Marju", "initials": "M"}, {"family": "Parsa", "given": "Afshin", "initials": "A"}, {"family": "Pendergrass", "given": "Sarah A", "initials": "SA"}, {"family": "Penninx", "given": "Brenda W J H", "initials": "BWJH"}, {"family": "Pirastu", "given": "Mario", "initials": "M"}, {"family": "Preuss", "given": "Michael H", "initials": "MH"}, {"family": "Psaty", "given": "Bruce M", "initials": "BM"}, {"family": "Raffield", "given": "Laura M", "initials": "LM"}, {"family": "Raitakari", "given": "Olli T", "initials": "OT"}, {"family": "Rheinberger", "given": "Myriam", "initials": "M"}, {"family": "Rice", "given": "Kenneth M", "initials": "KM"}, {"family": "Rizzi", "given": "Federica", "initials": "F"}, {"family": "Rosenkranz", "given": "Alexander R", "initials": "AR"}, {"family": "Rossing", "given": "Peter", "initials": "P"}, {"family": "Rotter", "given": "Jerome I", "initials": "JI"}, {"family": "Ruggiero", "given": "Daniela", "initials": "D"}, {"family": "Ryan", "given": "Kathleen A", "initials": "KA"}, {"family": "Sabanayagam", "given": "Charumathi", "initials": "C"}, {"family": "Salvi", "given": "Erika", "initials": "E"}, {"family": "Schmidt", "given": "Helena", "initials": "H"}, {"family": "Schmidt", "given": "Reinhold", "initials": "R"}, {"family": "Scholz", "given": "Markus", "initials": "M"}, {"family": "Sch\u00f6ttker", "given": "Ben", "initials": "B"}, {"family": "Schulz", "given": "Christina-Alexandra", "initials": "CA"}, {"family": "Sedaghat", "given": "Sanaz", "initials": "S"}, {"family": "Shaffer", "given": "Christian M", "initials": "CM"}, {"family": "Sieber", "given": "Karsten B", "initials": "KB"}, {"family": "Sim", "given": "Xueling", "initials": "X"}, {"family": "Sims", "given": "Mario", "initials": "M"}, {"family": "Snieder", "given": "Harold", "initials": "H"}, {"family": "Stanzick", "given": "Kira J", "initials": "KJ"}, {"family": "Thorsteinsdottir", "given": "Unnur", "initials": "U"}, {"family": "Stocker", "given": "Hannah", "initials": "H"}, {"family": "Strauch", "given": "Konstantin", "initials": "K"}, {"family": "Stringham", "given": "Heather M", "initials": "HM"}, {"family": "Sulem", "given": "Patrick", "initials": "P"}, {"family": "Szymczak", "given": "Silke", "initials": "S"}, {"family": "Taylor", "given": "Kent D", "initials": "KD"}, {"family": "Thio", "given": "Chris H L", "initials": "CHL"}, {"family": "Tremblay", "given": "Johanne", "initials": "J"}, {"family": "Vaccargiu", "given": "Simona", "initials": "S"}, {"family": "van der Harst", "given": "Pim", "initials": "P"}, {"family": "van der Most", "given": "Peter J", "initials": "PJ"}, {"family": "Verweij", "given": "Niek", "initials": "N"}, {"family": "V\u00f6lker", "given": "Uwe", "initials": "U"}, {"family": "Wakai", "given": "Kenji", "initials": "K"}, {"family": "Waldenberger", "given": "Melanie", "initials": "M"}, {"family": "Wallentin", "given": "Lars", "initials": "L"}, {"family": "Wallner", "given": "Stefan", "initials": "S"}, {"family": "Wang", "given": "Judy", "initials": "J"}, {"family": "Waterworth", "given": "Dawn M", "initials": "DM"}, {"family": "White", "given": "Harvey D", "initials": "HD"}, {"family": "Willer", "given": "Cristen J", "initials": "CJ"}, {"family": "Wong", "given": "Tien-Yin", "initials": "TY"}, {"family": "Woodward", "given": "Mark", "initials": "M"}, {"family": "Yang", "given": "Qiong", "initials": "Q"}, {"family": "Yerges-Armstrong", "given": "Laura M", "initials": "LM"}, {"family": "Zimmermann", "given": "Martina", "initials": "M"}, {"family": "Zonderman", "given": "Alan B", "initials": "AB"}, {"family": "Bergler", "given": "Tobias", "initials": "T"}, {"family": "Stefansson", "given": "Kari", "initials": "K"}, {"family": "B\u00f6ger", "given": "Carsten A", "initials": "CA"}, {"family": "Pattaro", "given": "Cristian", "initials": "C"}, {"family": "K\u00f6ttgen", "given": "Anna", "initials": "A"}, {"family": "Kronenberg", "given": "Florian", "initials": "F"}, {"family": "Heid", "given": "Iris M", "initials": "IM"}], "type": "journal article", "published": "2022-06-16", "journal": {"title": "Kidney Int.", "issn": "1523-1755", "issn-l": "0085-2538"}, "abstract": "Estimated glomerular filtration rate (eGFR) reflects kidney function. Progressive eGFR-decline can lead to kidney failure, necessitating dialysis or transplantation. Hundreds of loci from genome-wide association studies (GWAS) for eGFR help explain population cross section variability. Since the contribution of these or other loci to eGFR-decline remains largely unknown, we derived GWAS for annual eGFR-decline and meta-analyzed 62 longitudinal studies with eGFR assessed twice over time in all 343,339 individuals and in high-risk groups. We also explored different covariate adjustment. Twelve genome-wide significant independent variants for eGFR-decline unadjusted or adjusted for eGFR-baseline (11 novel, one known for this phenotype), including nine variants robustly associated across models were identified. All loci for eGFR-decline were known for cross-sectional eGFR and thus distinguished a subgroup of eGFR loci. Seven of the nine variants showed variant-by-age interaction on eGFR cross section (further about 350,000 individuals), which linked genetic associations for eGFR-decline with age-dependency of genetic cross-section associations. Clinically important were two to four-fold greater genetic effects on eGFR-decline in high-risk subgroups. Five variants associated also with chronic kidney disease progression mapped to genes with functional in-silico evidence (UMOD, SPATA7, GALNTL5, TPPP). An unfavorable versus favorable nine-variant genetic profile showed increased risk odds ratios of 1.35 for kidney failure (95% confidence intervals 1.03-1.77) and 1.27 for acute kidney injury (95% confidence intervals 1.08-1.50) in over 2000 cases each, with matched controls). Thus, we provide a large data resource, genetic loci, and prioritized genes for kidney function decline, which help inform drug development pipelines revealing important insights into the age-dependency of kidney function genetics.", "doi": "10.1016/j.kint.2022.05.021", "pmid": "35716955", "labels": {"NGI SNP genotyping": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pii", "key": "S0085-2538(22)00454-9"}], "notes": [], "created": "2022-08-16T13:29:40.854Z", "modified": "2022-08-16T13:29:40.870Z"}, {"entity": "publication", "iuid": "20044ca7f045473daf17863e0344b451", "links": {"self": {"href": "https://publications.scilifelab.se/publication/20044ca7f045473daf17863e0344b451.json"}, "display": {"href": "https://publications.scilifelab.se/publication/20044ca7f045473daf17863e0344b451"}}, "title": "Differential and shared genetic effects on kidney function between diabetic and non-diabetic individuals.", 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"0000-0003-2544-4460", "researcher": {"href": "https://publications.scilifelab.se/researcher/b6b229457c2c4b25ae9c7d2cf029b82b.json"}}, {"family": "Gao", "given": "Xin", "initials": "X"}, {"family": "Sim", "given": "Xueling", "initials": "X", "orcid": "0000-0002-1233-7642", "researcher": {"href": "https://publications.scilifelab.se/researcher/3216a8d2a7264a1390a886fa09d5d648.json"}}, {"family": "Wang", "given": "Ya Xing", "initials": "YX", "orcid": "0000-0003-2749-7793", "researcher": {"href": "https://publications.scilifelab.se/researcher/a335d5361052470689def030e03e597b.json"}}, {"family": "Friedlander", "given": "Yechiel", "initials": "Y"}, {"family": "Tham", "given": "Yih-Chung", "initials": "YC", "orcid": "0000-0002-6752-797X", "researcher": {"href": "https://publications.scilifelab.se/researcher/8175b4e810bb4a1b9448d2e69be60a31.json"}}, {"family": "Kamatani", "given": "Yoichiro", "initials": "Y", "orcid": "0000-0001-8748-5597", "researcher": {"href": "https://publications.scilifelab.se/researcher/6cf00b09991c4b40bd77a4f2c5bfad97.json"}}, {"family": "Okada", "given": "Yukinori", "initials": "Y", "orcid": "0000-0002-0311-8472", "researcher": {"href": "https://publications.scilifelab.se/researcher/40b13860bfef41959c29be2de853b456.json"}}, {"family": "Milaneschi", "given": "Yuri", "initials": "Y"}, {"family": "Yu", "given": "Zhi", "initials": "Z", "orcid": "0000-0003-4810-3474", "researcher": {"href": "https://publications.scilifelab.se/researcher/df8600142a4249b6860fd0cbfa3bda5c.json"}}, {"family": "Lifelines cohort study", "given": "", "initials": ""}, {"family": "DiscovEHR/MyCode study", "given": "", "initials": ""}, {"family": "VA Million Veteran Program", "given": "", "initials": ""}, {"family": "Stark", "given": "Klaus J", "initials": "KJ"}, {"family": "Stefansson", "given": "Kari", "initials": "K", "orcid": "0000-0003-1676-864X", "researcher": {"href": "https://publications.scilifelab.se/researcher/679465193fba4887a68e2aec34ccfd8e.json"}}, {"family": "B\u00f6ger", "given": "Carsten A", "initials": "CA"}, {"family": "Hung", "given": "Adriana M", "initials": "AM"}, {"family": "Kronenberg", "given": "Florian", "initials": "F", "orcid": "0000-0003-2229-1120", "researcher": {"href": "https://publications.scilifelab.se/researcher/ebc59079554842ecb3512ef90249a2f2.json"}}, {"family": "K\u00f6ttgen", "given": "Anna", "initials": "A", "orcid": "0000-0002-4671-3714", "researcher": {"href": "https://publications.scilifelab.se/researcher/fe4cb85a14da4db6bc932a8bc4148efb.json"}}, {"family": "Pattaro", "given": "Cristian", "initials": "C", "orcid": "0000-0002-4119-0109", "researcher": {"href": "https://publications.scilifelab.se/researcher/3a6a570bbec647b188c4a7a5da03caac.json"}}, {"family": "Heid", "given": "Iris M", "initials": "IM", "orcid": "0000-0002-4122-5308", "researcher": {"href": "https://publications.scilifelab.se/researcher/34990140a9604dd7b61807dafc8fabc6.json"}}], "type": "journal article", "published": "2022-06-13", "journal": {"title": "Commun Biol", "issn": "2399-3642", "volume": "5", "issue": "1", "pages": "580", "issn-l": "2399-3642"}, "abstract": "Reduced glomerular filtration rate (GFR) can progress to kidney failure. Risk factors include genetics and diabetes mellitus (DM), but little is known about their interaction. We conducted genome-wide association meta-analyses for estimated GFR based on serum creatinine (eGFR), separately for individuals with or without DM (nDM = 178,691, nnoDM = 1,296,113). Our genome-wide searches identified (i) seven eGFR loci with significant DM/noDM-difference, (ii) four additional novel loci with suggestive difference and (iii) 28 further novel loci (including CUBN) by allowing for potential difference. GWAS on eGFR among DM individuals identified 2 known and 27 potentially responsible loci for diabetic kidney disease. Gene prioritization highlighted 18 genes that may inform reno-protective drug development. We highlight the existence of DM-only and noDM-only effects, which can inform about the target group, if respective genes are advanced as drug targets. Largely shared effects suggest that most drug interventions to alter eGFR should be effective in DM and noDM.", "doi": "10.1038/s42003-022-03448-z", "pmid": "35697829", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI SNP genotyping": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s42003-022-03448-z"}, {"db": "pmc", "key": "PMC9192715"}], "notes": [], "created": "2022-06-14T13:16:22.813Z", "modified": "2022-11-21T15:40:40.440Z"}, {"entity": "publication", "iuid": "af20ba6362a54f1bb72479cd4ba927c2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/af20ba6362a54f1bb72479cd4ba927c2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/af20ba6362a54f1bb72479cd4ba927c2"}}, "title": "Accelerated epigenetic aging in suicide attempters uninfluenced by high intent-to-die and choice of lethal methods.", "authors": [{"family": "Jokinen", "given": "Jussi", "initials": "J"}, {"family": "Andersson", "given": "Peter", "initials": "P"}, {"family": "Chatzittofis", "given": "Andreas", "initials": "A", "orcid": "0000-0002-6635-9564", "researcher": {"href": "https://publications.scilifelab.se/researcher/35583d0beb824e068ffd9c015d46309d.json"}}, {"family": "Savard", "given": "Josephine", "initials": "J", "orcid": "0000-0002-0140-4109", "researcher": {"href": "https://publications.scilifelab.se/researcher/19be5afe66ea42d5a2d5cb1695ff0da6.json"}}, {"family": "Rask-Andersen", "given": "Mathias", "initials": "M"}, {"family": "\u00c5sberg", "given": "Marie", "initials": "M"}, {"family": "Bostr\u00f6m", "given": "Adrian Desai E", "initials": "ADE", "orcid": "0000-0001-8604-9638", "researcher": {"href": "https://publications.scilifelab.se/researcher/5ace74b9a4894d82a16e7ff445bbcea6.json"}}], "type": "journal article", "published": "2022-06-02", "journal": {"title": "Transl Psychiatry", "issn": "2158-3188", "volume": "12", "issue": "1", "pages": "224", "issn-l": "2158-3188"}, "abstract": "Suicide attempts (SA) are associated with excess non-suicidal mortality, putatively mediated in part by premature cellular senescence. Epigenetic age (EA) estimators of biological age have been previously demonstrated to strongly predict physiological dysregulation and mortality risk. Herein, we investigate if violent SA with high intent-to-die is predictive of epigenetics-derived estimates of biological aging. The genome-wide methylation pattern was measured using the Illumina Infinium Methylation EPIC BeadChip in whole blood of 88 suicide attempters. Subjects were stratified into two groups based on the putative risk of later committed suicide (low- [n = 58] and high-risk [n = 30]) in dependency of SA method (violent or non-violent) and/or intent-to-die (high/low). Estimators of intrinsic and extrinsic EA acceleration, one marker optimized to predict physiological dysregulation (DNAmPhenoAge/AgeAccelPheno) and one optimized to predict lifespan (DNAmGrimAge/AgeAccelGrim) were investigated for associations to severity of SA, by univariate and multivariate analyses. The study was adequately powered to detect differences of 2.2 years in AgeAccelGrim in relation to SA severity. Baseline DNAmGrimAge exceeded chronological age by 7.3 years on average across all samples, conferring a mean 24.6% increase in relation to actual age. No individual EA acceleration marker was differentiated by suicidal risk group (p > 0.1). Thus, SA per se but not severity of SA is related to EA, implicating that excess non-suicidal mortality in SA is unrelated to risk of committed suicide. Preventative healthcare efforts aimed at curtailing excess mortality after SA may benefit from acting equally powerful to recognize somatic comorbidities irrespective of the severity inherent in the act itself.", "doi": "10.1038/s41398-022-01998-8", "pmid": "35654772", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI SNP genotyping": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41398-022-01998-8"}], "notes": [], "created": "2022-06-14T13:16:27.182Z", "modified": "2022-06-14T13:16:27.377Z"}, {"entity": "publication", "iuid": "93a04540a4c2419ca466a44ebbe062b8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/93a04540a4c2419ca466a44ebbe062b8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/93a04540a4c2419ca466a44ebbe062b8"}}, "title": "The HDAC9-associated risk locus promotes coronary artery disease by governing TWIST1.", "authors": [{"family": "Ma", "given": "Lijiang", "initials": "L", "orcid": "0000-0001-6498-5556", "researcher": {"href": "https://publications.scilifelab.se/researcher/f000e91a6c8c4ab081846c120683edc2.json"}}, {"family": "Bryce", "given": "Nicole S", "initials": "NS", "orcid": "0000-0001-9799-7393", "researcher": {"href": "https://publications.scilifelab.se/researcher/78e70822e0584633874053649f608dd1.json"}}, {"family": "Turner", "given": "Adam W", "initials": "AW"}, {"family": "Di Narzo", "given": "Antonio F", "initials": "AF", "orcid": "0000-0002-4033-5038", "researcher": {"href": "https://publications.scilifelab.se/researcher/c826b7a4f7cb446cb60410e167150312.json"}}, {"family": "Rahman", "given": "Karishma", "initials": "K", "orcid": "0000-0002-7675-9596", "researcher": {"href": "https://publications.scilifelab.se/researcher/7fa895ec4c8449b0b6e0841259ab7101.json"}}, {"family": "Xu", "given": "Yang", "initials": "Y", "orcid": "0000-0003-4669-0003", "researcher": {"href": "https://publications.scilifelab.se/researcher/0b571d6393af4cacbc53cf9208201266.json"}}, {"family": "Ermel", "given": "Raili", "initials": "R"}, {"family": "Sukhavasi", "given": "Katyayani", "initials": "K", "orcid": "0000-0001-5627-0163", "researcher": {"href": "https://publications.scilifelab.se/researcher/147dcf0d2b604e219e5b9b5cd7089a55.json"}}, {"family": "d'Escamard", "given": "Valentina", "initials": "V"}, {"family": "Chandel", "given": "Nirupama", "initials": "N"}, {"family": "V'Gangula", "given": "Bhargavi", "initials": "B"}, {"family": "Wolhuter", "given": "Kathryn", "initials": "K", "orcid": "0000-0001-6293-9820", "researcher": {"href": "https://publications.scilifelab.se/researcher/363b5011d58d412290824444e3e51399.json"}}, {"family": "Kadian-Dodov", "given": "Daniella", "initials": "D"}, {"family": "Franzen", "given": "Oscar", "initials": "O"}, {"family": "Ruusalepp", "given": "Arno", "initials": "A"}, {"family": "Hao", "given": "Ke", "initials": "K"}, {"family": "Miller", "given": "Clint L", "initials": "CL", "orcid": "0000-0003-4276-3607", "researcher": {"href": "https://publications.scilifelab.se/researcher/f126f09351544045a13bae1ff4391e78.json"}}, {"family": "Bj\u00f6rkegren", "given": "Johan L M", "initials": "JLM"}, {"family": "Kovacic", "given": "Jason C", "initials": "JC", "orcid": "0000-0003-4555-769X", "researcher": {"href": "https://publications.scilifelab.se/researcher/caefcca7394142918b01b3660da6551d.json"}}], "type": "journal article", "published": "2022-06-00", "journal": {"title": "PLoS Genet.", "issn": "1553-7404", "volume": "18", "issue": "6", "pages": "e1010261", "issn-l": "1553-7390"}, "abstract": "Genome wide association studies (GWAS) have identified thousands of single nucleotide polymorphisms (SNPs) associated with the risk of common disorders. However, since the large majority of these risk SNPs reside outside gene-coding regions, GWAS generally provide no information about causal mechanisms regarding the specific gene(s) that are affected or the tissue(s) in which these candidate gene(s) exert their effect. The 'gold standard' method for understanding causal genes and their mechanisms of action are laborious basic science studies often involving sophisticated knockin or knockout mouse lines, however, these types of studies are impractical as a high-throughput means to understand the many risk variants that cause complex diseases like coronary artery disease (CAD). As a solution, we developed a streamlined, data-driven informatics pipeline to gain mechanistic insights on complex genetic loci. The pipeline begins by understanding the SNPs in a given locus in terms of their relative location and linkage disequilibrium relationships, and then identifies nearby expression quantitative trait loci (eQTLs) to determine their relative independence and the likely tissues that mediate their disease-causal effects. The pipeline then seeks to understand associations with other disease-relevant genes, disease sub-phenotypes, potential causality (Mendelian randomization), and the regulatory and functional involvement of these genes in gene regulatory co-expression networks (GRNs). Here, we applied this pipeline to understand a cluster of SNPs associated with CAD within and immediately adjacent to the gene encoding HDAC9. Our pipeline demonstrated, and validated, that this locus is causal for CAD by modulation of TWIST1 expression levels in the arterial wall, and by also governing a GRN related to metabolic function in skeletal muscle. Our results reconciled numerous prior studies, and also provided clear evidence that this locus does not govern HDAC9 expression, structure or function. This pipeline should be considered as a powerful and efficient way to understand GWAS risk loci in a manner that better reflects the highly complex nature of genetic risk associated with common disorders.", "doi": "10.1371/journal.pgen.1010261", "pmid": "35714152", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9246173"}, {"db": "pii", "key": "PGENETICS-D-21-01392"}], "notes": [], "created": "2022-11-29T12:12:39.019Z", "modified": "2022-11-29T12:12:39.361Z"}, {"entity": "publication", "iuid": "0b04ba3887a041eab29ed76faa76295d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0b04ba3887a041eab29ed76faa76295d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0b04ba3887a041eab29ed76faa76295d"}}, "title": "Single base substitution and insertion/deletion mutational signatures in adult core binding factor acute myeloid leukemia.", "authors": [{"family": "Gunnarsson", "given": "Rebeqa", "initials": "R", "orcid": "0000-0002-2283-786X", "researcher": {"href": "https://publications.scilifelab.se/researcher/12601745d2c74562bf83d22879f212eb.json"}}, {"family": "Yang", "given": "Minjun", "initials": "M", "orcid": "0000-0002-3324-1498", "researcher": {"href": "https://publications.scilifelab.se/researcher/62822d0b9c6c4a01a53829b9b05443ba.json"}}, {"family": "Biloglav", "given": "Andrea", "initials": "A"}, {"family": "Lazarevic", "given": "Vladimir", "initials": "V", "orcid": "0000-0002-1782-4423", "researcher": {"href": "https://publications.scilifelab.se/researcher/7113f0d0569247d4ac94b73ddc6ca74e.json"}}, {"family": "Paulsson", "given": "Kajsa", "initials": "K", "orcid": "0000-0001-7950-222X", "researcher": {"href": "https://publications.scilifelab.se/researcher/2033b23811f1432c90ad860dd993e7a8.json"}}, {"family": "Johansson", "given": "Bertil", "initials": "B"}], "type": "letter", "published": "2022-06-00", "journal": {"title": "Leukemia", "issn": "1476-5551", "volume": "36", "issue": "6", "pages": "1681-1684", "issn-l": "0887-6924"}, "abstract": null, "doi": "10.1038/s41375-022-01552-x", "pmid": "35365774", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9162923"}, {"db": "pii", "key": "10.1038/s41375-022-01552-x"}], "notes": [], "created": "2022-11-29T09:20:02.714Z", "modified": "2022-11-29T09:20:02.768Z"}, {"entity": "publication", "iuid": "abd2fc3cd35d4629bddfad68f4bfab4f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/abd2fc3cd35d4629bddfad68f4bfab4f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/abd2fc3cd35d4629bddfad68f4bfab4f"}}, "title": "Improving lithium dose prediction using population pharmacokinetics and pharmacogenomics: a cohort genome-wide association study in Sweden", "authors": [{"family": "Millischer", "given": "Vincent", "initials": "V"}, {"family": "Matheson", "given": "Granville J", "initials": "GJ"}, {"family": "Bergen", "given": "Sarah E", "initials": "SE"}, {"family": "Coombes", "given": "Brandon J", "initials": "BJ"}, {"family": "Ponzer", "given": "Katja", "initials": "K"}, {"family": "Wikstr\u00f6m", "given": "Fredrik", "initials": "F"}, {"family": "Jagiello", "given": "Karolina", "initials": "K"}, {"family": "Lundberg", "given": "Martin", "initials": "M"}, {"family": "Stenvinkel", "given": "Peter", "initials": "P"}, {"family": "Biernacka", "given": "Joanna M", "initials": "JM"}, {"family": "Breuer", "given": "Olof", "initials": "O"}, {"family": "Martinsson", "given": "Lina", "initials": "L"}, {"family": "Land\u00e9n", "given": "Mikael", "initials": "M"}, {"family": "Backlund", "given": "Lena", "initials": "L"}, {"family": "Lavebratt", "given": "Catharina", "initials": "C"}, {"family": "Schalling", "given": "Martin", "initials": "M"}], "type": "journal-article", "published": "2022-06-00", "journal": {"title": "The Lancet Psychiatry", "issn": "2215-0374", "issn-l": null, "volume": "9", "issue": "6", "pages": "447-457"}, "abstract": null, "doi": "10.1016/s2215-0366(22)00100-6", "pmid": null, "labels": {"National Genomics Infrastructure": "Service", "NGI SNP genotyping": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [], "notes": [], "created": "2022-05-23T13:59:34.257Z", "modified": "2024-01-19T12:52:11.397Z"}, {"entity": "publication", "iuid": "2bd624ebafa942a99f4c19129a9f55e3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2bd624ebafa942a99f4c19129a9f55e3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2bd624ebafa942a99f4c19129a9f55e3"}}, "title": "Genetic determinants of mannose-binding lectin activity predispose to thromboembolic complications in critical COVID-19.", "authors": [{"family": "Hultstr\u00f6m", "given": "Michael", "initials": "M", "orcid": "0000-0003-4675-1099", "researcher": {"href": "https://publications.scilifelab.se/researcher/c9a74d3380a24c31930e6e671e685b5b.json"}}, {"family": "Frithiof", "given": "Robert", "initials": "R", "orcid": "0000-0003-2278-7951", "researcher": {"href": "https://publications.scilifelab.se/researcher/8fec11dd18f941b7842610ad14237a35.json"}}, {"family": "Grip", "given": "Jonathan", "initials": "J"}, {"family": "Lindel\u00f6f", "given": "Linnea", "initials": "L", "orcid": "0000-0002-3654-8874", "researcher": {"href": "https://publications.scilifelab.se/researcher/65f6c8233c5547f2885b3e55bbec2601.json"}}, {"family": "Rooijackers", "given": "Olav", "initials": "O"}, {"family": "Pigazzini", "given": "Sara", "initials": "S"}, {"family": "Niemi", "given": "Mari", "initials": "M"}, {"family": "Cordioli", "given": "Mattia", "initials": "M"}, {"family": "Nkambule", "given": "Lindo", "initials": "L"}, {"family": "Maricic", "given": "Tomislav", "initials": "T"}, {"family": "Ekdahl", "given": "Kristina Nilsson", "initials": "KN"}, {"family": "Nilsson", "given": "Bo", "initials": "B"}, {"family": "Lipcsey", "given": "Mikl\u00f3s", "initials": "M"}, {"family": "Zeberg", "given": "Hugo", "initials": "H", "orcid": "0000-0001-7118-1249", "researcher": {"href": "https://publications.scilifelab.se/researcher/090e842ed8ff4cf2a3fe5f8e58118e58.json"}}, {"family": "Eriksson", "given": "Oskar", "initials": "O", "orcid": "0000-0003-2418-6463", "researcher": {"href": "https://publications.scilifelab.se/researcher/be37c57d144c443d8d52df450b86a3fe.json"}}], "type": "letter", "published": "2022-06-00", "journal": {"title": "Nat. Immunol.", "issn": "1529-2916", "volume": "23", "issue": "6", "pages": "861-864", "issn-l": "1529-2908"}, "abstract": null, "doi": "10.1038/s41590-022-01227-w", "pmid": "35624204", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "NGI SNP genotyping": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41590-022-01227-w"}], "notes": [], "created": "2022-08-29T14:11:07.067Z", "modified": "2024-01-16T13:48:36.311Z"}, {"entity": "publication", "iuid": "5bdee259698b486498433b1d0d8dfda6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5bdee259698b486498433b1d0d8dfda6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5bdee259698b486498433b1d0d8dfda6"}}, "title": "Chronic Obstructive Pulmonary Disease Is Associated with Epigenome-Wide Differential Methylation in BAL Lung Cells.", "authors": [{"family": "Eriksson Str\u00f6m", "given": "Jonas", "initials": "J", "orcid": "0000-0002-3434-988X", "researcher": {"href": "https://publications.scilifelab.se/researcher/fb26be62d048452d97790f704c4456e5.json"}}, {"family": "Kebede Merid", "given": "Simon", "initials": "S"}, {"family": "Pourazar", "given": "Jamshid", "initials": "J"}, {"family": "Blomberg", "given": "Anders", "initials": "A"}, {"family": "Lindberg", "given": "Anne", "initials": "A", "orcid": "0000-0002-3292-7471", "researcher": {"href": "https://publications.scilifelab.se/researcher/7ae273fae3f74964b42c6cc110951d64.json"}}, {"family": "Ringh", "given": "Mikael V", "initials": "MV"}, {"family": "Hagemann-Jensen", "given": "Michael", "initials": "M"}, {"family": "Ekstr\u00f6m", "given": "Tomas J", "initials": "TJ"}, {"family": "Behndig", "given": "Annelie F", "initials": "AF"}, {"family": "Mel\u00e9n", "given": "Erik", "initials": "E"}], "type": "journal article", "published": "2022-06-00", "journal": {"title": "Am J Respir Cell Mol Biol", "issn": "1535-4989", "volume": "66", "issue": "6", "pages": "638-647", "issn-l": null}, "abstract": "DNA methylation patterns in chronic pulmonary obstructive disease (COPD) might offer new insights into disease pathogenesis. To assess methylation profiles in the main COPD target organ, we performed an epigenome-wide association study on BAL cells. Bronchoscopies were performed in 18 subjects with COPD and 15 control subjects (ex- and current smokers). DNA methylation was measured using the Illumina MethylationEPIC BeadChip Kit, covering more than 850,000 CpGs. Differentially methylated positions (DMPs) were examined for 1) enrichment in pathways and functional gene relationships using the Kyoto Encyclopedia of Genes and Genomes and Gene Ontology, 2) accelerated aging using Horvath's epigenetic clock, 3) correlation with gene expression, and 4) colocalization with genetic variation. We found 1,155 Bonferroni-significant (P < 6.74 \u00d7 10-8) DMPs associated with COPD, many with large effect sizes. Functional analysis identified biologically plausible pathways and gene relationships, including enrichment for transcription factor activity. Strong correlation was found between DNA methylation and chronological age but not between COPD and accelerated aging. For 79 unique DMPs, DNA methylation correlated significantly with gene expression in BAL cells. Thirty-nine percent of DMPs were colocalized with COPD-associated SNPs. To the best of our knowledge, this is the first epigenome-wide association study of COPD on BAL cells, and our analyses revealed many differential methylation sites. Integration with mRNA data showed a strong functional readout for relevant genes, identifying sites where DNA methylation might directly affect expression. Almost half of DMPs were colocated with SNPs identified in previous genome-wide association studies of COPD, suggesting joint genetic and epigenetic pathways related to disease.", "doi": "10.1165/rcmb.2021-0403OC", "pmid": "35286818", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "NGI SNP genotyping": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9163645"}], "notes": [], "created": "2022-05-06T10:18:18.738Z", "modified": "2024-01-16T13:48:36.334Z"}, {"entity": "publication", "iuid": "c2b2bd4639fc4fee871c6ab8e77b0a9f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c2b2bd4639fc4fee871c6ab8e77b0a9f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c2b2bd4639fc4fee871c6ab8e77b0a9f"}}, "title": "Ancient DNA from a 2700-year-old goitered gazelle (Gazella subgutturosa) supports gazelle hunting in Iron Age Central Asia.", "authors": [{"family": "Rodrigues Soares", "given": "Andr\u00e9 Elias", "initials": "AE"}, {"family": "Boroffka", "given": "Nikolaus", "initials": "N"}, {"family": "Schr\u00f6der", "given": "Oskar", "initials": "O"}, {"family": "Sverchkov", "given": "Leonid", "initials": "L"}, {"family": "Benecke", "given": "Norbert", "initials": "N"}, {"family": "G\u00fcnther", "given": "Torsten", "initials": "T", "orcid": "0000-0001-9460-390X", "researcher": {"href": "https://publications.scilifelab.se/researcher/84159bff82a64a938bcff107f550c901.json"}}], "type": "journal article", "published": "2022-06-00", "journal": {"title": "R. Soc. open sci.", "issn": "2054-5703", "volume": "9", "issue": "6", "pages": "220104", "issn-l": "2054-5703"}, "abstract": "Central Asia has been an important region connecting the different parts of Eurasia throughout history and prehistory, with large states developing in this region during the Iron Age. Archaeogenomics is a powerful addition to the zooarchaeological toolkit for understanding the relation of these societies to animals. Here, we present the genetic identification of a goitered gazelle specimen (Gazella subgutturosa) at the site Gazimulla-Tepa, in modern-day Uzbekistan, supporting hunting of the species in the region during the Iron Age. The sample was directly radiocarbon dated to 2724-2439 calBP. A phylogenetic analysis of the mitochondrial genome places the individual into the modern variation of G. subgutturosa. Our data do represent both the first ancient DNA and the first nuclear DNA sequences of this species. The lack of genomic resources available for this gazelle and related species prevented us from performing a more in-depth analysis of the nuclear sequences generated. Therefore, we are making our sequence data available to the research community to facilitate other research of this nowadays threatened species which has been subject to human hunting for several millennia across its entire range on the Asian continent.", "doi": "10.1098/rsos.220104", "pmid": "35719876", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9198508"}, {"db": "pii", "key": "rsos220104"}, {"db": "figshare", "key": "10.6084/m9.figshare.c.6024060"}], "notes": [], "created": "2022-11-29T12:33:09.400Z", "modified": "2024-01-16T13:48:36.352Z"}, {"entity": "publication", "iuid": "304b49e6219a4beb9a932d515c6e1453", "links": {"self": {"href": "https://publications.scilifelab.se/publication/304b49e6219a4beb9a932d515c6e1453.json"}, "display": {"href": "https://publications.scilifelab.se/publication/304b49e6219a4beb9a932d515c6e1453"}}, "title": "Development of gut microbiota during the first 2 years of life.", "authors": [{"family": "Wernroth", "given": "Mona-Lisa", "initials": "ML"}, {"family": "Peura", "given": "Sari", "initials": "S"}, {"family": "Hedman", "given": "Anna M", "initials": "AM"}, {"family": "Hetty", "given": "Susanne", "initials": "S"}, {"family": "Vicenzi", "given": "Silvia", "initials": "S"}, {"family": "Kennedy", "given": "Beatrice", "initials": "B"}, {"family": "Fall", "given": "Katja", "initials": "K"}, {"family": "Svennblad", "given": "Bodil", "initials": "B"}, {"family": "Andolf", "given": "Ellika", "initials": "E"}, {"family": "Pershagen", "given": "G\u00f6ran", "initials": "G"}, {"family": "Theorell-Hagl\u00f6w", "given": "Jenny", "initials": "J"}, {"family": "Nguyen", "given": "Diem", "initials": "D"}, {"family": "Sayols-Baixeras", "given": "Sergi", "initials": "S"}, {"family": "Dekkers", "given": "Koen F", "initials": "KF"}, {"family": "Bertilsson", "given": "Stefan", "initials": "S"}, {"family": "Almqvist", "given": "Catarina", "initials": "C"}, {"family": "Dicksved", "given": "Johan", "initials": "J"}, {"family": "Fall", "given": "Tove", "initials": "T"}], "type": "journal article", "published": "2022-05-31", "journal": {"title": "Sci Rep", "issn": "2045-2322", "issn-l": "2045-2322", "volume": "12", "issue": "1", "pages": "9080"}, "abstract": "Although development of microbiota in childhood has been linked to chronic immune-related conditions, early childhood determinants of microbiota development have not been fully elucidated. We used 16S rRNA sequencing to analyse faecal and saliva samples from 83 children at four time-points during their first 2 years of life and from their mothers. Our findings confirm that gut microbiota in infants have low diversity and highlight that some properties are shared with the oral microbiota, although inter-individual differences are present. A considerable convergence in gut microbiota composition was noted across the first 2 years of life, towards a more diverse adult-like microbiota. Mode of delivery accounted for some of the inter-individual variation in early childhood, but with a pronounced attenuation over time. Our study extends previous research with further characterization of the major shift in gut microbiota composition during the first 2 years of life.", "doi": "10.1038/s41598-022-13009-3", "pmid": "35641542", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-022-13009-3"}, {"db": "pmc", "key": "PMC9156670"}], "notes": [], "created": "2022-06-03T06:21:52.597Z", "modified": "2024-01-16T13:48:36.379Z"}, {"entity": "publication", "iuid": "265d3081559d435081d2d22b8a2e97da", "links": {"self": {"href": "https://publications.scilifelab.se/publication/265d3081559d435081d2d22b8a2e97da.json"}, "display": {"href": "https://publications.scilifelab.se/publication/265d3081559d435081d2d22b8a2e97da"}}, "title": "An empirical evaluation of genotype imputation of ancient DNA.", "authors": [{"family": "Ausmees", "given": "Kristiina", "initials": "K", "orcid": "0000-0002-6212-539X", "researcher": {"href": "https://publications.scilifelab.se/researcher/9d6a0fd5017647a7acb70bf4c667c73e.json"}}, {"family": "Sanchez-Quinto", "given": "Federico", "initials": "F"}, {"family": "Jakobsson", "given": "Mattias", "initials": "M", "orcid": "0000-0001-7840-7853", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a4abe0fcb20492d9ec849c9fbf58a71.json"}}, {"family": "Nettelblad", "given": "Carl", "initials": "C", "orcid": "0000-0003-0458-6902", "researcher": {"href": "https://publications.scilifelab.se/researcher/c300f2900aff429d8a3bbc72ee006df7.json"}}], "type": "journal article", "published": "2022-05-30", "journal": {"title": "G3 (Bethesda)", "issn": "2160-1836", "volume": "12", "issue": "6", "issn-l": "2160-1836"}, "abstract": "With capabilities of sequencing ancient DNA to high coverage often limited by sample quality or cost, imputation of missing genotypes presents a possibility to increase the power of inference as well as cost-effectiveness for the analysis of ancient data. However, the high degree of uncertainty often associated with ancient DNA poses several methodological challenges, and performance of imputation methods in this context has not been fully explored. To gain further insights, we performed a systematic evaluation of imputation of ancient data using Beagle v4.0 and reference data from phase 3 of the 1000 Genomes project, investigating the effects of coverage, phased reference, and study sample size. Making use of five ancient individuals with high-coverage data available, we evaluated imputed data for accuracy, reference bias, and genetic affinities as captured by principal component analysis. We obtained genotype concordance levels of over 99% for data with 1\u00d7 coverage, and similar levels of accuracy and reference bias at levels as low as 0.75\u00d7. Our findings suggest that using imputed data can be a realistic option for various population genetic analyses even for data in coverage ranges below 1\u00d7. We also show that a large and varied phased reference panel as well as the inclusion of low- to moderate-coverage ancient individuals in the study sample can increase imputation performance, particularly for rare alleles. In-depth analysis of imputed data with respect to genetic variants and allele frequencies gave further insight into the nature of errors arising during imputation, and can provide practical guidelines for postprocessing and validation prior to downstream analysis.", "doi": "10.1093/g3journal/jkac089", "pmid": "35482488", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9157144"}, {"db": "pii", "key": "6575448"}], "notes": [], "created": "2022-11-29T09:07:08.055Z", "modified": "2024-01-16T13:48:36.386Z"}, {"entity": "publication", "iuid": "bc12467f5df540deb9a014812f7caf7d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/bc12467f5df540deb9a014812f7caf7d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/bc12467f5df540deb9a014812f7caf7d"}}, "title": "Inflammation and Interferon Signatures in Peripheral B-Lymphocytes and Sera of Individuals With Fibromyalgia.", "authors": [{"family": "Fineschi", "given": "Serena", "initials": "S"}, {"family": "Klar", "given": "Joakim", "initials": "J"}, {"family": "Gustafsson", "given": "Kristin Ayoola", "initials": "KA"}, {"family": "Jonsson", "given": "Kent", "initials": "K"}, {"family": "Karlsson", "given": "Bo", "initials": "B"}, {"family": "Dahl", "given": "Niklas", "initials": "N"}], "type": "journal article", "published": "2022-05-26", "journal": {"title": "Front Immunol", "issn": "1664-3224", "volume": "13", "pages": "874490", "issn-l": "1664-3224"}, "abstract": "Fibromyalgia (FM) is an idiopathic chronic disease characterized by widespread musculoskeletal pain, hyperalgesia and allodynia, often accompanied by fatigue, cognitive dysfunction and other symptoms. Autoimmunity and neuroinflammatory mechanisms have been suggested to play important roles in the pathophysiology of FM supported by recently identified interferon signatures in affected individuals. However, the contribution of different components in the immune system, such as the B-lymphocytes, in the progression to FM are yet unknown. Furthermore, there is a great need for biomarkers that may improve diagnostics of FM. Herein, we investigated the gene expression profile in peripheral B-cells, as well as a panel of inflammatory serum proteins, in 30 FM patients and 23 healthy matched control individuals. RNA sequence analysis revealed 60 differentially expressed genes when comparing the two groups. The group of FM patients showed increased expression of twenty-five interferon-regulated genes, such as S100A8 and S100A9, VCAM, CD163, SERPINA1, ANXA1, and an increased interferon score. Furthermore, FM was associated with elevated levels of 19 inflammatory serum proteins, such as IL8, AXIN1, SIRT2 and STAMBP, that correlated with the FM severity score. Together, the results shows that FM is associated with an interferon signature in B-cells and increased levels of a set of inflammatory serum proteins. Our findings bring further support for immune activation in the pathogenesis of FM and highlight candidate biomarkers for diagnosis and intervention in the management of FM.", "doi": "10.3389/fimmu.2022.874490", "pmid": "35693781", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support and Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9177944"}], "notes": [], "created": "2022-06-13T14:53:56.387Z", "modified": "2024-01-16T13:48:36.443Z"}, {"entity": "publication", "iuid": "125725b7b2fe4b5f8fc3e6674ca1d421", "links": {"self": {"href": "https://publications.scilifelab.se/publication/125725b7b2fe4b5f8fc3e6674ca1d421.json"}, "display": {"href": "https://publications.scilifelab.se/publication/125725b7b2fe4b5f8fc3e6674ca1d421"}}, "title": "Challenges in Analyzing Functional Epigenetic Data in Perspective of Adolescent Psychiatric Health.", "authors": [{"family": "Manu", "given": "Diana M", "initials": "DM", "orcid": "0000-0001-6377-0270", "researcher": {"href": "https://publications.scilifelab.se/researcher/1facf036e83a4fd1934204cc1dc7ee4d.json"}}, {"family": "Mwinyi", "given": "Jessica", "initials": "J"}, {"family": "Schi\u00f6th", "given": "Helgi B", "initials": "HB"}], "type": "journal article", "published": "2022-05-23", "journal": {"title": "Int J Mol Sci", "issn": "1422-0067", "volume": "23", "issue": "10", "issn-l": null}, "abstract": "The formative period of adolescence plays a crucial role in the development of skills and abilities for adulthood. Adolescents who are affected by mental health conditions are at risk of suicide and social and academic impairments. Gene-environment complementary contributions to the molecular mechanisms involved in psychiatric disorders have emphasized the need to analyze epigenetic marks such as DNA methylation (DNAm) and non-coding RNAs. However, the large and diverse bioinformatic and statistical methods, referring to the confounders of the statistical models, application of multiple-testing adjustment methods, questions regarding the correlation of DNAm across tissues, and sex-dependent differences in results, have raised challenges regarding the interpretation of the results. Based on the example of generalized anxiety disorder (GAD) and depressive disorder (MDD), we shed light on the current knowledge and usage of methodological tools in analyzing epigenetics. Statistical robustness is an essential prerequisite for a better understanding and interpretation of epigenetic modifications and helps to find novel targets for personalized therapeutics in psychiatric diseases.", "doi": "10.3390/ijms23105856", "pmid": "35628666", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI SNP genotyping": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pii", "key": "ijms23105856"}], "notes": [], "created": "2022-06-14T13:16:29.585Z", "modified": "2022-06-14T13:16:29.624Z"}, {"entity": "publication", "iuid": "25a29e9b946b4f01b58409c5d20272c4", "links": {"self": {"href": "https://publications.scilifelab.se/publication/25a29e9b946b4f01b58409c5d20272c4.json"}, "display": {"href": "https://publications.scilifelab.se/publication/25a29e9b946b4f01b58409c5d20272c4"}}, "title": "Environmentally induced DNA methylation is inherited across generations in an aquatic keystone species.", "authors": [{"family": "Feiner", "given": "Nathalie", "initials": "N", "orcid": "0000-0003-4648-6950", "researcher": {"href": "https://publications.scilifelab.se/researcher/4dfa523d52b348359775994be5d69640.json"}}, {"family": "Radersma", "given": "Reinder", "initials": "R"}, {"family": "Vasquez", "given": "Louella", "initials": "L"}, {"family": "Ringn\u00e9r", "given": "Markus", "initials": "M"}, {"family": "Nystedt", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Raine", "given": "Amanda", "initials": "A"}, {"family": "Tobi", "given": "Elmar W", "initials": "EW"}, {"family": "Heijmans", "given": "Bastiaan T", "initials": "BT"}, {"family": "Uller", "given": "Tobias", "initials": "T"}], "type": "journal article", "published": "2022-05-20", "journal": {"title": "iScience", "issn": "2589-0042", "issn-l": "2589-0042", "volume": "25", "issue": "5", "pages": "104303"}, "abstract": "Transgenerational inheritance of environmentally induced epigenetic marks can have significant impacts on eco-evolutionary dynamics, but the phenomenon remains controversial in ecological model systems. We used whole-genome bisulfite sequencing of individual water fleas (Daphnia magna) to assess whether environmentally induced DNA methylation is transgenerationally inherited. Genetically identical females were exposed to one of three natural stressors, or a de-methylating drug, and their offspring were propagated clonally for four generations under control conditions. We identified between 70 and 225 differentially methylated CpG positions (DMPs) in F1 individuals whose mothers were exposed to a natural stressor. Roughly half of these environmentally induced DMPs persisted until generation F4. In contrast, treatment with the drug demonstrated that pervasive hypomethylation upon exposure is reset almost completely after one generation. These results suggest that environmentally induced DNA methylation is non-random and stably inherited across generations in Daphnia, making epigenetic inheritance a putative factor in the eco-evolutionary dynamics of freshwater communities.", "doi": "10.1016/j.isci.2022.104303", "pmid": "35573201", "labels": {"Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "NGI Short read": "Collaborative", "NGI Uppsala (SNP&SEQ Technology Platform)": "Collaborative", "National Genomics Infrastructure": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "S2589-0042(22)00573-9"}, {"db": "pmc", "key": "PMC9097707"}, {"db": "Dryad", "key": "10.5061/dryad.f4qrfj6xq"}], "notes": [], "created": "2022-05-06T10:42:50.020Z", "modified": "2024-01-16T13:48:36.473Z"}, {"entity": "publication", "iuid": "290244e1fc43467897f79ecf0ffdbcb8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/290244e1fc43467897f79ecf0ffdbcb8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/290244e1fc43467897f79ecf0ffdbcb8"}}, "title": "Genome-wide association meta-analysis identifies 48 risk variants and highlights the role of the stria vascularis in hearing loss.", "authors": [{"family": "Trpchevska", "given": "Natalia", "initials": "N"}, {"family": "Freidin", "given": "Maxim B", "initials": "MB"}, {"family": "Broer", "given": "Linda", "initials": "L"}, {"family": "Oosterloo", "given": "Berthe C", "initials": "BC"}, {"family": "Yao", "given": "Shuyang", "initials": "S"}, {"family": "Zhou", "given": "Yitian", "initials": "Y"}, {"family": "Vona", "given": "Barbara", "initials": "B"}, {"family": "Bishop", "given": "Charles", "initials": "C"}, {"family": "Bizaki-Vallaskangas", "given": "Argyro", "initials": "A"}, {"family": "Canlon", "given": "Barbara", "initials": "B"}, {"family": "Castellana", "given": "Fabio", "initials": "F"}, {"family": "Chasman", "given": "Daniel I", "initials": "DI"}, {"family": "Cherny", "given": "Stacey", "initials": "S"}, {"family": "Christensen", "given": "Kaare", "initials": "K"}, {"family": "Concas", "given": "Maria Pina", "initials": "MP"}, {"family": "Correa", "given": "Adolfo", "initials": "A"}, {"family": "Elkon", "given": "Ran", "initials": "R"}, {"family": "Estonian Biobank Research Team", "given": "", "initials": ""}, {"family": "Mengel-From", "given": "Jonas", "initials": "J"}, {"family": "Gao", "given": "Yan", "initials": "Y"}, {"family": "Giersch", "given": "Anne B S", "initials": "ABS"}, {"family": "Girotto", "given": "Giorgia", "initials": "G"}, {"family": "Gudjonsson", "given": "Alexander", "initials": "A"}, {"family": "Gudnason", "given": "Vilmundur", "initials": "V"}, {"family": "Heard-Costa", "given": "Nancy L", "initials": "NL"}, {"family": "Hertzano", "given": "Ronna", "initials": "R"}, {"family": "Hjelmborg", "given": "Jacob V B", "initials": "JVB"}, {"family": "Hjerling-Leffler", "given": "Jens", "initials": "J"}, {"family": "Hoffman", "given": "Howard J", "initials": "HJ"}, {"family": "Kaprio", "given": "Jaakko", "initials": "J"}, {"family": "Kettunen", "given": "Johannes", "initials": "J"}, {"family": "Krebs", "given": "Kristi", "initials": "K"}, {"family": "K\u00e4hler", "given": "Anna K", "initials": "AK"}, {"family": "Lallemend", "given": "Francois", "initials": "F"}, {"family": "Launer", "given": "Lenore J", "initials": "LJ"}, {"family": "Lee", "given": "I-Min", "initials": "I"}, {"family": "Leonard", "given": "Hampton", "initials": "H"}, {"family": "Li", "given": "Chuan-Ming", "initials": "C"}, {"family": "Lowenheim", "given": "Hubert", "initials": "H"}, {"family": "Magnusson", "given": "Patrik K E", "initials": "PKE"}, {"family": "van Meurs", "given": "Joyce", "initials": "J"}, {"family": "Milani", "given": "Lili", "initials": "L"}, {"family": "Morton", "given": "Cynthia C", "initials": "CC"}, {"family": "M\u00e4kitie", "given": "Antti", "initials": "A"}, {"family": "Nalls", "given": "Mike A", "initials": "MA"}, {"family": "Nardone", "given": "Giuseppe Giovanni", "initials": "GG"}, {"family": "Nygaard", "given": "Marianne", "initials": "M"}, {"family": "Palviainen", "given": "Teemu", "initials": "T"}, {"family": "Pratt", "given": "Sheila", "initials": "S"}, {"family": "Quaranta", "given": "Nicola", "initials": "N"}, {"family": "R\u00e4m\u00f6", "given": "Joel", "initials": "J"}, {"family": "Saarentaus", "given": "Elmo", "initials": "E"}, {"family": "Sardone", "given": "Rodolfo", "initials": "R"}, {"family": "Satizabal Barrera", "given": "Claudia L", "initials": "CL"}, {"family": "Schweinfurth", "given": "John M", "initials": "JM"}, {"family": "Seshadri", "given": "Sudha", "initials": "S"}, {"family": "Shiroma", "given": "Eric", "initials": "E"}, {"family": "Shulman", "given": "Eldad", "initials": "E"}, {"family": "Simonsick", "given": "Eleanor", "initials": "E"}, {"family": "Spankovich", "given": "Christopher", "initials": "C"}, {"family": "Tropitzsch", "given": "Anke", "initials": "A"}, {"family": "Lauschke", "given": "Volker M", "initials": "VM"}, {"family": "Sullivan", "given": "Patrick F", "initials": "PF"}, {"family": "Goedegebure", "given": "Andre", "initials": "A"}, {"family": "Cederroth", "given": "Christopher R", "initials": "CR"}, {"family": "Williams", "given": "Frances M K", "initials": "FMK"}, {"family": "Nagtegaal", "given": "Andries Paul", "initials": "AP"}], "type": "journal article", "published": "2022-05-12", "journal": {"title": "Am. J. Hum. Genet.", "issn": "1537-6605", "issn-l": "0002-9297", "volume": "109", "issue": "6", "pages": "1077-1091"}, "abstract": "Hearing loss is one of the top contributors to years lived with disability and is a risk factor for dementia. Molecular evidence on the cellular origins of hearing loss in humans is growing. Here, we performed a genome-wide association meta-analysis of clinically diagnosed and self-reported hearing impairment on 723,266 individuals and identified 48 significant loci, 10 of which are novel. A large proportion of associations comprised missense variants, half of which lie within known familial hearing loss loci. We used single-cell RNA-sequencing data from mouse cochlea and brain and mapped common-variant genomic results to spindle, root, and basal cells from the stria vascularis, a structure in the cochlea necessary for normal hearing. Our findings indicate the importance of the stria vascularis in the mechanism of hearing impairment, providing future paths for developing targets for therapeutic intervention in hearing loss.", "doi": "10.1016/j.ajhg.2022.04.010", "pmid": "35580588", "labels": {"National Genomics Infrastructure": "Service", "NGI SNP genotyping": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "S0002-9297(22)00158-6"}], "notes": [], "created": "2022-05-23T13:59:36.677Z", "modified": "2022-11-29T12:04:55.870Z"}, {"entity": "publication", "iuid": "a037a3c54c4049f5abc112ffb15baca4", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a037a3c54c4049f5abc112ffb15baca4.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a037a3c54c4049f5abc112ffb15baca4"}}, "title": "Ivermectin-induced gene expression changes in adult Parascaris univalens and Caenorhabditis elegans: a comparative approach to study anthelminthic metabolism and resistance in vitro.", "authors": [{"family": "Dube", "given": "Faruk", "initials": "F", "orcid": "0000-0003-1340-9123", "researcher": {"href": "https://publications.scilifelab.se/researcher/efd709b6ebf04946bf70f1ab4c8c5cbf.json"}}, {"family": "Hinas", "given": "Andrea", "initials": "A"}, {"family": "Roy", "given": "Shweta", "initials": "S"}, {"family": "Martin", "given": "Frida", "initials": "F"}, {"family": "\u00c5brink", "given": "Magnus", "initials": "M"}, {"family": "Sv\u00e4rd", "given": "Staffan", "initials": "S"}, {"family": "Tyd\u00e9n", "given": "Eva", "initials": "E"}], "type": "journal article", "published": "2022-05-05", "journal": {"title": "Parasit Vectors", "issn": "1756-3305", "volume": "15", "issue": "1", "pages": "158", "issn-l": "1756-3305"}, "abstract": "The nematode Parascaris univalens is one of the most prevalent parasitic pathogens infecting horses but anthelmintic resistance undermines treatment approaches. The molecular mechanisms underlying drug activity and resistance remain poorly understood in this parasite since experimental in vitro models are lacking. The aim of this study was to evaluate the use of Caenorhabditis elegans as a model for P. univalens drug metabolism/resistance studies by a comparative gene expression approach after in vitro exposure to the anthelmintic drug ivermectin (IVM).\n\nTwelve adult P. univalens worms in groups of three were exposed to ivermectin (IVM, 10-13 M, 10-11 M, 10-9 M) or left unexposed for 24 h at 37 \u00b0C, and total RNA, extracted from the anterior end of the worms, was sequenced using Illumina NovaSeq. Differentially expressed genes (DEGs) involved in metabolism, transportation, or gene expression with annotated Caernorhabditis elegans orthologues were identified as candidate genes to be involved in IVM metabolism/resistance. Similarly, groups of 300 adult C. elegans worms were exposed to IVM (10-9 M, 10-8 M and 10-7 M) or left unexposed for 4 h at 20 \u00b0C. Quantitative RT-PCR of RNA extracted from the C. elegans worm pools was used to compare against the expression of selected P. univalens candidate genes after drug treatment.\n\nAfter IVM exposure, 1085 DEGs were found in adult P. univalens worms but the relative gene expression changes were small and large variabilities were found between different worms. Fifteen of the DEGs were chosen for further characterization in C. elegans after comparative bioinformatics analyses. Candidate genes, including the putative drug target lgc-37, responded to IVM in P. univalens, but marginal to no responses were observed in C. elegans despite dose-dependent behavioral effects observed in C. elegans after IVM exposure. Thus, the overlap in IVM-induced gene expression in this small set of genes was minor in adult worms of the two nematode species.\n\nThis is the first time to our knowledge that a comparative gene expression approach has evaluated C. elegans as a model to understand IVM metabolism/resistance in P. univalens. Genes in P. univalens adults that responded to IVM treatment were identified. However, identifying conserved genes in P. univalens and C. elegans involved in IVM metabolism/resistance by comparing gene expression of candidate genes proved challenging. The approach appears promising but was limited by the number of genes studied (n = 15). Future studies comparing a larger number of genes between the two species may result in identification of additional candidate genes involved in drug metabolism and/or resistance.", "doi": "10.1186/s13071-022-05260-4", "pmid": "35513885", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9074254"}, {"db": "pii", "key": "10.1186/s13071-022-05260-4"}], "notes": [], "created": "2022-11-29T12:03:10.370Z", "modified": "2024-01-16T13:48:36.731Z"}, {"entity": "publication", "iuid": "959380267d6149ad8c41e56a069865c6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/959380267d6149ad8c41e56a069865c6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/959380267d6149ad8c41e56a069865c6"}}, "title": "Comparison of methodological approaches to the study of young sex chromosomes: A case study in Poecilia.", "authors": [{"family": "Darolti", "given": "Iulia", "initials": "I"}, {"family": "Almeida", "given": "Pedro", "initials": "P"}, {"family": "Wright", "given": "Alison E", "initials": "AE"}, {"family": "Mank", "given": "Judith E", "initials": "JE", "orcid": "0000-0002-2450-513X", "researcher": {"href": "https://publications.scilifelab.se/researcher/42f3e1ac3beb4d9cb0c6687ec7d94c68.json"}}], "type": "journal article", "published": "2022-05-04", "journal": {"title": "J. Evol. Biol.", "issn": "1420-9101", "issn-l": "1010-061X", "volume": "35", "issue": "12", "pages": "1646-1658"}, "abstract": "Studies of sex chromosome systems at early stages of divergence are key to understanding the initial process and underlying causes of recombination suppression. However, identifying signatures of divergence in homomorphic sex chromosomes can be challenging due to high levels of sequence similarity between the X and the Y. Variations in methodological precision and underlying data can make all the difference between detecting subtle divergence patterns or missing them entirely. Recent efforts to test for X-Y sequence differentiation in the guppy have led to contradictory results. Here, we apply different analytical methodologies to the same data set to test for the accuracy of different approaches in identifying patterns of sex chromosome divergence in the guppy. Our comparative analysis reveals that the most substantial source of variation in the results of the different analyses lies in the reference genome used. Analyses using custom-made genome assemblies for the focal population or species successfully recover a signal of divergence across different methodological approaches. By contrast, using the distantly related Xiphophorus reference genome results in variable patterns, due to both sequence evolution and structural variations on the sex chromosomes between the guppy and Xiphophorus. Changes in mapping and filtering parameters can additionally introduce noise and obscure the signal. Our results illustrate how analytical differences can alter perceived results and we highlight best practices for the study of nascent sex chromosomes.", "doi": "10.1111/jeb.14013", "pmid": "35506576", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [], "notes": [], "created": "2022-11-29T11:58:52.373Z", "modified": "2022-12-07T08:53:17.615Z"}, {"entity": "publication", "iuid": "0f40db40a4a744a193d075e875abdbf1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0f40db40a4a744a193d075e875abdbf1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0f40db40a4a744a193d075e875abdbf1"}}, "title": "Genetic Landscape of the ACE2 Coronavirus Receptor.", "authors": [{"family": "Yang", "given": "Zhijian", "initials": "Z", "orcid": "0000-0003-4803-8633", "researcher": {"href": "https://publications.scilifelab.se/researcher/104e44a8c1e949d18d371fad8b2c9fa9.json"}}, {"family": "Macdonald-Dunlop", "given": "Erin", "initials": "E"}, {"family": "Chen", "given": "Jiantao", "initials": "J", "orcid": "0000-0002-7214-2257", "researcher": {"href": "https://publications.scilifelab.se/researcher/3e8d1f3a3d2f499cb948355fa256d5b9.json"}}, {"family": "Zhai", "given": "Ranran", "initials": "R", "orcid": "0000-0002-5834-9120", "researcher": {"href": "https://publications.scilifelab.se/researcher/43424d9c39ae413096249b0abecc08ee.json"}}, {"family": "Li", "given": "Ting", "initials": "T"}, {"family": "Richmond", "given": "Anne", "initials": "A"}, {"family": "Klari\u0107", "given": "Lucija", "initials": "L", "orcid": "0000-0003-3105-8929", "researcher": {"href": "https://publications.scilifelab.se/researcher/4e9259ccc4aa49e8bf6ea82b71d9be0f.json"}}, {"family": "Pirastu", "given": "Nicola", "initials": "N", "orcid": "0000-0002-5363-3886", "researcher": {"href": "https://publications.scilifelab.se/researcher/badf4678d37546ce993bccb3880d4f12.json"}}, {"family": "Ning", "given": "Zheng", "initials": "Z", "orcid": "0000-0002-0451-6536", "researcher": {"href": "https://publications.scilifelab.se/researcher/fa6cf2d38b5e428a9ce6120f4e6cb46c.json"}}, {"family": "Zheng", "given": "Chenqing", "initials": "C"}, {"family": "Wang", "given": "Yipeng", "initials": "Y"}, {"family": "Huang", "given": "Tingting", "initials": "T", "orcid": "0000-0003-2314-4448", "researcher": {"href": "https://publications.scilifelab.se/researcher/c764a0dc5d6f4358a46638a7098de3a3.json"}}, {"family": "He", "given": "Yazhou", "initials": "Y", "orcid": "0000-0003-2358-0143", "researcher": {"href": "https://publications.scilifelab.se/researcher/4699263c60454108a44731efc3800cc6.json"}}, {"family": "Guo", "given": "Huiming", "initials": "H"}, {"family": "Ying", "given": "Kejun", "initials": "K", "orcid": "0000-0002-1791-6176", "researcher": {"href": "https://publications.scilifelab.se/researcher/6485f7e370b44c5db723352f811ceae5.json"}}, {"family": "Gustafsson", "given": "Stefan", "initials": "S"}, {"family": "Prins", "given": "Bram", "initials": "B"}, {"family": "Ramisch", "given": "Anna", "initials": "A", "orcid": "0000-0002-0641-4330", "researcher": {"href": "https://publications.scilifelab.se/researcher/65cf286b1a1f41a7be0fdf02c92dcdbc.json"}}, {"family": "Dermitzakis", "given": "Emmanouil T", "initials": "ET"}, {"family": "Png", "given": "Grace", "initials": "G", "orcid": "0000-0003-3962-7436", "researcher": {"href": "https://publications.scilifelab.se/researcher/a065c580d09948b398573339800385b1.json"}}, {"family": "Eriksson", "given": "Niclas", "initials": "N", "orcid": "0000-0002-2152-4343", "researcher": {"href": "https://publications.scilifelab.se/researcher/64611a83caba46d597f45371b77de26b.json"}}, {"family": "Haessler", "given": "Jeffrey", "initials": "J"}, {"family": "Hu", "given": "Xiaowei", "initials": "X"}, {"family": "Zanetti", "given": "Daniela", "initials": "D", "orcid": "0000-0002-1225-1021", "researcher": {"href": "https://publications.scilifelab.se/researcher/88b1725b56034ad18aa0e4a6cc73126e.json"}}, {"family": "Boutin", "given": "Thibaud", "initials": "T"}, {"family": "Hwang", "given": "Shih-Jen", "initials": "SJ", "orcid": "0000-0002-2129-5704", "researcher": {"href": "https://publications.scilifelab.se/researcher/eb2b949d7dd0449b841f40d6ae246fcb.json"}}, {"family": "Wheeler", "given": "Eleanor", "initials": "E"}, {"family": "Pietzner", "given": "Maik", "initials": "M"}, {"family": "Raffield", "given": "Laura M", "initials": "LM", "orcid": "0000-0002-7892-193X", "researcher": {"href": "https://publications.scilifelab.se/researcher/202a2d2ab8a54b93bcd728d74a7724ce.json"}}, {"family": "Kalnapenkis", "given": "Anette", "initials": "A"}, {"family": "Peters", "given": "James E", "initials": "JE"}, {"family": "Vi\u00f1uela", "given": "Ana", "initials": "A", "orcid": "0000-0003-3771-8537", "researcher": {"href": "https://publications.scilifelab.se/researcher/e6551fc3132f4fa597378c565247a315.json"}}, {"family": "Gilly", "given": "Arthur", "initials": "A"}, {"family": "Elmst\u00e5hl", "given": "S\u00f6lve", "initials": "S"}, {"family": "Dedoussis", "given": "George", "initials": "G"}, {"family": "Petrie", "given": "John R", "initials": "JR"}, {"family": "Pola\u0161ek", "given": "Ozren", "initials": "O"}, {"family": "Folkersen", "given": "Lasse", "initials": "L", "orcid": "0000-0003-0708-9530", "researcher": {"href": "https://publications.scilifelab.se/researcher/7202a83ff6484d5c9d77f448f93c6520.json"}}, {"family": "Chen", "given": "Yan", "initials": "Y", "orcid": "0000-0001-9673-9712", "researcher": {"href": "https://publications.scilifelab.se/researcher/8ad31a2d328b47d59d84972db72bd37d.json"}}, {"family": "Yao", "given": "Chen", "initials": "C"}, {"family": "V\u00f5sa", "given": "Urmo", "initials": "U"}, {"family": "Pairo-Castineira", "given": "Erola", "initials": "E"}, {"family": "Clohisey", "given": "Sara", "initials": "S"}, {"family": "Bretherick", "given": "Andrew D", "initials": "AD"}, {"family": "Rawlik", "given": "Konrad", "initials": "K"}, {"family": "GenOMICC Consortium\u2020", "given": "", "initials": ""}, {"family": "IMI-DIRECT Consortium\u2020", "given": "", "initials": ""}, {"family": "Esko", "given": "T\u00f5nu", "initials": "T"}, {"family": "Enroth", "given": "Stefan", "initials": "S"}, {"family": "Johansson", "given": "\u00c5sa", "initials": "\u00c5"}, {"family": "Gyllensten", "given": "Ulf", "initials": "U"}, {"family": "Langenberg", "given": "Claudia", "initials": "C", "orcid": "0000-0002-5017-7344", "researcher": {"href": "https://publications.scilifelab.se/researcher/ca19370bb4d6437aa9df3905db9d3dd2.json"}}, {"family": "Levy", "given": "Daniel", "initials": "D", "orcid": "0000-0003-1843-8724", "researcher": {"href": "https://publications.scilifelab.se/researcher/86bfd3e65ead428c93dc1a461004adab.json"}}, {"family": "Hayward", "given": "Caroline", "initials": "C", "orcid": "0000-0002-9405-9550", "researcher": {"href": "https://publications.scilifelab.se/researcher/cd49e9ad5a024c7ca2f1aa97d9e58eba.json"}}, {"family": "Assimes", "given": "Themistocles L", "initials": "TL", "orcid": "0000-0003-2349-0009", "researcher": {"href": "https://publications.scilifelab.se/researcher/9e155ca3dd01486580be888d1ded405c.json"}}, {"family": "Kooperberg", "given": "Charles", "initials": "C", "orcid": "0000-0002-7986-8560", "researcher": {"href": "https://publications.scilifelab.se/researcher/ede9a05559a041fa92259322da5e7151.json"}}, {"family": "Manichaikul", "given": "Ani W", "initials": "AW"}, {"family": "Siegbahn", "given": "Agneta", "initials": "A"}, {"family": "Wallentin", "given": "Lars", "initials": "L"}, {"family": "Lind", "given": "Lars", "initials": "L", "orcid": "0000-0003-2335-8542", "researcher": {"href": "https://publications.scilifelab.se/researcher/4c517dacca7c4ec58a3e03b59ffb4044.json"}}, {"family": "Zeggini", "given": "Eleftheria", "initials": "E"}, {"family": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications.scilifelab.se/researcher/aba5822711b246b397fffacb7ae403b3.json"}}, {"family": "Butterworth", "given": "Adam S", "initials": "AS", "orcid": "0000-0002-6915-9015", "researcher": {"href": "https://publications.scilifelab.se/researcher/7b8c140c80d942c4b1b684876e4d6180.json"}}, {"family": "Micha\u00eblsson", "given": "Karl", "initials": "K", "orcid": "0000-0003-2815-1217", "researcher": {"href": "https://publications.scilifelab.se/researcher/eff63868e95240f695d47e871e31947f.json"}}, {"family": "Pawitan", "given": "Yudi", "initials": "Y"}, {"family": "Joshi", "given": "Peter K", "initials": "PK", "orcid": "0000-0002-6361-5059", "researcher": {"href": "https://publications.scilifelab.se/researcher/46050ddec8f64054b3bab46c5016aebf.json"}}, {"family": "Baillie", "given": "J Kenneth", "initials": "JK"}, {"family": "M\u00e4larstig", "given": "Anders", "initials": "A"}, {"family": "Reiner", "given": "Alexander P", "initials": "AP", "orcid": "0000-0002-1427-4470", "researcher": {"href": "https://publications.scilifelab.se/researcher/931fcf4444904ec398a450a9ec4f4389.json"}}, {"family": "Wilson", "given": "James F", "initials": "JF"}, {"family": "Shen", "given": "Xia", "initials": "X", "orcid": "0000-0003-4390-1979", "researcher": {"href": "https://publications.scilifelab.se/researcher/b40d1f7f07ed482b9c95f56c61f0a836.json"}}], "type": "journal article", "published": "2022-05-03", "journal": {"title": "Circulation", "issn": "1524-4539", "volume": "145", "issue": "18", "pages": "1398-1411", "issn-l": "0009-7322"}, "abstract": "SARS-CoV-2, the causal agent of COVID-19, enters human cells using the ACE2 (angiotensin-converting enzyme 2) protein as a receptor. ACE2 is thus key to the infection and treatment of the coronavirus. ACE2 is highly expressed in the heart and respiratory and gastrointestinal tracts, playing important regulatory roles in the cardiovascular and other biological systems. However, the genetic basis of the ACE2 protein levels is not well understood.\n\nWe have conducted the largest genome-wide association meta-analysis of plasma ACE2 levels in >28 000 individuals of the SCALLOP Consortium (Systematic and Combined Analysis of Olink Proteins). We summarize the cross-sectional epidemiological correlates of circulating ACE2. Using the summary statistics-based high-definition likelihood method, we estimate relevant genetic correlations with cardiometabolic phenotypes, COVID-19, and other human complex traits and diseases. We perform causal inference of soluble ACE2 on vascular disease outcomes and COVID-19 severity using mendelian randomization. We also perform in silico functional analysis by integrating with other types of omics data.\n\nWe identified 10 loci, including 8 novel, capturing 30% of the heritability of the protein. We detected that plasma ACE2 was genetically correlated with vascular diseases, severe COVID-19, and a wide range of human complex diseases and medications. An X-chromosome cis-protein quantitative trait loci-based mendelian randomization analysis suggested a causal effect of elevated ACE2 levels on COVID-19 severity (odds ratio, 1.63 [95% CI, 1.10-2.42]; P=0.01), hospitalization (odds ratio, 1.52 [95% CI, 1.05-2.21]; P=0.03), and infection (odds ratio, 1.60 [95% CI, 1.08-2.37]; P=0.02). Tissue- and cell type-specific transcriptomic and epigenomic analysis revealed that the ACE2 regulatory variants were enriched for DNA methylation sites in blood immune cells.\n\nHuman plasma ACE2 shares a genetic basis with cardiovascular disease, COVID-19, and other related diseases. The genetic architecture of the ACE2 protein is mapped, providing a useful resource for further biological and clinical studies on this coronavirus receptor.", "doi": "10.1161/CIRCULATIONAHA.121.057888", "pmid": "35387486", "labels": {"National Genomics Infrastructure": "Service", "NGI SNP genotyping": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Affinity Proteomics Stockholm": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9047645"}], "notes": [], "created": "2022-05-06T10:18:12.729Z", "modified": "2022-12-05T01:33:32.862Z"}, {"entity": "publication", "iuid": "c90c79135ed64cf4bdbb70b9d59e87ab", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c90c79135ed64cf4bdbb70b9d59e87ab.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c90c79135ed64cf4bdbb70b9d59e87ab"}}, "title": "HLA variants associated with azathioprine-induced pancreatitis in patients with Crohn's disease.", "authors": [{"family": "\u00c5s", "given": "Joel", "initials": "J"}, {"family": "Bertulyte", "given": "Ilma", "initials": "I"}, {"family": "Eriksson", "given": "Niclas", "initials": "N"}, {"family": "Magnusson", "given": "Patrik K E", "initials": "PKE"}, {"family": "Wadelius", "given": "Mia", "initials": "M"}, {"family": "Hallberg", "given": "P\u00e4r", "initials": "P"}], "type": "journal article", "published": "2022-05-00", "journal": {"title": "Clin Transl Sci", "issn": "1752-8062", "volume": "15", "issue": "5", "pages": "1249-1256", "issn-l": null}, "abstract": "The immunosuppressant drug azathioprine is associated with a 4% risk of acute pancreatitis in patients with inflammatory bowel disease (IBD). Studies have demonstrated an increased risk in carriers of HLA-DQA1*02:01 and HLA-DRB1*07:01. We investigated whether these human leukocyte antigen (HLA) types were associated with azathioprine-induced pancreatitis also in Swedish patients with IBD, and whether the type of disease affected the association. Nineteen individuals with IBD who developed acute pancreatitis after initiation of azathioprine were genotyped and compared with a population control cohort (n = 4891) and a control group matched for disease (n = 81). HLA-DQA1*02:01 and HLA-DRB1*07:01 were in full linkage disequilibrium, and were significantly associated with acute pancreatitis both when cases were compared with population controls (OR 3.97 [95% CI 1.57-9.97], p = 0.0035) and matched controls (OR 3.55 [95% CI 1.23-10.98], p = 0.0275). In a disease-specific analysis, the correlation was positive in patients with Crohn's disease versus matched controls (OR 9.27 [95% CI 1.86-46.19], p = 0.0066), but not in those with ulcerative colitis versus matched controls (OR 0.69 [95% CI 0.07-6.74], p = 0.749). In patients with Crohn's disease, we estimated the conditional risk of carriers of HLA-DQA1*02:01-HLA-DRB1*07:01 to 7.3%, and the conditional risk of a non-carrier to 2.2%. We conclude that HLA-DQA1*02:01-HLA-DRB1*07:01 is a marker for increased risk of acute pancreatitis in individuals of Swedish genetic origin, treated with azathioprine for Crohn's disease.", "doi": "10.1111/cts.13244", "pmid": "35120281", "labels": {"National Genomics Infrastructure": "Service", "NGI SNP genotyping": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9099136"}], "notes": [], "created": "2022-05-06T10:18:07.980Z", "modified": "2024-01-16T13:48:36.820Z"}, {"entity": "publication", "iuid": "28a281acd45f4ed7a0999df336aa4840", "links": {"self": {"href": "https://publications.scilifelab.se/publication/28a281acd45f4ed7a0999df336aa4840.json"}, "display": {"href": "https://publications.scilifelab.se/publication/28a281acd45f4ed7a0999df336aa4840"}}, "title": "Dual RNA Sequencing Reveals Key Events When Different Giardia Life Cycle Stages Interact With Human Intestinal Epithelial Cells In Vitro.", "authors": [{"family": "Rojas", "given": "Laura", "initials": "L"}, {"family": "Gr\u00fcttner", "given": "Jana", "initials": "J"}, {"family": "Ma'ayeh", "given": "Showgy", "initials": "S"}, {"family": "Xu", "given": "Feifei", "initials": "F"}, {"family": "Sv\u00e4rd", "given": "Staffan G", "initials": "SG"}], "type": "journal article", "published": "2022-04-27", "journal": {"title": "Front. Cell. Infect. Microbiol.", "issn": "2235-2988", "volume": "12", "pages": "862211", "issn-l": "2235-2988"}, "abstract": "Giardia intestinalis is a protozoan parasite causing diarrheal disease, giardiasis, after extracellular infection of humans and other mammals' intestinal epithelial cells (IECs) of the upper small intestine. The parasite has two main life cycle stages: replicative trophozoites and transmissive cysts. Differentiating parasites (encysting cells) and trophozoites have recently been shown to be present in the same regions of the upper small intestine, whereas most mature cysts are found further down in the intestinal system. To learn more about host-parasite interactions during Giardia infections, we used an in vitro model of the parasite's interaction with host IECs (differentiated Caco-2 cells) and Giardia WB trophozoites, early encysting cells (7 h), and cysts. Dual RNA sequencing (Dual RNAseq) was used to identify differentially expressed genes (DEGs) in both Giardia and the IECs, which might relate to establishing infection and disease induction. In the human cells, the largest gene expression changes were found in immune and MAPK signaling, transcriptional regulation, apoptosis, cholesterol metabolism and oxidative stress. The different life cycle stages of Giardia induced a core of similar DEGs but at different levels and there are many life cycle stage-specific DEGs. The metabolic protein PCK1, the transcription factors HES7, HEY1 and JUN, the peptide hormone CCK and the mucins MUC2 and MUC5A are up-regulated in the IECs by trophozoites but not cysts. Cysts specifically induce the chemokines CCL4L2, CCL5 and CXCL5, the signaling protein TRKA and the anti-bacterial protein WFDC12. The parasite, in turn, up-regulated a large number of hypothetical genes, high cysteine membrane proteins (HCMPs) and oxidative stress response genes. Early encysting cells have unique DEGs compared to trophozoites (e.g. several uniquely up-regulated HCMPs) and interaction of these cells with IECs affected the encystation process. Our data show that different life cycle stages of Giardia induce different gene expression responses in the host cells and that the IECs in turn differentially affect the gene expression in trophozoites and early encysting cells. This life cycle stage-specific host-parasite cross-talk is an important aspect to consider during further studies of Giardia's molecular pathogenesis.", "doi": "10.3389/fcimb.2022.862211", "pmid": "35573800", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9094438"}], "notes": [], "created": "2022-11-29T12:13:42.089Z", "modified": "2022-11-29T12:13:42.093Z"}, {"entity": "publication", "iuid": "d42d2a62ff4a4fd492c94539d79ed06f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d42d2a62ff4a4fd492c94539d79ed06f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d42d2a62ff4a4fd492c94539d79ed06f"}}, "title": "Cell-lineage controlled epigenetic regulation in glioblastoma stem cells determines functionally distinct subgroups and predicts patient survival.", "authors": [{"family": "Lu", "given": "Xi", "initials": "X", "orcid": "0000-0002-1650-9974", "researcher": {"href": "https://publications.scilifelab.se/researcher/a2fc905a0497492c964e10e0f1f82f4c.json"}}, {"family": "Maturi", "given": "Naga Prathyusha", "initials": "NP", "orcid": "0000-0002-7726-8617", "researcher": {"href": "https://publications.scilifelab.se/researcher/12f69dfe618f48c9bd4aa6075525975c.json"}}, {"family": "Jarvius", "given": "Malin", "initials": "M"}, {"family": "Yildirim", "given": "Irem", "initials": "I", "orcid": "0000-0003-3602-5544", "researcher": {"href": "https://publications.scilifelab.se/researcher/a29421803962496880443d5772f4c97a.json"}}, {"family": "Dang", "given": "Yonglong", "initials": "Y"}, {"family": "Zhao", "given": "Linxuan", "initials": "L"}, {"family": "Xie", "given": "Yuan", "initials": "Y"}, {"family": "Tan", "given": "E-Jean", "initials": "EJ", "orcid": "0000-0002-4631-174X", "researcher": {"href": "https://publications.scilifelab.se/researcher/03d12f8cf5714430a7297ed0c3f0e1f6.json"}}, {"family": "Xing", "given": "Pengwei", "initials": "P"}, {"family": "Larsson", "given": "Rolf", "initials": "R"}, {"family": "Frykn\u00e4s", "given": "M\u00e5rten", "initials": "M"}, {"family": "Uhrbom", "given": "Lene", "initials": "L", "orcid": "0000-0001-8595-5698", "researcher": {"href": "https://publications.scilifelab.se/researcher/67bb8672ad514a9bb5f86c8d6b494269.json"}}, {"family": "Chen", "given": "Xingqi", "initials": "X", "orcid": "0000-0002-5657-2839", "researcher": {"href": "https://publications.scilifelab.se/researcher/ef7ddc09e57745909175e41ac2d1b647.json"}}], "type": "journal article", "published": "2022-04-25", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "13", "issue": "1", "pages": "2236", "issn-l": "2041-1723"}, "abstract": "There is ample support for developmental regulation of glioblastoma stem cells. To examine how cell lineage controls glioblastoma stem cell function, we present a cross-species epigenome analysis of mouse and human glioblastoma stem cells. We analyze and compare the chromatin-accessibility landscape of nine mouse glioblastoma stem cell cultures of three defined origins and 60 patient-derived glioblastoma stem cell cultures by assay for transposase-accessible chromatin using sequencing. This separates the mouse cultures according to cell of origin and identifies three human glioblastoma stem cell clusters that show overlapping characteristics with each of the mouse groups, and a distribution along an axis of proneural to mesenchymal phenotypes. The epigenetic-based human glioblastoma stem cell clusters display distinct functional properties and can separate patient survival. Cross-species analyses reveals conserved epigenetic regulation of mouse and human glioblastoma stem cells. We conclude that epigenetic control of glioblastoma stem cells primarily is dictated by developmental origin which impacts clinically relevant glioblastoma stem cell properties and patient survival.", "doi": "10.1038/s41467-022-29912-2", "pmid": "35469026", "labels": {"NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-022-29912-2"}], "notes": [], "created": "2022-04-29T09:50:33.950Z", "modified": "2022-04-29T09:50:34.131Z"}, {"entity": "publication", "iuid": "e8791e5840a54822a2cd0d8fe70d5836", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e8791e5840a54822a2cd0d8fe70d5836.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e8791e5840a54822a2cd0d8fe70d5836"}}, "title": "Auxilin is a novel susceptibility gene for congenital heart block which directly impacts fetal heart function.", "authors": [{"family": "Meisgen", "given": "Sabrina", "initials": "S"}, {"family": "Hedlund", "given": "Malin", "initials": "M"}, {"family": "Ambrosi", "given": "Aurelie", "initials": "A"}, {"family": "Folkersen", "given": "Lasse", "initials": "L"}, {"family": "Ottosson", "given": "Vijole", "initials": "V"}, {"family": "Forsberg", "given": "David", "initials": "D"}, {"family": "Thorlacius", "given": "Gudny Ella", "initials": "GE"}, {"family": "Biavati", "given": "Luca", "initials": "L"}, {"family": "Strandberg", "given": "Linn", "initials": "L"}, {"family": "Mofors", "given": "Johannes", "initials": "J"}, {"family": "Ramskold", "given": "Daniel", "initials": "D"}, {"family": "Ruhrmann", "given": "Sabrina", "initials": "S"}, {"family": "Meneghel", "given": "Lauro", "initials": "L"}, {"family": "Nyberg", "given": "William", "initials": "W"}, {"family": "Espinosa", "given": "Alexander", "initials": "A"}, {"family": "Hamilton", "given": "Robert Murray", "initials": "RM"}, {"family": "Franco-Cereceda", "given": "Anders", "initials": "A"}, {"family": "Hamsten", "given": "Anders", "initials": "A"}, {"family": "Olsson", "given": "Tomas", "initials": "T"}, {"family": "Greene", "given": "Lois", "initials": "L"}, {"family": "Eriksson", "given": "Per", "initials": "P"}, {"family": "Gemzell-Danielsson", "given": "Kristina", "initials": "K"}, {"family": "Salomonsson", "given": "Stina", "initials": "S"}, {"family": "Kuchroo", "given": "Vijay K", "initials": "VK"}, {"family": "Herlenius", "given": "Eric", "initials": "E"}, {"family": "Kockum", "given": "Ingrid", "initials": "I"}, {"family": "Sonesson", "given": "Sven-Erik", "initials": "S"}, {"family": "Wahren-Herlenius", "given": "Marie", "initials": "M", "orcid": "0000-0002-0915-7245", "researcher": {"href": "https://publications.scilifelab.se/researcher/a8451e7f5e6e4e4da0bace3dfafaeb38.json"}}], "type": "journal article", "published": "2022-04-25", "journal": {"title": "Ann. Rheum. Dis.", "issn": "1468-2060", "issn-l": "0003-4967", "volume": "81", "issue": "8", "pages": "1151-1161"}, "abstract": "Neonatal lupus erythematosus (NLE) may develop after transplacental transfer of maternal autoantibodies with cardiac manifestations (congenital heart block, CHB) including atrioventricular block, atrial and ventricular arrhythmias, and cardiomyopathies. The association with anti-Ro/SSA antibodies is well established, but a recurrence rate of only 12%-16% despite persisting maternal autoantibodies suggests that additional factors are required for CHB development. Here, we identify fetal genetic variants conferring risk of CHB and elucidate their effects on cardiac function.\r\n\r\nA genome-wide association study was performed in families with at least one case of CHB. Gene expression was analysed by microarrays, RNA sequencing and PCR and protein expression by western blot, immunohistochemistry, immunofluorescence and flow cytometry. Calcium regulation and connectivity were analysed in primary cardiomyocytes and cells induced from pleuripotent stem cells. Fetal heart performance was analysed by Doppler/echocardiography.\r\n\r\nWe identified DNAJC6 as a novel fetal susceptibility gene, with decreased cardiac expression of DNAJC6 associated with the disease risk genotype. We further demonstrate that fetal cardiomyocytes deficient in auxilin, the protein encoded by DNAJC6, have abnormal connectivity and Ca2+ homoeostasis in culture, as well as decreased cell surface expression of the Cav1.3 calcium channel. Doppler echocardiography of auxilin-deficient fetal mice revealed cardiac NLE abnormalities in utero, including abnormal heart rhythm with atrial and ventricular ectopias, as well as a prolonged atrioventricular time intervals.\r\n\r\nOur study identifies auxilin as the first genetic susceptibility factor in NLE modulating cardiac function, opening new avenues for the development of screening and therapeutic strategies in CHB.", "doi": "10.1136/annrheumdis-2021-221714", "pmid": "35470161", "labels": {"National Genomics Infrastructure": "Service", "NGI SNP genotyping": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "annrheumdis-2021-221714"}], "notes": [], "created": "2022-05-06T10:18:16.352Z", "modified": "2022-11-29T12:02:18.509Z"}, {"entity": "publication", "iuid": "3607abce5d57420abd7f4b3689913959", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3607abce5d57420abd7f4b3689913959.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3607abce5d57420abd7f4b3689913959"}}, "title": "Influence of cysteine, serine, sulfate, and sulfide on anaerobic conversion of unsaturated long-chain fatty acid, oleate, to methane.", "authors": [{"family": "Shakeri Yekta", "given": "Sepehr", "initials": "S"}, {"family": "Elreedy", "given": "Ahmed", "initials": "A"}, {"family": "Liu", "given": "Tong", "initials": "T"}, {"family": "Hedenstr\u00f6m", "given": "Mattias", "initials": "M"}, {"family": "Isaksson", "given": "Simon", "initials": "S"}, {"family": "Fujii", "given": "Manabu", "initials": "M"}, {"family": "Schn\u00fcrer", "given": "Anna", "initials": "A"}], "type": "journal article", "published": "2022-04-15", "journal": {"title": "Sci. Total Environ.", "issn": "1879-1026", "issn-l": "0048-9697", "volume": "817", "issue": null, "pages": "152967"}, "abstract": "This study aims to elucidate the role of sulfide and its precursors in anaerobic digestion (i.e., cysteine, representing sulfur-containing amino acids, and sulfate) on microbial oleate conversion to methane. Serine, with a similar structure to cysteine but with a hydroxyl group instead of a thiol, was included as a control to assess potential effects on methane formation that were not related to sulfur functionalities. The results showed that copresence of sulfide and oleate in anaerobic batch assays accelerated the methane formation compared to assays with only oleate and mitigated negative effect on methane formation caused by increased sulfide level. Nuclear magnetic resonance spectroscopy of sulfide-exposed oleate suggested that sulfide reaction with oleate double bonds likely contributed to negation of the negative effect on the methanogenic activity. Methane formation from oleate was also accelerated in the presence of cysteine or serine, while sulfate decreased the cumulative methane formation from oleate. Neither cysteine nor serine was converted to methane, and their accelerating effects was associated to different mechanisms due to establishment of microbial communities with different structures, as evidenced by high-throughput sequencing of 16S rRNA gene. These outcomes contribute with new knowledge to develop strategies for optimum use of sulfur- and lipid-rich wastes in anaerobic digestion processes.", "doi": "10.1016/j.scitotenv.2022.152967", "pmid": "35016947", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Short read": "Service", "National Genomics Infrastructure": "Service", "Swedish NMR Centre": "Collaborative"}, "xrefs": [{"db": "pii", "key": "S0048-9697(22)00056-0"}], "notes": [], "created": "2022-01-13T16:12:31.063Z", "modified": "2025-10-17T13:03:54.839Z"}, {"entity": "publication", "iuid": "e632f026baa44e0e80541b5040017234", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e632f026baa44e0e80541b5040017234.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e632f026baa44e0e80541b5040017234"}}, "title": "HPA-axis dysregulation is not associated with accelerated epigenetic aging in patients with hypersexual disorder.", "authors": [{"family": "Bostr\u00f6m", "given": "Adrian Desai E", "initials": "ADE"}, {"family": "Andersson", "given": "Peter", "initials": "P"}, {"family": "Chatzittofis", "given": "Andreas", "initials": "A"}, {"family": "Savard", "given": "Josephine", "initials": "J"}, {"family": "Rask-Andersen", "given": "Mathias", "initials": "M"}, {"family": "\u00d6berg", "given": "Katarina G", "initials": "KG"}, {"family": "Arver", "given": "Stefan", "initials": "S"}, {"family": "Jokinen", "given": "Jussi", "initials": "J"}], "type": "journal article", "published": "2022-04-14", "journal": {"title": "Psychoneuroendocrinology", "issn": "1873-3360", "volume": "141", "pages": "105765", "issn-l": "0306-4530"}, "abstract": "Hypersexual disorder (HD) - a nonparaphilic sexual desire disorder with impulsivity component - was evaluated for inclusion as a diagnosis in the DSM-5 and the diagnosis compulsive sexual behavior disorder is included as an impulse control disorder in the ICD-11. Hypothalamic-pituitary-adrenal (HPA)-axis hyperactivity is believed to affect cellular senescence and has been implicated in HD. No previous study investigated HD or HPA-axis dysregulation in relation to measures of epigenetic age (EA) acceleration.\n\nThis study reports on a case-control study set-up from a well-characterized cohort, contrasting EA predictors in relation to 60 HD patients and 33 healthy volunteers (HV) and 19 mixed HD/HV exhibiting dexamethasone suppression test (DST) non-suppression to 73 mixed HD/HV DST controls. The genome-wide methylation pattern was measured in whole blood from 94 subjects using the Illumina Infinium Methylation EPIC BeadChip and preprocessed according to specialized protocols suitable for epigenetic age estimation. The online DNAm Age Calculator (https://dnamage.\n\nucla.edu/) was implemented to retrieve various EA predictors, which were compared between the in-silico generated subgroups.\n\nQuality control analyses indicated strong correlations between the EA measure DNA methylation GrimAge (DNAm GrimAge - the EA clock most reliably associated with mortality risk) and chronological age in all sub-groups. The study was adequately powered to detect differences of 2.5 and 3.0 years in DNAm GrimAge minus age in relation to both HD and HPA-axis dysregulation, respectively. Baseline DNAm GrimAge exceeded chronological age by 2.8 years on average across all samples. No EA acceleration marker was associated with HD or DST suppression status (p > 0.05).\n\nEA acceleration markers shown to be strongly predictive of physiological dysregulation and mortality-risk, are not related to HD or DST non-suppression status (measured after 0.5 mg dexamethasone). The independency of HPA-axis dysregulation to EA acceleration does not support the biological relevance of this dosage-regimen when applied to patients with HD. These findings do not support the notion of accelerated cellular senescence in HD. Studies stratifying DST non-suppressors according to established dosage-regimens in somatic settings are needed to fully elucidate the putative contribution of HPA-axis dysregulation to EA.", "doi": "10.1016/j.psyneuen.2022.105765", "pmid": "35452872", "labels": {"National Genomics Infrastructure": "Service", "NGI SNP genotyping": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "S0306-4530(22)00106-8"}], "notes": [], "created": "2022-05-06T10:18:10.293Z", "modified": "2022-05-06T10:18:10.339Z"}, {"entity": "publication", "iuid": "bc870a45f0344e1e8e4a7fe8930a4fcc", "links": {"self": {"href": "https://publications.scilifelab.se/publication/bc870a45f0344e1e8e4a7fe8930a4fcc.json"}, "display": {"href": "https://publications.scilifelab.se/publication/bc870a45f0344e1e8e4a7fe8930a4fcc"}}, "title": "scSPLAT, a scalable plate-based protocol for single cell WGBS library preparation.", "authors": [{"family": "Raine", "given": "Amanda", "initials": "A"}, {"family": "Lundmark", "given": "Anders", "initials": "A"}, {"family": "Annett", "given": "Alva", "initials": "A"}, {"family": "Wiman", "given": "Ann-Christin", "initials": "AC"}, {"family": "Cavalli", "given": "Marco", "initials": "M"}, {"family": "Wadelius", "given": "Claes", "initials": "C"}, {"family": "Bergin", "given": "Claudia", "initials": "C"}, {"family": "Nordlund", "given": "Jessica", "initials": "J"}], "type": "journal article", "published": "2022-04-06", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "12", "issue": "1", "pages": "5772", "issn-l": "2045-2322"}, "abstract": "DNA methylation is a central epigenetic mark that has diverse roles in gene regulation, development, and maintenance of genome integrity. 5 methyl cytosine (5mC) can be interrogated at base resolution in single cells by using bisulfite sequencing (scWGBS). Several different scWGBS strategies have been described in recent years to study DNA methylation in single cells. However, there remain limitations with respect to cost-efficiency and yield. Herein, we present a new development in the field of scWGBS library preparation; single cell Splinted Ligation Adapter Tagging (scSPLAT). scSPLAT employs a pooling strategy to facilitate sample preparation at a higher scale and throughput than previously possible. We demonstrate the accuracy and robustness of the method by generating data from 225 single K562 cells and from 309 single liver nuclei and compare scSPLAT against other scWGBS methods.", "doi": "10.1038/s41598-022-09798-2", "pmid": "35388090", "labels": {"National Genomics Infrastructure": "Technology development", "NGI Single cell": "Technology development", "NGI Uppsala (SNP&SEQ Technology Platform)": "Technology development", "Microbial Single Cell Genomics": null, "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC8986790"}, {"db": "pii", "key": "10.1038/s41598-022-09798-2"}], "notes": [], "created": "2022-05-09T11:05:24.613Z", "modified": "2024-01-16T13:48:37.083Z"}, {"entity": "publication", "iuid": "84a78d53a4334fc19fc2291e44e6e963", "links": {"self": {"href": "https://publications.scilifelab.se/publication/84a78d53a4334fc19fc2291e44e6e963.json"}, "display": {"href": "https://publications.scilifelab.se/publication/84a78d53a4334fc19fc2291e44e6e963"}}, "title": "Next Generation Plasma Proteomics Identifies High-Precision Biomarker Candidates for Ovarian Cancer.", "authors": [{"family": "Gyllensten", "given": "Ulf", "initials": "U"}, {"family": "Hedlund-Lindberg", "given": "Julia", "initials": "J"}, {"family": "Svensson", "given": "Johanna", "initials": "J"}, {"family": "Manninen", "given": "Johanna", "initials": "J"}, {"family": "\u00d6st", "given": "Torbj\u00f6rn", "initials": "T"}, {"family": "Ramsell", "given": "Jon", "initials": "J"}, {"family": "\u00c5slin", "given": "Matilda", "initials": "M", "orcid": "0000-0002-2450-6415", "researcher": {"href": "https://publications.scilifelab.se/researcher/f3f0bf2483a543d689fb6e95804066dd.json"}}, {"family": "Ivansson", "given": "Emma", "initials": "E"}, {"family": "Lomnytska", "given": "Marta", "initials": "M"}, {"family": "Lycke", "given": "Maria", "initials": "M"}, {"family": "Axelsson", "given": "Tomas", "initials": "T"}, {"family": "Liljedahl", "given": "Ulrika", "initials": "U"}, {"family": "Nordlund", "given": "Jessica", "initials": "J", "orcid": "0000-0001-8699-9959", "researcher": {"href": "https://publications.scilifelab.se/researcher/ddf48c9262134821bcc6ce1180049753.json"}}, {"family": "Edqvist", "given": "Per-Henrik", "initials": "PH", "orcid": "0000-0002-8330-0134", "researcher": {"href": "https://publications.scilifelab.se/researcher/dd5ff31463cd4345a1fc8351e797ac7f.json"}}, {"family": "Sj\u00f6blom", "given": "Tobias", "initials": "T", "orcid": "0000-0001-6668-4140", "researcher": {"href": "https://publications.scilifelab.se/researcher/909f00a5bf6e465f9ff560b12bcd863a.json"}}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M"}, {"family": "St\u00e5lberg", "given": "Karin", "initials": "K", "orcid": "0000-0001-5527-8796", "researcher": {"href": "https://publications.scilifelab.se/researcher/47a9c8e243994dccb4730266b0431d6d.json"}}, {"family": "Sundfeldt", "given": "Karin", "initials": "K", "orcid": "0000-0002-7135-3132", "researcher": {"href": "https://publications.scilifelab.se/researcher/fb40cfcba9154502ad1d530c5e4a8a66.json"}}, {"family": "\u00c5berg", "given": "Mikael", "initials": "M"}, {"family": "Enroth", "given": "Stefan", "initials": "S", "orcid": "0000-0002-5056-9137", "researcher": {"href": "https://publications.scilifelab.se/researcher/16bb97ef16ee49f3ae0c7ea0495fd971.json"}}], "type": "journal article", "published": "2022-03-30", "journal": {"title": "Cancers (Basel)", "issn": "2072-6694", "volume": "14", "issue": "7", "issn-l": "2072-6694"}, "abstract": "Ovarian cancer is the eighth most common cancer among women and has a 5-year survival of only 30-50%. The survival is close to 90% for patients in stage I but only 20% for patients in stage IV. The presently available biomarkers have insufficient sensitivity and specificity for early detection and there is an urgent need to identify novel biomarkers.\n\nWe employed the Explore PEA technology for high-precision analysis of 1463 plasma proteins and conducted a discovery and replication study using two clinical cohorts of previously untreated patients with benign or malignant ovarian tumours (N = 111 and N = 37).\n\nThe discovery analysis identified 32 proteins that had significantly higher levels in malignant cases as compared to benign diagnoses, and for 28 of these, the association was replicated in the second cohort. Multivariate modelling identified three highly accurate models based on 4 to 7 proteins each for separating benign tumours from early-stage and/or late-stage ovarian cancers, all with AUCs above 0.96 in the replication cohort. We also developed a model for separating the early-stage from the late-stage achieving an AUC of 0.81 in the replication cohort. These models were based on eleven proteins in total (ALPP, CXCL8, DPY30, IL6, IL12, KRT19, PAEP, TSPAN1, SIGLEC5, VTCN1, and WFDC2), notably without MUCIN-16. The majority of the associated proteins have been connected to ovarian cancer but not identified as potential biomarkers.\n\nThe results show the ability of using high-precision proteomics for the identification of novel plasma protein biomarker candidates for the early detection of ovarian cancer.", "doi": "10.3390/cancers14071757", "pmid": "35406529", "labels": {"National Genomics Infrastructure": "Collaborative", "NGI Proteomics": "Collaborative", "NGI Uppsala (SNP&SEQ Technology Platform)": "Collaborative", "Affinity Proteomics Uppsala": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC8997113"}, {"db": "pii", "key": "cancers14071757"}], "notes": [], "created": "2022-05-06T10:19:41.790Z", "modified": "2022-12-02T08:50:06.321Z"}, {"entity": "publication", "iuid": "d43e6d14232747caa43602a9dbe3b086", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d43e6d14232747caa43602a9dbe3b086.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d43e6d14232747caa43602a9dbe3b086"}}, "title": "Inflammation and neutrophil extracellular traps in cerebral cavernous malformation.", "authors": [{"family": "Yau", "given": "Anthony C Y", "initials": "ACY", "orcid": "0000-0002-1570-7813", "researcher": {"href": "https://publications.scilifelab.se/researcher/5d050ac252ce4b8e82ae73ed9f4aa6b4.json"}}, {"family": "Globisch", "given": "Maria Ascencion", "initials": "MA", "orcid": "0000-0002-2251-9810", "researcher": {"href": "https://publications.scilifelab.se/researcher/eec1b44eb73f410f8c27f642ec061a67.json"}}, {"family": "Onyeogaziri", "given": "Favour Chinyere", "initials": "FC"}, {"family": "Conze", "given": "Lei L", "initials": "LL", "orcid": "0000-0001-8698-3842", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff4ce9ba49a5461f9247f3d1220bed18.json"}}, {"family": "Smith", "given": "Ross", "initials": "R", "orcid": "0000-0003-4239-3204", "researcher": {"href": "https://publications.scilifelab.se/researcher/a464f28ad47c4706a08645b9616198b7.json"}}, {"family": "Jauhiainen", "given": "Suvi", "initials": "S"}, {"family": "Corada", "given": "Monica", "initials": "M", "orcid": "0000-0001-8220-0871", "researcher": {"href": "https://publications.scilifelab.se/researcher/2e75cbe437524e2d87d202eaefc0ccca.json"}}, {"family": "Orsenigo", "given": "Fabrizio", "initials": "F", "orcid": "0000-0001-9135-8478", "researcher": {"href": "https://publications.scilifelab.se/researcher/f03f2f483b8f491582245a256bef8ccb.json"}}, {"family": "Huang", "given": "Hua", "initials": "H", "orcid": "0000-0002-0914-6562", "researcher": {"href": "https://publications.scilifelab.se/researcher/35186228c92646e891ea31b4cf65a577.json"}}, {"family": "Herre", "given": "Melanie", "initials": "M"}, {"family": "Olsson", "given": "Anna-Karin", "initials": "AK", "orcid": "0000-0002-5438-7293", "researcher": {"href": "https://publications.scilifelab.se/researcher/57ec91022afd4c1390433d6383a06fc0.json"}}, {"family": "Malinverno", "given": "Matteo", "initials": "M", "orcid": "0000-0001-8242-7937", "researcher": {"href": "https://publications.scilifelab.se/researcher/bb8715aae8fe48f6b2cbacb997401749.json"}}, {"family": "Sundell", "given": "Veronica", "initials": "V"}, {"family": "Rezai Jahromi", "given": "Behnam", "initials": "B", "orcid": "0000-0003-3937-2816", "researcher": {"href": "https://publications.scilifelab.se/researcher/5b1eedb302484555b1451aa283157a04.json"}}, {"family": "Niemel\u00e4", "given": "Mika", "initials": "M", "orcid": "0000-0003-1526-0684", "researcher": {"href": "https://publications.scilifelab.se/researcher/41d032a4f170424f8c24657bb282a48e.json"}}, {"family": "Laakso", "given": "Aki", "initials": "A", "orcid": "0000-0002-5312-4926", "researcher": {"href": "https://publications.scilifelab.se/researcher/d34aba099f9044c88997da8ab113a7c2.json"}}, {"family": "Garlanda", "given": "Cecilia", "initials": "C", "orcid": "0000-0002-1510-7703", "researcher": {"href": "https://publications.scilifelab.se/researcher/c40dc1a52b364e2194ac072873d5efc9.json"}}, {"family": "Mantovani", "given": "Alberto", "initials": "A", "orcid": "0000-0001-5578-236X", "researcher": {"href": "https://publications.scilifelab.se/researcher/99eeed4b00c6456d8d4fc1b6832f677b.json"}}, {"family": "Lampugnani", "given": "Maria Grazia", "initials": "MG", "orcid": "0000-0002-4802-7064", "researcher": {"href": "https://publications.scilifelab.se/researcher/9aca420b37904fceac0b4bbc7f634c70.json"}}, {"family": "Dejana", "given": "Elisabetta", "initials": "E", "orcid": "0000-0002-0007-0426", "researcher": {"href": "https://publications.scilifelab.se/researcher/44cc4a690a194c5bbc2193213c98c5e1.json"}}, {"family": "Magnusson", "given": "Peetra U", "initials": "PU", "orcid": "0000-0003-1142-854X", "researcher": {"href": "https://publications.scilifelab.se/researcher/2b1a74b677b145fc81a2d4bd7f3bf498.json"}}], "type": "journal article", "published": "2022-03-25", "journal": {"title": "Cell. Mol. Life Sci.", "issn": "1420-9071", "volume": "79", "issue": "4", "pages": "206", "issn-l": "1420-682X"}, "abstract": "Cerebral Cavernous Malformation (CCM) is a brain vascular disease with various neurological symptoms. In this study, we describe the inflammatory profile in CCM and show for the first time the formation of neutrophil extracellular traps (NETs) in rodents and humans with CCM. Through RNA-seq analysis of cerebellum endothelial cells from wild-type mice and mice with an endothelial cell-specific ablation of the Ccm3 gene (Ccm3iECKO), we show that endothelial cells from Ccm3iECKO mice have an increased expression of inflammation-related genes. These genes encode proinflammatory cytokines and chemokines, as well as adhesion molecules, which promote recruitment of inflammatory and immune cells. Similarly, immunoassays showed elevated levels of these cytokines and chemokines in the cerebellum of the Ccm3iECKO mice. Consistently, both flow cytometry and immunofluorescence analysis showed infiltration of different subsets of leukocytes into the CCM lesions. Neutrophils, which are known to fight against infection through different strategies, including the formation of NETs, represented the leukocyte subset within the most pronounced increase in CCM. Here, we detected elevated levels of NETs in the blood and the deposition of NETs in the cerebral cavernomas of Ccm3iECKO mice. Degradation of NETs by DNase I treatment improved the vascular barrier. The deposition of NETs in the cavernomas of patients with CCM confirms the clinical relevance of NETs in CCM.", "doi": "10.1007/s00018-022-04224-2", "pmid": "35333979", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC8949649"}, {"db": "pii", "key": "10.1007/s00018-022-04224-2"}], "notes": [], "created": "2022-11-29T09:50:27.050Z", "modified": "2022-11-29T09:50:27.560Z"}, {"entity": "publication", "iuid": "8f169041de1f4c60ad274706cf0739bc", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8f169041de1f4c60ad274706cf0739bc.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8f169041de1f4c60ad274706cf0739bc"}}, "title": "Near Chromosome-Level Genome Assembly and Annotation of Rhodotorula babjevae Strains Reveals High Intraspecific Divergence.", "authors": [{"family": "Mart\u00edn-Hern\u00e1ndez", "given": "Giselle C", "initials": "GC", "orcid": "0000-0003-1497-7755", "researcher": {"href": "https://publications.scilifelab.se/researcher/5289a4b7aa8e476eaadb6d7773be8db8.json"}}, {"family": "M\u00fcller", "given": "Bettina", "initials": "B", "orcid": "0000-0002-0030-7710", "researcher": {"href": "https://publications.scilifelab.se/researcher/4c1cb5bfdb1a4ceaa551d5908b54e062.json"}}, {"family": "Brandt", "given": "Christian", "initials": "C", "orcid": "0000-0002-7199-3957", "researcher": {"href": "https://publications.scilifelab.se/researcher/f760c98ca3844c50a684346e41733263.json"}}, {"family": "H\u00f6lzer", "given": "Martin", "initials": "M", "orcid": "0000-0001-7090-8717", "researcher": {"href": "https://publications.scilifelab.se/researcher/87dee9193083480d9be8784de5431626.json"}}, {"family": "Viehweger", "given": "Adrian", "initials": "A"}, {"family": "Passoth", "given": "Volkmar", "initials": "V", "orcid": "0000-0002-2059-9044", "researcher": {"href": "https://publications.scilifelab.se/researcher/b44de438fbf14bda83267d133a19f488.json"}}], "type": "journal article", "published": "2022-03-22", "journal": {"title": "JoF", "issn": "2309-608X", "volume": "8", "issue": "4", "issn-l": null}, "abstract": "The genus Rhodotorula includes basidiomycetous oleaginous yeast species. Rhodotorula babjevae can produce compounds of biotechnological interest such as lipids, carotenoids, and biosurfactants from low value substrates such as lignocellulose hydrolysate. High-quality genome assemblies are needed to develop genetic tools and to understand fungal evolution and genetics. Here, we combined short- and long-read sequencing to resolve the genomes of two R. babjevae strains, CBS 7808 (type strain) and DBVPG 8058, at chromosomal level. Both genomes are 21 Mbp in size and have a GC content of 68.2%. Allele frequency analysis indicates that both strains are tetraploid. The genomes consist of a maximum of 21 chromosomes with a size of 0.4 to 2.4 Mbp. In both assemblies, the mitochondrial genome was recovered in a single contig, that shared 97% pairwise identity. Pairwise identity between most chromosomes ranges from 82 to 87%. We also found indications for strain-specific extrachromosomal endogenous DNA. A total of 7591 and 7481 protein-coding genes were annotated in CBS 7808 and DBVPG 8058, respectively. CBS 7808 accumulated a higher number of tandem duplications than DBVPG 8058. We identified large translocation events between putative chromosomes. Genome divergence values between the two strains indicate that they may belong to different species.", "doi": "10.3390/jof8040323", "pmid": "35448555", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9027234"}, {"db": "pii", "key": "jof8040323"}], "notes": [], "created": "2022-11-29T12:27:36.058Z", "modified": "2022-11-29T12:27:36.232Z"}, {"entity": "publication", "iuid": "51bed1dfb07142a79ddc3a8d820cc598", "links": {"self": {"href": "https://publications.scilifelab.se/publication/51bed1dfb07142a79ddc3a8d820cc598.json"}, "display": {"href": "https://publications.scilifelab.se/publication/51bed1dfb07142a79ddc3a8d820cc598"}}, "title": "GWAS in people of Middle Eastern descent reveals a locus protective of kidney function-a cross-sectional study.", "authors": [{"family": "Mohamed", "given": "Siham A", "initials": "SA", "orcid": "0000-0001-8572-0848", "researcher": {"href": "https://publications.scilifelab.se/researcher/fa4c325b0a854172b69ecae7292712a1.json"}}, {"family": "Fernadez-Tajes", "given": "Juan", "initials": "J", "orcid": "0000-0003-1515-2421", "researcher": {"href": "https://publications.scilifelab.se/researcher/dad51251fc8d42f793e4c991c4102667.json"}}, {"family": "Franks", "given": "Paul W", "initials": "PW", "orcid": "0000-0002-0520-7604", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ebbf40c0f7e49dd8c75a2b6cbf27276.json"}}, {"family": "Bennet", "given": "Louise", "initials": "L", "orcid": "0000-0001-7101-1290", "researcher": {"href": "https://publications.scilifelab.se/researcher/4be856882c2a40bd9fbde780816af7e1.json"}}], "type": "journal article", "published": "2022-03-01", "journal": {"title": "BMC Med", "issn": "1741-7015", "volume": "20", "issue": "1", "pages": "76", "issn-l": "1741-7015"}, "abstract": "Type 2 diabetes is one of the leading causes of chronic kidney failure, which increases globally and represents a significant threat to public health. People from the Middle East represent one of the largest immigrant groups in Europe today. Despite poor glucose regulation and high risk for early-onset insulin-deficient type 2 diabetes, they have better kidney function and lower rates of all-cause and cardiovascular-specific mortality compared with people of European ancestry. Here, we assessed the genetic basis of estimated glomerular filtration rate (eGFR) and other metabolic traits in people of Iraqi ancestry living in southern Sweden.\n\nGenome-wide association study (GWAS) analyses were performed in 1201 Iraqi-born residents of the city of Malm\u00f6 for eGFR and ten other metabolic traits using linear mixed-models to account for family structure.\n\nThe strongest association signal was detected for eGFR in CST9 (rs13037490; P value = 2.4 \u00d7 10-13), a locus previously associated with cystatin C-based eGFR; importantly, the effect (major) allele here contrasts the effect (minor) allele in other populations, suggesting favorable selection at this locus. Additional novel genome-wide significant loci for eGFR (ERBB4), fasting glucose (CAMTA1, NDUFA10, TRIO, WWC1, TRAPPC9, SH3GL2, ABCC11), quantitative insulin-sensitivity check index (METTL16), and HbA1C (CAMTA1, ME1, PAK1, RORA) were identified.\n\nThe genetic effects discovered here may help explain why people from the Middle East have better kidney function than those of European descent. Genetic predisposition to preserved kidney function may also underlie the observed survival benefits in Middle Eastern immigrants with type 2 diabetes.", "doi": "10.1186/s12916-022-02267-7", "pmid": "35227251", "labels": {"National Genomics Infrastructure": "Service", "NGI SNP genotyping": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1186/s12916-022-02267-7"}, {"db": "pmc", "key": "PMC8886846"}], "notes": [], "created": "2022-05-06T10:18:21.346Z", "modified": "2022-05-06T10:18:21.491Z"}, {"entity": "publication", "iuid": "2ac617985f284c5da4d79ca90e3b6931", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2ac617985f284c5da4d79ca90e3b6931.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2ac617985f284c5da4d79ca90e3b6931"}}, "title": "Whole-genome resequencing of temporally stratified samples reveals substantial loss of haplotype diversity in the highly inbred Scandinavian wolf population.", "authors": [{"family": "Viluma", "given": "Agnese", "initials": "A", "orcid": "0000-0003-3388-5020", "researcher": {"href": "https://publications.scilifelab.se/researcher/1df731227e824bb5a8dade435f9571aa.json"}}, {"family": "Flagstad", "given": "\u00d8ystein", "initials": "\u00d8"}, {"family": "\u00c5kesson", "given": "Mikael", "initials": "M"}, {"family": "Wikenros", "given": "Camilla", "initials": "C"}, {"family": "Sand", "given": "H\u00e5kan", "initials": "H"}, {"family": "Wabakken", "given": "Petter", "initials": "P"}, {"family": "Ellegren", "given": "Hans", "initials": "H"}], "type": "journal article", "published": "2022-03-00", "journal": {"title": "Genome Res.", "issn": "1549-5469", "volume": "32", "issue": "3", "pages": "449-458", "issn-l": "1088-9051"}, "abstract": "Genetic drift can dramatically change allele frequencies in small populations and lead to reduced levels of genetic diversity, including loss of segregating variants. However, there is a shortage of quantitative studies of how genetic diversity changes over time in natural populations, especially on genome-wide scales. Here, we analyzed whole-genome sequences from 76 wolves of a highly inbred Scandinavian population, founded by only one female and two males, sampled over a period of 30 yr. We obtained chromosome-level haplotypes of all three founders and found that 10%-24% of their diploid genomes had become lost after about 20 yr of inbreeding (which approximately corresponds to five generations). Lost haplotypes spanned large genomic regions, as expected from the amount of recombination during this limited time period. Altogether, 160,000 SNP alleles became lost from the population, which may include adaptive variants as well as wild-type alleles masking recessively deleterious alleles. Although not sampled, we could indirectly infer that the two male founders had megabase-sized runs of homozygosity and that all three founders showed significant haplotype sharing, meaning that there were on average only 4.2 unique haplotypes in the six copies of each autosome that the founders brought into the population. This violates the assumption of unrelated founder haplotypes often made in conservation and management of endangered species. Our study provides a novel view of how whole-genome resequencing of temporally stratified samples can be used to visualize and directly quantify the consequences of genetic drift in a small inbred population.", "doi": "10.1101/gr.276070.121", "pmid": "35135873", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Short read": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC8896455"}, {"db": "pii", "key": "gr.276070.121"}, {"db": "medline", "key": "9509184"}], "notes": [], "created": "2022-09-28T13:51:59.123Z", "modified": "2024-01-16T13:48:37.319Z"}, {"entity": "publication", "iuid": "2680a2abced44ef5951849e303ee5cf6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2680a2abced44ef5951849e303ee5cf6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2680a2abced44ef5951849e303ee5cf6"}}, "title": "The Genetic Architecture of Obsessive-Compulsive Disorder: Contribution of Liability to OCD From Alleles Across the Frequency Spectrum.", "authors": [{"family": "Mahjani", "given": "Behrang", "initials": "B", "orcid": "0000-0001-6087-9537", "researcher": {"href": "https://publications.scilifelab.se/researcher/ec48acf0ec354881bc2ea4e277489718.json"}}, {"family": "Klei", "given": "Lambertus", "initials": "L"}, {"family": "Mattheisen", "given": "Manuel", "initials": "M"}, {"family": "Halvorsen", "given": "Matthew W", "initials": "MW"}, {"family": "Reichenberg", "given": "Abraham", "initials": "A"}, {"family": "Roeder", "given": "Kathryn", "initials": "K"}, {"family": "Pedersen", "given": "Nancy L", "initials": "NL"}, {"family": "Boberg", "given": "Julia", "initials": "J"}, {"family": "de Schipper", "given": "Elles", "initials": "E"}, {"family": "Bulik", "given": "Cynthia M", "initials": "CM"}, {"family": "Land\u00e9n", "given": "Mikael", "initials": "M"}, {"family": "Fund\u00edn", "given": "Bengt", "initials": "B"}, {"family": "Mataix-Cols", "given": "David", "initials": "D"}, {"family": "Sandin", "given": "Sven", "initials": "S"}, {"family": "Hultman", "given": "Christina M", "initials": "CM"}, {"family": "Crowley", "given": "James J", "initials": "JJ"}, {"family": "Buxbaum", "given": "Joseph D", "initials": "JD"}, {"family": "R\u00fcck", "given": "Christian", "initials": "C"}, {"family": "Devlin", "given": "Bernie", "initials": "B"}, {"family": "Grice", "given": "Dorothy E", "initials": "DE"}], "type": "journal article", "published": "2022-03-00", "journal": {"title": "Am J Psychiatry", "issn": "1535-7228", "issn-l": "0002-953X", "volume": "179", "issue": "3", "pages": "216-225"}, "abstract": "Obsessive-compulsive disorder (OCD) is known to be substantially heritable; however, the contribution of genetic variation across the allele frequency spectrum to this heritability remains uncertain. The authors used two new homogeneous cohorts to estimate the heritability of OCD from inherited genetic variation and contrasted the results with those of previous studies.\n\nThe sample consisted of 2,090 Swedish-born individuals diagnosed with OCD and 4,567 control subjects, all genotyped for common genetic variants, specifically >400,000 single-nucleotide polymorphisms (SNPs) with minor allele frequency (MAF) \u22650.01. Using genotypes of these SNPs to estimate distant familial relationships among individuals, the authors estimated the heritability of OCD, both overall and partitioned according to MAF bins.\n\nNarrow-sense heritability of OCD was estimated at 29% (SE=4%). The estimate was robust, varying only modestly under different models. Contrary to an earlier study, however, SNPs with MAF between 0.01 and 0.05 accounted for 10% of heritability, and estimated heritability per MAF bin roughly followed expectations based on a simple model for SNP-based heritability.\n\nThese results indicate that common inherited risk variation (MAF \u22650.01) accounts for most of the heritable variation in OCD. SNPs with low MAF contribute meaningfully to the heritability of OCD, and the results are consistent with expectation under the \"infinitesimal model\" (also referred to as the \"polygenic model\"), where risk is influenced by a large number of loci across the genome and across MAF bins.", "doi": "10.1176/appi.ajp.2021.21010101", "pmid": "34789012", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC8897260"}, {"db": "mid", "key": "NIHMS1745008"}], "notes": [], "created": "2021-11-26T16:27:54.676Z", "modified": "2024-01-16T13:48:37.338Z"}, {"entity": "publication", "iuid": "c5707d7f269941cb9e6716038a773c9b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c5707d7f269941cb9e6716038a773c9b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c5707d7f269941cb9e6716038a773c9b"}}, "title": "Loss of Y and clonal hematopoiesis in blood-two sides of the same coin?", "authors": [{"family": "Ljungstr\u00f6m", "given": "Viktor", "initials": "V"}, {"family": "Mattisson", "given": "Jonas", "initials": "J"}, {"family": "Halvardson", "given": "Jonatan", "initials": "J"}, {"family": "Pandzic", "given": "Tatjana", "initials": "T"}, {"family": "Davies", "given": "Hanna", "initials": "H"}, {"family": "Rychlicka-Buniowska", "given": "Edyta", "initials": "E"}, {"family": "Danielsson", "given": "Marcus", "initials": "M", "orcid": "0000-0003-4418-0165", "researcher": {"href": "https://publications.scilifelab.se/researcher/d6b237ce613e4ef8a6d7ab2654c2c41e.json"}}, {"family": "Lacaze", "given": "Paul", "initials": "P"}, {"family": "Cavelier", "given": "Lucia", "initials": "L"}, {"family": "Dumanski", "given": "Jan P", "initials": "JP", "orcid": "0000-0002-1489-1452", "researcher": {"href": "https://publications.scilifelab.se/researcher/15b14282209342cfa9c82cdbf02999f6.json"}}, {"family": "Baliakas", "given": "Panagiotis", "initials": "P", "orcid": "0000-0002-5634-7156", "researcher": {"href": "https://publications.scilifelab.se/researcher/17370bd509dc4b1081af5aed9e5117c7.json"}}, {"family": "Forsberg", "given": "Lars A", "initials": "LA", "orcid": "0000-0002-1701-755X", "researcher": {"href": "https://publications.scilifelab.se/researcher/9ac2d8e983764a82982118b6db84029e.json"}}], "type": "letter", "published": "2022-03-00", "journal": {"title": "Leukemia", "issn": "1476-5551", "issn-l": "0887-6924", "volume": "36", "issue": "3", "pages": "889-891"}, "abstract": null, "doi": "10.1038/s41375-021-01456-2", "pmid": "34725452", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Clinical Genomics Uppsala": "Service", "NGI SNP genotyping": "Service", "Bioinformatics Support for Computational Resources": "Service", "Clinical Genomics": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC8885420"}, {"db": "pii", "key": "10.1038/s41375-021-01456-2"}], "notes": [], "created": "2021-11-26T16:27:55.997Z", "modified": "2024-01-16T13:48:37.346Z"}, {"entity": "publication", "iuid": "08f15b6b8d674af294f91bd5ad4005d3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/08f15b6b8d674af294f91bd5ad4005d3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/08f15b6b8d674af294f91bd5ad4005d3"}}, "title": "The Value of Whole-Genome Sequencing for Mitochondrial DNA Population Studies: Strategies and Criteria for Extracting High-Quality Mitogenome Haplotypes.", "authors": [{"family": "Sturk-Andreaggi", "given": "Kimberly", "initials": "K", "orcid": "0000-0001-6857-923X", "researcher": {"href": "https://publications.scilifelab.se/researcher/3f1cbf7b4fd94b17b1c37712634b7638.json"}}, {"family": "Ring", "given": "Joseph D", "initials": "JD"}, {"family": "Ameur", "given": "Adam", "initials": "A", "orcid": "0000-0001-6085-6749", "researcher": {"href": "https://publications.scilifelab.se/researcher/e960811513664a78b2804a00ee70f7c3.json"}}, {"family": "Gyllensten", "given": "Ulf", "initials": "U"}, {"family": "Bodner", "given": "Martin", "initials": "M", "orcid": "0000-0002-3870-9862", "researcher": {"href": "https://publications.scilifelab.se/researcher/455fefcf430d4b7e8433b3c7b3856b4b.json"}}, {"family": "Parson", "given": "Walther", "initials": "W", "orcid": "0000-0002-5692-2392", "researcher": {"href": "https://publications.scilifelab.se/researcher/84574a9a6f03419ea3a37a6dd0470082.json"}}, {"family": "Marshall", "given": "Charla", "initials": "C", "orcid": "0000-0002-8495-1748", "researcher": {"href": "https://publications.scilifelab.se/researcher/75b9e14fcfae4eeea425cf685cf6d6ba.json"}}, {"family": "Allen", "given": "Marie", "initials": "M"}], "type": "journal article", "published": "2022-02-17", "journal": {"title": "Int J Mol Sci", "issn": "1422-0067", "issn-l": null, "volume": "23", "issue": "4", "pages": null}, "abstract": "Whole-genome sequencing (WGS) data present a readily available resource for mitochondrial genome (mitogenome) haplotypes that can be utilized for genetics research including population studies. However, the reconstruction of the mitogenome is complicated by nuclear mitochondrial DNA (mtDNA) segments (NUMTs) that co-align with the mtDNA sequences and mimic authentic heteroplasmy. Two minimum variant detection thresholds, 5% and 10%, were assessed for the ability to produce authentic mitogenome haplotypes from a previously generated WGS dataset. Variants associated with NUMTs were detected in the mtDNA alignments for 91 of 917 (~8%) Swedish samples when the 5% frequency threshold was applied. The 413 observed NUMT variants were predominantly detected in two regions (nps 12,612-13,105 and 16,390-16,527), which were consistent with previously documented NUMTs. The number of NUMT variants was reduced by ~97% (400) using a 10% frequency threshold. Furthermore, the 5% frequency data were inconsistent with a platinum-quality mitogenome dataset with respect to observed heteroplasmy. These analyses illustrate that a 10% variant detection threshold may be necessary to ensure the generation of reliable mitogenome haplotypes from WGS data resources.", "doi": "10.3390/ijms23042244", "pmid": "35216360", "labels": {"National Genomics Infrastructure": "Collaborative", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Uppsala (Uppsala Genome Center)": "Collaborative", "NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC8876724"}, {"db": "pii", "key": "ijms23042244"}], "notes": [], "created": "2022-03-29T04:39:22.438Z", "modified": "2024-01-16T13:48:37.438Z"}, {"entity": "publication", "iuid": "70304e2e74c14f8c98b28d736df71cf4", "links": {"self": {"href": "https://publications.scilifelab.se/publication/70304e2e74c14f8c98b28d736df71cf4.json"}, "display": {"href": "https://publications.scilifelab.se/publication/70304e2e74c14f8c98b28d736df71cf4"}}, "title": "The miRNome function transitions from regulating developmental genes to transposable elements during pollen maturation.", "authors": [{"family": "Oliver", "given": "Cecilia", "initials": "C", "orcid": "0000-0002-5231-7910", "researcher": {"href": "https://publications.scilifelab.se/researcher/8fdb426c5e2e48e985eb8939a1c40d6e.json"}}, {"family": "Annacondia", "given": "Maria Luz", "initials": "ML", "orcid": "0000-0001-7998-8362", "researcher": {"href": "https://publications.scilifelab.se/researcher/7b4d89a422254e47a38fe438fe99bdaf.json"}}, {"family": "Wang", "given": "Zhenxing", "initials": "Z", "orcid": "0000-0001-5102-7121", "researcher": {"href": "https://publications.scilifelab.se/researcher/4b6c9f88c65d4fbc94da6d7598102335.json"}}, {"family": "Jullien", "given": "Pauline E", "initials": "PE", "orcid": "0000-0003-1212-3246", "researcher": {"href": "https://publications.scilifelab.se/researcher/7a97f95d2f1046b3a7027dedf5a31082.json"}}, {"family": "Slotkin", "given": "R Keith", "initials": "RK", "orcid": "0000-0001-9582-3533", "researcher": {"href": "https://publications.scilifelab.se/researcher/ac639e0390ef4140a566e5cbbf65084a.json"}}, {"family": "K\u00f6hler", "given": "Claudia", "initials": "C", "orcid": "0000-0002-2619-4857", "researcher": {"href": "https://publications.scilifelab.se/researcher/accd3f9307614c8ab67154dd5e50cdac.json"}}, {"family": "Martinez", "given": "German", "initials": "G", "orcid": "0000-0002-5215-0866", "researcher": {"href": "https://publications.scilifelab.se/researcher/591f629ea8ed44c2bd9cd417dcebd8bc.json"}}], "type": "journal article", "published": "2022-02-03", "journal": {"title": "Plant Cell", "issn": "1532-298X", "volume": "34", "issue": "2", "pages": "784-801", "issn-l": "1040-4651"}, "abstract": "Animal and plant microRNAs (miRNAs) are essential for the spatio-temporal regulation of development. Together with this role, plant miRNAs have been proposed to target transposable elements (TEs) and stimulate the production of epigenetically active small interfering RNAs. This activity is evident in the plant male gamete containing structure, the male gametophyte or pollen grain. How the dual role of plant miRNAs, regulating both genes and TEs, is integrated during pollen development and which mRNAs are regulated by miRNAs in this cell type at a genome-wide scale are unknown. Here, we provide a detailed analysis of miRNA dynamics and activity during pollen development in Arabidopsis thaliana using small RNA and degradome parallel analysis of RNA end high-throughput sequencing. Furthermore, we uncover miRNAs loaded into the two main active Argonaute (AGO) proteins in the uninuclear and mature pollen grain, AGO1 and AGO5. Our results indicate that the developmental progression from microspore to mature pollen grain is characterized by a transition from miRNAs targeting developmental genes to miRNAs regulating TE activity.", "doi": "10.1093/plcell/koab280", "pmid": "34755870", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC8824631"}, {"db": "pii", "key": "6424912"}], "notes": [], "created": "2022-11-29T09:51:29.116Z", "modified": "2022-11-29T09:51:29.270Z"}, {"entity": "publication", "iuid": "47a4b84cdcfc498c8e898c032a1c6b57", "links": {"self": {"href": "https://publications.scilifelab.se/publication/47a4b84cdcfc498c8e898c032a1c6b57.json"}, "display": {"href": "https://publications.scilifelab.se/publication/47a4b84cdcfc498c8e898c032a1c6b57"}}, "title": "Heterochiasmy and the establishment of gsdf as a novel sex determining gene in Atlantic halibut.", "authors": [{"family": "Edvardsen", "given": "Rolf Brudvik", "initials": "RB", "orcid": "0000-0001-8430-8042", "researcher": {"href": "https://publications.scilifelab.se/researcher/07efd6f7e7b04bbd8af5221f78e982c7.json"}}, {"family": "Wallerman", "given": "Ola", "initials": "O", "orcid": "0000-0003-1037-7904", "researcher": {"href": "https://publications.scilifelab.se/researcher/9b32e1cfd3084b10a4c220416a6bc589.json"}}, {"family": "Furmanek", "given": "Tomasz", "initials": "T", "orcid": "0000-0001-8577-9604", "researcher": {"href": "https://publications.scilifelab.se/researcher/5a02b990970e46409613ca730ced5914.json"}}, {"family": "Kleppe", "given": "Lene", "initials": "L"}, {"family": "Jern", "given": "Patric", "initials": "P", "orcid": "0000-0003-3393-5825", "researcher": {"href": "https://publications.scilifelab.se/researcher/8baed28572fd470ba1e7b18fccd2e275.json"}}, {"family": "Wallberg", "given": "Andreas", "initials": "A", "orcid": "0000-0002-9081-9663", "researcher": {"href": "https://publications.scilifelab.se/researcher/b67a52aca631482d8b8f58e525a82d14.json"}}, {"family": "Kj\u00e6rner-Semb", "given": "Erik", "initials": "E", "orcid": "0000-0001-7160-6710", "researcher": {"href": "https://publications.scilifelab.se/researcher/44013d14287f43a29ca482f5dcdc988a.json"}}, {"family": "M\u00e6hle", "given": "Stig", "initials": "S"}, {"family": "Olausson", "given": "Sara Karolina", "initials": "SK"}, {"family": "Sundstr\u00f6m", "given": "Elisabeth", "initials": "E", "orcid": "0000-0001-9526-8541", "researcher": {"href": "https://publications.scilifelab.se/researcher/20f87b64e71b4a00a9474ec4d898601d.json"}}, {"family": "Harboe", "given": "Torstein", "initials": "T"}, {"family": "Mangor-Jensen", "given": "Ragnfrid", "initials": "R"}, {"family": "M\u00f8gster", "given": "Margareth", "initials": "M"}, {"family": "Perrichon", "given": "Prescilla", "initials": "P", "orcid": "0000-0002-1410-878X", "researcher": {"href": "https://publications.scilifelab.se/researcher/fd8005cb7ec44f569ffc2d457d6e8bf9.json"}}, {"family": "Norberg", "given": "Birgitta", "initials": "B", "orcid": "0000-0003-1550-5725", "researcher": {"href": "https://publications.scilifelab.se/researcher/c178dcf0ef364f14b6cdb7661540070f.json"}}, {"family": "Rubin", "given": "Carl-Johan", "initials": "CJ", "orcid": "0000-0001-8238-5052", "researcher": {"href": "https://publications.scilifelab.se/researcher/0bd98ada4083444e8336ef3ec53df488.json"}}], "type": "journal article", "published": "2022-02-00", "journal": {"title": "PLoS Genet.", "issn": "1553-7404", "volume": "18", "issue": "2", "pages": "e1010011", "issn-l": "1553-7390"}, "abstract": "Atlantic Halibut (Hippoglossus hippoglossus) has a X/Y genetic sex determination system, but the sex determining factor is not known. We produced a high-quality genome assembly from a male and identified parts of chromosome 13 as the Y chromosome due to sequence divergence between sexes and segregation of sex genotypes in pedigrees. Linkage analysis revealed that all chromosomes exhibit heterochiasmy, i.e. male-only and female-only meiotic recombination regions (MRR/FRR). We show that FRR/MRR intervals differ in nucleotide diversity and repeat class content and that this is true also for other Pleuronectidae species. We further show that remnants of a Gypsy-like transposable element insertion on chr13 promotes early male specific expression of gonadal somatic cell derived factor (gsdf). Less than 4.5 MYA, this male-determining element evolved on an autosomal FRR segment featuring pre-existing male meiotic recombination barriers, thereby creating a Y chromosome. Our findings indicate that heterochiasmy may facilitate the evolution of genetic sex determination systems relying on linkage of sexually antagonistic loci to a sex-determining factor.", "doi": "10.1371/journal.pgen.1010011", "pmid": "35134055", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC8824383"}, {"db": "pii", "key": "PGENETICS-D-21-00885"}], "notes": [], "created": "2022-11-29T09:16:18.063Z", "modified": "2024-01-16T13:48:37.634Z"}, {"entity": "publication", "iuid": "bac07fae3c0e4214bca1d4ff1a326f39", "links": {"self": {"href": "https://publications.scilifelab.se/publication/bac07fae3c0e4214bca1d4ff1a326f39.json"}, "display": {"href": "https://publications.scilifelab.se/publication/bac07fae3c0e4214bca1d4ff1a326f39"}}, "title": "A genomic and morphometric analysis of alpine bumblebees: Ongoing reductions in tongue length but no clear genetic component.", "authors": [{"family": "Christmas", "given": "Matthew J", "initials": "MJ"}, {"family": "Jones", "given": "Julia C", "initials": "JC"}, {"family": "Olsson", "given": "Anna", "initials": "A"}, {"family": "Wallerman", "given": "Ola", "initials": "O"}, {"family": "Bunikis", "given": "Ignas", "initials": "I"}, {"family": "Kierczak", "given": "Marcin", "initials": "M", "orcid": "0000-0003-2629-5655", "researcher": {"href": "https://publications.scilifelab.se/researcher/6c13f96fb81f4ae2bfff5e91ac45388e.json"}}, {"family": "Whitley", "given": "Kaitlyn M", "initials": "KM"}, {"family": "Sullivan", "given": "Isabel", "initials": "I"}, {"family": "Geib", "given": "Jennifer C", "initials": "JC"}, {"family": "Miller-Struttmann", "given": "Nicole E", "initials": "NE"}, {"family": "Webster", "given": "Matthew T", "initials": "MT", "orcid": "0000-0003-1141-2863", "researcher": {"href": "https://publications.scilifelab.se/researcher/579df0da95b94e5087512b76d7f1c058.json"}}], "type": "journal article", "published": "2022-02-00", "journal": {"title": "Mol. Ecol.", "issn": "1365-294X", "issn-l": "0962-1083", "volume": "31", "issue": "4", "pages": "1111-1127"}, "abstract": "Over the last six decades, populations of the bumblebees Bombus sylvicola and Bombus balteatus in Colorado have experienced decreases in tongue length, a trait important for plant-pollinator mutualisms. It has been hypothesized that this observation reflects selection resulting from shifts in floral composition under climate change. Here we used morphometrics and population genomics to determine whether morphological change is ongoing, investigate the genetic basis of morphological variation, and analyse population structure in these populations. We generated a genome assembly of B. balteatus. We then analysed whole-genome sequencing data and morphometric measurements of 580 samples of both species from seven high-altitude localities. Out of 281 samples originally identified as B. sylvicola, 67 formed a separate genetic cluster comprising a newly-discovered cryptic species (\"incognitus\"). However, an absence of genetic structure within species suggests that gene flow is common between mountains. We found a significant decrease in tongue length between bees collected between 2012-2014 and in 2017, indicating that morphological shifts are ongoing. We did not discover any genetic associations with tongue length, but a SNP related to production of a proteolytic digestive enzyme was implicated in body size variation. We identified evidence of covariance between kinship and both tongue length and body size, which is suggestive of a genetic component of these traits, although it is possible that shared environmental effects between colonies are responsible. Our results provide evidence for ongoing modification of a morphological trait important for pollination and indicate that this trait probably has a complex genetic and environmental basis.", "doi": "10.1111/mec.16291", "pmid": "34837435", "labels": {"NGI Uppsala (Uppsala Genome Center)": "Collaborative", "National Genomics Infrastructure": "Collaborative", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "NGI Long read": "Collaborative", "NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [], "notes": [], "created": "2021-11-30T12:41:55.744Z", "modified": "2024-01-16T13:48:37.663Z"}, {"entity": "publication", "iuid": "c7e444c1c6864297b04b31cb10b66b98", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c7e444c1c6864297b04b31cb10b66b98.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c7e444c1c6864297b04b31cb10b66b98"}}, "title": "A Verticillium longisporum pleiotropic drug transporter determines tolerance to the plant host \u03b2-pinene monoterpene.", "authors": [{"family": "Rafiei", "given": "Vahideh", "initials": "V", "orcid": "0000-0003-0021-9734", "researcher": {"href": "https://publications.scilifelab.se/researcher/c453e43d63594937aa2efd03e37bee1e.json"}}, {"family": "Ruffino", "given": "Alessandra", "initials": "A", "orcid": "0000-0002-7039-2957", "researcher": {"href": "https://publications.scilifelab.se/researcher/acfbbc82f59b4fbc8a9ea0e6b8515e51.json"}}, {"family": "Persson Hod\u00e9n", "given": "Kristian", "initials": "K", "orcid": "0000-0003-0354-0662", "researcher": {"href": "https://publications.scilifelab.se/researcher/e8b41e8e41574ee6bcb55df3b0d145d9.json"}}, {"family": "Tornkvist", "given": "Anna", "initials": "A", "orcid": "0000-0002-6215-6727", "researcher": {"href": "https://publications.scilifelab.se/researcher/d36e5404f2a841019aa1aeac9c8c7ec9.json"}}, {"family": "Mozuraitis", "given": "Raimondas", "initials": "R", "orcid": "0000-0002-1719-2294", "researcher": {"href": "https://publications.scilifelab.se/researcher/213ecb5deb7d4d06901f461424d964cf.json"}}, {"family": "Dubey", "given": "Mukesh", "initials": "M", "orcid": "0000-0001-7393-366X", "researcher": {"href": "https://publications.scilifelab.se/researcher/da047e9540e344cc93b54a96d5c82b72.json"}}, {"family": "Tzelepis", "given": "Georgios", "initials": "G", "orcid": "0000-0001-6144-2185", "researcher": {"href": "https://publications.scilifelab.se/researcher/60b2114dba0640d3aeecba0c4e729ce0.json"}}], "type": "journal article", "published": "2022-02-00", "journal": {"title": "Mol. Plant Pathol.", "issn": "1364-3703", "volume": "23", "issue": "2", "pages": "291-303", "issn-l": null}, "abstract": "Terpenes constitute a major part of secondary metabolites secreted by plants in the rhizosphere. However, their specific functions in fungal-plant interactions have not been investigated thoroughly. In this study we investigated the role of monoterpenes in interactions between oilseed rape (Brassica napus) and the soilborne pathogen Verticillium longisporum. We identified seven monoterpenes produced by B. napus, and production of \u03b1-pinene, \u03b2-pinene, 3-carene, and camphene was significantly increased upon fungal infection. Among them, \u03b2-pinene was chosen for further analysis. Transcriptome analysis of V. longisporum on exposure to \u03b2-pinene resulted in identification of two highly expressed pleotropic drug transporters paralog genes named VlAbcG1a and VlAbcG1b. Overexpression of VlAbcG1a in Saccharomyces cerevisiae increased tolerance to \u03b2-pinene, while deletion of the VlAbcG1a homologous gene in Verticillium dahliae resulted in mutants with increased sensitivity to certain monoterpenes. Furthermore, the VlAbcG1a overexpression strain displayed an increased tolerance to \u03b2-pinene and increased virulence in tomato plants. Data from this study give new insights into the roles of terpenes in plant-fungal pathogen interactions and the mechanisms fungi deploy to cope with the toxicity of these secondary metabolites.", "doi": "10.1111/mpp.13162", "pmid": "34825755", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC8743018"}], "notes": [], "created": "2022-11-29T09:34:58.011Z", "modified": "2022-11-29T09:34:58.198Z"}, {"entity": "publication", "iuid": "00097c342d474f85a1fe229a74798c7b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/00097c342d474f85a1fe229a74798c7b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/00097c342d474f85a1fe229a74798c7b"}}, "title": "Massive genome inversion drives coexistence of divergent morphs in common quails.", "authors": [{"family": "Sanchez-Donoso", "given": "Ines", "initials": "I", "orcid": "0000-0003-2773-9844", "researcher": {"href": "https://publications.scilifelab.se/researcher/917f54b110bd4aca8efbcf3cd9aef4e7.json"}}, {"family": "Ravagni", "given": "Sara", "initials": "S", "orcid": "0000-0003-0320-3447", "researcher": {"href": "https://publications.scilifelab.se/researcher/8cb16a7faa1a4952b3247d440d2cdf5f.json"}}, {"family": "Rodr\u00edguez-Teijeiro", "given": "J Domingo", "initials": "JD"}, {"family": "Christmas", "given": "Matthew J", "initials": "MJ", "orcid": "0000-0002-6355-7581", "researcher": {"href": "https://publications.scilifelab.se/researcher/76e069a0271e4a1fbc31fd3cb440366f.json"}}, {"family": "Huang", "given": "Yan", "initials": "Y"}, {"family": "Maldonado-Linares", "given": "Andros", "initials": "A"}, {"family": "Puigcerver", "given": "Manel", "initials": "M"}, {"family": "Jim\u00e9nez-Blasco", "given": "Irene", "initials": "I"}, {"family": "Andrade", "given": "Pedro", "initials": "P"}, {"family": "Gon\u00e7alves", "given": "David", "initials": "D"}, {"family": "Friis", "given": "Guillermo", "initials": "G", "orcid": "0000-0002-0731-6468", "researcher": {"href": "https://publications.scilifelab.se/researcher/aa844934c3544b37ba2c9874ed8f9b8d.json"}}, {"family": "Roig", "given": "Ignasi", "initials": "I", "orcid": "0000-0003-0313-3581", "researcher": {"href": "https://publications.scilifelab.se/researcher/138805893cb940d39e98c8347f909260.json"}}, {"family": "Webster", "given": "Matthew T", "initials": "MT", "orcid": "0000-0003-1141-2863", "researcher": {"href": "https://publications.scilifelab.se/researcher/579df0da95b94e5087512b76d7f1c058.json"}}, {"family": "Leonard", "given": "Jennifer A", "initials": "JA"}, {"family": "Vil\u00e0", "given": "Carles", "initials": "C"}], "type": "journal article", "published": "2022-01-24", "journal": {"title": "Curr. Biol.", "issn": "1879-0445", "issn-l": "0960-9822", "volume": "32", "issue": "2", "pages": "462-469.e6"}, "abstract": "The presence of population-specific phenotypes often reflects local adaptation or barriers to gene flow. The co-occurrence of phenotypic polymorphisms that are restricted within the range of a highly mobile species is more difficult to explain. An example of such polymorphisms is in the common quail Coturnix coturnix, a small migratory bird that moves widely during the breeding season in search of new mating opportunities, following ephemeral habitats,1,2 and whose females may lay successive clutches at different locations while migrating.3 In spite of this vagility, previous studies reported a higher frequency of heavier males with darker throat coloration in the southwest of the distribution (I. Jim\u00e9nez-Blasco et al., 2015, Int. Union Game Biol., conference). We used population genomics and cytogenetics to explore the basis of this polymorphism and discovered a large inversion in the genome of the common quail. This inversion extends 115 Mbp in length and encompasses more than 7,000 genes (about 12% of the genome), producing two very different forms. Birds with the inversion are larger, have darker throat coloration and rounder wings, are inferred to have poorer flight efficiency, and are geographically restricted despite the high mobility of the species. Stable isotope analyses confirmed that birds carrying the inversion have shorter migratory distances or do not migrate. However, we found no evidence of pre- or post-zygotic isolation, indicating the two forms commonly interbreed and that the polymorphism remains locally restricted because of the effect on behavior. This illustrates a genomic mechanism underlying maintenance of geographically structured polymorphisms despite interbreeding with a lineage with high mobility.", "doi": "10.1016/j.cub.2021.11.019", "pmid": "34847353", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pii", "key": "S0960-9822(21)01543-8"}], "notes": [], "created": "2021-11-30T12:50:56.211Z", "modified": "2022-08-19T08:57:48.552Z"}, {"entity": "publication", "iuid": "e0d583dfe4c3412cbdc9356197a1f6ac", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e0d583dfe4c3412cbdc9356197a1f6ac.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e0d583dfe4c3412cbdc9356197a1f6ac"}}, "title": "Transcriptomic analysis reveals proinflammatory signatures associated with acute myeloid leukemia progression.", "authors": [{"family": "Stratmann", "given": "Svea", "initials": "S", "orcid": "0000-0002-7438-9093", "researcher": {"href": "https://publications.scilifelab.se/researcher/3927efe3aaf84399b26355d92c3a15cf.json"}}, {"family": "Yones", "given": "Sara A", "initials": "SA", "orcid": "0000-0002-7201-2604", "researcher": {"href": "https://publications.scilifelab.se/researcher/17817db9549947578bbe96ba93524cf5.json"}}, {"family": "Garbulowski", "given": "Mateusz", "initials": "M", "orcid": "0000-0002-2497-194X", "researcher": {"href": "https://publications.scilifelab.se/researcher/ad0d6d37b2a04400a8dc407fc78523ec.json"}}, {"family": "Sun", "given": "Jitong", "initials": "J"}, {"family": "Skaftason", "given": "Aron", "initials": "A"}, {"family": "Mayrhofer", "given": "Markus", "initials": "M"}, {"family": "Norgren", "given": "Nina", "initials": "N", "orcid": "0000-0002-3823-1555", "researcher": {"href": "https://publications.scilifelab.se/researcher/a14a423eff78442daffe57aff0130f33.json"}}, {"family": "Herlin", "given": "Morten Krogh", "initials": "MK", "orcid": "0000-0001-7179-4643", "researcher": {"href": "https://publications.scilifelab.se/researcher/fc2efb7b874d46879e3f34e3d7a1b8ef.json"}}, {"family": "Sundstr\u00f6m", "given": "Christer", "initials": "C", "orcid": "0000-0002-8160-5647", "researcher": {"href": "https://publications.scilifelab.se/researcher/dfac750a70664f9986b3cc06334638cc.json"}}, {"family": "Eriksson", "given": "Anna", "initials": "A"}, {"family": "H\u00f6glund", "given": "Martin", "initials": "M", "orcid": "0000-0003-2468-0226", "researcher": {"href": "https://publications.scilifelab.se/researcher/8717164448ee4e2797fefd365103ddc8.json"}}, {"family": "Palle", "given": "Josefine", "initials": "J"}, {"family": "Abrahamsson", "given": "Jonas", "initials": "J"}, {"family": "Jahnukainen", "given": "Kirsi", "initials": "K"}, {"family": "Munthe-Kaas", "given": "Monica Cheng", "initials": "MC"}, {"family": "Zeller", "given": "Bernward", "initials": "B"}, {"family": "Tamm", "given": "Katja Pokrovskaja", "initials": "KP"}, {"family": "Cavelier", "given": "Lucia", "initials": "L"}, {"family": "Komorowski", "given": "Jan", "initials": "J", "orcid": "0000-0002-0766-8789", "researcher": {"href": "https://publications.scilifelab.se/researcher/b2d1190dfa864e4089c58c864857b114.json"}}, {"family": "Holmfeldt", "given": "Linda", "initials": "L", "orcid": "0000-0003-4140-3423", "researcher": {"href": "https://publications.scilifelab.se/researcher/12b8b368e61e48d3b800516f006fbb7d.json"}}], "type": "journal article", "published": "2022-01-11", "journal": {"title": "Blood Adv", "issn": "2473-9537", "issn-l": "2473-9529", "volume": "6", "issue": "1", "pages": "152-164"}, "abstract": "Numerous studies have been performed over the last decade to exploit the complexity of genomic and transcriptomic lesions driving the initiation of acute myeloid leukemia (AML). These studies have helped improve risk classification and treatment options. Detailed molecular characterization of longitudinal AML samples is sparse, however; meanwhile, relapse and therapy resistance represent the main challenges in AML care. To this end, we performed transcriptome-wide RNA sequencing of longitudinal diagnosis, relapse, and/or primary resistant samples from 47 adult and 23 pediatric AML patients with known mutational background. Gene expression analysis revealed the association of short event-free survival with overexpression of GLI2 and IL1R1, as well as downregulation of ST18. Moreover, CR1 downregulation and DPEP1 upregulation were associated with AML relapse both in adults and children. Finally, machine learning-based and network-based analysis identified overexpressed CD6 and downregulated INSR as highly copredictive genes depicting important relapse-associated characteristics among adult patients with AML. Our findings highlight the importance of a tumor-promoting inflammatory environment in leukemia progression, as indicated by several of the herein identified differentially expressed genes. Together, this knowledge provides the foundation for novel personalized drug targets and has the potential to maximize the benefit of current treatments to improve cure rates in AML.", "doi": "10.1182/bloodadvances.2021004962", "pmid": "34619772", "labels": {"Clinical Genomics Uppsala": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "NGI Short read": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative", "Clinical Genomics": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC8753201"}, {"db": "pii", "key": "477210"}], "notes": [], "created": "2021-12-06T08:28:43.286Z", "modified": "2024-01-16T13:48:37.758Z"}, {"entity": "publication", "iuid": "6afe7eb5e9a94df680b83253610f4fcf", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6afe7eb5e9a94df680b83253610f4fcf.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6afe7eb5e9a94df680b83253610f4fcf"}}, "title": "Genomic Signatures of Sexual Selection on Pollen-Expressed Genes in Arabis alpina.", "authors": [{"family": "Guti\u00e9rrez-Valencia", "given": "Juanita", "initials": "J"}, {"family": "Fracassetti", "given": "Marco", "initials": "M"}, {"family": "Horvath", "given": "Robert", "initials": "R", "orcid": "0000-0002-3221-8835", "researcher": {"href": "https://publications.scilifelab.se/researcher/fd1f411c815a49bf91ada0eac39dee8b.json"}}, {"family": "Laenen", "given": "Benjamin", "initials": "B"}, {"family": "D\u00e9samore", "given": "Aur\u00e9lie", "initials": "A"}, {"family": "Drouzas", "given": "Andreas D", "initials": "AD"}, {"family": "Friberg", "given": "Magne", "initials": "M"}, {"family": "Kol\u00e1\u0159", "given": "Filip", "initials": "F"}, {"family": "Slotte", "given": "Tanja", "initials": "T", "orcid": "0000-0001-6020-5102", "researcher": {"href": "https://publications.scilifelab.se/researcher/67c69ee78bae41478465a7e5fa63b946.json"}}], "type": "journal article", "published": "2022-01-07", "journal": {"title": "Mol. Biol. Evol.", "issn": "1537-1719", "issn-l": "0737-4038", "volume": "39", "issue": "1", "pages": null}, "abstract": "Fertilization in angiosperms involves the germination of pollen on the stigma, followed by the extrusion of a pollen tube that elongates through the style and delivers two sperm cells to the embryo sac. Sexual selection could occur throughout this process when male gametophytes compete for fertilization. The strength of sexual selection during pollen competition should be affected by the number of genotypes deposited on the stigma. As increased self-fertilization reduces the number of mating partners, and the genetic diversity and heterozygosity of populations, it should thereby reduce the intensity of sexual selection during pollen competition. Despite the prevalence of mating system shifts, few studies have directly compared the molecular signatures of sexual selection during pollen competition in populations with different mating systems. Here we analyzed whole-genome sequences from natural populations of Arabis alpina, a species showing mating system variation across its distribution, to test whether shifts from cross- to self-fertilization result in molecular signatures consistent with sexual selection on genes involved in pollen competition. We found evidence for efficient purifying selection on genes expressed in vegetative pollen, and overall weaker selection on sperm-expressed genes. This pattern was robust when controlling for gene expression level and specificity. In agreement with the expectation that sexual selection intensifies under cross-fertilization, we found that the efficacy of purifying selection on male gametophyte-expressed genes was significantly stronger in genetically more diverse and outbred populations. Our results show that intra-sexual competition shapes the evolution of pollen-expressed genes, and that its strength fades with increasing self-fertilization rates.", "doi": "10.1093/molbev/msab349", "pmid": "34878144", "labels": {"Bioinformatics Long-term Support WABI": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Short read": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC8788238"}, {"db": "pii", "key": "6456311"}], "notes": [], "created": "2022-02-17T12:52:26.583Z", "modified": "2024-01-16T13:48:37.803Z"}, {"entity": "publication", "iuid": "dab2208caeea405eac67dbba14f79339", "links": {"self": {"href": "https://publications.scilifelab.se/publication/dab2208caeea405eac67dbba14f79339.json"}, "display": {"href": "https://publications.scilifelab.se/publication/dab2208caeea405eac67dbba14f79339"}}, "title": "Risk of Revision After Arthroplasty Associated with Specific Gene Loci: A Genomewide Association Study of Single-Nucleotide Polymorphisms in 1,130 Twins Treated with Arthroplasty.", "authors": [{"family": "Br\u00fcggemann", "given": "Anders", "initials": "A", "orcid": "0000-0002-3600-253", "researcher": {"href": "https://publications.scilifelab.se/researcher/cbd0a479f8464bc6b309e1ecd9b7a9ea.json"}}, {"family": "Eriksson", "given": "Niclas", "initials": "N", "orcid": "0000-0002-2152-4343", "researcher": {"href": "https://publications.scilifelab.se/researcher/64611a83caba46d597f45371b77de26b.json"}}, {"family": "Micha\u00eblsson", "given": "Karl", "initials": "K", "orcid": "0000-0003-2815-1217", "researcher": {"href": "https://publications.scilifelab.se/researcher/eff63868e95240f695d47e871e31947f.json"}}, {"family": "Hailer", "given": "Nils P", "initials": "NP", "orcid": "0000-0002-3233-2638", "researcher": {"href": "https://publications.scilifelab.se/researcher/4c8bb8c013184ef7b482ffe6f8f1380b.json"}}], "type": "journal article", "published": "2022-01-04", "journal": {"title": "J Bone Joint Surg Am", "issn": "1535-1386", "issn-l": null, "volume": "104", "issue": "7", "pages": "610-620"}, "abstract": "The risk of revision surgery following total joint arthroplasty (TJA) may be influenced by genetic factors. Therefore, we sought to identify genetic variants associated with the risk of revision surgery in a genomewide association study.\r\n\r\nWe investigated a cohort of 1,130 twins from the Swedish Twin Registry treated with TJA. During a mean of 9.4 years of follow-up, 75 individuals underwent revision surgery for aseptic loosening (the primary outcome) and 94, for any reason (the secondary outcome). Genetic information was collected using the Illumina OmniExpress and PsychArray panels, and the Haplotype Reference Consortium served as the reference for gene imputation. Adjusted Cox regression models were fitted to calculate hazard ratios (HRs) with 95% confidence intervals (CIs).\r\n\r\nNine single-nucleotide polymorphisms (SNPs) reached genomewide significance for aseptic loosening. The first SNP, rs77149046, located in the endosome-lysosome associated apoptosis and autophagy regulator family member 2 (ELAPOR2) gene, conferred an HR of 5.40 (CI, 3.23-9.02; p = 1.32\u00d710-10), followed by 4 SNPs within the region coding for sodium-dependent taurine and beta-alanine transporter (SLC6A6), with HRs ranging from 3.35 to 3.43. The sixth SNP, rs7853989 (HR, 3.46; CI, 2.33-5.13; p = 6.91\u00d710-10), was located in a region coding for the ABO blood group system. This SNP has been described as predictive for blood type B. Seven significant SNPs were found for the risk of revision for any reason, with the first 4 again being located in the SLC6A6 region. The leading SNP, rs62233562, conferred an HR of 3.11 (CI, 2.19-4.40; p = 1.74\u00d710-10) for revision surgery. Similar HRs were found for SNPs 3:14506680 (p = 1.78\u00d710-10), rs2289129 (p = 1.78\u00d710-10), and rs17309567 (p = 3.16\u00d710-10). The fifth SNP, rs11120968, was located in the calmodulin-binding transcription activator 1 (CAMTA1) gene (HR, 2.34; CI, 1.74-3.13, p = 1.45\u00d710-8).\r\n\r\nWe identified 12 unique SNPs associated with an increased risk of revision surgery. Among these, 2 were in ELAPOR2, which is closely linked to bone formation. Another SNP is located in a gene region encoding for the ABO system, which merits further studies of causal relationships.\r\n\r\nPrognostic Level III. See Instructions for Authors for a complete description of levels of evidence.", "doi": "10.2106/JBJS.21.00750", "pmid": "34982741", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "NGI SNP genotyping": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "00004623-990000000-00431"}], "notes": [], "created": "2022-01-20T12:59:36.162Z", "modified": "2024-01-16T13:48:37.826Z"}, {"entity": "publication", "iuid": "d42a9507c5ac44fa9396fc9e67645fe3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d42a9507c5ac44fa9396fc9e67645fe3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d42a9507c5ac44fa9396fc9e67645fe3"}}, "title": "Transcriptome sequencing of archived lymphoma specimens is feasible and clinically relevant using exome capture technology.", "authors": [{"family": "Skaftason", "given": "Aron", "initials": "A"}, {"family": "Qu", "given": "Ying", "initials": "Y"}, {"family": "Abdulla", "given": "Maysaa", "initials": "M"}, {"family": "Nordlund", "given": "Jessica", "initials": "J"}, {"family": "Berglund", "given": "Mattias", "initials": "M"}, {"family": "Ednersson", "given": "Susanne Bram", "initials": "SB"}, {"family": "Andersson", "given": "Per-Ola", "initials": "PO"}, {"family": "Enblad", "given": "Gunilla", "initials": "G"}, {"family": "Amini", "given": "Rose-Marie", "initials": "RM"}, {"family": "Rosenquist", "given": "Richard", "initials": "R"}, {"family": "Mansouri", "given": "Larry", "initials": "L"}], "type": "journal article", "published": "2022-01-00", "journal": {"title": "Genes Chromosomes Cancer", "issn": "1098-2264", "issn-l": "1045-2257", "volume": "61", "issue": "1", "pages": "27-36"}, "abstract": "Formalin-fixed, paraffin-embedded (FFPE) specimens are an underutilized resource in medical research, particularly in the setting of transcriptome sequencing, as RNA from these samples is often degraded. We took advantage of an exome capture-based RNA-sequencing protocol to explore global gene expression in paired fresh-frozen (FF) and FFPE samples from 16 diffuse large B-cell lymphoma (DLBCL) patients. While FFPE samples generated fewer mapped reads compared to their FF counterparts, these reads captured the same library complexity and had a similar number of genes expressed on average. Furthermore, gene expression demonstrated a high correlation when comparing housekeeping genes only or across the entire transcriptome (r = 0.99 for both comparisons). Differences in gene expression were primarily seen in lowly expressed genes and genes with small or large coding sequences. Using cell-of-origin classifiers and clinically relevant gene expression signatures for DLBCL, FF, and FFPE samples from the same biopsy paired nearly perfectly in clustering analysis. This was further confirmed in a validation cohort of 50 FFPE DLBCL samples. In summary, we found the biological differences between tumors to be far greater than artifacts created as a result of degraded RNA. We conclude that exome capture transcriptome sequencing data from archival samples can confidently be used for cell-of-origin classification of DLBCL samples.", "doi": "10.1002/gcc.23002", "pmid": "34647650", "labels": {"Clinical Genomics Uppsala": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Technology development", "National Genomics Infrastructure": "Technology development", "NGI Short read": "Technology development", "Clinical Genomics": "Service"}, "xrefs": [], "notes": [], "created": "2021-12-06T08:28:42.125Z", "modified": "2023-06-20T15:58:04.919Z"}, {"entity": "publication", "iuid": "1e01d5c737c9470d84510a8f3be208e7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1e01d5c737c9470d84510a8f3be208e7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1e01d5c737c9470d84510a8f3be208e7"}}, "title": "Common, low-frequency, rare, and ultra-rare coding variants contribute to COVID-19 severity.", "authors": [{"family": "Fallerini", "given": "Chiara", "initials": "C"}, {"family": "Picchiotti", "given": "Nicola", "initials": "N"}, {"family": "Baldassarri", "given": "Margherita", "initials": "M"}, {"family": "Zguro", "given": "Kristina", "initials": "K"}, {"family": "Daga", "given": "Sergio", "initials": "S"}, {"family": "Fava", "given": "Francesca", "initials": "F"}, {"family": "Benetti", "given": "Elisa", "initials": "E"}, {"family": "Amitrano", "given": "Sara", "initials": "S"}, {"family": "Bruttini", "given": "Mirella", "initials": "M"}, {"family": "Palmieri", "given": "Maria", "initials": "M"}, {"family": "Croci", "given": "Susanna", "initials": "S"}, {"family": "Lista", "given": "Mirjam", "initials": "M"}, {"family": "Beligni", "given": "Giada", "initials": "G"}, {"family": "Valentino", "given": "Floriana", "initials": "F"}, {"family": "Meloni", "given": "Ilaria", "initials": "I"}, {"family": "Tanfoni", "given": "Marco", "initials": "M"}, {"family": "Minnai", "given": "Francesca", "initials": "F"}, {"family": "Colombo", "given": "Francesca", "initials": "F"}, {"family": "Cabri", "given": "Enrico", "initials": "E"}, {"family": "Fratelli", "given": "Maddalena", "initials": "M"}, {"family": "Gabbi", "given": "Chiara", "initials": "C"}, {"family": "Mantovani", "given": "Stefania", "initials": "S"}, {"family": "Frullanti", "given": "Elisa", "initials": "E"}, {"family": "Gori", "given": "Marco", "initials": "M"}, {"family": "Crawley", "given": "Francis P", "initials": "FP"}, {"family": "Butler-Laporte", "given": "Guillaume", "initials": "G"}, {"family": "Richards", "given": "Brent", "initials": "B"}, {"family": "Zeberg", "given": "Hugo", "initials": "H"}, {"family": "Lipcsey", "given": "Miklos", "initials": "M"}, {"family": "Hultstr\u00f6m", "given": "Michael", "initials": "M"}, {"family": "Ludwig", "given": "Kerstin U", "initials": "KU"}, {"family": "Schulte", "given": "Eva C", "initials": "EC"}, {"family": "Pairo-Castineira", "given": "Erola", "initials": "E"}, {"family": "Baillie", "given": "John Kenneth", "initials": "JK"}, {"family": "Schmidt", "given": "Axel", "initials": "A"}, {"family": "Frithiof", "given": "Robert", "initials": "R"}, {"family": "WES/WGS Working Group Within the HGI", "given": "", "initials": ""}, {"family": "GenOMICC Consortium", "given": "", "initials": ""}, {"family": "GEN-COVID Multicenter Study", "given": "", "initials": ""}, {"family": "Mari", "given": "Francesca", "initials": "F"}, {"family": "Renieri", "given": "Alessandra", "initials": "A", "orcid": "0000-0002-0846-9220", "researcher": {"href": "https://publications.scilifelab.se/researcher/3dbf990f1e0c4fd99e45c945915f25b0.json"}}, {"family": "Furini", "given": "Simone", "initials": "S"}], "type": "journal article", "published": "2022-01-00", "journal": {"title": "Hum. Genet.", "issn": "1432-1203", "volume": "141", "issue": "1", "pages": "147-173", "issn-l": "0340-6717"}, "abstract": "The combined impact of common and rare exonic variants in COVID-19 host genetics is currently insufficiently understood. Here, common and rare variants from whole-exome sequencing data of about 4000 SARS-CoV-2-positive individuals were used to define an interpretable machine-learning model for predicting COVID-19 severity. First, variants were converted into separate sets of Boolean features, depending on the absence or the presence of variants in each gene. An ensemble of LASSO logistic regression models was used to identify the most informative Boolean features with respect to the genetic bases of severity. The Boolean features selected by these logistic models were combined into an Integrated PolyGenic Score that offers a synthetic and interpretable index for describing the contribution of host genetics in COVID-19 severity, as demonstrated through testing in several independent cohorts. Selected features belong to ultra-rare, rare, low-frequency, and common variants, including those in linkage disequilibrium with known GWAS loci. Noteworthily, around one quarter of the selected genes are sex-specific. Pathway analysis of the selected genes associated with COVID-19 severity reflected the multi-organ nature of the disease. The proposed model might provide useful information for developing diagnostics and therapeutics, while also being able to guide bedside disease management.", "doi": "10.1007/s00439-021-02397-7", "pmid": "34889978", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pii", "key": "10.1007/s00439-021-02397-7"}, {"db": "pmc", "key": "PMC8661833"}], "notes": [], "created": "2022-01-16T20:25:36.805Z", "modified": "2022-01-16T20:25:36.857Z"}, {"entity": "publication", "iuid": "c6fcde1c149146be8ea0b5308f8ec628", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c6fcde1c149146be8ea0b5308f8ec628.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c6fcde1c149146be8ea0b5308f8ec628"}}, "title": "Meta-analyses identify DNA methylation associated with kidney function and damage.", "authors": [{"family": "Schlosser", "given": "Pascal", "initials": "P", "orcid": "0000-0002-8460-0462", "researcher": {"href": "https://publications.scilifelab.se/researcher/b69be66d160c4cdc8030a07ebcb8f150.json"}}, {"family": "Tin", "given": "Adrienne", "initials": "A", "orcid": "0000-0002-4207-5866", "researcher": {"href": "https://publications.scilifelab.se/researcher/b9c33ed3b64348be904a14698402445e.json"}}, {"family": "Matias-Garcia", "given": "Pamela R", "initials": "PR"}, {"family": "Thio", "given": "Chris H L", "initials": "CHL", "orcid": "0000-0003-2623-7172", "researcher": {"href": "https://publications.scilifelab.se/researcher/47fba5312ce6449fb9cfc45f6e1717e1.json"}}, {"family": "Joehanes", "given": "Roby", "initials": "R"}, {"family": "Liu", "given": "Hongbo", "initials": "H", "orcid": "0000-0002-0733-8616", "researcher": {"href": "https://publications.scilifelab.se/researcher/ed1bef0b625f42249a5f5364e3759e71.json"}}, {"family": "Weihs", "given": "Antoine", "initials": "A", "orcid": "0000-0002-7113-0027", "researcher": {"href": "https://publications.scilifelab.se/researcher/f1328f6e263640e99a047d68e82a2db3.json"}}, {"family": "Yu", "given": "Zhi", "initials": "Z", "orcid": "0000-0003-4810-3474", "researcher": {"href": "https://publications.scilifelab.se/researcher/df8600142a4249b6860fd0cbfa3bda5c.json"}}, {"family": "Hoppmann", "given": "Anselm", "initials": "A"}, {"family": "Grundner-Culemann", "given": "Franziska", "initials": "F", "orcid": "0000-0001-9649-281X", "researcher": {"href": "https://publications.scilifelab.se/researcher/e201128d0a6348dcbbfd0e8f3c71f828.json"}}, {"family": "Min", "given": "Josine L", "initials": "JL", "orcid": "0000-0003-4456-9824", "researcher": {"href": "https://publications.scilifelab.se/researcher/5896cbc0cb8d427a954b194839adda52.json"}}, {"family": "Adeyemo", "given": "Adebowale A", "initials": "AA", "orcid": "0000-0002-3105-3231", "researcher": {"href": "https://publications.scilifelab.se/researcher/762f3602e6324dfc991b1d90e21d9ade.json"}}, {"family": "Agyemang", "given": "Charles", "initials": "C", "orcid": "0000-0002-3882-7295", "researcher": {"href": "https://publications.scilifelab.se/researcher/0731c8e87d0f44c3895f01d44cfacaeb.json"}}, {"family": "\u00c4rnl\u00f6v", "given": "Johan", "initials": "J"}, {"family": "Aziz", "given": "Nasir A", "initials": "NA", "orcid": "0000-0001-6184-458X", "researcher": {"href": "https://publications.scilifelab.se/researcher/d1753010c5124e1f85318f62d70611e2.json"}}, {"family": "Baccarelli", "given": "Andrea", "initials": "A", "orcid": "0000-0002-3436-0640", "researcher": {"href": "https://publications.scilifelab.se/researcher/7e842a0969914ba89d930e7d6eb7dd85.json"}}, {"family": "Bochud", "given": "Murielle", "initials": "M", "orcid": "0000-0002-5727-0218", "researcher": {"href": "https://publications.scilifelab.se/researcher/8ef45ef924eb46508d318bc39070ac25.json"}}, {"family": "Brenner", "given": "Hermann", "initials": "H"}, {"family": "Breteler", "given": "Monique M B", "initials": "MMB", "orcid": "0000-0002-0626-9305", "researcher": {"href": "https://publications.scilifelab.se/researcher/523a79be871d433f8efb817ba0358277.json"}}, {"family": "Carmeli", "given": "Cristian", "initials": "C", "orcid": "0000-0002-1463-4587", "researcher": {"href": "https://publications.scilifelab.se/researcher/777f4f02217b42878a281d047df2b128.json"}}, {"family": "Chaker", "given": "Layal", "initials": "L"}, {"family": "Chambers", "given": "John C", "initials": "JC"}, {"family": "Cole", "given": "Shelley A", "initials": "SA"}, {"family": "Coresh", "given": "Josef", "initials": "J", "orcid": "0000-0002-4598-0669", "researcher": {"href": "https://publications.scilifelab.se/researcher/c69274bcafbe4c6e82fe945c74cb7bc6.json"}}, {"family": "Corre", "given": "Tanguy", "initials": "T"}, {"family": "Correa", "given": "Adolfo", "initials": "A", "orcid": "0000-0002-9501-600X", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a12b716143c4156b060f87d5373b87d.json"}}, {"family": "Cox", "given": "Simon R", "initials": "SR", "orcid": "0000-0003-4036-3642", "researcher": {"href": "https://publications.scilifelab.se/researcher/52416a98fd6e44bcb8092baa8837ff04.json"}}, {"family": "de Klein", "given": "Niek", "initials": "N", "orcid": "0000-0003-4640-9904", "researcher": {"href": "https://publications.scilifelab.se/researcher/b20c6c778c1d4508acc72a04561b7c72.json"}}, {"family": "Delgado", "given": "Graciela E", "initials": "GE"}, {"family": "Domingo-Relloso", "given": "Arce", "initials": "A"}, {"family": "Eckardt", "given": "Kai-Uwe", "initials": "KU", "orcid": "0000-0003-3823-0920", "researcher": {"href": "https://publications.scilifelab.se/researcher/9a29c97073404c5182735051d113999b.json"}}, {"family": "Ekici", "given": "Arif B", "initials": "AB", "orcid": "0000-0001-6099-7066", "researcher": {"href": "https://publications.scilifelab.se/researcher/d12ffb30f50d4c45adf31b328ce4d8fd.json"}}, {"family": "Endlich", "given": "Karlhans", "initials": "K", "orcid": "0000-0001-6052-6061", "researcher": {"href": "https://publications.scilifelab.se/researcher/da4d7341c495488f82994b45756c8de7.json"}}, {"family": "Evans", "given": "Kathryn L", "initials": "KL", "orcid": "0000-0002-7884-5877", "researcher": {"href": "https://publications.scilifelab.se/researcher/2985078354be4ab19f96d66fa9b2c8cc.json"}}, {"family": "Floyd", "given": "James S", "initials": "JS"}, {"family": "Fornage", "given": "Myriam", "initials": "M", "orcid": "0000-0003-0677-8158", "researcher": {"href": "https://publications.scilifelab.se/researcher/b5de431c325e40f4adfe13c06cf1e0b9.json"}}, {"family": "Franke", "given": "Lude", "initials": "L"}, {"family": "Fraszczyk", "given": "Eliza", "initials": "E"}, {"family": "Gao", "given": "Xu", "initials": "X", "orcid": "0000-0001-6506-6084", "researcher": {"href": "https://publications.scilifelab.se/researcher/82092a375cb8470c97ea5bcfeb15eb47.json"}}, {"family": "G\u00e0o", "given": "X\u012bn", "initials": "X", "orcid": "0000-0003-0108-6961", "researcher": {"href": "https://publications.scilifelab.se/researcher/5eb7f388567b4514a237f2303077a46a.json"}}, {"family": "Ghanbari", "given": "Mohsen", "initials": "M", "orcid": "0000-0002-9476-7143", "researcher": {"href": "https://publications.scilifelab.se/researcher/52ef9606de1144c994e0e854c5a85569.json"}}, {"family": "Ghasemi", "given": "Sahar", "initials": "S"}, {"family": "Gieger", "given": "Christian", "initials": "C", "orcid": "0000-0001-6986-9554", "researcher": {"href": "https://publications.scilifelab.se/researcher/86f44e76061c403fadd97b768e2a7e62.json"}}, {"family": "Greenland", "given": "Philip", "initials": "P"}, {"family": "Grove", "given": "Megan L", "initials": "ML"}, {"family": "Harris", "given": "Sarah E", "initials": "SE", "orcid": "0000-0002-4941-5106", "researcher": {"href": "https://publications.scilifelab.se/researcher/1bbd06383e594035ab80af3bcdb29f91.json"}}, {"family": "Hemani", "given": "Gibran", "initials": "G", "orcid": "0000-0003-0920-1055", "researcher": {"href": "https://publications.scilifelab.se/researcher/cd71462e306f446bae17d8991b97b24e.json"}}, {"family": "Henneman", "given": "Peter", "initials": "P"}, {"family": "Herder", "given": "Christian", "initials": "C", "orcid": "0000-0002-2050-093X", "researcher": {"href": "https://publications.scilifelab.se/researcher/71627ac8638d4f95bd5cd84e7b07a952.json"}}, {"family": "Horvath", "given": "Steve", "initials": "S", "orcid": "0000-0002-4110-3589", "researcher": {"href": "https://publications.scilifelab.se/researcher/d9fd917cfb8e43329e4dadb4e14e32ef.json"}}, {"family": "Hou", "given": "Lifang", "initials": "L"}, {"family": "Hurme", "given": "Mikko A", "initials": "MA", "orcid": "0000-0002-2149-0630", "researcher": {"href": "https://publications.scilifelab.se/researcher/a7d00b649d284101b0501e2024fb651a.json"}}, {"family": "Hwang", "given": "Shih-Jen", "initials": "SJ"}, {"family": "Jarvelin", "given": "Marjo-Riitta", "initials": "MR"}, {"family": "Kardia", "given": "Sharon L R", "initials": "SLR"}, {"family": "Kasela", "given": "Silva", "initials": "S"}, {"family": "Kleber", "given": "Marcus E", "initials": "ME", "orcid": "0000-0003-0663-7275", "researcher": {"href": "https://publications.scilifelab.se/researcher/a51175112cfb4721b8c9fbfdc71c4307.json"}}, {"family": "Koenig", "given": "Wolfgang", "initials": "W", "orcid": "0000-0002-2064-9603", "researcher": {"href": "https://publications.scilifelab.se/researcher/b358f3d797814a07a05a63364ae37d27.json"}}, {"family": "Kooner", "given": "Jaspal S", "initials": "JS"}, {"family": "Kramer", "given": "Holly", "initials": "H"}, {"family": "Kronenberg", "given": "Florian", "initials": "F", "orcid": "0000-0003-2229-1120", "researcher": {"href": "https://publications.scilifelab.se/researcher/ebc59079554842ecb3512ef90249a2f2.json"}}, {"family": "K\u00fchnel", "given": "Brigitte", "initials": "B"}, {"family": "Lehtim\u00e4ki", "given": "Terho", "initials": "T", "orcid": 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"initials": "DL", "orcid": "0000-0003-3242-0360", "researcher": {"href": "https://publications.scilifelab.se/researcher/e324cff97e2c49599c0474948c3a1470.json"}}, {"family": "Meeks", "given": "Karlijn A C", "initials": "KAC", "orcid": "0000-0003-3032-405X", "researcher": {"href": "https://publications.scilifelab.se/researcher/d7492fa21d4b46da87e4a328a983f55e.json"}}, {"family": "Milani", "given": "Lili", "initials": "L", "orcid": "0000-0002-5323-3102", "researcher": {"href": "https://publications.scilifelab.se/researcher/dec8d00c4b9d43458c5c895b164695d5.json"}}, {"family": "Mishra", "given": "Pashupati P", "initials": "PP"}, {"family": "Nauck", "given": "Matthias", "initials": "M", "orcid": "0000-0002-6678-7964", "researcher": {"href": "https://publications.scilifelab.se/researcher/c4b3ce009b2641eda8ad26665e7183f7.json"}}, {"family": "Navas-Acien", "given": "Ana", "initials": "A"}, {"family": "Nowak", "given": "Christoph", "initials": "C", "orcid": "0000-0001-8435-3978", "researcher": 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"researcher": {"href": "https://publications.scilifelab.se/researcher/dd8f1e7f80ee4aa8b853ef31295f5709.json"}}, {"family": "Estonian Biobank Research Team", "given": "", "initials": ""}, {"family": "Genetics of DNA Methylation Consortium", "given": "", "initials": ""}, {"family": "Loh", "given": "Marie", "initials": "M", "orcid": "0000-0003-3626-8466", "researcher": {"href": "https://publications.scilifelab.se/researcher/70e1d986dce444f889fda8d47e9cb355.json"}}, {"family": "Snieder", "given": "Harold", "initials": "H", "orcid": "0000-0003-1949-2298", "researcher": {"href": "https://publications.scilifelab.se/researcher/e9276827839a4f3cb50dcaa2ad4708a5.json"}}, {"family": "Levy", "given": "Daniel", "initials": "D", "orcid": "0000-0003-1843-8724", "researcher": {"href": "https://publications.scilifelab.se/researcher/86bfd3e65ead428c93dc1a461004adab.json"}}, {"family": "Waldenberger", "given": "Melanie", "initials": "M", "orcid": "0000-0003-0583-5093", "researcher": {"href": "https://publications.scilifelab.se/researcher/c8de22214f2448c6a7f86fc1040d0104.json"}}, {"family": "Susztak", "given": "Katalin", "initials": "K", "orcid": "0000-0002-1005-3726", "researcher": {"href": "https://publications.scilifelab.se/researcher/1382eacb5f28444396132254487e3ed9.json"}}, {"family": "K\u00f6ttgen", "given": "Anna", "initials": "A", "orcid": "0000-0002-4671-3714", "researcher": {"href": "https://publications.scilifelab.se/researcher/fe4cb85a14da4db6bc932a8bc4148efb.json"}}, {"family": "Teumer", "given": "Alexander", "initials": "A", "orcid": "0000-0002-8309-094X", "researcher": {"href": "https://publications.scilifelab.se/researcher/dc9c2667a55b47a6a08aea764fab0946.json"}}], "type": "journal article", "published": "2021-12-09", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "12", "issue": "1", "pages": "7174", "issn-l": "2041-1723"}, "abstract": "Chronic kidney disease is a major public health burden. Elevated urinary albumin-to-creatinine ratio is a measure of kidney damage, and used to diagnose and stage chronic kidney disease. To extend the knowledge on regulatory mechanisms related to kidney function and disease, we conducted a blood-based epigenome-wide association study for estimated glomerular filtration rate (n = 33,605) and urinary albumin-to-creatinine ratio (n = 15,068) and detected 69 and seven CpG sites where DNA methylation was associated with the respective trait. The majority of these findings showed directionally consistent associations with the respective clinical outcomes chronic kidney disease and moderately increased albuminuria. Associations of DNA methylation with kidney function, such as CpGs at JAZF1, PELI1 and CHD2 were validated in kidney tissue. Methylation at PHRF1, LDB2, CSRNP1 and IRF5 indicated causal effects on kidney function. Enrichment analyses revealed pathways related to hemostasis and blood cell migration for estimated glomerular filtration rate, and immune cell activation and response for urinary albumin-to-creatinineratio-associated CpGs.", "doi": "10.1038/s41467-021-27234-3", "pmid": "34887417", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-021-27234-3"}], "notes": [], "created": "2021-12-22T19:39:46.207Z", "modified": "2021-12-22T19:39:47.563Z"}, {"entity": "publication", "iuid": "08350a98d5d042829c1d154c715361d9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/08350a98d5d042829c1d154c715361d9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/08350a98d5d042829c1d154c715361d9"}}, "title": "Epigenome-wide association study of serum urate reveals insights into urate co-regulation and the SLC2A9 locus.", "authors": [{"family": "Tin", 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"https://publications.scilifelab.se/researcher/d7492fa21d4b46da87e4a328a983f55e.json"}}, {"family": "Milani", "given": "Lili", "initials": "L", "orcid": "0000-0002-5323-3102", "researcher": {"href": "https://publications.scilifelab.se/researcher/dec8d00c4b9d43458c5c895b164695d5.json"}}, {"family": "Mishra", "given": "Pashupati P", "initials": "PP"}, {"family": "Nauck", "given": "Matthias", "initials": "M", "orcid": "0000-0002-6678-7964", "researcher": {"href": "https://publications.scilifelab.se/researcher/c4b3ce009b2641eda8ad26665e7183f7.json"}}, {"family": "Nowak", "given": "Christoph", "initials": "C", "orcid": "0000-0001-8435-3978", "researcher": {"href": "https://publications.scilifelab.se/researcher/f8be03e2acc84b07b342725a768a1f53.json"}}, {"family": "Peters", "given": "Annette", "initials": "A", "orcid": "0000-0001-6645-0985", "researcher": {"href": "https://publications.scilifelab.se/researcher/05465e52a0f6412e81752d2249af30de.json"}}, {"family": "Prokisch", "given": "Holger", "initials": "H", "orcid": "0000-0003-2379-6286", "researcher": {"href": "https://publications.scilifelab.se/researcher/48fcadf9621143d78b89116929aceb79.json"}}, {"family": "Psaty", "given": "Bruce M", "initials": "BM", "orcid": "0000-0002-7278-2190", "researcher": {"href": "https://publications.scilifelab.se/researcher/b18d7cad2e604bcbbb41b8e5d206c22c.json"}}, {"family": "Raitakari", "given": "Olli T", "initials": "OT"}, {"family": "Ratliff", "given": "Scott M", "initials": "SM"}, {"family": "Reiner", "given": "Alex P", "initials": "AP", "orcid": "0000-0002-1427-4470", "researcher": {"href": "https://publications.scilifelab.se/researcher/931fcf4444904ec398a450a9ec4f4389.json"}}, {"family": "Sch\u00f6ttker", "given": "Ben", "initials": "B", "orcid": "0000-0002-1217-4521", "researcher": {"href": "https://publications.scilifelab.se/researcher/cfbda7c479a54690a046ef88ebbd5be8.json"}}, {"family": "Schwartz", "given": "Joel", "initials": "J"}, {"family": "Sedaghat", "given": "Sanaz", "initials": "S"}, {"family": "Smith", "given": "Jennifer A", "initials": "JA", "orcid": "0000-0002-3575-5468", "researcher": {"href": "https://publications.scilifelab.se/researcher/311c7381092b4143bcd2e4ef93250526.json"}}, {"family": "Sotoodehnia", "given": "Nona", "initials": "N"}, {"family": "Stocker", "given": "Hannah R", "initials": "HR", "orcid": "0000-0001-5281-2455", "researcher": {"href": "https://publications.scilifelab.se/researcher/1b29536e37004e708b1c75abc369d1f2.json"}}, {"family": "Stringhini", "given": "Silvia", "initials": "S", "orcid": "0000-0002-4387-8943", "researcher": {"href": "https://publications.scilifelab.se/researcher/e670989692024cc581612a876237d6a7.json"}}, {"family": "Sundstr\u00f6m", "given": "Johan", "initials": "J", "orcid": "0000-0003-2247-8454", "researcher": {"href": "https://publications.scilifelab.se/researcher/91a40d3c138d43f2b0d38f66be4b71c7.json"}}, {"family": "Swenson", "given": "Brenton R", "initials": "BR"}, {"family": "van Meurs", "given": "Joyce B J", "initials": "JBJ"}, {"family": "van Vliet-Ostaptchouk", "given": "Jana V", "initials": "JV", "orcid": "0000-0002-7943-3153", "researcher": {"href": "https://publications.scilifelab.se/researcher/babcbf8d8f124eceaf0a06dffd39b5cb.json"}}, {"family": "Venema", "given": "Andrea", "initials": "A"}, {"family": "V\u00f6lker", "given": "Uwe", "initials": "U", "orcid": "0000-0002-5689-3448", "researcher": {"href": "https://publications.scilifelab.se/researcher/e529a40052644d83bdef588a3e4f4e99.json"}}, {"family": "Winkelmann", "given": "Juliane", "initials": "J"}, {"family": "Wolffenbuttel", "given": "Bruce H R", "initials": "BHR", "orcid": "0000-0001-9262-6921", "researcher": {"href": "https://publications.scilifelab.se/researcher/705d5bb109c443289feef937e695dc7d.json"}}, {"family": "Zhao", "given": "Wei", "initials": "W", "orcid": "0000-0001-7388-0692", "researcher": {"href": "https://publications.scilifelab.se/researcher/a0c2246e69494086bab7ead8e6f1f717.json"}}, {"family": "Zheng", "given": "Yinan", "initials": "Y", "orcid": "0000-0002-2006-7320", "researcher": {"href": "https://publications.scilifelab.se/researcher/dd8f1e7f80ee4aa8b853ef31295f5709.json"}}, {"family": "Estonian Biobank Research Team", "given": "", "initials": ""}, {"family": "Genetics of DNA Methylation Consortium", "given": "", "initials": ""}, {"family": "Loh", "given": "Marie", "initials": "M", "orcid": "0000-0003-3626-8466", "researcher": {"href": "https://publications.scilifelab.se/researcher/70e1d986dce444f889fda8d47e9cb355.json"}}, {"family": "Snieder", "given": "Harold", "initials": "H", "orcid": "0000-0003-1949-2298", "researcher": {"href": "https://publications.scilifelab.se/researcher/e9276827839a4f3cb50dcaa2ad4708a5.json"}}, {"family": "Waldenberger", "given": "Melanie", "initials": "M", "orcid": "0000-0003-0583-5093", "researcher": {"href": "https://publications.scilifelab.se/researcher/c8de22214f2448c6a7f86fc1040d0104.json"}}, {"family": "Levy", "given": "Daniel", "initials": "D", "orcid": "0000-0003-1843-8724", "researcher": {"href": "https://publications.scilifelab.se/researcher/86bfd3e65ead428c93dc1a461004adab.json"}}, {"family": "Akilesh", "given": "Shreeram", "initials": "S", "orcid": "0000-0003-3152-7991", "researcher": {"href": "https://publications.scilifelab.se/researcher/1cb143e90633471486dbad753d06e3fe.json"}}, {"family": "Woodward", "given": "Owen M", "initials": "OM", "orcid": "0000-0001-9514-2180", "researcher": {"href": "https://publications.scilifelab.se/researcher/669278c697764d249d6668a7d59269a6.json"}}, {"family": "Susztak", "given": "Katalin", "initials": "K", "orcid": "0000-0002-1005-3726", "researcher": {"href": "https://publications.scilifelab.se/researcher/1382eacb5f28444396132254487e3ed9.json"}}, {"family": "Teumer", "given": "Alexander", "initials": "A", "orcid": "0000-0002-8309-094X", "researcher": {"href": "https://publications.scilifelab.se/researcher/dc9c2667a55b47a6a08aea764fab0946.json"}}, {"family": "K\u00f6ttgen", "given": "Anna", "initials": "A", "orcid": "0000-0002-4671-3714", "researcher": {"href": "https://publications.scilifelab.se/researcher/fe4cb85a14da4db6bc932a8bc4148efb.json"}}], "type": "journal article", "published": "2021-12-09", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "12", "issue": "1", "pages": "7173", "issn-l": "2041-1723"}, "abstract": "Elevated serum urate levels, a complex trait and major risk factor for incident gout, are correlated with cardiometabolic traits via incompletely understood mechanisms. DNA methylation in whole blood captures genetic and environmental influences and is assessed in transethnic meta-analysis of epigenome-wide association studies (EWAS) of serum urate (discovery, n = 12,474, replication, n = 5522). The 100 replicated, epigenome-wide significant (p < 1.1E-7) CpGs explain 11.6% of the serum urate variance. At SLC2A9, the serum urate locus with the largest effect in genome-wide association studies (GWAS), five CpGs are associated with SLC2A9 gene expression. Four CpGs at SLC2A9 have significant causal effects on serum urate levels and/or gout, and two of these partly mediate the effects of urate-associated GWAS variants. In other genes, including SLC7A11 and PHGDH, 17 urate-associated CpGs are associated with conditions defining metabolic syndrome, suggesting that these CpGs may represent a blood DNA methylation signature of cardiometabolic risk factors. This study demonstrates that EWAS can provide new insights into GWAS loci and the correlation of serum urate with other complex traits.", "doi": "10.1038/s41467-021-27198-4", "pmid": "34887389", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-021-27198-4"}], "notes": [], "created": "2021-12-22T19:39:57.979Z", "modified": "2021-12-22T19:39:58.563Z"}, {"entity": "publication", "iuid": "d2ceef178633481b9e77a29553a89c32", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d2ceef178633481b9e77a29553a89c32.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d2ceef178633481b9e77a29553a89c32"}}, "title": "Male-biased migration from East Africa introduced pastoralism into southern Africa.", "authors": [{"family": "Vicente", "given": "M\u00e1rio", "initials": "M"}, {"family": "Lankheet", "given": "Imke", "initials": "I"}, {"family": "Russell", "given": "Thembi", "initials": "T"}, {"family": "Hollfelder", "given": "Nina", "initials": "N"}, {"family": "Coetzee", "given": "Vinet", "initials": "V"}, {"family": "Soodyall", "given": "Himla", "initials": "H"}, {"family": "Jongh", "given": "Michael De", "initials": "M"}, {"family": "Schlebusch", "given": "Carina M", "initials": "CM", "orcid": "0000-0002-8160-9621", "researcher": {"href": "https://publications.scilifelab.se/researcher/682f10853c1145649b8c76680605dd9b.json"}}], "type": "journal article", "published": "2021-12-07", "journal": {"title": "BMC Biol.", "issn": "1741-7007", "volume": "19", "issue": "1", "pages": "259", "issn-l": "1741-7007"}, "abstract": "Hunter-gatherer lifestyles dominated the southern African landscape up to ~ 2000 years ago, when herding and farming groups started to arrive in the area. First, herding and livestock, likely of East African origin, appeared in southern Africa, preceding the arrival of the large-scale Bantu-speaking agro-pastoralist expansion that introduced West African-related genetic ancestry into the area. Present-day Khoekhoe-speaking Namaqua (or Nama in short) pastoralists show high proportions of East African admixture, linking the East African ancestry with Khoekhoe herders. Most other historical Khoekhoe populations have, however, disappeared over the last few centuries and their contribution to the genetic structure of present-day populations is not well understood. In our study, we analyzed genome-wide autosomal and full mitochondrial data from a population who trace their ancestry to the Khoekhoe-speaking Hessequa herders from the southern Cape region of what is now South Africa.\n\nWe generated genome-wide data from 162 individuals and mitochondrial DNA data of a subset of 87 individuals, sampled in the Western Cape Province, South Africa, where the Hessequa population once lived. Using available comparative data from Khoe-speaking and related groups, we aligned genetic date estimates and admixture proportions to the archaeological proposed dates and routes for the arrival of the East African pastoralists in southern Africa. We identified several Afro-Asiatic-speaking pastoralist groups from Ethiopia and Tanzania who share high affinities with the East African ancestry present in southern Africa. We also found that the East African pastoralist expansion was heavily male-biased, akin to a pastoralist migration previously observed on the genetic level in ancient Europe, by which Pontic-Caspian Steppe pastoralist groups represented by the Yamnaya culture spread across the Eurasian continent during the late Neolithic/Bronze Age.\n\nWe propose that pastoralism in southern Africa arrived through male-biased migration of an East African Afro-Asiatic-related group(s) who introduced new subsistence and livestock practices to local southern African hunter-gatherers. Our results add to the understanding of historical human migration and mobility in Africa, connected to the spread of food-producing and livestock practices.", "doi": "10.1186/s12915-021-01193-z", "pmid": "34872534", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1186/s12915-021-01193-z"}, {"db": "pmc", "key": "PMC8650298"}], "notes": [], "created": "2021-12-22T19:40:00.864Z", "modified": "2021-12-22T19:40:00.905Z"}, {"entity": "publication", "iuid": "4323b87bc1e449628432f3792dd208b8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4323b87bc1e449628432f3792dd208b8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4323b87bc1e449628432f3792dd208b8"}}, "title": "The SEQC2 epigenomics quality control (EpiQC) study.", "authors": [{"family": "Foox", "given": "Jonathan", "initials": "J"}, {"family": "Nordlund", "given": "Jessica", "initials": "J"}, {"family": "Lalancette", "given": "Claudia", "initials": "C"}, {"family": "Gong", "given": "Ting", "initials": "T"}, {"family": "Lacey", "given": "Michelle", "initials": "M"}, {"family": "Lent", "given": "Samantha", "initials": "S"}, {"family": "Langhorst", "given": "Bradley W", "initials": "BW"}, {"family": "Ponnaluri", "given": "V K Chaithanya", "initials": "VKC"}, {"family": "Williams", "given": "Louise", "initials": "L"}, {"family": "Padmanabhan", "given": "Karthik Ramaswamy", "initials": "KR"}, {"family": "Cavalcante", "given": "Raymond", "initials": "R"}, {"family": "Lundmark", "given": "Anders", "initials": "A"}, {"family": "Butler", "given": "Daniel", "initials": "D"}, {"family": "Mozsary", "given": "Christopher", "initials": "C"}, {"family": "Gurvitch", "given": "Justin", "initials": "J"}, {"family": "Greally", "given": "John M", "initials": "JM"}, {"family": "Suzuki", "given": "Masako", "initials": "M"}, {"family": "Menor", "given": "Mark", "initials": "M"}, {"family": "Nasu", "given": "Masaki", "initials": "M"}, {"family": "Alonso", "given": "Alicia", "initials": "A"}, {"family": "Sheridan", "given": "Caroline", "initials": "C"}, {"family": "Scherer", "given": "Andreas", "initials": "A"}, {"family": "Bruinsma", "given": "Stephen", "initials": "S"}, {"family": "Golda", "given": "Gosia", "initials": "G"}, {"family": "Muszynska", "given": "Agata", "initials": "A"}, {"family": "\u0141abaj", "given": "Pawe\u0142 P", "initials": "PP"}, {"family": "Campbell", "given": "Matthew A", "initials": "MA"}, {"family": "Wos", "given": "Frank", "initials": "F"}, {"family": "Raine", "given": "Amanda", "initials": "A"}, {"family": "Liljedahl", "given": "Ulrika", "initials": "U"}, {"family": "Axelsson", "given": "Tomas", "initials": "T"}, {"family": "Wang", "given": "Charles", "initials": "C"}, {"family": "Chen", "given": "Zhong", "initials": "Z"}, {"family": "Yang", "given": "Zhaowei", "initials": "Z"}, {"family": "Li", "given": "Jing", "initials": "J"}, {"family": "Yang", "given": "Xiaopeng", "initials": "X"}, {"family": "Wang", "given": "Hongwei", "initials": "H"}, {"family": "Melnick", "given": "Ari", "initials": "A"}, {"family": "Guo", "given": "Shang", "initials": "S"}, {"family": "Blume", "given": "Alexander", "initials": "A"}, {"family": "Franke", "given": "Vedran", "initials": "V"}, {"family": "Ibanez de Caceres", "given": "Inmaculada", "initials": "I"}, {"family": "Rodriguez-Antolin", "given": "Carlos", "initials": "C"}, {"family": "Rosas", "given": "Rocio", "initials": "R"}, {"family": "Davis", "given": "Justin Wade", "initials": "JW"}, {"family": "Ishii", "given": "Jennifer", "initials": "J"}, {"family": "Megherbi", "given": "Dalila B", "initials": "DB"}, {"family": "Xiao", "given": "Wenming", "initials": "W"}, {"family": "Liao", "given": "Will", "initials": "W"}, {"family": "Xu", "given": "Joshua", "initials": "J"}, {"family": "Hong", "given": "Huixiao", "initials": "H"}, {"family": "Ning", "given": "Baitang", "initials": "B"}, {"family": "Tong", "given": "Weida", "initials": "W"}, {"family": "Akalin", "given": "Altuna", "initials": "A"}, {"family": "Wang", "given": "Yunliang", "initials": "Y"}, {"family": "Deng", "given": "Youping", "initials": "Y"}, {"family": "Mason", "given": "Christopher E", "initials": "CE", "orcid": "0000-0002-1850-1642", "researcher": {"href": "https://publications.scilifelab.se/researcher/2af4cb8577d34907b22b030f9e79e90e.json"}}], "type": "journal article", "published": "2021-12-06", "journal": {"title": "Genome Biol.", "issn": "1474-760X", "volume": "22", "issue": "1", "pages": "332", "issn-l": "1474-7596"}, "abstract": "Cytosine modifications in DNA such as 5-methylcytosine (5mC) underlie a broad range of developmental processes, maintain cellular lineage specification, and can define or stratify types of cancer and other diseases. However, the wide variety of approaches available to interrogate these modifications has created a need for harmonized materials, methods, and rigorous benchmarking to improve genome-wide methylome sequencing applications in clinical and basic research. Here, we present a multi-platform assessment and cross-validated resource for epigenetics research from the FDA's Epigenomics Quality Control Group.\n\nEach sample is processed in multiple replicates by three whole-genome bisulfite sequencing (WGBS) protocols (TruSeq DNA methylation, Accel-NGS MethylSeq, and SPLAT), oxidative bisulfite sequencing (TrueMethyl), enzymatic deamination method (EMSeq), targeted methylation sequencing (Illumina Methyl Capture EPIC), single-molecule long-read nanopore sequencing from Oxford Nanopore Technologies, and 850k Illumina methylation arrays. After rigorous quality assessment and comparison to Illumina EPIC methylation microarrays and testing on a range of algorithms (Bismark, BitmapperBS, bwa-meth, and BitMapperBS), we find overall high concordance between assays, but also differences in efficiency of read mapping, CpG capture, coverage, and platform performance, and variable performance across 26 microarray normalization algorithms.\n\nThe data provided herein can guide the use of these DNA reference materials in epigenomics research, as well as provide best practices for experimental design in future studies. By leveraging seven human cell lines that are designated as publicly available reference materials, these data can be used as a baseline to advance epigenomics research.", "doi": "10.1186/s13059-021-02529-2", "pmid": "34872606", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Collaborative", "National Genomics Infrastructure": "Collaborative", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1186/s13059-021-02529-2"}, {"db": "pmc", "key": "PMC8650396"}], "notes": [], "created": "2021-12-08T14:28:40.112Z", "modified": "2024-01-16T13:48:37.984Z"}, {"entity": "publication", "iuid": "e389be71822d45d6ac04d848bfb48df6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e389be71822d45d6ac04d848bfb48df6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e389be71822d45d6ac04d848bfb48df6"}}, "title": "The power of genetic diversity in genome-wide association studies of lipids.", 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"Hirschhorn", "given": "Joel N", "initials": "JN", "orcid": "0000-0002-1650-7901", "researcher": {"href": "https://publications.scilifelab.se/researcher/79e3bb42733c4904a4543cb3b6397c0f.json"}}, {"family": "Kathiresan", "given": "Sekar", "initials": "S"}, {"family": "VA Million Veteran Program", "given": "", "initials": ""}, {"family": "Global Lipids Genetics Consortium*", "given": "", "initials": ""}, {"family": "Boehnke", "given": "Michael", "initials": "M", "orcid": "0000-0002-6442-7754", "researcher": {"href": "https://publications.scilifelab.se/researcher/b8cb72bdcea4492199a1b9d8ac406ac7.json"}}, {"family": "Natarajan", "given": "Pradeep", "initials": "P"}, {"family": "Peloso", "given": "Gina M", "initials": "GM", "orcid": "0000-0002-5355-8636", "researcher": {"href": "https://publications.scilifelab.se/researcher/3a0c07ebec3741efa6ef71d416e7c66a.json"}}, {"family": "Brown", "given": "Christopher D", "initials": "CD"}, {"family": "Morris", "given": "Andrew P", "initials": "AP", "orcid": "0000-0002-6805-6014", "researcher": {"href": "https://publications.scilifelab.se/researcher/991fd686a4a040a1a197c1f32d5b731b.json"}}, {"family": "Assimes", "given": "Themistocles L", "initials": "TL", "orcid": "0000-0003-2349-0009", "researcher": {"href": "https://publications.scilifelab.se/researcher/9e155ca3dd01486580be888d1ded405c.json"}}, {"family": "Deloukas", "given": "Panos", "initials": "P", "orcid": "0000-0001-9251-070X", "researcher": {"href": "https://publications.scilifelab.se/researcher/eb59dbd2f2204d41b801c41188611a9e.json"}}, {"family": "Sun", "given": "Yan V", "initials": "YV", "orcid": "0000-0002-2838-1824", "researcher": {"href": "https://publications.scilifelab.se/researcher/c6299caf6b6342fdbfab4c0d9738b28f.json"}}, {"family": "Willer", "given": "Cristen J", "initials": "CJ", "orcid": "0000-0001-5645-4966", "researcher": {"href": "https://publications.scilifelab.se/researcher/b3a8e1d33146452b87e7e21eb5339f80.json"}}], "type": "journal article", "published": "2021-12-00", "journal": {"title": "Nature", "issn": "1476-4687", "volume": "600", "issue": "7890", "pages": "675-679", "issn-l": "0028-0836"}, "abstract": "Increased blood lipid levels are heritable risk factors of cardiovascular disease with varied prevalence worldwide owing to different dietary patterns and medication use1. Despite advances in prevention and treatment, in particular through reducing low-density lipoprotein cholesterol levels2, heart disease remains the leading cause of death worldwide3. Genome-wideassociation studies (GWAS) of blood lipid levels have led to important biological and clinical insights, as well as new drug targets, for cardiovascular disease. However, most previous GWAS4-23 have been conducted in European ancestry populations and may have missed genetic variants that contribute to lipid-level variation in other ancestry groups. These include differences in allele frequencies, effect sizes and linkage-disequilibrium patterns24. Here we conduct a multi-ancestry, genome-wide genetic discovery meta-analysis of lipid levels in approximately 1.65 million individuals, including 350,000 of non-European ancestries. We quantify the gain in studying non-European ancestries and provide evidence to support the expansion of recruitment of additional ancestries, even with relatively small sample sizes. We find that increasing diversity rather than studying additional individuals of European ancestry results in substantial improvements in fine-mapping functional variants and portability of polygenic prediction (evaluated in approximately 295,000 individuals from 7 ancestry groupings). Modest gains in the number of discovered loci and ancestry-specific variants were also achieved. As GWAS expand emphasis beyond the identification of genes and fundamental biology towards the use of genetic variants for preventive and precision medicine25, we anticipate that increased diversity of participants will lead to more accurate and equitable26 application of polygenic scores in clinical practice.", "doi": "10.1038/s41586-021-04064-3", "pmid": "34887591", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "mid", "key": "NIHMS1758809"}, {"db": "pmc", "key": "PMC8730582"}, {"db": "pii", "key": "10.1038/s41586-021-04064-3"}], "notes": [], "created": "2021-12-22T19:39:50.082Z", "modified": "2023-06-19T12:31:07.699Z"}, {"entity": "publication", "iuid": "bd53cdd9312a4daeb054082f3ef37158", "links": {"self": {"href": "https://publications.scilifelab.se/publication/bd53cdd9312a4daeb054082f3ef37158.json"}, "display": {"href": "https://publications.scilifelab.se/publication/bd53cdd9312a4daeb054082f3ef37158"}}, "title": "The genomics of heart failure: design and rationale of the HERMES consortium.", "authors": [{"family": "Lumbers", "given": "R Thomas", "initials": "RT"}, {"family": "Shah", "given": "Sonia", "initials": "S"}, {"family": "Lin", "given": "Honghuang", "initials": "H"}, {"family": "Czuba", "given": "Tomasz", "initials": "T"}, {"family": "Henry", "given": "Albert", "initials": "A"}, {"family": "Swerdlow", "given": "Daniel I", "initials": "DI"}, {"family": "M\u00e4larstig", "given": "Anders", "initials": "A"}, {"family": "Andersson", "given": "Charlotte", "initials": "C"}, {"family": "Verweij", "given": "Niek", "initials": "N"}, {"family": "Holmes", "given": "Michael V", "initials": "MV"}, {"family": "\u00c4rnl\u00f6v", "given": "Johan", "initials": "J"}, {"family": "Svensson", "given": "Per", "initials": "P"}, {"family": "Hemingway", "given": "Harry", "initials": "H"}, {"family": "Sallah", "given": "Neneh", "initials": "N"}, {"family": "Almgren", "given": "Peter", "initials": "P"}, {"family": "Aragam", "given": "Krishna G", "initials": "KG"}, {"family": "Asselin", "given": "Geraldine", "initials": "G"}, {"family": "Backman", "given": "Joshua D", "initials": "JD"}, {"family": "Biggs", "given": "Mary L", "initials": "ML"}, {"family": "Bloom", "given": "Heather L", "initials": "HL"}, {"family": "Boersma", "given": "Eric", "initials": "E"}, {"family": "Brandimarto", "given": "Jeffrey", "initials": "J"}, {"family": "Brown", "given": "Michael R", "initials": "MR"}, {"family": "Brunner-La Rocca", "given": "Hans-Peter", "initials": "HP"}, {"family": "Carey", "given": "David J", "initials": "DJ"}, {"family": "Chaffin", "given": "Mark D", "initials": "MD"}, {"family": "Chasman", "given": "Daniel I", "initials": "DI"}, {"family": "Chazara", "given": "Olympe", "initials": "O"}, {"family": "Chen", "given": "Xing", "initials": "X"}, {"family": "Chen", "given": "Xu", "initials": "X"}, {"family": "Chung", "given": "Jonathan H", "initials": "JH"}, {"family": "Chutkow", "given": "William", "initials": "W"}, {"family": "Cleland", "given": "John G F", "initials": "JGF"}, {"family": "Cook", "given": "James P", "initials": "JP"}, {"family": "de Denus", "given": "Simon", "initials": "S"}, {"family": "Dehghan", "given": "Abbas", "initials": "A"}, {"family": "Delgado", "given": "Graciela E", "initials": "GE"}, {"family": "Denaxas", "given": "Spiros", "initials": "S"}, {"family": "Doney", "given": "Alexander S", "initials": "AS"}, {"family": "D\u00f6rr", "given": "Marcus", "initials": "M"}, {"family": "Dudley", "given": "Samuel C", "initials": "SC"}, {"family": "Engstr\u00f6m", "given": "Gunnar", "initials": "G"}, {"family": "Esko", "given": "T\u00f5nu", "initials": "T"}, {"family": "Fatemifar", "given": "Ghazaleh", "initials": "G"}, {"family": "Felix", "given": "Stephan B", "initials": "SB"}, {"family": "Finan", "given": "Chris", "initials": "C"}, {"family": "Ford", "given": "Ian", "initials": "I"}, {"family": "Fougerousse", "given": "Francoise", "initials": "F"}, {"family": "Fouodjio", "given": "Ren\u00e9", "initials": "R"}, {"family": "Ghanbari", "given": "Mohsen", "initials": "M"}, {"family": "Ghasemi", "given": "Sahar", "initials": "S"}, {"family": "Giedraitis", "given": "Vilmantas", "initials": "V"}, {"family": "Giulianini", "given": "Franco", "initials": "F"}, {"family": "Gottdiener", "given": "John S", "initials": "JS"}, {"family": "Gross", "given": "Stefan", "initials": "S"}, {"family": "Gu\u00f0bjartsson", "given": "Dan\u00edel F", "initials": "DF"}, {"family": "Gui", "given": "Hongsheng", "initials": "H"}, {"family": "Gutmann", "given": "Rebecca", "initials": "R"}, {"family": "Haggerty", "given": "Christopher M", "initials": "CM"}, {"family": "van der Harst", "given": "Pim", "initials": "P"}, {"family": "Hedman", "given": "\u00c5sa K", "initials": "\u00c5K"}, {"family": "Helgadottir", "given": "Anna", "initials": "A"}, {"family": "Hillege", "given": "Hans", "initials": "H"}, {"family": "Hyde", "given": "Craig L", "initials": "CL"}, {"family": "Jacob", "given": "Jaison", "initials": "J"}, {"family": "Jukema", "given": "J Wouter", "initials": "JW"}, {"family": "Kamanu", "given": "Frederick", "initials": "F"}, {"family": "Kardys", "given": "Isabella", "initials": "I"}, {"family": "Kavousi", "given": "Maryam", "initials": "M"}, {"family": "Khaw", "given": "Kay-Tee", "initials": "KT"}, {"family": "Kleber", "given": "Marcus E", "initials": "ME"}, {"family": "K\u00f8ber", "given": "Lars", "initials": "L"}, {"family": "Koekemoer", "given": "Andrea", "initials": "A"}, {"family": "Kraus", "given": "Bill", "initials": "B"}, {"family": "Kuchenbaecker", "given": "Karoline", "initials": "K"}, {"family": "Langenberg", "given": "Claudia", "initials": "C"}, {"family": "Lind", "given": "Lars", "initials": "L"}, {"family": "Lindgren", "given": "Cecilia M", "initials": "CM"}, {"family": "London", "given": "Barry", "initials": "B"}, {"family": "Lotta", "given": "Luca A", "initials": "LA"}, {"family": "Lovering", "given": "Ruth C", "initials": "RC"}, {"family": "Luan", "given": "Jian'an", "initials": "J"}, {"family": "Magnusson", "given": "Patrik", "initials": "P"}, {"family": "Mahajan", "given": "Anubha", "initials": "A"}, {"family": "Mann", "given": "Douglas", "initials": "D"}, {"family": "Margulies", "given": "Kenneth B", "initials": "KB"}, {"family": "Marston", "given": "Nicholas A", "initials": "NA"}, {"family": "M\u00e4rz", "given": "Winfried", "initials": "W"}, {"family": "McMurray", "given": "John J V", "initials": "JJV"}, {"family": "Melander", "given": "Olle", "initials": "O"}, {"family": "Melloni", "given": "Giorgio", "initials": "G"}, {"family": "Mordi", "given": "Ify R", "initials": "IR"}, {"family": "Morley", "given": "Michael P", "initials": "MP"}, {"family": "Morris", "given": "Andrew D", "initials": "AD"}, {"family": "Morris", "given": "Andrew P", "initials": "AP"}, {"family": "Morrison", "given": "Alanna C", "initials": "AC"}, {"family": "Nagle", "given": "Michael W", "initials": "MW"}, {"family": "Nelson", "given": "Christopher P", "initials": "CP"}, {"family": "Newton-Cheh", "given": "Christopher", "initials": "C"}, {"family": "Niessner", "given": "Alexander", "initials": "A"}, {"family": "Niiranen", "given": "Teemu", "initials": "T"}, {"family": "Nowak", "given": "Christoph", "initials": "C"}, {"family": "O'Donoghue", "given": "Michelle L", "initials": "ML"}, {"family": "Owens", "given": "Anjali T", "initials": "AT"}, {"family": "Palmer", "given": "Colin N A", "initials": "CNA"}, {"family": "Par\u00e9", "given": "Guillaume", "initials": "G"}, {"family": "Perola", "given": "Markus", "initials": "M"}, {"family": "Perreault", "given": "Louis-Philippe Lemieux", "initials": "LL"}, {"family": "Portilla-Fernandez", "given": "Eliana", "initials": "E"}, {"family": "Psaty", "given": "Bruce M", "initials": "BM"}, {"family": "Rice", "given": "Kenneth M", "initials": "KM"}, {"family": "Ridker", "given": "Paul M", "initials": "PM"}, {"family": "Romaine", "given": "Simon P R", "initials": "SPR"}, {"family": "Roselli", "given": "Carolina", "initials": "C"}, {"family": "Rotter", "given": "Jerome I", "initials": "JI"}, {"family": "Ruff", "given": "Christian T", "initials": "CT"}, {"family": "Sabatine", "given": "Marc S", "initials": "MS"}, {"family": "Salo", "given": "Perttu", "initials": "P"}, {"family": "Salomaa", "given": "Veikko", "initials": "V"}, {"family": "van Setten", "given": "Jessica", "initials": "J"}, {"family": "Shalaby", "given": "Alaa A", "initials": "AA"}, {"family": "Smelser", "given": "Diane T", "initials": "DT"}, {"family": "Smith", "given": "Nicholas L", "initials": "NL"}, {"family": "Stefansson", "given": "Kari", "initials": "K"}, {"family": "Stender", "given": "Steen", "initials": "S"}, {"family": "Stott", "given": "David J", "initials": "DJ"}, {"family": "Sveinbj\u00f6rnsson", "given": "Gar\u00f0ar", "initials": "G"}, {"family": "Tammesoo", "given": "Mari-Liis", "initials": "ML"}, {"family": "Tardif", "given": "Jean-Claude", "initials": "JC"}, {"family": "Taylor", "given": "Kent D", "initials": "KD"}, {"family": "Teder-Laving", "given": "Maris", "initials": "M"}, {"family": "Teumer", "given": "Alexander", "initials": "A"}, {"family": "Thorgeirsson", "given": "Gu\u00f0mundur", "initials": "G"}, {"family": "Thorsteinsdottir", "given": "Unnur", "initials": "U"}, {"family": "Torp-Pedersen", "given": "Christian", "initials": "C"}, {"family": "Trompet", "given": "Stella", "initials": "S"}, {"family": "Tuckwell", "given": "Danny", "initials": "D"}, {"family": "Tyl", "given": "Benoit", "initials": "B"}, {"family": "Uitterlinden", "given": "Andre G", "initials": "AG"}, {"family": "Vaura", "given": "Felix", "initials": "F"}, {"family": "Veluchamy", "given": "Abirami", "initials": "A"}, {"family": "Visscher", "given": "Peter M", "initials": "PM"}, {"family": "V\u00f6lker", "given": "Uwe", "initials": "U"}, {"family": "Voors", "given": "Adriaan A", "initials": "AA"}, {"family": "Wang", "given": "Xiaosong", "initials": "X"}, {"family": "Wareham", "given": "Nicholas J", "initials": "NJ"}, {"family": "Weeke", "given": "Peter E", "initials": "PE"}, {"family": "Weiss", "given": "Raul", "initials": "R"}, {"family": "White", "given": "Harvey D", "initials": "HD"}, {"family": "Wiggins", "given": "Kerri L", "initials": "KL"}, {"family": "Xing", "given": "Heming", "initials": "H"}, {"family": "Yang", "given": "Jian", "initials": "J"}, {"family": "Yang", "given": "Yifan", "initials": "Y"}, {"family": "Yerges-Armstrong", "given": "Laura M", "initials": "LM"}, {"family": "Yu", "given": "Bing", "initials": "B"}, {"family": "Zannad", "given": "Faiez", "initials": "F"}, {"family": "Zhao", "given": "Faye", "initials": "F"}, {"family": "Regeneron Genetics Center", "given": "", "initials": ""}, {"family": "Wilk", "given": "Jemma B", "initials": "JB"}, {"family": "Holm", "given": "Hilma", "initials": "H"}, {"family": "Sattar", "given": "Naveed", "initials": "N"}, {"family": "Lubitz", "given": "Steven A", "initials": "SA"}, {"family": "Lanfear", "given": "David E", "initials": "DE"}, {"family": "Shah", "given": "Svati", "initials": "S"}, {"family": "Dunn", "given": "Michael E", "initials": "ME"}, {"family": "Wells", "given": "Quinn S", "initials": "QS"}, {"family": "Asselbergs", "given": "Folkert W", "initials": "FW"}, {"family": "Hingorani", "given": "Aroon D", "initials": "AD"}, {"family": "Dub\u00e9", "given": "Marie-Pierre", "initials": "MP"}, {"family": "Samani", "given": "Nilesh J", "initials": "NJ"}, {"family": "Lang", "given": "Chim C", "initials": "CC"}, {"family": "Cappola", "given": "Thomas P", "initials": "TP"}, {"family": "Ellinor", "given": "Patrick T", "initials": "PT"}, {"family": "Vasan", "given": "Ramachandran S", "initials": "RS"}, {"family": "Smith", "given": "J Gustav", "initials": "JG"}], "type": "journal article", "published": "2021-12-00", "journal": {"title": "ESC Heart Failure", "issn": "2055-5822", "issn-l": null, "volume": "8", "issue": "6", "pages": "5531-5541"}, "abstract": "The HERMES (HEart failure Molecular Epidemiology for Therapeutic targetS) consortium aims to identify the genomic and molecular basis of heart failure.\n\nThe consortium currently includes 51 studies from 11 countries, including 68 157 heart failure cases and 949 888 controls, with data on heart failure events and prognosis. All studies collected biological samples and performed genome-wide genotyping of common genetic variants. The enrolment of subjects into participating studies ranged from 1948 to the present day, and the median follow-up following heart failure diagnosis ranged from 2 to 116 months. Forty-nine of 51 individual studies enrolled participants of both sexes; in these studies, participants with heart failure were predominantly male (34-90%). The mean age at diagnosis or ascertainment across all studies ranged from 54 to 84 years. Based on the aggregate sample, we estimated 80% power to genetic variant associations with risk of heart failure with an odds ratio of \u22651.10 for common variants (allele frequency \u2265 0.05) and \u22651.20 for low-frequency variants (allele frequency 0.01-0.05) at P < 5 \u00d7 10-8 under an additive genetic model.\n\nHERMES is a global collaboration aiming to (i) identify the genetic determinants of heart failure; (ii) generate insights into the causal pathways leading to heart failure and enable genetic approaches to target prioritization; and (iii) develop genomic tools for disease stratification and risk prediction.", "doi": "10.1002/ehf2.13517", "pmid": "34480422", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC8712846"}], "notes": [], "created": "2021-09-07T11:11:45.925Z", "modified": "2023-06-19T13:01:08.136Z"}, {"entity": "publication", "iuid": "adaf9a93a2bd4c25a95e6c65cbef74c7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/adaf9a93a2bd4c25a95e6c65cbef74c7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/adaf9a93a2bd4c25a95e6c65cbef74c7"}}, "title": "Pyramiding of scald resistance genes in four spring barley MAGIC populations.", "authors": [{"family": "Hautsalo", "given": "Juho", "initials": "J", "orcid": "0000-0003-2501-2297", "researcher": {"href": "https://publications.scilifelab.se/researcher/838159575f394d7f8a4ddf4e00ef716c.json"}}, {"family": "Novakazi", "given": "Flutur\u00eb", "initials": "F", "orcid": "0000-0001-7151-6811", "researcher": {"href": "https://publications.scilifelab.se/researcher/5812b915262d44e4972483c8314675c3.json"}}, {"family": "Jalli", "given": "Marja", "initials": "M"}, {"family": "G\u00f6ransson", "given": "Magnus", "initials": "M", "orcid": "0000-0002-0081-2207", "researcher": {"href": "https://publications.scilifelab.se/researcher/13cca49312994a8fa45dc1fb7db8a42f.json"}}, {"family": "Manninen", "given": "Outi", "initials": "O", "orcid": "0000-0001-9641-6657", "researcher": {"href": "https://publications.scilifelab.se/researcher/ec5965b7edd0413791c990a978f17045.json"}}, {"family": "Isolahti", "given": "Mika", "initials": "M"}, {"family": "Reitan", "given": "Lars", "initials": "L"}, {"family": "Bergersen", "given": "Stein", "initials": "S"}, {"family": "Krusell", "given": "Lene", "initials": "L"}, {"family": "Damsg\u00e5rd Robertsen", "given": "Charlotte", "initials": "C"}, {"family": "Orabi", "given": "Jihad", "initials": "J"}, {"family": "Due Jensen", "given": "Jens", "initials": "J"}, {"family": "Jahoor", "given": "Ahmed", "initials": "A"}, {"family": "Bengtsson", "given": "Ther\u00e9se", "initials": "T", "orcid": "0000-0003-4784-1723", "researcher": {"href": "https://publications.scilifelab.se/researcher/0ec4d4a00bcf4fd59113eb264283b92a.json"}}, {"family": "PPP Barley Consortium", "given": "", "initials": ""}], "type": "journal article", "published": "2021-12-00", "journal": {"title": "Theor. Appl. Genet.", "issn": "1432-2242", "issn-l": "0040-5752", "volume": "134", "issue": "12", "pages": "3829-3843"}, "abstract": "Genome-Wide Association Studies (GWAS) of four Multi-parent Advanced Generation Inter-Cross (MAGIC) populations identified nine regions on chromosomes 1H, 3H, 4H, 5H, 6H and 7H associated with resistance against barley scald disease. Three of these regions are putatively novel resistance Quantitative Trait Loci (QTL). Barley scald is caused by Rhynchosporium commune, one of the most important barley leaf diseases that are prevalent in most barley-growing regions. Up to 40% yield losses can occur in susceptible barley cultivars. Four MAGIC populations were generated in a Nordic Public-Private Pre-breeding of spring barley project (PPP Barley) to introduce resistance to several important diseases. Here, these MAGIC populations consisting of six to eight founders each were tested for scald resistance in field trials in Finland and Iceland. Eight different model covariate combinations were compared for GWAS studies, and the models that deviated the least from the expected p-values were selected. For all QTL, candidate genes were identified that are predicted to be involved in pathogen defence. The MAGIC progenies contained new haplotypes of significant SNP-markers with high resistance levels. The lines with successfully pyramided resistance against scald and mildew and the significant markers are now distributed among Nordic plant breeders and will benefit development of disease-resistant cultivars.", "doi": "10.1007/s00122-021-03930-y", "pmid": "34350474", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pii", "key": "10.1007/s00122-021-03930-y"}, {"db": "pmc", "key": "PMC8580920"}], "notes": [], "created": "2021-08-19T13:41:40.899Z", "modified": "2021-12-07T06:55:41.799Z"}, {"entity": "publication", "iuid": "bebd66235c6f4826bce9732aff4c705d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/bebd66235c6f4826bce9732aff4c705d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/bebd66235c6f4826bce9732aff4c705d"}}, "title": "Genetic variants at the RTP4/MASP1 locus are associated with fatigue in Scandinavian patients with primary Sj\u00f6gren's syndrome.", "authors": [{"family": "Norheim", "given": "Katrine Br\u00e6kke", "initials": "KB"}, {"family": "Imgenberg-Kreuz", "given": "Juliana", "initials": "J"}, {"family": "Alexsson", "given": "Andrei", "initials": "A"}, {"family": "Johnsen", "given": "Svein Joar Augl\u00e6nd", "initials": "SJA"}, {"family": "B\u00e5rdsen", "given": "Kjetil", "initials": "K"}, {"family": "Brun", "given": "Johan Gorgas", "initials": "JG"}, {"family": "Dehkordi", "given": "Rezvan Kiani", "initials": "RK"}, {"family": "Theander", "given": "Elke", "initials": "E"}, {"family": "Mandl", "given": "Thomas", "initials": "T"}, {"family": "Jonsson", "given": "Roland", "initials": "R"}, {"family": "Ng", "given": "Wan-Fai", "initials": "WF"}, {"family": "Lessard", "given": "Christopher J", "initials": "CJ"}, {"family": "Rasmussen", "given": "Astrid", "initials": "A"}, {"family": "Sivilis", "given": "Kathy", "initials": "K"}, {"family": "Ronnblom", "given": "Lars", "initials": "L"}, {"family": "Omdal", "given": "Roald", "initials": "R", "orcid": "0000-0002-6051-4658", "researcher": {"href": "https://publications.scilifelab.se/researcher/0a73cb2f66b24c10beebe981f470b495.json"}}], "type": "journal article", "published": "2021-12-00", "journal": {"title": "RMD Open", "issn": "2056-5933", "volume": "7", "issue": "3", "issn-l": "2056-5933"}, "abstract": "Fatigue is common and severe in primary Sj\u00f6gren's syndrome (pSS). The aim of this study was to identify genetic determinants of fatigue in pSS through a genome-wide association study.\n\nPatients with pSS from Norway, Sweden, UK and USA with fatigue and genotype data available were included. After genotype imputation and quality control, 682 patients and 4 966 157 genetic markers were available. Association analysis in each cohort using linear regression with fatigue as a continuous variable and meta-analyses between the cohorts were performed.\n\nMeta-analysis of the Norwegian and Swedish cohorts identified five polymorphisms within the same linkage disequilibrium block at the receptor transporter protein 4 (RTP4)/MASP1 locus associated with fatigue with genome-wide significance (GWS) (p<5\u00d710-8). Patients homozygous for the major allele scored 25 mm higher on the fatigue Visual Analogue Scale than patients homozygous for the minor allele. There were no variants associated with fatigue with GWS in meta-analyses of the US/UK cohorts, or all four cohorts. RTP4 expression in pSS B cells was upregulated and positively correlated with the type I interferon score. Expression quantitative trait loci effects in whole blood for fatigue-associated variants at RTP4/MASP1 and levels of RTP4 and MASP1 expression were identified.\n\nGenetic variations at RTP4/MASP1 are associated with fatigue in Scandinavian pSS patients. RTP4 encodes a Golgi chaperone that influences opioid pain receptor function and MASP1 is involved in complement activation. These results add evidence for genetic influence over fatigue in pSS.", "doi": "10.1136/rmdopen-2021-001832", "pmid": "34907023", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "rmdopen-2021-001832"}], "notes": [], "created": "2021-12-22T19:39:55.571Z", "modified": "2021-12-22T19:39:55.682Z"}, {"entity": "publication", "iuid": "3611028adfd841ac88242da67bb97158", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3611028adfd841ac88242da67bb97158.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3611028adfd841ac88242da67bb97158"}}, "title": "Expression of BCL6 in paediatric B-cell acute lymphoblastic leukaemia and association with prognosis.", "authors": [{"family": "M\u00e4kinen", "given": "Artturi", "initials": "A"}, {"family": "Nikkil\u00e4", "given": "Atte", "initials": "A"}, {"family": "Mehtonen", "given": "Juha", "initials": "J"}, {"family": "Teppo", "given": "Susanna", "initials": "S"}, {"family": "Oksa", "given": "Laura", "initials": "L"}, {"family": "Nordlund", "given": "Jessica", "initials": "J"}, {"family": "Rounioja", "given": "Samuli", "initials": "S"}, {"family": "Pohjolainen", "given": "Virva", "initials": "V"}, {"family": "Laukkanen", "given": "Saara", "initials": "S"}, {"family": "Hein\u00e4niemi", "given": "Merja", "initials": "M"}, {"family": "Paavonen", "given": "Timo", "initials": "T"}, {"family": "Lohi", "given": "Olli", "initials": "O"}], "type": "journal article", "published": "2021-12-00", "journal": {"title": "Pathology", "issn": "1465-3931", "issn-l": null, "volume": "53", "issue": "7", "pages": "875-882"}, "abstract": "B-cell lineage acute lymphoblastic leukaemia (B-ALL) is the most common paediatric malignancy. Transcription factor B-cell lymphoma 6 (BCL6) is essential to germinal centre formation and antibody affinity maturation and plays a major role in mature B-cell malignancies. More recently, it was shown to act as a critical downstream regulator in pre-BCR+ B-ALL. We investigated the expression of the BCL6 protein in a population-based cohort of paediatric B-ALL cases and detected moderate to strong positivity through immunohistochemistry in 7% of cases (8/117); however, only two of eight BCL6 cases (25%) co-expressed the ZAP70 protein. In light of these data, the subtype with active pre-BCR signalling constitutes a rare entity in paediatric B-ALL. In three independent larger cohorts with gene expression data, high BCL6 mRNA levels were associated with the TCF3-PBX1, Ph-like, NUTM1, MEF2D and PAX5-alt subgroups and the 'metagene' signature for pre-BCR-associated genes. However, higher-than-median BCL6 mRNA level alone was associated with favourable event free survival in the Nordic paediatric cohort, indicating that using BCL6 as a diagnostic marker requires careful design, and evaluation of protein level is needed alongside the genetic or transcriptomic data.", "doi": "10.1016/j.pathol.2021.02.013", "pmid": "34049715", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pii", "key": "S0031-3025(21)00109-4"}], "notes": [], "created": "2021-12-10T10:33:38.923Z", "modified": "2023-05-22T14:24:21.445Z"}, {"entity": "publication", "iuid": "0c150c7610fb4d7ab0600f04c6610e36", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0c150c7610fb4d7ab0600f04c6610e36.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0c150c7610fb4d7ab0600f04c6610e36"}}, "title": "Single cell genomics reveals plastid-lacking Picozoa are close relatives of red algae.", "authors": [{"family": "Sch\u00f6n", "given": "Max E", "initials": "ME", "orcid": "0000-0002-4453-4173", "researcher": {"href": "https://publications.scilifelab.se/researcher/ac8236efee89497bacf5fa9ada6ee8a5.json"}}, {"family": "Zlatogursky", "given": "Vasily V", "initials": "VV", "orcid": "0000-0002-2688-3900", "researcher": {"href": "https://publications.scilifelab.se/researcher/bd1807f8bc0b4990bb1d4a4037ae4566.json"}}, {"family": "Singh", "given": "Rohan P", "initials": "RP"}, {"family": "Poirier", "given": "Camille", "initials": "C"}, {"family": "Wilken", "given": "Susanne", "initials": "S"}, {"family": "Mathur", "given": "Varsha", "initials": "V"}, {"family": "Strassert", "given": "J\u00fcrgen F H", "initials": "JFH", "orcid": "0000-0001-6786-7563", "researcher": {"href": "https://publications.scilifelab.se/researcher/079bf03f0b2c438ab4e01346eb0be1af.json"}}, {"family": "Pinhassi", "given": "Jarone", "initials": "J", "orcid": "0000-0002-6405-1347", "researcher": {"href": "https://publications.scilifelab.se/researcher/b352d814c2534b06a79992fda3bbb075.json"}}, {"family": "Worden", "given": "Alexandra Z", "initials": "AZ", "orcid": "0000-0002-9888-9324", "researcher": {"href": "https://publications.scilifelab.se/researcher/d5c3bd7ac29e4564a25fcd334fd4c24a.json"}}, {"family": "Keeling", "given": "Patrick J", "initials": "PJ", "orcid": "0000-0002-7644-0745", "researcher": {"href": "https://publications.scilifelab.se/researcher/1f5e2df178884dd6bc124ebcde2e1483.json"}}, {"family": "Ettema", "given": "Thijs J G", "initials": "TJG", "orcid": "0000-0002-6898-6377", "researcher": {"href": "https://publications.scilifelab.se/researcher/42fc4acc111f4c488b23fa41341705e2.json"}}, {"family": "Wideman", "given": "Jeremy G", "initials": "JG", "orcid": "0000-0002-4426-9533", "researcher": {"href": "https://publications.scilifelab.se/researcher/c3403a41c09c480d982a8c1ec018aede.json"}}, {"family": "Burki", "given": "Fabien", "initials": "F", "orcid": "0000-0002-8248-8462", "researcher": {"href": "https://publications.scilifelab.se/researcher/c386a8e440344f25bea35d570450b09b.json"}}], "type": "journal article", "published": "2021-11-17", "journal": {"title": "Nat Commun", "issn": "2041-1723", "issn-l": "2041-1723", "volume": "12", "issue": "1", "pages": "6651"}, "abstract": "The endosymbiotic origin of plastids from cyanobacteria gave eukaryotes photosynthetic capabilities and launched the diversification of countless forms of algae. These primary plastids are found in members of the eukaryotic supergroup Archaeplastida. All known archaeplastids still retain some form of primary plastids, which are widely assumed to have a single origin. Here, we use single-cell genomics from natural samples combined with phylogenomics to infer the evolutionary origin of the phylum Picozoa, a globally distributed but seemingly rare group of marine microbial heterotrophic eukaryotes. Strikingly, the analysis of 43 single-cell genomes shows that Picozoa belong to Archaeplastida, specifically related to red algae and the phagotrophic rhodelphids. These picozoan genomes support the hypothesis that Picozoa lack a plastid, and further reveal no evidence of an early cryptic endosymbiosis with cyanobacteria. These findings change our understanding of plastid evolution as they either represent the first complete plastid loss in a free-living taxon, or indicate that red algae and rhodelphids obtained their plastids independently of other archaeplastids.", "doi": "10.1038/s41467-021-26918-0", "pmid": "34789758", "labels": {"Microbial Single Cell Genomics": "Service", "National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-021-26918-0"}, {"db": "pmc", "key": "PMC8599508"}, {"db": "figshare", "key": "10.6084/m9.figshare.c.5388176"}], "notes": [], "created": "2021-11-17T12:35:08.815Z", "modified": "2024-01-16T13:48:38.070Z"}, {"entity": "publication", "iuid": "e2e0b1cdb60c40dabbccb4597711b1ea", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e2e0b1cdb60c40dabbccb4597711b1ea.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e2e0b1cdb60c40dabbccb4597711b1ea"}}, "title": "Comparison of EM-seq and PBAT methylome library methods for low-input DNA.", "authors": [{"family": "Han", "given": "Yanan", "initials": "Y", "orcid": "0000-0002-3464-2656", "researcher": {"href": "https://publications.scilifelab.se/researcher/9dbd01317d224156a002d298de5112ac.json"}}, {"family": "Zheleznyakova", "given": "Galina Yurevna", "initials": "GY"}, {"family": "Marincevic-Zuniga", "given": "Yanara", "initials": "Y"}, {"family": "Kakhki", "given": "Majid Pahlevan", "initials": "MP"}, {"family": "Raine", "given": "Amanda", "initials": "A"}, {"family": "Needhamsen", "given": "Maria", "initials": "M"}, {"family": "Jagodic", "given": "Maja", "initials": "M"}], "type": "journal article", "published": "2021-11-17", "journal": {"title": "Epigenetics", "issn": "1559-2308", "issn-l": "1559-2294", "volume": "17", "issue": "10", "pages": "1195-1204"}, "abstract": "DNA methylation is the most studied epigenetic mark involved in regulation of gene expression. For low input samples, a limited number of methods for quantifying DNA methylation genome-wide has been evaluated. Here, we compared a series of input DNA amounts (1-10ng) from two methylome library preparation protocols, enzymatic methyl-seq (EM-seq) and post-bisulfite adaptor tagging (PBAT) adapted from single-cell PBAT. EM-seq takes advantage of enzymatic activity while PBAT relies on conventional bisulfite conversion for detection of DNA methylation. We found that both methods accurately quantified DNA methylation genome-wide. They produced expected distribution patterns around genomic features, high C-T transition efficiency at non-CpG sites and high correlation between input amounts. However, EM-seq performed better in regard to library and sequencing quality, i.e. EM-seq produced larger insert sizes, higher alignment rates and higher library complexity with lower duplication rate compared to PBAT. Moreover, EM-seq demonstrated higher CpG coverage, better CpG site overlap and higher consistency between input series. In summary, our data suggests that EM-seq overall performed better than PBAT in whole-genome methylation quantification of low input samples.", "doi": "10.1080/15592294.2021.1997406", "pmid": "34709110", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Collaborative", "National Genomics Infrastructure": "Collaborative", "NGI Short read": "Collaborative"}, "xrefs": [], "notes": [], "created": "2021-12-10T11:22:58.275Z", "modified": "2022-11-29T09:19:22.428Z"}, {"entity": "publication", "iuid": "a16477100ca44690afdb66e882fc52d2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a16477100ca44690afdb66e882fc52d2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a16477100ca44690afdb66e882fc52d2"}}, "title": "Rare variant analysis in eczema identifies exonic variants in DUSP1, NOTCH4 and SLC9A4.", "authors": [{"family": "Grosche", "given": "Sarah", "initials": "S"}, {"family": "Marenholz", "given": "Ingo", "initials": "I"}, {"family": "Esparza-Gordillo", "given": "Jorge", "initials": "J"}, {"family": "Arnau-Soler", "given": "Aleix", "initials": "A"}, {"family": "Pairo-Castineira", "given": "Erola", "initials": "E", "orcid": "0000-0002-2423-3090", "researcher": {"href": "https://publications.scilifelab.se/researcher/c8cc869b85f64312b03d353912f1fba4.json"}}, {"family": "R\u00fcschendorf", "given": "Franz", "initials": "F", "orcid": "0000-0001-5640-810X", "researcher": {"href": "https://publications.scilifelab.se/researcher/e02ac817ef224343ba9d9a9ac7cdc43e.json"}}, {"family": "Ahluwalia", "given": "Tarunveer S", "initials": "TS", "orcid": "0000-0002-7464-3354", "researcher": {"href": "https://publications.scilifelab.se/researcher/2fde142189574b44a72155785763a327.json"}}, {"family": "Almqvist", "given": "Catarina", "initials": "C"}, {"family": "Arnold", "given": "Andreas", "initials": "A"}, {"family": "Australian Asthma Genetics Consortium (AAGC)", "given": "", "initials": ""}, {"family": "Baurecht", "given": "Hansj\u00f6rg", "initials": "H", "orcid": "0000-0002-9265-5594", "researcher": {"href": "https://publications.scilifelab.se/researcher/65098dade92d4b87a691906582cc4fa9.json"}}, {"family": "Bisgaard", "given": "Hans", "initials": "H", "orcid": "0000-0003-4131-7592", "researcher": {"href": "https://publications.scilifelab.se/researcher/5179e5b6e16e482c9d2a9d8250bfc44d.json"}}, {"family": "B\u00f8nnelykke", "given": "Klaus", "initials": "K", "orcid": "0000-0003-2003-1018", "researcher": {"href": "https://publications.scilifelab.se/researcher/2e0992f23e69443c8bf08589711cb9b9.json"}}, {"family": "Brown", "given": "Sara J", "initials": "SJ", "orcid": "0000-0002-3232-5251", "researcher": {"href": "https://publications.scilifelab.se/researcher/f3d24ef4a0034f3fbe0bdf273ffc25fc.json"}}, {"family": "Bustamante", "given": "Mariona", "initials": "M", "orcid": "0000-0003-0127-2860", "researcher": {"href": "https://publications.scilifelab.se/researcher/7283551b36ce4d99851d8eb166af3bf9.json"}}, {"family": "Curtin", "given": "John A", "initials": "JA"}, {"family": "Custovic", "given": "Adnan", "initials": "A", "orcid": "0000-0001-5218-7071", "researcher": {"href": "https://publications.scilifelab.se/researcher/54b6c2bf8fc54ae68fec26ea7d6bc158.json"}}, {"family": "Dharmage", "given": "Shyamali C", "initials": "SC"}, {"family": "Esplugues", "given": "Ana", "initials": "A"}, {"family": "Falchi", "given": "Mario", "initials": "M", "orcid": "0000-0002-5646-1004", "researcher": {"href": "https://publications.scilifelab.se/researcher/74b676eb136243318749e1a4e265d71e.json"}}, {"family": "Fernandez-Orth", "given": "Dietmar", "initials": "D", "orcid": "0000-0002-1237-3192", "researcher": {"href": "https://publications.scilifelab.se/researcher/119682064dc44f92ba9dffdcc9652e46.json"}}, {"family": "Ferreira", "given": "Manuel A R", "initials": "MAR"}, {"family": "Franke", "given": "Andre", "initials": "A", "orcid": "0000-0003-1530-5811", "researcher": {"href": "https://publications.scilifelab.se/researcher/8fffe3df068c4283a8b8b583717e6bb6.json"}}, {"family": "Gerdes", "given": "Sascha", "initials": "S"}, {"family": "Gieger", "given": "Christian", "initials": "C", "orcid": "0000-0001-6986-9554", "researcher": {"href": "https://publications.scilifelab.se/researcher/86f44e76061c403fadd97b768e2a7e62.json"}}, {"family": "Hakonarson", "given": "Hakon", "initials": "H", "orcid": "0000-0003-2814-7461", "researcher": {"href": "https://publications.scilifelab.se/researcher/bd650cc09eb84d669c55c3f0ef690955.json"}}, {"family": "Holt", "given": "Patrick G", "initials": "PG", "orcid": "0000-0003-1193-0935", "researcher": {"href": "https://publications.scilifelab.se/researcher/3e746298fc4143a3bf5d8a6250d88254.json"}}, {"family": "Homuth", "given": "Georg", "initials": "G"}, {"family": "Hubner", "given": "Norbert", "initials": "N", "orcid": "0000-0002-1218-6223", "researcher": {"href": "https://publications.scilifelab.se/researcher/1d84f34739c743838cea107286522e42.json"}}, {"family": "Hysi", "given": "Pirro G", "initials": "PG", "orcid": "0000-0001-5752-2510", "researcher": {"href": "https://publications.scilifelab.se/researcher/8d756a9f3294490fa137e2308ccb353e.json"}}, {"family": "Jarvelin", "given": "Marjo-Riitta", "initials": "M"}, {"family": "Karlsson", "given": "Robert", "initials": "R", "orcid": "0000-0002-8949-2587", "researcher": {"href": "https://publications.scilifelab.se/researcher/9df14bf33f3342408d624caa70d45b7c.json"}}, {"family": "Koppelman", "given": "Gerard H", "initials": "GH", "orcid": "0000-0001-8567-3252", "researcher": {"href": "https://publications.scilifelab.se/researcher/cd7e0158050a4ab3860e288c4eb9ae87.json"}}, {"family": "Lau", "given": "Susanne", "initials": "S"}, {"family": "Lutz", "given": "Manuel", "initials": "M"}, {"family": "Magnusson", "given": "Patrik K E", "initials": "PKE", "orcid": "0000-0002-7315-7899", "researcher": {"href": "https://publications.scilifelab.se/researcher/b277b6387de142bbab91fad82d9eff09.json"}}, {"family": "Marks", "given": "Guy B", "initials": "GB"}, {"family": "M\u00fcller-Nurasyid", "given": "Martina", "initials": "M", "orcid": "0000-0003-3793-5910", "researcher": {"href": "https://publications.scilifelab.se/researcher/4d21299bb41343f88142255e64a9da57.json"}}, {"family": "N\u00f6then", "given": "Markus M", "initials": "MM", "orcid": "0000-0002-8770-2464", "researcher": {"href": "https://publications.scilifelab.se/researcher/903aa25b88bc48adbe60be2a7179929b.json"}}, {"family": "Paternoster", "given": "Lavinia", "initials": "L", "orcid": "0000-0003-2514-0889", "researcher": {"href": "https://publications.scilifelab.se/researcher/826f9852c56d4922ab255ab83d26faa8.json"}}, {"family": "Pennell", "given": "Craig E", "initials": "CE", "orcid": "0000-0002-0937-6165", "researcher": {"href": "https://publications.scilifelab.se/researcher/9e35a98141ce4350b6775593f87e40a5.json"}}, {"family": "Peters", "given": "Annette", "initials": "A", "orcid": "0000-0001-6645-0985", "researcher": {"href": "https://publications.scilifelab.se/researcher/05465e52a0f6412e81752d2249af30de.json"}}, {"family": "Rawlik", "given": "Konrad", "initials": "K", "orcid": "0000-0002-0010-370X", "researcher": {"href": "https://publications.scilifelab.se/researcher/3c46ce845e5a43b98ba496c13ca987cd.json"}}, {"family": "Robertson", "given": "Colin F", "initials": "CF"}, {"family": "Rodriguez", "given": "Elke", "initials": "E", "orcid": "0000-0003-3692-3950", "researcher": {"href": "https://publications.scilifelab.se/researcher/4e8669678dc94c32bda1a12b81a22743.json"}}, {"family": "Sebert", "given": "Sylvain", "initials": "S", "orcid": "0000-0001-6681-6983", "researcher": {"href": "https://publications.scilifelab.se/researcher/c007e85f69d4421bb6cf76dc52a01eb8.json"}}, {"family": "Simpson", "given": "Angela", "initials": "A"}, {"family": "Sleiman", "given": "Patrick M A", "initials": "PMA"}, {"family": "Standl", "given": "Marie", "initials": "M"}, {"family": "St\u00f6lzl", "given": "Dora", "initials": "D"}, {"family": "Strauch", "given": "Konstantin", "initials": "K"}, {"family": "Szwajda", "given": "Agnieszka", "initials": "A"}, {"family": "Tenesa", "given": "Albert", "initials": "A", "orcid": "0000-0003-4884-4475", "researcher": {"href": "https://publications.scilifelab.se/researcher/99ef99f1a6d5469facdbc8faa2b0ef39.json"}}, {"family": "Thompson", "given": "Philip J", "initials": "PJ"}, {"family": "Ullemar", "given": "Vilhelmina", "initials": "V"}, {"family": "Visconti", "given": "Alessia", "initials": "A", "orcid": "0000-0003-4144-2019", "researcher": {"href": "https://publications.scilifelab.se/researcher/d6b388c130a94f66819774f44a4c6e38.json"}}, {"family": "Vonk", "given": "Judith M", "initials": "JM", "orcid": "0000-0001-7531-4547", "researcher": {"href": "https://publications.scilifelab.se/researcher/e57100a0e5bc48c59590c043897a8bbd.json"}}, {"family": "Wang", "given": "Carol A", "initials": "CA", "orcid": "0000-0002-4301-3974", "researcher": {"href": "https://publications.scilifelab.se/researcher/bf99a43c27034a68976e978b104a91d7.json"}}, {"family": "Weidinger", "given": "Stephan", "initials": "S"}, {"family": "Wielscher", "given": "Matthias", "initials": "M"}, {"family": "Worth", "given": "Catherine L", "initials": "CL", "orcid": "0000-0002-1796-9606", "researcher": {"href": "https://publications.scilifelab.se/researcher/7a8a93c773b54b288809d04813441600.json"}}, {"family": "Xu", "given": "Chen-Jian", "initials": "C"}, {"family": "Lee", "given": "Young-Ae", "initials": "Y"}], "type": "journal article", "published": "2021-11-16", "journal": {"title": "Nat Commun", "issn": "2041-1723", "issn-l": "2041-1723", "volume": "12", "issue": "1", "pages": "6618"}, "abstract": "Previous genome-wide association studies revealed multiple common variants involved in eczema but the role of rare variants remains to be elucidated. Here, we investigate the role of rare variants in eczema susceptibility. We meta-analyze 21 study populations including 20,016 eczema cases and 380,433 controls. Rare variants are imputed with high accuracy using large population-based reference panels. We identify rare exonic variants in DUSP1, NOTCH4, and SLC9A4 to be associated with eczema. In DUSP1 and NOTCH4 missense variants are predicted to impact conserved functional domains. In addition, five novel common variants at SATB1-AS1/KCNH8, TRIB1/LINC00861, ZBTB1, TBX21/OSBPL7, and CSF2RB are discovered. While genes prioritized based on rare variants are significantly up-regulated in the skin, common variants point to immune cell function. Over 20% of the single nucleotide variant-based heritability is attributable to rare and low-frequency variants. The identified rare/low-frequency variants located in functional protein domains point to promising targets for novel therapeutic approaches to eczema.", "doi": "10.1038/s41467-021-26783-x", "pmid": "34785669", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-021-26783-x"}, {"db": "pmc", "key": "PMC8595373"}], "notes": [], "created": "2021-11-26T16:27:57.327Z", "modified": "2021-12-07T06:56:28.734Z"}, {"entity": "publication", "iuid": "0b34b7db41124b8eb5f36bf6e8077154", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0b34b7db41124b8eb5f36bf6e8077154.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0b34b7db41124b8eb5f36bf6e8077154"}}, "title": "Palmdelphin Regulates Nuclear Resilience to Mechanical Stress in the Endothelium.", "authors": [{"family": "S\u00e1inz-Jaspeado", "given": "Miguel", "initials": "M"}, {"family": "Smith", "given": "Ross O", "initials": "RO", "orcid": "0000-0003-4239-3204", "researcher": {"href": "https://publications.scilifelab.se/researcher/a464f28ad47c4706a08645b9616198b7.json"}}, {"family": "Plunde", "given": "Oscar", "initials": "O"}, {"family": "Pawelzik", "given": "Sven-Christian", "initials": "SC"}, {"family": "Jin", "given": "Yi", "initials": "Y", "orcid": "0000-0001-9704-973X", "researcher": {"href": "https://publications.scilifelab.se/researcher/deff30d686dd469f907bc80b8f628390.json"}}, {"family": "Nordling", "given": "Sofia", "initials": "S"}, {"family": "Ding", "given": "Yindi", "initials": "Y", "orcid": "0000-0003-4672-7611", "researcher": {"href": "https://publications.scilifelab.se/researcher/cda52c187d0e49f4b1f09b76bbfa0202.json"}}, {"family": "Aspenstr\u00f6m", "given": "Pontus", "initials": "P"}, {"family": "Hedlund", "given": "Marie", "initials": "M"}, {"family": "Bastianello", "given": "Giulia", "initials": "G"}, {"family": "Ascione", "given": "Flora", "initials": "F"}, {"family": "Li", "given": "Qingsen", "initials": "Q"}, {"family": "Demir", "given": "Cansaran Saygili", "initials": "CS"}, {"family": "Fernando", "given": "Dinesh", "initials": "D", "orcid": "0000-0003-2487-0599", "researcher": {"href": "https://publications.scilifelab.se/researcher/85093375f68a4e70912f07bb5c05ad48.json"}}, {"family": "Daniel", "given": "Geoffrey", "initials": "G", "orcid": "0000-0002-8886-1942", "researcher": {"href": "https://publications.scilifelab.se/researcher/628aeb01d86b47c1b09e2d070356dde8.json"}}, {"family": "Franco-Cereceda", "given": "Anders", "initials": "A"}, {"family": "Kroon", "given": "Jeffrey", "initials": "J", "orcid": "0000-0001-9983-6614", "researcher": {"href": "https://publications.scilifelab.se/researcher/df348c68131743d1a78d5058aacd20b4.json"}}, {"family": "Foiani", "given": "Marco", "initials": "M"}, {"family": "Petrova", "given": "Tatiana V", "initials": "TV"}, {"family": "Kilimann", "given": "Manfred W", "initials": "MW"}, {"family": "B\u00e4ck", "given": "Magnus", "initials": "M", "orcid": "0000-0003-0853-5141", "researcher": {"href": "https://publications.scilifelab.se/researcher/2208efeca524405f8162841b2d2e5910.json"}}, {"family": "Claesson-Welsh", "given": "Lena", "initials": "L", "orcid": "0000-0003-4275-2000", "researcher": {"href": "https://publications.scilifelab.se/researcher/647e2a349efd4e11827209883e86079b.json"}}], "type": "journal article", "published": "2021-11-16", "journal": {"title": "Circulation", "issn": "1524-4539", "issn-l": "0009-7322", "volume": "144", "issue": "20", "pages": "1629-1645"}, "abstract": "PALMD (palmdelphin) belongs to the family of paralemmin proteins implicated in cytoskeletal regulation. Single nucleotide polymorphisms in the PALMD locus that result in reduced expression are strong risk factors for development of calcific aortic valve stenosis and predict severity of the disease.\n\nImmunodetection and public database screening showed dominant expression of PALMD in endothelial cells (ECs) in brain and cardiovascular tissues including aortic valves. Mass spectrometry, coimmunoprecipitation, and immunofluorescent staining allowed identification of PALMD partners. The consequence of loss of PALMD expression was assessed in small interferring RNA-treated EC cultures, knockout mice, and human valve samples. RNA sequencing of ECs and transcript arrays on valve samples from an aortic valve study cohort including patients with the single nucleotide polymorphism rs7543130 informed about gene regulatory changes.\n\nECs express the cytosolic PALMD-KKVI splice variant, which associated with RANGAP1 (RAN GTP hydrolyase activating protein 1). RANGAP1 regulates the activity of the GTPase RAN and thereby nucleocytoplasmic shuttling via XPO1 (Exportin1). Reduced PALMD expression resulted in subcellular relocalization of RANGAP1 and XPO1, and nuclear arrest of the XPO1 cargoes p53 and p21. This indicates an important role for PALMD in nucleocytoplasmic transport and consequently in gene regulation because of the effect on localization of transcriptional regulators. Changes in EC responsiveness on loss of PALMD expression included failure to form a perinuclear actin cap when exposed to flow, indicating lack of protection against mechanical stress. Loss of the actin cap correlated with misalignment of the nuclear long axis relative to the cell body, observed in PALMD-deficient ECs, Palmd mouse aorta, and human aortic valve samples derived from patients with calcific aortic valve stenosis. In agreement with these changes in EC behavior, gene ontology analysis showed enrichment of nuclear- and cytoskeleton-related terms in -/-PALMD-silenced ECs.\n\nWe identify RANGAP1 as a PALMD partner in ECs. Disrupting the PALMD/RANGAP1 complex alters the subcellular localization of RANGAP1 and XPO1, and leads to nuclear arrest of the XPO1 cargoes p53 and p21, accompanied by gene regulatory changes and loss of actin-dependent nuclear resilience. Combined, these consequences of reduced PALMD expression provide a mechanistic underpinning for PALMD's contribution to calcific aortic valve stenosis pathology.", "doi": "10.1161/CIRCULATIONAHA.121.054182", "pmid": "34636652", "labels": {"Global Proteomics and Proteogenomics": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC8589083"}], "notes": [], "created": "2022-03-29T10:27:37.036Z", "modified": "2023-11-16T12:06:34.222Z"}, {"entity": "publication", "iuid": "34a48de26bb1448da0afb5d96f1a811d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/34a48de26bb1448da0afb5d96f1a811d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/34a48de26bb1448da0afb5d96f1a811d"}}, "title": "Whole genome and exome sequencing reference datasets from a multi-center and cross-platform benchmark study.", "authors": [{"family": "Zhao", "given": "Yongmei", "initials": "Y", "orcid": "0000-0003-0800-4658", "researcher": {"href": "https://publications.scilifelab.se/researcher/3a5a787c429e416da061067ec701a3b1.json"}}, {"family": "Fang", "given": "Li Tai", "initials": "LT", "orcid": "0000-0003-3201-5162", "researcher": {"href": "https://publications.scilifelab.se/researcher/b580a1ef08e04613adc5824605d9d442.json"}}, {"family": "Shen", "given": "Tsai-Wei", "initials": "T"}, {"family": "Choudhari", "given": "Sulbha", "initials": "S"}, {"family": "Talsania", "given": "Keyur", "initials": "K"}, {"family": "Chen", "given": "Xiongfong", "initials": "X"}, {"family": "Shetty", "given": "Jyoti", "initials": "J"}, {"family": "Kriga", "given": "Yuliya", "initials": "Y"}, {"family": "Tran", "given": "Bao", "initials": "B"}, {"family": "Zhu", "given": "Bin", "initials": "B", "orcid": "0000-0003-0172-5516", "researcher": {"href": "https://publications.scilifelab.se/researcher/67eaeee64f3741c58132c76ba8d33d2b.json"}}, {"family": "Chen", "given": "Zhong", "initials": "Z"}, {"family": "Chen", "given": "Wanqiu", "initials": "W", "orcid": "0000-0003-3706-7834", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff236616beef483ea11661874e91b7d1.json"}}, {"family": "Wang", "given": "Charles", "initials": "C", "orcid": "0000-0001-8861-2121", "researcher": {"href": "https://publications.scilifelab.se/researcher/6f245b91838442ef859874ad23d0aae8.json"}}, {"family": "Jaeger", "given": "Erich", "initials": "E"}, {"family": "Meerzaman", "given": "Daoud", "initials": "D"}, {"family": "Lu", "given": "Charles", "initials": "C"}, {"family": "Idler", "given": "Kenneth", "initials": "K"}, {"family": "Ren", "given": "Luyao", "initials": "L"}, {"family": "Zheng", "given": "Yuanting", "initials": "Y"}, {"family": "Shi", "given": "Leming", "initials": "L"}, {"family": "Petitjean", "given": "Virginie", "initials": "V"}, {"family": "Sultan", "given": "Marc", "initials": "M"}, {"family": "Hung", "given": "Tiffany", "initials": "T"}, {"family": "Peters", "given": "Eric", "initials": "E"}, {"family": "Drabek", "given": "Jiri", "initials": "J"}, {"family": "Vojta", "given": "Petr", "initials": "P"}, {"family": "Maestro", "given": "Roberta", "initials": "R"}, {"family": "Gasparotto", "given": "Daniela", "initials": "D"}, {"family": "K\u00f5ks", "given": "Sulev", "initials": "S", "orcid": "0000-0001-6087-6643", "researcher": {"href": "https://publications.scilifelab.se/researcher/dea893f45b1b45a5a92890878fa044e5.json"}}, {"family": "Reimann", "given": "Ene", "initials": "E", "orcid": "0000-0002-5410-4433", "researcher": {"href": "https://publications.scilifelab.se/researcher/25325fa20b3940a6acd1ebd0a58629ef.json"}}, {"family": "Scherer", "given": "Andreas", "initials": "A"}, {"family": "Nordlund", "given": "Jessica", "initials": "J"}, {"family": "Liljedahl", "given": "Ulrika", "initials": "U"}, {"family": "Foox", "given": "Jonathan", "initials": "J"}, {"family": "Mason", "given": "Christopher E", "initials": "CE", "orcid": "0000-0002-1850-1642", "researcher": {"href": "https://publications.scilifelab.se/researcher/2af4cb8577d34907b22b030f9e79e90e.json"}}, {"family": "Xiao", "given": "Chunlin", "initials": "C", "orcid": "0000-0001-8702-4889", "researcher": {"href": "https://publications.scilifelab.se/researcher/8b1a63c56506470cba459c6e60378ba2.json"}}, {"family": "Hong", "given": "Huixiao", "initials": "H", "orcid": "0000-0001-8087-3968", "researcher": {"href": "https://publications.scilifelab.se/researcher/158916b8a0cc4a28b2dceb12514d4a88.json"}}, {"family": "Xiao", "given": "Wenming", "initials": "W", "orcid": "0000-0003-4096-9724", "researcher": {"href": "https://publications.scilifelab.se/researcher/633df103f81f4142ace7a3763b56af54.json"}}], "type": "dataset", "published": "2021-11-09", "journal": {"title": "Sci Data", "issn": "2052-4463", "issn-l": "2052-4463", "volume": "8", "issue": "1", "pages": "296"}, "abstract": "With the rapid advancement of sequencing technologies, next generation sequencing (NGS) analysis has been widely applied in cancer genomics research. More recently, NGS has been adopted in clinical oncology to advance personalized medicine. Clinical applications of precision oncology require accurate tests that can distinguish tumor-specific mutations from artifacts introduced during NGS processes or data analysis. Therefore, there is an urgent need to develop best practices in cancer mutation detection using NGS and the need for standard reference data sets for systematically measuring accuracy and reproducibility across platforms and methods. Within the SEQC2 consortium context, we established paired tumor-normal reference samples and generated whole-genome (WGS) and whole-exome sequencing (WES) data using sixteen library protocols, seven sequencing platforms at six different centers. We systematically interrogated somatic mutations in the reference samples to identify factors affecting detection reproducibility and accuracy in cancer genomes. These large cross-platform/site WGS and WES datasets using well-characterized reference samples will represent a powerful resource for benchmarking NGS technologies, bioinformatics pipelines, and for the cancer genomics studies.", "doi": "10.1038/s41597-021-01077-5", "pmid": "34753956", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Collaborative", "National Genomics Infrastructure": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1038/s41597-021-01077-5"}, {"db": "pmc", "key": "PMC8578599"}], "notes": [], "created": "2022-02-22T16:04:58.400Z", "modified": "2022-03-31T15:20:05.415Z"}, {"entity": "publication", "iuid": "6962e840304c4a2ea97234ee06ee9e8c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6962e840304c4a2ea97234ee06ee9e8c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6962e840304c4a2ea97234ee06ee9e8c"}}, "title": "A common polymorphism in the dopamine transporter gene predicts working memory performance and in vivo dopamine integrity in aging.", "authors": [{"family": "Karalija", "given": "Nina", "initials": "N"}, {"family": "K\u00f6hncke", "given": "Ylva", "initials": "Y"}, {"family": "D\u00fczel", "given": "Sandra", "initials": "S"}, {"family": "Bertram", "given": "Lars", "initials": "L"}, {"family": "Papenberg", "given": "Goran", "initials": "G"}, {"family": "Demuth", "given": "Ilja", "initials": "I"}, {"family": "Lill", "given": "Christina M", "initials": "CM"}, {"family": "Johansson", "given": "Jarkko", "initials": "J"}, {"family": "Riklund", "given": "Katrine", "initials": "K"}, {"family": "L\u00f6vd\u00e9n", "given": "Martin", "initials": "M"}, {"family": "B\u00e4ckman", "given": "Lars", "initials": "L"}, {"family": "Nyberg", "given": "Lars", "initials": "L"}, {"family": "Lindenberger", "given": "Ulman", "initials": "U"}, {"family": "Brandmaier", "given": "Andreas M", "initials": "AM"}], "type": "journal article", "published": "2021-11-03", "journal": {"title": "Neuroimage", "issn": "1095-9572", "issn-l": "1053-8119", "volume": "245", "issue": null, "pages": "118707"}, "abstract": "Dopamine (DA) integrity is suggested as a potential cause of individual differences in working memory (WM) performance among older adults. Still, the principal dopaminergic mechanisms giving rise to WM differences remain unspecified. Here, 61 single-nucleotide polymorphisms, located in or adjacent to various dopamine-related genes, were assessed for their links to WM performance in a sample of 1313 adults aged 61-80 years from the Berlin Aging Study II. Least Absolute Shrinkage and Selection Operator (LASSO) regression was conducted to estimate associations between polymorphisms and WM. Rs40184 in the DA transporter gene, SLC6A3, showed allelic group differences in WM, with T-carriers performing better than C homozygotes (p<0.01). This finding was replicated in an independent sample from the Cognition, Brain, and Aging study (COBRA; baseline: n = 181, ages: 64-68 years; 5-year follow up: n = 129). In COBRA, in vivo DA integrity was measured with 11C-raclopride and positron emission tomography. Notably, WM as well as in vivo DA integrity was higher for rs40184 T-carriers at baseline (p<0.05 for WM and caudate and hippocampal D2-receptor availability) and at the 5-year follow-up (p<0.05 for WM and hippocampal D2 availability). Our findings indicate that individual differences in DA transporter function contribute to differences in WM performance in old age, presumably by regulating DA availability.", "doi": "10.1016/j.neuroimage.2021.118707", "pmid": "34742942", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pii", "key": "S1053-8119(21)00979-4"}], "notes": [], "created": "2021-11-26T16:27:52.009Z", "modified": "2021-12-07T06:55:08.618Z"}, {"entity": "publication", "iuid": "6b1e9e477a224713ae67aa09319e2f6b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6b1e9e477a224713ae67aa09319e2f6b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6b1e9e477a224713ae67aa09319e2f6b"}}, "title": "BMP2-induction of FN14 promotes protumorigenic signaling in gynecologic cancer cells.", "authors": [{"family": "Fukuda", "given": "Tomohiko", "initials": "T"}, {"family": "Fukuda", "given": "Risa", "initials": "R"}, {"family": "Koinuma", "given": "Daizo", "initials": "D"}, {"family": "Moustakas", "given": "Aristidis", "initials": "A"}, {"family": "Miyazono", "given": "Kohei", "initials": "K"}, {"family": "Heldin", "given": "Carl-Henrik", "initials": "CH"}], "type": "journal article", "published": "2021-11-00", "journal": {"title": "Cell. Signal.", "issn": "1873-3913", "volume": "87", "pages": "110146", "issn-l": "0898-6568"}, "abstract": "We previously reported that bone morphogenetic protein (BMP) signaling promotes tumorigenesis in gynecologic cancer cells. BMP2 enhances proliferation of ovarian and endometrial cancer cells via c-KIT induction, and triggers epithelial-mesenchymal transition (EMT) by SNAIL and/or SLUG induction, leading to increased cell migration. However, the downstream effectors of BMP signaling in gynecological cancer cells have not been clearly elucidated. In this study, we performed RNA-sequencing of Ishikawa endometrial and SKOV3 ovarian cancer cells after BMP2 stimulation, and identified TNFRSF12A, encoding fibroblast growth factor-inducible 14 (FN14) as a common BMP2-induced gene. FN14 knockdown suppressed BMP2-induced cell proliferation and migration, confirmed by MTS and scratch assays, respectively. In addition, FN14 silencing augmented chemosensitivity of SKOV3 cells. As a downstream effector of BMP signaling, FN14 modulated both c-KIT and SNAIL expression, which are important for growth and migration of ovarian and endometrial cancer cells. These results support the notion that the tumor promoting effects of BMP signaling in gynecological cancers are partially attributed to FN14 induction.", "doi": "10.1016/j.cellsig.2021.110146", "pmid": "34517088", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pii", "key": "S0898-6568(21)00235-7"}], "notes": [], "created": "2021-12-08T14:26:59.223Z", "modified": "2021-12-08T14:26:59.229Z"}, {"entity": "publication", "iuid": "4f8a0c83dae54eb198f28abf5760d51e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4f8a0c83dae54eb198f28abf5760d51e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4f8a0c83dae54eb198f28abf5760d51e"}}, "title": "The oral microbiota of wild bears in Sweden reflects the history of antibiotic use by humans.", "authors": [{"family": "Brealey", "given": "Jaelle C", "initials": "JC"}, {"family": "Leit\u00e3o", "given": "Henrique G", "initials": "HG"}, {"family": "Hofstede", "given": "Thijs", "initials": "T"}, {"family": "Kalthoff", "given": "Daniela C", "initials": "DC"}, {"family": "Guschanski", "given": "Katerina", "initials": "K"}], "type": "journal article", "published": "2021-10-25", "journal": {"title": "Curr. Biol.", "issn": "1879-0445", "volume": "31", "issue": "20", "pages": "4650-4658.e6", "issn-l": "0960-9822"}, "abstract": "Following the advent of industrial-scale antibiotic production in the 1940s,1 antimicrobial resistance (AMR) has been on the rise and now poses a major global health threat in terms of mortality, morbidity, and economic burden.2,3 Because AMR can be exchanged between humans, livestock, and wildlife, wild animals can be used as indicators of human-associated AMR contamination of the environment.4 However, AMR is a normal function of natural environments and is present in host-associated microbiomes, which makes it challenging to distinguish between anthropogenic and natural sources.4,5 One way to overcome this difficulty is to use historical samples that span the period from before the mass production of antibiotics to today. We used shotgun metagenomic sequencing of dental calculus, the calcified form of the oral microbial biofilm, to determine the abundance and repertoire of AMR genes in the oral microbiome of Swedish brown bears collected over the last 180 years. Our temporal metagenomics approach allowed us to establish a baseline of natural AMR in the pre-antibiotics era and to quantify a significant increase in total AMR load and diversity of AMR genes that is consistent with patterns of national human antibiotic use. We also demonstrated a significant decrease in total AMR load in bears in the last two decades, which coincides with Swedish strategies to mitigate AMR. Our study suggests that public health policies can be effective in limiting human-associated AMR contamination of the environment and wildlife.", "doi": "10.1016/j.cub.2021.08.010", "pmid": "34437844", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "S0960-9822(21)01112-X"}], "notes": [], "created": "2021-12-07T21:45:43.466Z", "modified": "2024-01-16T13:48:38.192Z"}, {"entity": "publication", "iuid": "7038d1529975473fb56885bcdf066f24", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7038d1529975473fb56885bcdf066f24.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7038d1529975473fb56885bcdf066f24"}}, "title": "Milking system and premilking routines have strong effect on the microbial community in bulk tank milk.", "authors": [{"family": "Sun", "given": "Li", "initials": "L"}, {"family": "Lundh", "given": "\u00c5se", "initials": "\u00c5"}, {"family": "H\u00f6jer", "given": "Annika", "initials": "A"}, {"family": "Bernes", "given": "Gun", "initials": "G"}, {"family": "Nilsson", "given": "David", "initials": "D"}, {"family": "Johansson", "given": "Monika", "initials": "M"}, {"family": "Hetta", "given": "M\u00e5rten", "initials": "M"}, {"family": "Gustafsson", "given": "Anders H", "initials": "AH"}, {"family": "Saed\u00e9n", "given": "Karin Hallin", "initials": "KH"}, {"family": "Dicksved", "given": "Johan", "initials": "J"}], "type": "journal article", "published": "2021-10-22", "journal": {"title": "J Dairy Sci", "issn": "1525-3198", "issn-l": null}, "abstract": "In this study, we investigated the variation in the microbial community present in bulk tank milk samples and the potential effect of different farm management factors. Bulk tank milk samples were collected repeatedly over one year from 42 farms located in northern Sweden. Total and thermoresistant bacteria counts and 16S rRNA gene-based amplicon sequencing were used to characterize microbial community composition. The microbial community was in general heterogeneous both within and between different farms and the community composition in the bulk tank milk was commonly dominated by Pseudomonas, Acinetobacter, Streptococcus, unclassified Peptostreptococcaceae, and Staphylococcus. Principal component analysis including farm factor variables and microbial taxa data revealed that the microbial community in milk was affected by type of milking system. Milk from farms using an automatic (robot) milking system (AMS) and loose housing showed different microbial community composition compared with milk from tiestall farms. A discriminant analysis model revealed that this difference was dependent on several microbial taxa. Among farms using an automatic milking system, there were further differences in the microbial community composition depending on the brand of the milking robot used. On tiestall farms, routines for teat preparation and cleaning of the milking equipment affected the microbial community composition in milk. Total bacteria count (TBC) in milk differed between the farm types, and TBC were higher on AMS than tiestall farms (log 4.05 vs. log 3.79 TBC/mL for AMS and tiestalls, respectively). Among tiestall farms, milk from farms using a chemical agent in connection to teat preparation and a more frequent use of acid to clean the milking equipment had lower TBC in milk, than milk from farms using water for teat preparation and a less frequent use of acid to clean the milking equipment (log 3.68 vs. 4.02 TBC/mL). There were no significant differences in the number of thermoresistant bacteria between farm types. The evaluated factors explained only a small proportion of total variation in the microbiota data, however, despite this, the study highlights the effect of routines associated with teat preparation and cleaning of the milking equipment on raw milk microbiota, irrespective of type of milking system used.", "doi": "10.3168/jds.2021-20661", "pmid": "34696914", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pii", "key": "S0022-0302(21)00969-3"}], "notes": [], "created": "2021-12-08T13:56:57.088Z", "modified": "2021-12-08T13:56:57.123Z"}, {"entity": "publication", "iuid": "cf64d8d5c8d0433d86e6b162465f5973", "links": {"self": {"href": "https://publications.scilifelab.se/publication/cf64d8d5c8d0433d86e6b162465f5973.json"}, "display": {"href": "https://publications.scilifelab.se/publication/cf64d8d5c8d0433d86e6b162465f5973"}}, "title": "Frailty and the risk of dementia: is the association explained by shared environmental and genetic factors?", "authors": [{"family": "Bai", "given": "Ge", "initials": "G"}, {"family": "Wang", "given": "Yunzhang", "initials": "Y"}, {"family": "Kuja-Halkola", "given": "Ralf", "initials": "R"}, {"family": "Li", "given": "Xia", "initials": "X"}, {"family": "Tomata", "given": "Yasutake", "initials": "Y"}, {"family": "Karlsson", "given": "Ida K", "initials": "IK"}, {"family": "Pedersen", "given": "Nancy L", "initials": "NL"}, {"family": "H\u00e4gg", "given": "Sara", "initials": "S"}, {"family": "Jylh\u00e4v\u00e4", "given": "Juulia", "initials": "J", "orcid": "0000-0003-0250-4491", "researcher": {"href": "https://publications.scilifelab.se/researcher/5193964678264255adaaf5005ab59a87.json"}}], "type": "journal article", "published": "2021-10-18", "journal": {"title": "BMC Med", "issn": "1741-7015", "issn-l": "1741-7015", "volume": "19", "issue": "1", "pages": "248"}, "abstract": "Frailty has been identified as a risk factor for cognitive impairment and dementia. However, it is not known whether familial factors, such as genetics and shared environmental factors, underlie this association. We analyzed the association between frailty and the risk of dementia in a large twin cohort and examined the role of familial factors in the association.\n\nThe Rockwood frailty index (FI) based on 44 health deficits was used to assess frailty. The population-level association between FI and the risk of all-cause dementia was analyzed in 41,550 participants of the Screening Across the Lifespan Twin (SALT) study (full sample, aged 41-97 years at baseline), using Cox and competing risk models. A subsample of 10,487 SALT participants aged 65 and older who received a cognitive assessment (cognitive sample) was used in a sensitivity analysis to assess the effect of baseline cognitive level on the FI-dementia association. To analyze the influence of familial effects on the FI-dementia association, a within-pair analysis was performed. The within-pair model was also used to assess whether the risk conferred by frailty varies by age at FI assessment.\n\nA total of 3183 individuals were diagnosed with dementia during the 19-year follow-up. A 10% increase in FI was associated with an increased risk of dementia (hazard ratio [HR] 1.17 (95% confidence interval [CI] 1.07, 1.18)) in the full sample adjusted for age, sex, education, and tobacco use. A significant association was likewise found in the cognitive sample, with an HR of 1.13 (95% CI 1.09, 1.20), adjusted for age, sex, and cognitive level at baseline. The associations were not attenuated when adjusted for APOE \u025b4 carrier status or considering the competing risk of death. After adjusting for familial effects, we found no evidence for statistically significant attenuation of the effect. The risk conferred by higher FI on dementia was constant after age 50 until very old age.\n\nA higher level of frailty predicts the risk of dementia and the association appears independent of familial factors. Targeting frailty might thus contribute to preventing or delaying dementia.", "doi": "10.1186/s12916-021-02104-3", "pmid": "34657626", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1186/s12916-021-02104-3"}, {"db": "pmc", "key": "PMC8522144"}], "notes": [], "created": "2021-10-19T14:10:09.688Z", "modified": "2024-01-16T13:48:38.230Z"}, {"entity": "publication", "iuid": "039e2f3bd92446c48fe798ff1e76bc1d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/039e2f3bd92446c48fe798ff1e76bc1d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/039e2f3bd92446c48fe798ff1e76bc1d"}}, "title": "RNA sequencing reveals metabolic and regulatory changes leading to more robust fermentation performance during short-term adaptation of Saccharomyces cerevisiae to lignocellulosic inhibitors.", "authors": [{"family": "van Dijk", "given": "Marlous", "initials": "M", "orcid": "0000-0002-2342-6456", "researcher": {"href": "https://publications.scilifelab.se/researcher/d00b5a4f307845adb69ec15731344b72.json"}}, {"family": "Rugbjerg", "given": "Peter", "initials": "P", "orcid": "0000-0003-2561-5063", "researcher": {"href": "https://publications.scilifelab.se/researcher/23a7c1f85a584c0b942200752205804a.json"}}, {"family": "Nyg\u00e5rd", "given": "Yvonne", "initials": "Y", "orcid": "0000-0001-6117-0343", "researcher": {"href": "https://publications.scilifelab.se/researcher/a136743764bc4dc4aa4d363c5a930592.json"}}, {"family": "Olsson", "given": "Lisbeth", "initials": "L", "orcid": "0000-0002-0827-5442", "researcher": {"href": "https://publications.scilifelab.se/researcher/5fa7036912fb4073be4a4365937f2232.json"}}], "type": "journal article", "published": "2021-10-15", "journal": {"title": "Biotechnol Biofuels", "issn": "1754-6834", "volume": "14", "issue": "1", "pages": "201", "issn-l": "1754-6834"}, "abstract": "The limited tolerance of Saccharomyces cerevisiae to inhibitors is a major challenge in second-generation bioethanol production, and our understanding of the molecular mechanisms providing tolerance to inhibitor-rich lignocellulosic hydrolysates is incomplete. Short-term adaptation of the yeast in the presence of dilute hydrolysate can improve its robustness and productivity during subsequent fermentation.\n\nWe utilized RNA sequencing to investigate differential gene expression in the industrial yeast strain CR01 during short-term adaptation, mimicking industrial conditions for cell propagation. In this first transcriptomic study of short-term adaption of S. cerevisiae to lignocellulosic hydrolysate, we found that cultures respond by fine-tuned up- and down-regulation of a subset of general stress response genes. Furthermore, time-resolved RNA sequencing allowed for identification of genes that were differentially expressed at 2 or more sampling points, revealing the importance of oxidative stress response, thiamin and biotin biosynthesis. furan-aldehyde reductases and specific drug:H+ antiporters, as well as the down-regulation of certain transporter genes.\n\nThese findings provide a better understanding of the molecular mechanisms governing short-term adaptation of S. cerevisiae to lignocellulosic hydrolysate, and suggest new genetic targets for improving fermentation robustness.", "doi": "10.1186/s13068-021-02049-y", "pmid": "34654441", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pii", "key": "10.1186/s13068-021-02049-y"}, {"db": "pmc", "key": "PMC8518171"}], "notes": [], "created": "2021-12-08T13:56:24.073Z", "modified": "2021-12-08T13:56:24.235Z"}, {"entity": "publication", "iuid": "a51b73263a6d4b939a0085b5f33e1f97", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a51b73263a6d4b939a0085b5f33e1f97.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a51b73263a6d4b939a0085b5f33e1f97"}}, "title": "Cis-acting mutation affecting GJA5 transcription is underlying the Melanotic within-feather pigmentation pattern in chickens.", "authors": [{"family": "Li", "given": "Jingyi", "initials": "J"}, {"family": "Lee", "given": "Mi-Ok", "initials": "MO"}, {"family": "Chen", "given": "Junfeng", "initials": "J"}, {"family": "Davis", "given": "Brian W", "initials": "BW", "orcid": "0000-0002-6121-135X", "researcher": {"href": "https://publications.scilifelab.se/researcher/63981f53ab2e4dc09a4a2a62ae0b7a84.json"}}, {"family": "Dorshorst", "given": "Benjamin J", "initials": "BJ"}, {"family": "Siegel", "given": "Paul B", "initials": "PB", "orcid": "0000-0003-1415-7781", "researcher": {"href": "https://publications.scilifelab.se/researcher/7945724419eb443c84341086cca382cf.json"}}, {"family": "Inaba", "given": "Masafumi", "initials": "M"}, {"family": "Jiang", "given": "Ting-Xin", "initials": "TX", "orcid": "0000-0003-1972-8985", "researcher": {"href": "https://publications.scilifelab.se/researcher/4dacf1a76c35436fa36cc75b0dbe28d7.json"}}, {"family": "Chuong", "given": "Cheng-Ming", "initials": "CM", "orcid": "0000-0001-9673-3994", "researcher": {"href": "https://publications.scilifelab.se/researcher/4396f32b3ded4decb329859b5d14f420.json"}}, {"family": "Andersson", "given": "Leif", "initials": "L", "orcid": "0000-0002-4085-6968", "researcher": {"href": "https://publications.scilifelab.se/researcher/bd3343c12f994b1fabcae23027d3a76d.json"}}], "type": "journal article", "published": "2021-10-12", "journal": {"title": "Proc. Natl. Acad. Sci. U.S.A.", "issn": "1091-6490", "volume": "118", "issue": "41", "issn-l": "0027-8424"}, "abstract": "Melanotic (Ml) is a mutation in chickens that extends black (eumelanin) pigmentation in normally brown or red (pheomelanin) areas, thus affecting multiple within-feather patterns [J. W. Moore, J. R. Smyth Jr, J. Hered. 62, 215-219 (1971)]. In the present study, linkage mapping using a back-cross between Dark Cornish (Ml/Ml) and Partridge Plymouth Rock (ml +/ml ) chickens assigned +Ml to an 820-kb region on chromosome 1. Identity-by-descent mapping, via whole-genome sequencing and diagnostic tests using a diverse set of chickens, refined the localization to the genomic region harboring GJA5 encoding gap-junction protein 5 (alias connexin 40) previously associated with pigmentation patterns in zebrafish. An insertion/deletion polymorphism located in the vicinity of the GJA5 promoter region was identified as the candidate causal mutation. Four different GJA5 transcripts were found to be expressed in feather follicles and at least two showed differential expression between genotypes. The results showed that Melanotic constitutes a cis-acting regulatory mutation affecting GJA5 expression. A recent study established the melanocortin-1 receptor (MC1R) locus and the interaction between the MC1R receptor and its antagonist agouti-signaling protein as the primary mechanism underlying variation in within-feather pigmentation patterns in chickens. The present study advances understanding the mechanisms underlying variation in plumage color in birds because it demonstrates that the activity of connexin 40/GJA5 can modulate the periodic pigmentation patterns within individual feathers.", "doi": "10.1073/pnas.2109363118", "pmid": "34607956", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "2109363118"}, {"db": "pmc", "key": "PMC8521658"}], "notes": [], "created": "2021-12-10T11:08:58.593Z", "modified": "2024-01-16T13:48:38.245Z"}, {"entity": "publication", "iuid": "9d11c94d2fc948afa5b9d4e1573e1d8e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9d11c94d2fc948afa5b9d4e1573e1d8e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9d11c94d2fc948afa5b9d4e1573e1d8e"}}, "title": "Philippine Ayta possess the highest level of Denisovan ancestry in the world.", "authors": [{"family": "Larena", "given": "Maximilian", "initials": "M"}, {"family": "McKenna", "given": "James", "initials": "J"}, {"family": "Sanchez-Quinto", "given": "Federico", "initials": "F"}, {"family": "Bernhardsson", "given": "Carolina", "initials": "C"}, {"family": "Ebeo", "given": "Carlo", "initials": "C"}, {"family": "Reyes", "given": "Rebecca", "initials": "R"}, {"family": "Casel", "given": "Ophelia", "initials": "O"}, {"family": "Huang", "given": "Jin-Yuan", "initials": "JY"}, {"family": "Hagada", "given": "Kim Pullupul", "initials": "KP"}, {"family": "Guilay", "given": "Dennis", "initials": "D"}, {"family": "Reyes", "given": "Jennelyn", "initials": "J"}, {"family": "Allian", "given": "Fatima Pir", "initials": "FP"}, {"family": "Mori", "given": "Virgilio", "initials": "V"}, {"family": "Azarcon", "given": "Lahaina Sue", "initials": "LS"}, {"family": "Manera", "given": "Alma", "initials": "A"}, {"family": "Terando", "given": "Celito", "initials": "C"}, {"family": "Jamero", "given": "Lucio", "initials": "L"}, {"family": "Sireg", "given": "Gauden", "initials": "G"}, {"family": "Manginsay-Tremedal", "given": "Renefe", "initials": "R"}, {"family": "Labos", "given": "Maria Shiela", "initials": "MS"}, {"family": "Vilar", "given": "Richard Dian", "initials": "RD"}, {"family": "Latiph", "given": "Acram", "initials": "A"}, {"family": "Saway", "given": "Rodelio Linsahay", "initials": "RL"}, {"family": "Marte", "given": "Erwin", "initials": "E"}, {"family": "Magbanua", "given": "Pablito", "initials": "P"}, {"family": "Morales", "given": "Amor", "initials": "A"}, {"family": "Java", "given": "Ismael", "initials": "I"}, {"family": "Reveche", "given": "Rudy", "initials": "R"}, {"family": "Barrios", "given": "Becky", "initials": "B"}, {"family": "Burton", "given": "Erlinda", "initials": "E"}, {"family": "Salon", "given": "Jesus Christopher", "initials": "JC"}, {"family": "Kels", "given": "Ma Junaliah Tuazon", "initials": "MJT"}, {"family": "Albano", "given": "Adrian", "initials": "A"}, {"family": "Cruz-Angeles", "given": "Rose Beatrix", "initials": "RB"}, {"family": "Molanida", "given": "Edison", "initials": "E"}, {"family": "Graneh\u00e4ll", "given": "Lena", "initials": "L"}, {"family": "Vicente", "given": "M\u00e1rio", "initials": "M"}, {"family": "Edlund", "given": "Hanna", "initials": "H"}, {"family": "Loo", "given": "Jun-Hun", "initials": "JH"}, {"family": "Trejaut", "given": "Jean", "initials": "J"}, {"family": "Ho", "given": "Simon Y W", "initials": "SYW"}, {"family": "Reid", "given": "Lawrence", "initials": "L"}, {"family": "Lambeck", "given": "Kurt", "initials": "K"}, {"family": "Malmstr\u00f6m", "given": "Helena", "initials": "H"}, {"family": "Schlebusch", "given": "Carina", "initials": "C"}, {"family": "Endicott", "given": "Phillip", "initials": "P"}, {"family": "Jakobsson", "given": "Mattias", "initials": "M"}], "type": "journal article", "published": "2021-10-11", "journal": {"title": "Curr. Biol.", "issn": "1879-0445", "volume": "31", "issue": "19", "pages": "4219-4230.e10", "issn-l": "0960-9822"}, "abstract": "Multiple lines of evidence show that modern humans interbred with archaic Denisovans. Here, we report an account of shared demographic history between Australasians and Denisovans distinctively in Island Southeast Asia. Our analyses are based on \u223c2.3 million genotypes from 118 ethnic groups of the Philippines, including 25 diverse self-identified Negrito populations, along with high-coverage genomes of Australopapuans and Ayta Magbukon Negritos. We show that Ayta Magbukon possess the highest level of Denisovan ancestry in the world-\u223c30%-40% greater than that of Australians and Papuans-consistent with an independent admixture event into Negritos from Denisovans. Together with the recently described Homo luzonensis, we suggest that there were multiple archaic species that inhabited the Philippines prior to the arrival of modern humans and that these archaic groups may have been genetically related. Altogether, our findings unveil a complex intertwined history of modern and archaic humans in the Asia-Pacific region, where distinct Islander Denisovan populations differentially admixed with incoming Australasians across multiple locations and at various points in time.", "doi": "10.1016/j.cub.2021.07.022", "pmid": "34388371", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "S0960-9822(21)00977-5"}, {"db": "pmc", "key": "PMC8596304"}], "notes": [], "created": "2021-12-07T21:42:50.941Z", "modified": "2024-01-16T13:48:38.253Z"}, {"entity": "publication", "iuid": "58a8042a127b4e0b849ec2354eada4a0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/58a8042a127b4e0b849ec2354eada4a0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/58a8042a127b4e0b849ec2354eada4a0"}}, "title": "HPA axis dysregulation is associated with differential methylation of CpG-sites in related genes.", "authors": [{"family": "Chatzittofis", "given": "Andreas", "initials": "A"}, {"family": "Bostr\u00f6m", "given": "Adrian Desai E", "initials": "ADE"}, {"family": "Ciuculete", "given": "Diana M", "initials": "DM"}, {"family": "\u00d6berg", "given": "Katarina G\u00f6rts", "initials": "KG"}, {"family": "Arver", "given": "Stefan", "initials": "S"}, {"family": "Schi\u00f6th", "given": "Helgi B", "initials": "HB"}, {"family": "Jokinen", "given": "Jussi", "initials": "J"}], "type": "journal article", "published": "2021-10-11", "journal": {"title": "Sci Rep", "issn": "2045-2322", "issn-l": "2045-2322", "volume": "11", "issue": "1", "pages": "20134"}, "abstract": "DNA methylation shifts in Hypothalamic-pituitary-adrenal (HPA) axis related genes is reported in psychiatric disorders including hypersexual disorder. This study, comprising 20 dexamethasone suppression test (DST) non-suppressors and 73 controls, examined the association between the HPA axis dysregulation, shifts in DNA methylation of HPA axis related genes and importantly, gene expression. Individuals with cortisol level \u2265 138 nmol/l, after the low dose (0.5 mg) dexamethasone suppression test (DST) were classified as non-suppressors. Genome-wide methylation pattern, measured in whole blood using the EPIC BeadChip, investigated CpG sites located within 2000 bp of the transcriptional start site of key HPA axis genes, i.e.: CRH, CRHBP, CRHR-1, CRHR-2, FKBP5 and NR3C1. Regression models including DNA methylation M-values and the binary outcome (DST non-suppression status) were performed. Gene transcripts with an abundance of differentially methylated CpG sites were identified with binomial tests. Pearson correlations and robust linear regressions were performed between CpG methylation and gene expression in two independent cohorts. Six of 76 CpG sites were significantly hypermethylated in DST non-suppressors (nominal P < 0.05), associated with genes CRH, CRHR1, CRHR2, FKBP5 and NR3C1. NR3C1 transcript AJ877169 showed statistically significant abundance of probes differentially methylated by DST non-suppression status and correlated with DST cortisol levels. Further, methylation levels of cg07733851 and cg27122725 were positively correlated with gene expression levels of the NR3C1 gene. Methylation levels of cg08636224 (FKBP5) correlated with baseline cortisol and gene expression. Our findings revealed that DNA methylation shifts are involved in the altered mechanism of the HPA axis suggesting that new epigenetic targets should be considered behind psychiatric disorders.", "doi": "10.1038/s41598-021-99714-x", "pmid": "34635736", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-021-99714-x"}, {"db": "pmc", "key": "PMC8505644"}], "notes": [], "created": "2021-10-19T14:10:12.164Z", "modified": "2024-01-16T13:48:38.261Z"}, {"entity": "publication", "iuid": "7da881e6bd1c41e59a6db035fcd40b87", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7da881e6bd1c41e59a6db035fcd40b87.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7da881e6bd1c41e59a6db035fcd40b87"}}, "title": "Chromosome-level genome assembly and transcriptome-based annotation of the oleaginous yeast Rhodotorula toruloides CBS 14.", "authors": [{"family": "Mart\u00edn-Hern\u00e1ndez", "given": "Giselle C", "initials": "GC"}, {"family": "M\u00fcller", "given": "Bettina", "initials": "B"}, {"family": "Chmielarz", "given": "Miko\u0142aj", "initials": "M"}, {"family": "Brandt", "given": "Christian", "initials": "C"}, {"family": "H\u00f6lzer", "given": "Martin", "initials": "M"}, {"family": "Viehweger", "given": "Adrian", "initials": "A"}, {"family": "Passoth", "given": "Volkmar", "initials": "V"}], "type": "journal article", "published": "2021-10-11", "journal": {"title": "Genomics", "issn": "1089-8646", "volume": "113", "issue": "6", "pages": "4022-4027", "issn-l": "0888-7543"}, "abstract": "Rhodotorula toruloides is an oleaginous yeast with high biotechnological potential. In order to understand the molecular physiology of lipid synthesis in R. toruloides and to advance metabolic engineering, a high-resolution genome is required. We constructed a genome draft of R. toruloides CBS 14, using a hybrid assembly approach, consisting of short and long reads generated by Illumina and Nanopore sequencing, respectively. The genome draft consists of 23 contigs and 3 scaffolds, with a N50 length of 1,529,952 bp, thus largely representing chromosomal organization. The total size of the genome is 20,534,857 bp and the overall GC content is 61.83%. Transcriptomic data from different growth conditions was used to aid species-specific gene annotation. We annotated 9464 genes and identified 11,691 transcripts. Furthermore, we demonstrated the presence of a potential plasmid, an extrachromosomal circular structure of about 11 kb with a copy number about three times as high as the other chromosomes.", "doi": "10.1016/j.ygeno.2021.10.006", "pmid": "34648882", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pii", "key": "S0888-7543(21)00369-4"}], "notes": [], "created": "2021-12-08T13:55:49.083Z", "modified": "2021-12-08T13:55:49.096Z"}, {"entity": "publication", "iuid": "9de64a0e085e4158a4b9af7a44d7b319", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9de64a0e085e4158a4b9af7a44d7b319.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9de64a0e085e4158a4b9af7a44d7b319"}}, "title": "Distinct B cell subsets in Peyer's patches convey probiotic effects by Limosilactobacillus reuteri.", "authors": [{"family": "Liu", "given": "Hao-Yu", "initials": "HY"}, {"family": "Giraud", "given": "Antoine", "initials": "A"}, {"family": "Seignez", "given": "Cedric", "initials": "C"}, {"family": "Ahl", "given": "David", "initials": "D"}, {"family": "Guo", "given": "Feilong", "initials": "F"}, {"family": "Sedin", "given": "John", "initials": "J"}, {"family": "Walden", "given": "Tomas", "initials": "T"}, {"family": "Oh", "given": "Jee-Hwan", "initials": "JH"}, {"family": "van Pijkeren", "given": "Jan Peter", "initials": "JP"}, {"family": "Holm", "given": "Lena", "initials": "L"}, {"family": "Roos", "given": "Stefan", "initials": "S"}, {"family": "Bertilsson", "given": "Stefan", "initials": "S"}, {"family": "Phillipson", "given": "Mia", "initials": "M", "orcid": "0000-0002-2387-0266", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ebf9ffcab3e4a19add4c6dd51b727b1.json"}}], "type": "journal article", "published": "2021-10-03", "journal": {"title": "Microbiome", "issn": "2049-2618", "volume": "9", "issue": "1", "pages": "198", "issn-l": "2049-2618"}, "abstract": "Intestinal Peyer's patches (PPs) form unique niches for bacteria-immune cell interactions that direct host immunity and shape the microbiome. Here we investigate how peroral administration of probiotic bacterium Limosilactobacillus reuteri R2LC affects B lymphocytes and IgA induction in the PPs, as well as the downstream consequences on intestinal microbiota and susceptibility to inflammation.\n\nThe B cells of PPs were separated by size to circumvent activation-dependent cell identification biases due to dynamic expression of markers, which resulted in two phenotypically, transcriptionally, and spatially distinct subsets: small IgD+/GL7-/S1PR1+/Bcl6, CCR6-expressing pre-germinal center (GC)-like B cells with innate-like functions located subepithelially, and large GL7+/S1PR1-/Ki67+/Bcl6, CD69-expressing B cells with strong metabolic activity found in the GC. Peroral L. reuteri administration expanded both B cell subsets and enhanced the innate-like properties of pre-GC-like B cells while retaining them in the sub-epithelial compartment by increased sphingosine-1-phosphate/S1PR1 signaling. Furthermore, L. reuteri promoted GC-like B cell differentiation, which involved expansion of the GC area and autocrine TGF\u03b2-1 activation. Consequently, PD-1-T follicular helper cell-dependent IgA induction and production was increased by L. reuteri, which shifted the intestinal microbiome and protected against dextran-sulfate-sodium induced colitis and dysbiosis.\n\nThe Peyer's patches sense, enhance and transmit probiotic signals by increasing the numbers and effector functions of distinct B cell subsets, resulting in increased IgA production, altered intestinal microbiota, and protection against inflammation. Video abstract.", "doi": "10.1186/s40168-021-01128-4", "pmid": "34602091", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pii", "key": "10.1186/s40168-021-01128-4"}, {"db": "pmc", "key": "PMC8487498"}], "notes": [], "created": "2022-05-31T05:45:27.828Z", "modified": "2022-05-31T05:45:27.844Z"}, {"entity": "publication", "iuid": "7c2dbf0e2d434e6187454643c879f6e3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7c2dbf0e2d434e6187454643c879f6e3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7c2dbf0e2d434e6187454643c879f6e3"}}, "title": "Pregnancy-related hormones and COMT genotype: Associations with maternal working memory.", "authors": [{"family": "Amiel Castro", "given": "Rita", "initials": "R"}, {"family": "Kunovac Kallak", "given": "Theodora", "initials": "T"}, {"family": "Sundstr\u00f6m Poromaa", "given": "Inger", "initials": "I"}, {"family": "Willebrand", "given": "Mimmie", "initials": "M"}, {"family": "Lager", "given": "Susanne", "initials": "S"}, {"family": "Ehlert", "given": "Ulrike", "initials": "U"}, {"family": "Skalkidou", "given": "Alkistis", "initials": "A"}], "type": "journal article", "published": "2021-10-00", "journal": {"title": "Psychoneuroendocrinology", "issn": "1873-3360", "issn-l": "0306-4530", "volume": "132", "issue": null, "pages": "105361"}, "abstract": "Women experience different degrees of subjective cognitive changes during pregnancy. The exact mechanism underlying these changes is unknown, although endocrine alterations and genetics may be contributing factors. We investigated whether multiple pregnancy-related hormones were associated with working memory function assessed with the Digit Span Test (DST) in late pregnancy. Moreover, we examined whether the catechol-O-methyltransferase (COMT) genotype, previously related to working memory, was an effect modifier in this association. In this population-based panel study, we recorded psychiatric history, medication use, socio-demographic characteristics, and psychological well-being, gathered blood and saliva samples, and administered the DST at gestational weeks 35-39 (N = 216). We conducted multivariate linear regressions with DST as outcome, with different hormones and COMT genotype, adjusting for covariates including maternal age, BMI, education, depressive symptoms, and parity. We repeated these analyses excluding women with elevated depressive symptoms. Higher DST total scores were associated with increased free estradiol concentrations (B = 0.01, p = 0.03; B = 0.01, p = 0.02) in all participants and in participants without depressive symptoms, respectively, whereas DST forward was positively associated with free estradiol only in women without depressive symptoms (B = 0.01, p = 0.04). Lower total testosterone concentrations (B = -0.03, p = 0.01) enhanced DST backward performance in non-depressed women. Maternal higher education was significantly associated with the DST subscales in all participants. No significant differences emerged when considering the COMT genotype. Our results suggest differential associations of free estradiol and total testosterone levels with working memory function in late pregnancy.", "doi": "10.1016/j.psyneuen.2021.105361", "pmid": "34333317", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "S0306-4530(21)00235-3"}], "notes": [], "created": "2021-08-19T13:41:30.271Z", "modified": "2024-01-16T13:48:38.347Z"}, {"entity": "publication", "iuid": "f6799d3e01e6445788993dca4c841552", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f6799d3e01e6445788993dca4c841552.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f6799d3e01e6445788993dca4c841552"}}, "title": "Maternal genetic origin of the late and final Neolithic human populations from present-day Poland.", "authors": [{"family": "Juras", "given": "Anna", "initials": "A", "orcid": "0000-0002-2585-127X", "researcher": {"href": "https://publications.scilifelab.se/researcher/21890fe291bb4e8e913c5eb5963bcdce.json"}}, {"family": "Ehler", "given": "Edvard", "initials": "E"}, {"family": "Chyle\u0144ski", "given": "Maciej", "initials": "M"}, {"family": "Pospieszny", "given": "\u0141ukasz", "initials": "\u0141"}, {"family": "Spinek", "given": "Anna El\u017cbieta", "initials": "AE", "orcid": "0000-0003-0304-081X", "researcher": {"href": "https://publications.scilifelab.se/researcher/cb733a1bd8454c729d03ebd221cdf9ef.json"}}, {"family": "Malmstr\u00f6m", "given": "Helena", "initials": "H"}, {"family": "Krzewi\u0144ska", "given": "Maja", "initials": "M"}, {"family": "Szostek", "given": "Krzysztof", "initials": "K"}, {"family": "Pasterkiewicz", "given": "Wojciech", "initials": "W"}, {"family": "Florek", "given": "Marek", "initials": "M"}, {"family": "Wilk", "given": "Stanis\u0142aw", "initials": "S"}, {"family": "Mnich", "given": "Barbara", "initials": "B"}, {"family": "Kruk", "given": "Janusz", "initials": "J"}, {"family": "Szmyt", "given": "Marzena", "initials": "M"}, {"family": "Kozie\u0142", "given": "S\u0142awomir", "initials": "S"}, {"family": "G\u00f6therstr\u00f6m", "given": "Anders", "initials": "A"}, {"family": "Jakobsson", "given": "Mattias", "initials": "M", "orcid": "0000-0001-7840-7853", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a4abe0fcb20492d9ec849c9fbf58a71.json"}}, {"family": "Dabert", "given": "Miroslawa", "initials": "M"}], "type": "historical article", "published": "2021-10-00", "journal": {"title": "Am. J. Phys. Anthropol.", "issn": "1096-8644", "issn-l": "0002-9483", "volume": "176", "issue": "2", "pages": "223-236"}, "abstract": "We aim to identify maternal genetic affinities between the Middle to Final Neolithic (3850-2300 BC) populations from present-day Poland and possible genetic influences from the Pontic steppe.\n\nWe conducted ancient DNA studies from populations associated with Z\u0142ota, Globular Amphora, Funnel Beaker, and Corded Ware cultures (CWC). We sequenced genomic libraries on Illumina platform to generate 86 complete ancient mitochondrial genomes. Some of the samples were enriched for mitochondrial DNA using hybridization capture.\n\nThe maternal genetic composition found in Z\u0142ota-associated individuals resembled that found in people associated with the Globular Amphora culture which indicates that both groups likely originated from the same maternal genetic background. Further, these two groups were closely related to the Funnel Beaker culture-associated population. None of these groups shared a close affinity to CWC-associated people. Haplogroup U4 was present only in the CWC group and absent in Z\u0142ota group, Globular Amphora, and Funnel Beaker cultures.\n\nThe prevalence of mitochondrial haplogroups of Neolithic farmer origin identified in Early, Middle and Late Neolithic populations suggests a genetic continuity of these maternal lineages in the studied area. Although overlapping in time - and to some extent - in cultural expressions, none of the studied groups (Z\u0142ota, Globular Amphora, Funnel Beaker), shared a close genetic affinity to CWC-associated people, indicating a larger extent of cultural influence from the Pontic steppe than genetic exchange. The higher frequency of haplogroup U5b found in populations associated with Funnel Beaker, Globular Amphora, and Z\u0142ota cultures suggest a gradual maternal genetic influx from Mesolithic hunter-gatherers. Moreover, presence of haplogroup U4 in Corded Ware groups is most likely associated with the migrations from the Pontic steppe at the end of the Neolithic and supports the observed genetic distances.", "doi": "10.1002/ajpa.24372", "pmid": "34308549", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2021-10-01T09:03:18.631Z", "modified": "2024-01-16T13:48:38.387Z"}, {"entity": "publication", "iuid": "6dc0d1b807c54d67851f7551d0a1f0af", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6dc0d1b807c54d67851f7551d0a1f0af.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6dc0d1b807c54d67851f7551d0a1f0af"}}, "title": "Genome-wide association study of liver enzyme elevation in rheumatoid arthritis patients starting methotrexate.", "authors": [{"family": "Sundbaum", "given": "Johanna Karlsson", "initials": "JK", "orcid": "0000-0001-5313-7981", "researcher": {"href": "https://publications.scilifelab.se/researcher/aae0af5ecb664750a7fe9f482181e571.json"}}, {"family": "Baecklund", "given": "Eva", "initials": "E"}, {"family": "Eriksson", "given": "Niclas", "initials": "N", "orcid": "0000-0002-2152-4343", "researcher": {"href": "https://publications.scilifelab.se/researcher/64611a83caba46d597f45371b77de26b.json"}}, {"family": "Kohnke", "given": "Hugo", "initials": "H"}, {"family": "Wallenberg", "given": "Matilda", "initials": "M"}, {"family": "Cavalli", "given": "Marco", "initials": "M", "orcid": "0000-0003-1143-1431", "researcher": {"href": "https://publications.scilifelab.se/researcher/e35211c06385459baee12101121d2a15.json"}}, {"family": "Wadelius", "given": "Claes", "initials": "C", "orcid": "0000-0002-2033-7829", "researcher": {"href": "https://publications.scilifelab.se/researcher/2ec5ca1122024da4893b61e329a5ece5.json"}}, {"family": "Wadelius", "given": "Mia", "initials": "M", "orcid": "0000-0002-6368-2622", "researcher": {"href": "https://publications.scilifelab.se/researcher/ec07b9869a1f4b77b734c5dc567dc630.json"}}, {"family": "Hallberg", "given": "P\u00e4r", "initials": "P", "orcid": "0000-0003-3465-3280", "researcher": {"href": "https://publications.scilifelab.se/researcher/968cb3fe072d4ed09739e8be6668d168.json"}}], "type": "journal article", "published": "2021-10-00", "journal": {"title": "Pharmacogenomics", "issn": "1744-8042", "issn-l": "1462-2416", "volume": "22", "issue": "15", "pages": "973-982"}, "abstract": "Aim: To identify novel genetic variants predisposing to elevation of Alanine aminotransferase (ALT) in rheumatoid arthritis (RA) patients after initiation of methotrexate (MTX) treatment. Patients & methods: We performed genome-wide association studies in 198 RA patients starting MTX. Outcomes were maximum level of ALT and ALT >1.5-times the upper level of normal within the first 6 months of treatment. Results: RAVER2 (rs72675408) was significantly associated with maximum level of ALT (p = 4.36 \u00d7 10-8). This variant is in linkage disequilibrium with rs72675451, which is associated with differential expression of JAK1 and RAVER2. Conclusion: We found an association between ALT elevation and genetic variants that may regulate the expression of JAK1 and RAVER2. JAK1 encodes a janus kinase involved in the pathogenesis of RA.", "doi": "10.2217/pgs-2021-0064", "pmid": "34521259", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2021-09-17T14:54:04.269Z", "modified": "2024-01-16T13:48:38.408Z"}, {"entity": "publication", "iuid": "529981913bf64485865d384a5c90dac6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/529981913bf64485865d384a5c90dac6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/529981913bf64485865d384a5c90dac6"}}, "title": "DE-ETIOLATED1 has a role in the circadian clock of the liverwort Marchantia polymorpha.", "authors": [{"family": "Lagercrantz", "given": "Ulf", "initials": "U", "orcid": "0000-0003-2440-0677", "researcher": {"href": "https://publications.scilifelab.se/researcher/98afd2f15b94420f98013905e519f0ad.json"}}, {"family": "Billhardt", "given": "Anja", "initials": "A", "orcid": "0000-0003-0654-591X", "researcher": {"href": "https://publications.scilifelab.se/researcher/453482990e7f4597ae9a0d8b42af79fa.json"}}, {"family": "Rousku", "given": "Sabine N", "initials": "SN", "orcid": "0000-0002-0891-2130", "researcher": {"href": "https://publications.scilifelab.se/researcher/1b3d286164f54449961d5326036b9330.json"}}, {"family": "Leso", "given": "Martina", "initials": "M", "orcid": "0000-0003-4192-8027", "researcher": {"href": "https://publications.scilifelab.se/researcher/4ec4323cecc7419a8bcf1b8bd98c58e6.json"}}, {"family": "Reza", "given": "Salim Hossain", "initials": "SH", "orcid": "0000-0002-3646-3440", "researcher": {"href": "https://publications.scilifelab.se/researcher/1a412c7369804e06ab648436800db9fe.json"}}, {"family": "Eklund", "given": "D Magnus", "initials": "DM", "orcid": "0000-0002-0576-7636", "researcher": {"href": "https://publications.scilifelab.se/researcher/68452420738e4c97b3e04194eca2d519.json"}}], "type": "journal article", "published": "2021-10-00", "journal": {"title": "New Phytol.", "issn": "1469-8137", "volume": "232", "issue": "2", "pages": "595-609", "issn-l": "0028-646X"}, "abstract": "Previous studies of plant circadian clock evolution have often relied on clock models and genes defined in Arabidopsis. These studies identified homologues with seemingly conserved function, as well as frequent gene loss. In the present study, we aimed to identify candidate clock genes in the liverwort Marchantia polymorpha using a more unbiased approach. To identify genes with circadian rhythm we sequenced the transcriptomes of gemmalings in a time series in constant light conditions. Subsequently, we performed functional studies using loss-of-function mutants and gene expression reporters. Among the genes displaying circadian rhythm, a homologue to the transcriptional co-repressor Arabidopsis DE-ETIOLATED1 showed high amplitude and morning phase. Because AtDET1 is arrhythmic and associated with the morning gene function of AtCCA1/LHY, that lack a homologue in liverworts, we functionally studied DET1 in M. polymorpha. We found that the circadian rhythm of MpDET1 expression is disrupted in loss-of-function mutants of core clock genes and putative evening-complex genes. MpDET1 knock-down in turn results in altered circadian rhythm of nyctinastic thallus movement and clock gene expression. We could not detect any effect of MpDET1 knock-down on circadian response to light, suggesting that MpDET1 has a yet unknown function in the M. polymorpha circadian clock.", "doi": "10.1111/nph.17653", "pmid": "34320227", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2021-12-08T13:48:34.650Z", "modified": "2024-01-16T13:48:38.423Z"}, {"entity": "publication", "iuid": "e2c7e0df97dc45de9a909aafc53e6ff6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e2c7e0df97dc45de9a909aafc53e6ff6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e2c7e0df97dc45de9a909aafc53e6ff6"}}, "title": "ZBED6 regulates Igf2 expression partially through its regulation of miR483 expression.", "authors": [{"family": "Naboulsi", "given": "Rakan", "initials": "R"}, {"family": "Larsson", "given": "M\u00e5rten", "initials": "M"}, {"family": "Andersson", "given": "Leif", "initials": "L", "orcid": "0000-0002-4085-6968", "researcher": {"href": "https://publications.scilifelab.se/researcher/bd3343c12f994b1fabcae23027d3a76d.json"}}, {"family": "Younis", "given": "Shady", "initials": "S"}], "type": "journal article", "published": "2021-09-30", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "11", "issue": "1", "pages": "19484", "issn-l": "2045-2322"}, "abstract": "The expression of Igf2 in mammals shows a complex regulation involving multiple promoters and epigenetic mechanisms. We previously identified a novel regulatory mechanism based on the interaction between the transcriptional factor ZBED6 and Igf2 intron. Disruption of the ZBED6-Igf2 interaction leads to a dramatic up-regulation of IGF2 expression postnatally. In the current study we characterize an additional layer of regulation involving miR483 encoded by another Igf2 intron. We found a highly significant up-regulation of miR483 expression when the ZBED6-Igf2 axis is disrupted in transgenic mice. Furthermore, CRISPR/Cas9 mediated knock-out of miR483 in C2C12 myoblast cells, both wild-type and cells with disrupted ZBED6-Igf2 axis (Igf2dGGCT), resulted in down-regulation of Igf2 expression and a reduced proliferation rate. This was further validated using miR483 mimics and inhibitors. RNA-seq analysis revealed a significant enrichment of genes involved in the PI3K-Akt signaling pathway among genes down-regulated in miR483-/- cells, including Igf2 down-regulation. The opposite pattern was observed in Igf2dGGCT cells, where Igf2 is up-regulated. Our data suggest a positive feedback between miR483 and Igf2 promoter activity, strongly affecting how ZBED6 controls Igf2 expression in various cell types.", "doi": "10.1038/s41598-021-98777-0", "pmid": "34593874", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-021-98777-0"}, {"db": "pmc", "key": "PMC8484269"}], "notes": [], "created": "2022-01-16T20:56:35.213Z", "modified": "2022-01-16T20:56:35.229Z"}, {"entity": "publication", "iuid": "49d38abbaafa466faf21989eac9e3f23", "links": {"self": {"href": "https://publications.scilifelab.se/publication/49d38abbaafa466faf21989eac9e3f23.json"}, "display": {"href": "https://publications.scilifelab.se/publication/49d38abbaafa466faf21989eac9e3f23"}}, "title": "In-depth Phylogenomic Analysis of Arbuscular Mycorrhizal Fungi Based on a Comprehensive Set of de novo Genome Assemblies", "authors": [{"family": "Montoliu-Nerin", "given": "Merce", "initials": "M"}, {"family": "S\u00e1nchez-Garc\u00eda", "given": "Marisol", "initials": "M"}, {"family": "Bergin", "given": "Claudia", "initials": "C"}, {"family": "Kutschera", "given": "Verena Esther", "initials": "VE"}, {"family": "Johannesson", "given": "Hanna", "initials": "H"}, {"family": "Bever", "given": "James D", "initials": "JD"}, {"family": "Rosling", "given": "Anna", "initials": "A"}], "type": "journal-article", "published": "2021-09-29", "journal": {"title": "Front. Fungal Biol.", "issn": "2673-6128", "issn-l": null, "volume": "2", "issue": null, "pages": null}, "abstract": null, "doi": "10.3389/ffunb.2021.716385", "pmid": null, "labels": {"Microbial Single Cell Genomics": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [], "notes": [], "created": "2021-10-20T07:55:39.002Z", "modified": "2024-01-16T13:48:38.431Z"}, {"entity": "publication", "iuid": "1fafeea0c1fc4b21b45c073667f92be3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1fafeea0c1fc4b21b45c073667f92be3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1fafeea0c1fc4b21b45c073667f92be3"}}, "title": "Avian neo-sex chromosomes reveal dynamics of recombination suppression and W degeneration.", "authors": [{"family": "Sigeman", "given": "Hanna", "initials": "H", "orcid": "0000-0002-1457-4174", "researcher": {"href": "https://publications.scilifelab.se/researcher/f75fea472d1d495a92228c50bd63891e.json"}}, {"family": "Strandh", "given": "Maria", "initials": "M"}, {"family": "Proux-W\u00e9ra", "given": "Estelle", "initials": "E"}, {"family": "Kutschera", "given": "Verena E", "initials": "VE"}, {"family": "Ponnikas", "given": "Suvi", "initials": "S"}, {"family": "Zhang", "given": "Hongkai", "initials": "H"}, {"family": "Lundberg", "given": "Max", "initials": "M"}, {"family": "Soler", "given": "Lucile", "initials": "L"}, {"family": "Bunikis", "given": "Ignas", "initials": "I"}, {"family": "Tarka", "given": "Maja", "initials": "M"}, {"family": "Hasselquist", "given": "Dennis", "initials": "D"}, {"family": "Nystedt", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Westerdahl", "given": "Helena", "initials": "H"}, {"family": "Hansson", "given": "Bengt", "initials": "B", "orcid": "0000-0001-6694-8169", "researcher": {"href": "https://publications.scilifelab.se/researcher/01f0144e207c41dcbc4d5aec68690e4b.json"}}], "type": "journal article", "published": "2021-09-20", "journal": {"title": "Mol. Biol. Evol.", "issn": "1537-1719", "issn-l": "0737-4038", "volume": "38", "issue": "12", "pages": "5275-5291"}, "abstract": "How the avian sex chromosomes first evolved from autosomes remains elusive as 100 million years (Myr) of divergence and degeneration obscure their evolutionary history. The Sylvioidea group of songbirds is interesting for understanding avian sex chromosome evolution because a chromosome fusion event \u223c24 Myr ago formed \"neo-sex chromosomes\" consisting of an added (new) and an ancestral (old) part. Here, we report the complete female genome (ZW) of one Sylvioidea species, the great reed warbler (Acrocephalus arundinaceus). Our long-read assembly shows that the added region has been translocated to both Z and W, and while the added-Z has remained its gene order the added-W part has been heavily rearranged. Phylogenetic analyses show that recombination between the homologous added-Z and -W regions continued after the fusion event, and that recombination suppression across this region took several million years to be completed. Moreover, recombination suppression was initiated across multiple positions over the added-Z, which is not consistent with a simple linear progression starting from the fusion point. As expected following recombination suppression, the added-W show signs of degeneration including repeat accumulation and gene loss. Finally, we present evidence for non-random maintenance of slowly evolving and dosage-sensitive genes on both ancestral- and added-W, a process causing correlated evolution among orthologous genes across broad taxonomic groups, regardless of sex-linkage.", "doi": "10.1093/molbev/msab277", "pmid": "34542640", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "NGI Uppsala (Uppsala Genome Center)": "Collaborative", "National Genomics Infrastructure": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Short read": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "6372697"}], "notes": [], "created": "2021-10-29T14:04:51.682Z", "modified": "2024-01-16T13:48:38.463Z"}, {"entity": "publication", "iuid": "4f73084862574e6a8c628f2ab94e8780", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4f73084862574e6a8c628f2ab94e8780.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4f73084862574e6a8c628f2ab94e8780"}}, "title": "Dual RNA-seq transcriptome analysis of caecal tissue during primary Eimeria tenella infection in chickens.", "authors": [{"family": "Sandholt", "given": "Arnar K S", "initials": "AKS"}, {"family": "Wattrang", "given": "Eva", "initials": "E"}, {"family": "Lilja", "given": "Tobias", "initials": "T"}, {"family": "Ahola", "given": "Harri", "initials": "H"}, {"family": "Lund\u00e9n", "given": "Anna", "initials": "A"}, {"family": "Troell", "given": "Karin", "initials": "K"}, {"family": "Sv\u00e4rd", "given": "Staffan G", "initials": "SG"}, {"family": "S\u00f6derlund", "given": "Robert", "initials": "R"}], "type": "journal article", "published": "2021-09-14", "journal": {"title": "BMC Genomics", "issn": "1471-2164", "volume": "22", "issue": "1", "pages": "660", "issn-l": "1471-2164"}, "abstract": "Coccidiosis is an infectious disease with large negative impact on the poultry industry worldwide. It is an enteric infection caused by unicellular Apicomplexan parasites of the genus Eimeria. The present study aimed to gain more knowledge about interactions between parasites and the host immune system during the early asexual replication phase of E. tenella in chicken caeca. For this purpose, chickens were experimentally infected with E. tenella oocysts, sacrificed on days 1-4 and 10 after infection and mRNA from caecal tissues was extracted and sequenced.\n\nDual RNA-seq analysis revealed time-dependent changes in both host and parasite gene expression during the course of the infection. Chicken immune activation was detected from day 3 and onwards with the highest number of differentially expressed immune genes recorded on day 10. Among early (days 3-4) responses up-regulation of genes for matrix metalloproteinases, several chemokines, interferon (IFN)-\u03b3 along with IFN-stimulated genes GBP, IRF1 and RSAD2 were noted. Increased expression of genes with immune suppressive/regulatory effects, e.g. IL10, SOCS1, SOCS3, was also observed among early responses. For E. tenella a general up-regulation of genes involved in protein expression and energy metabolism as well as a general down-regulation genes for DNA and RNA processing were observed during the infection. Specific E. tenella genes with altered expression during the experiment include those for proteins in rhoptry and microneme organelles.\n\nThe present study provides novel information on both the transcriptional activity of E. tenella during schizogony in ceacal tissue and of the local host responses to parasite invasion during this phase of infection. Results indicate a role for IFN-\u03b3 and IFN-stimulated genes in the innate defence against Eimeria replication.", "doi": "10.1186/s12864-021-07959-7", "pmid": "34521339", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1186/s12864-021-07959-7"}, {"db": "pmc", "key": "PMC8438895"}], "notes": [], "created": "2021-12-08T13:53:57.547Z", "modified": "2024-01-16T13:48:38.495Z"}, {"entity": "publication", "iuid": "6f70e1a8af3e47a5a3fa4fba74483b35", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6f70e1a8af3e47a5a3fa4fba74483b35.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6f70e1a8af3e47a5a3fa4fba74483b35"}}, "title": "The avian W chromosome is a refugium for endogenous retroviruses with likely effects on female-biased mutational load and genetic incompatibilities.", "authors": [{"family": "Peona", "given": "Valentina", "initials": "V", "orcid": "0000-0001-5119-1837", "researcher": {"href": "https://publications.scilifelab.se/researcher/d4903a935025452f88e4f1c02483829b.json"}}, {"family": "Palacios-Gimenez", "given": "Octavio M", "initials": "OM", "orcid": "0000-0002-1472-9949", "researcher": {"href": "https://publications.scilifelab.se/researcher/f90e29ecd5724ff19509983e65891915.json"}}, {"family": "Blommaert", "given": "Julie", "initials": "J", "orcid": "0000-0003-1411-2313", "researcher": {"href": "https://publications.scilifelab.se/researcher/761067515ad240c9b82f0ea7625b1320.json"}}, {"family": "Liu", "given": "Jing", "initials": "J"}, {"family": "Haryoko", "given": "Tri", "initials": "T", "orcid": "0000-0002-8549-3662", "researcher": {"href": "https://publications.scilifelab.se/researcher/5e409936447e49ef9cb6fe1c75417fb0.json"}}, {"family": "J\u00f8nsson", "given": "Knud A", "initials": "KA", "orcid": "0000-0002-1875-9504", "researcher": {"href": "https://publications.scilifelab.se/researcher/ca007307f40c49d2baa3420c3fc61d02.json"}}, {"family": "Irestedt", "given": "Martin", "initials": "M", "orcid": "0000-0003-1680-6861", "researcher": {"href": "https://publications.scilifelab.se/researcher/f390f09c31994a01a88d8e0d82c01ce6.json"}}, {"family": "Zhou", "given": "Qi", "initials": "Q", "orcid": "0000-0002-7419-2047", "researcher": {"href": "https://publications.scilifelab.se/researcher/a69266aa587d4126a23aa91c5bedfff8.json"}}, {"family": "Jern", "given": "Patric", "initials": "P", "orcid": "0000-0003-3393-5825", "researcher": {"href": "https://publications.scilifelab.se/researcher/8baed28572fd470ba1e7b18fccd2e275.json"}}, {"family": "Suh", "given": "Alexander", "initials": "A", "orcid": "0000-0002-8979-9992", "researcher": {"href": "https://publications.scilifelab.se/researcher/4e39e1313d894596a6c4ed949e43e019.json"}}], "type": "journal article", "published": "2021-09-13", "journal": {"title": "Philos. Trans. R. Soc. Lond., B, Biol. Sci.", "issn": "1471-2970", "issn-l": "0962-8436", "volume": "376", "issue": "1833", "pages": "20200186"}, "abstract": "It is a broadly observed pattern that the non-recombining regions of sex-limited chromosomes (Y and W) accumulate more repeats than the rest of the genome, even in species like birds with a low genome-wide repeat content. Here, we show that in birds with highly heteromorphic sex chromosomes, the W chromosome has a transposable element (TE) density of greater than 55% compared to the genome-wide density of less than 10%, and contains over half of all full-length (thus potentially active) endogenous retroviruses (ERVs) of the entire genome. Using RNA-seq and protein mass spectrometry data, we were able to detect signatures of female-specific ERV expression. We hypothesize that the avian W chromosome acts as a refugium for active ERVs, probably leading to female-biased mutational load that may influence female physiology similar to the 'toxic-Y' effect in Drosophila males. Furthermore, Haldane's rule predicts that the heterogametic sex has reduced fertility in hybrids. We propose that the excess of W-linked active ERVs over the rest of the genome may be an additional explanatory variable for Haldane's rule, with consequences for genetic incompatibilities between species through TE/repressor mismatches in hybrids. Together, our results suggest that the sequence content of female-specific W chromosomes can have effects far beyond sex determination and gene dosage. This article is part of the theme issue 'Challenging the paradigm in sex chromosome evolution: empirical and theoretical insights with a focus on vertebrates (Part II)'.", "doi": "10.1098/rstb.2020.0186", "pmid": "34304594", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC8310711"}, {"db": "figshare", "key": "10.6084/m9.figshare.c.5450746"}], "notes": [], "created": "2021-10-01T09:03:22.481Z", "modified": "2024-01-16T13:48:38.503Z"}, {"entity": "publication", "iuid": "1f113046713249708a4fafa69935a04e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1f113046713249708a4fafa69935a04e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1f113046713249708a4fafa69935a04e"}}, "title": "Temporally balanced selection during development of larval Pacific oysters (Crassostrea gigas) inherently preserves genetic diversity within offspring.", "authors": [{"family": "Durland", "given": "Evan", "initials": "E", "orcid": "0000-0003-1322-6810", "researcher": {"href": "https://publications.scilifelab.se/researcher/95291dd15b084ed08c777fd2ff01f6de.json"}}, {"family": "De Wit", "given": "Pierre", "initials": "P", "orcid": "0000-0003-4709-3438", "researcher": {"href": "https://publications.scilifelab.se/researcher/95b69d4724ce4b69819c0a1578cd56eb.json"}}, {"family": "Langdon", "given": "Chris", "initials": "C"}], "type": "journal article", "published": "2021-09-08", "journal": {"title": "Proc. Biol. Sci.", "issn": "1471-2954", "volume": "288", "issue": "1958", "pages": "20203223", "issn-l": "0962-8452"}, "abstract": "Balancing selection is one of the mechanisms which has been proposed to explain the maintenance of genetic diversity in species across generations. For species with large populations and complex life histories, however, heterogeneous selection pressures may create a scenario in which the net effects of selection are balanced across developmental stages. With replicated cultures and a pooled sequencing approach, we show that genotype-dependent mortality in larvae of the Pacific oyster (Crassostrea gigas) is largely temporally dynamic and inconsistently in favour of a single genotype or allelic variant at each locus. Overall, the patterns of genetic change we observe to be taking place are more complex than what would be expected under classical examples of additive or dominant genetic interactions. They are also not easily explained by our current understanding of the effects of genetic load. Collectively, temporally heterogeneous selection pressures across different larval developmental stages may act to maintain genetic diversity, while also inherently sheltering genetic load within oyster populations.", "doi": "10.1098/rspb.2020.3223", "pmid": "34465244", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC8437028"}, {"db": "Dryad", "key": "10.5061/dryad.2z34tmpn5"}, {"db": "figshare", "key": "10.6084/m9.figshare.c.5571376"}], "notes": [], "created": "2021-12-10T14:54:29.625Z", "modified": "2021-12-10T14:54:29.708Z"}, {"entity": "publication", "iuid": "b28943ea48e64a49b14732c0033cd621", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b28943ea48e64a49b14732c0033cd621.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b28943ea48e64a49b14732c0033cd621"}}, "title": "Toward best practice in cancer mutation detection with whole-genome and whole-exome sequencing.", "authors": [{"family": "Xiao", "given": "Wenming", "initials": "W", "orcid": "0000-0003-4096-9724", "researcher": {"href": "https://publications.scilifelab.se/researcher/633df103f81f4142ace7a3763b56af54.json"}}, {"family": "Ren", "given": "Luyao", "initials": "L"}, {"family": "Chen", "given": "Zhong", "initials": "Z", "orcid": "0000-0003-2444-8216", "researcher": {"href": "https://publications.scilifelab.se/researcher/32a2952ea73345708fb30f2fdb331030.json"}}, {"family": "Fang", "given": "Li Tai", "initials": "LT", "orcid": "0000-0003-3201-5162", "researcher": {"href": "https://publications.scilifelab.se/researcher/b580a1ef08e04613adc5824605d9d442.json"}}, {"family": "Zhao", "given": "Yongmei", "initials": "Y", "orcid": "0000-0003-0800-4658", "researcher": {"href": "https://publications.scilifelab.se/researcher/3a5a787c429e416da061067ec701a3b1.json"}}, {"family": "Lack", "given": "Justin", "initials": "J"}, {"family": "Guan", "given": "Meijian", "initials": "M"}, {"family": "Zhu", "given": "Bin", "initials": "B", "orcid": "0000-0003-0172-5516", "researcher": {"href": "https://publications.scilifelab.se/researcher/67eaeee64f3741c58132c76ba8d33d2b.json"}}, {"family": "Jaeger", "given": "Erich", "initials": "E"}, {"family": "Kerrigan", "given": "Liz", "initials": "L"}, {"family": "Blomquist", "given": "Thomas M", "initials": "TM"}, {"family": "Hung", "given": "Tiffany", "initials": "T"}, {"family": "Sultan", "given": "Marc", "initials": "M"}, {"family": "Idler", "given": "Kenneth", "initials": "K"}, {"family": "Lu", "given": "Charles", "initials": "C"}, {"family": "Scherer", "given": "Andreas", "initials": "A", "orcid": "0000-0002-4254-7122", "researcher": {"href": "https://publications.scilifelab.se/researcher/a0fa00ba4b5a443ab92a281ba7ec897d.json"}}, {"family": "Kusko", "given": "Rebecca", "initials": "R", "orcid": "0000-0001-6730-5990", "researcher": {"href": "https://publications.scilifelab.se/researcher/a81dcb197b234869aeb588d5d6270224.json"}}, {"family": "Moos", "given": "Malcolm", "initials": "M"}, {"family": "Xiao", "given": "Chunlin", "initials": "C", "orcid": "0000-0001-8702-4889", "researcher": {"href": "https://publications.scilifelab.se/researcher/8b1a63c56506470cba459c6e60378ba2.json"}}, {"family": "Sherry", "given": "Stephen T", "initials": "ST"}, {"family": "Abaan", "given": "Ogan D", "initials": "OD"}, {"family": "Chen", "given": "Wanqiu", "initials": "W", "orcid": "0000-0003-3706-7834", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff236616beef483ea11661874e91b7d1.json"}}, {"family": "Chen", "given": "Xin", "initials": "X"}, {"family": "Nordlund", "given": "Jessica", "initials": "J"}, {"family": "Liljedahl", "given": "Ulrika", "initials": "U"}, {"family": "Maestro", "given": "Roberta", "initials": "R", "orcid": "0000-0002-6642-5592", "researcher": {"href": "https://publications.scilifelab.se/researcher/d722fdb372d748c3a4a0a5b9fea02b36.json"}}, {"family": "Polano", "given": "Maurizio", "initials": "M"}, {"family": "Drabek", "given": "Jiri", "initials": "J"}, {"family": "Vojta", "given": "Petr", "initials": "P", "orcid": "0000-0003-0036-1853", "researcher": {"href": "https://publications.scilifelab.se/researcher/ed2d113a90ca4afea526bedd0ca871c6.json"}}, {"family": "K\u00f5ks", "given": "Sulev", "initials": "S", "orcid": "0000-0001-6087-6643", "researcher": {"href": "https://publications.scilifelab.se/researcher/dea893f45b1b45a5a92890878fa044e5.json"}}, {"family": "Reimann", "given": "Ene", "initials": "E", "orcid": "0000-0002-5410-4433", "researcher": {"href": "https://publications.scilifelab.se/researcher/25325fa20b3940a6acd1ebd0a58629ef.json"}}, {"family": "Madala", "given": "Bindu Swapna", "initials": "BS"}, {"family": "Mercer", "given": "Timothy", "initials": "T", "orcid": "0000-0001-8780-894X", "researcher": {"href": "https://publications.scilifelab.se/researcher/19d5fd2d39e74c09a0794bfaebe83d7b.json"}}, {"family": "Miller", "given": "Chris", "initials": "C"}, {"family": "Jacob", "given": "Howard", "initials": "H"}, {"family": "Truong", "given": "Tiffany", "initials": "T"}, {"family": "Moshrefi", "given": "Ali", "initials": "A"}, {"family": "Natarajan", "given": "Aparna", "initials": "A"}, {"family": "Granat", "given": "Ana", "initials": "A"}, {"family": "Schroth", "given": "Gary P", "initials": "GP", "orcid": "0000-0002-3055-056X", "researcher": {"href": "https://publications.scilifelab.se/researcher/4bcf10fe362c4775a8e8e49fd189deaa.json"}}, {"family": "Kalamegham", "given": "Rasika", "initials": "R"}, {"family": "Peters", "given": "Eric", "initials": "E"}, {"family": "Petitjean", "given": "Virginie", "initials": "V"}, {"family": "Walton", "given": "Ashley", "initials": "A"}, {"family": "Shen", "given": "Tsai-Wei", "initials": "TW", "orcid": "0000-0001-9644-1748", "researcher": {"href": "https://publications.scilifelab.se/researcher/d4552cb624e84ab58bc6df541408c06e.json"}}, {"family": "Talsania", "given": "Keyur", "initials": "K"}, {"family": "Vera", "given": "Cristobal Juan", "initials": "CJ"}, {"family": "Langenbach", "given": "Kurt", "initials": "K"}, {"family": "de Mars", "given": "Maryellen", "initials": "M"}, {"family": "Hipp", "given": "Jennifer A", "initials": "JA"}, {"family": "Willey", "given": "James C", "initials": "JC"}, {"family": "Wang", "given": "Jing", "initials": "J"}, {"family": "Shetty", "given": "Jyoti", "initials": "J"}, {"family": "Kriga", "given": "Yuliya", "initials": "Y"}, {"family": "Raziuddin", "given": "Arati", "initials": "A", "orcid": "0000-0001-9361-8691", "researcher": {"href": "https://publications.scilifelab.se/researcher/1eeb7daae54a464cb0fd3b7b3c464a1b.json"}}, {"family": "Tran", "given": "Bao", "initials": "B"}, {"family": "Zheng", "given": "Yuanting", "initials": "Y"}, {"family": "Yu", "given": "Ying", "initials": "Y"}, {"family": "Cam", "given": "Margaret", "initials": "M"}, {"family": "Jailwala", "given": "Parthav", "initials": "P"}, {"family": "Nguyen", "given": "Cu", "initials": "C"}, {"family": "Meerzaman", "given": "Daoud", "initials": "D"}, {"family": "Chen", "given": "Qingrong", "initials": "Q"}, {"family": "Yan", "given": "Chunhua", "initials": "C"}, {"family": "Ernest", "given": "Ben", "initials": "B"}, {"family": "Mehra", "given": "Urvashi", "initials": "U"}, {"family": "Jensen", "given": "Roderick V", "initials": "RV"}, {"family": "Jones", "given": "Wendell", "initials": "W", "orcid": "0000-0002-9676-5387", "researcher": {"href": "https://publications.scilifelab.se/researcher/d75368d5a5b64aceb3bf9f2ac39a871a.json"}}, {"family": "Li", "given": "Jian-Liang", "initials": "JL", "orcid": "0000-0002-6487-081X", "researcher": {"href": "https://publications.scilifelab.se/researcher/41c588cc49234eefb8edd53408bbe71b.json"}}, {"family": "Papas", "given": "Brian N", "initials": "BN"}, {"family": "Pirooznia", "given": "Mehdi", "initials": "M", "orcid": "0000-0002-4210-6458", "researcher": {"href": "https://publications.scilifelab.se/researcher/1b65f2a816224c6f91b136a2a6e0ecc0.json"}}, {"family": "Chen", "given": "Yun-Ching", "initials": "YC"}, {"family": "Seifuddin", "given": "Fayaz", "initials": "F", "orcid": "0000-0003-3357-7888", "researcher": {"href": "https://publications.scilifelab.se/researcher/d2eb5599718047bb87bc765a057c9e80.json"}}, {"family": "Li", "given": "Zhipan", "initials": "Z"}, {"family": "Liu", "given": "Xuelu", "initials": "X"}, {"family": "Resch", "given": "Wolfgang", "initials": "W"}, {"family": "Wang", "given": "Jingya", "initials": "J"}, {"family": "Wu", "given": "Leihong", "initials": "L"}, {"family": "Yavas", "given": "Gokhan", "initials": "G"}, {"family": "Miles", "given": "Corey", "initials": "C"}, {"family": "Ning", "given": "Baitang", "initials": "B"}, {"family": "Tong", "given": "Weida", "initials": "W"}, {"family": "Mason", "given": "Christopher E", "initials": "CE", "orcid": "0000-0002-1850-1642", "researcher": {"href": "https://publications.scilifelab.se/researcher/2af4cb8577d34907b22b030f9e79e90e.json"}}, {"family": "Donaldson", "given": "Eric", "initials": "E"}, {"family": "Lababidi", "given": "Samir", "initials": "S"}, {"family": "Staudt", "given": "Louis M", "initials": "LM"}, {"family": "Tezak", "given": "Zivana", "initials": "Z"}, {"family": "Hong", "given": "Huixiao", "initials": "H", "orcid": "0000-0001-8087-3968", "researcher": {"href": "https://publications.scilifelab.se/researcher/158916b8a0cc4a28b2dceb12514d4a88.json"}}, {"family": "Wang", "given": "Charles", "initials": "C", "orcid": "0000-0001-8861-2121", "researcher": {"href": "https://publications.scilifelab.se/researcher/6f245b91838442ef859874ad23d0aae8.json"}}, {"family": "Shi", "given": "Leming", "initials": "L", "orcid": "0000-0002-2981-4150", "researcher": {"href": "https://publications.scilifelab.se/researcher/7389ba41b5f449f6b2f2dc7311235f92.json"}}], "type": "journal article", "published": "2021-09-00", "journal": {"title": "Nat. Biotechnol.", "issn": "1546-1696", "volume": "39", "issue": "9", "pages": "1141-1150", "issn-l": "1087-0156"}, "abstract": "Clinical applications of precision oncology require accurate tests that can distinguish true cancer-specific mutations from errors introduced at each step of next-generation sequencing (NGS). To date, no bulk sequencing study has addressed the effects of cross-site reproducibility, nor the biological, technical and computational factors that influence variant identification. Here we report a systematic interrogation of somatic mutations in paired tumor-normal cell lines to identify factors affecting detection reproducibility and accuracy at six different centers. Using whole-genome sequencing (WGS) and whole-exome sequencing (WES), we evaluated the reproducibility of different sample types with varying input amount and tumor purity, and multiple library construction protocols, followed by processing with nine bioinformatics pipelines. We found that read coverage and callers affected both WGS and WES reproducibility, but WES performance was influenced by insert fragment size, genomic copy content and the global imbalance score (GIV; G > T/C > A). Finally, taking into account library preparation protocol, tumor content, read coverage and bioinformatics processes concomitantly, we recommend actionable practices to improve the reproducibility and accuracy of NGS experiments for cancer mutation detection.", "doi": "10.1038/s41587-021-00994-5", "pmid": "34504346", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Collaborative", "National Genomics Infrastructure": "Collaborative", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41587-021-00994-5"}, {"db": "pmc", "key": "PMC8506910"}, {"db": "mid", "key": "NIHMS1740805"}], "notes": [], "created": "2021-09-13T06:39:01.703Z", "modified": "2024-01-16T13:48:38.567Z"}, {"entity": "publication", "iuid": "645dc13f41284da3a7f99f28a785e7e5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/645dc13f41284da3a7f99f28a785e7e5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/645dc13f41284da3a7f99f28a785e7e5"}}, "title": "The genetic consequences of dog breed formation-Accumulation of deleterious genetic variation and fixation of mutations associated with myxomatous mitral valve disease in cavalier King Charles spaniels.", "authors": [{"family": "Axelsson", "given": "Erik", "initials": "E", "orcid": "0000-0001-6748-5450", "researcher": {"href": "https://publications.scilifelab.se/researcher/36430335097c4864b97539aa8bd1d6f1.json"}}, {"family": "Ljungvall", "given": "Ingrid", "initials": "I", "orcid": "0000-0002-6617-0454", "researcher": {"href": "https://publications.scilifelab.se/researcher/12b19ecb541c4d13a685b574390e8104.json"}}, {"family": "Bhoumik", "given": "Priyasma", "initials": "P", "orcid": "0000-0002-0698-5213", "researcher": {"href": "https://publications.scilifelab.se/researcher/658bd7e9fa2544d4b074bbf3b398ee2d.json"}}, {"family": "Conn", "given": "Laura Bas", "initials": "LB", "orcid": "0000-0003-3063-7160", "researcher": {"href": "https://publications.scilifelab.se/researcher/0b2f8d9874f24dc48cbff4a22bc521e9.json"}}, {"family": "Muren", "given": "Eva", "initials": "E"}, {"family": "Ohlsson", "given": "\u00c5sa", "initials": "\u00c5", "orcid": "0000-0003-1116-0141", "researcher": {"href": "https://publications.scilifelab.se/researcher/91d12e64d2d740669ec499319b66c22e.json"}}, {"family": "Olsen", "given": "Lisbeth H\u00f8ier", "initials": "LH", "orcid": "0000-0002-0292-3111", "researcher": {"href": "https://publications.scilifelab.se/researcher/0ad86fe9b2c14f8a8cabce67fd97836a.json"}}, {"family": "Engdahl", "given": "Karolina", "initials": "K", "orcid": "0000-0003-2800-9990", "researcher": {"href": "https://publications.scilifelab.se/researcher/eae1015240ea4637ade953b6c6ffa084.json"}}, {"family": "Hagman", "given": "Ragnvi", "initials": "R", "orcid": "0000-0002-9853-4558", "researcher": {"href": "https://publications.scilifelab.se/researcher/5192e729c95c4653b1f3b258187ef5cc.json"}}, {"family": "Hanson", "given": "Jeanette", "initials": "J", "orcid": "0000-0001-5596-9538", "researcher": {"href": "https://publications.scilifelab.se/researcher/126ddee571444a5aaac298e3d60b7e49.json"}}, {"family": "Kryvokhyzha", "given": "Dmytro", "initials": "D", "orcid": "0000-0001-6498-1977", "researcher": {"href": "https://publications.scilifelab.se/researcher/a3ca1c441506436282871ecd40f7be35.json"}}, {"family": "Pettersson", "given": "Mats", "initials": "M", "orcid": "0000-0002-7372-9076", "researcher": {"href": "https://publications.scilifelab.se/researcher/27011c7fbb8a44dda536a4fc876675b0.json"}}, {"family": "Grenet", "given": "Olivier", "initials": "O"}, {"family": "Moggs", "given": "Jonathan", "initials": "J"}, {"family": "Del Rio-Espinola", "given": "Alberto", "initials": "A"}, {"family": "Epe", "given": "Christian", "initials": "C", "orcid": "0000-0001-9144-0930", "researcher": {"href": "https://publications.scilifelab.se/researcher/cdce7e5c483c43258c5082610ef46125.json"}}, {"family": "Taillon", "given": "Bruce", "initials": "B", "orcid": "0000-0002-2124-7921", "researcher": {"href": "https://publications.scilifelab.se/researcher/a2f6bdb3c1404cc88eb2771d2bb4d3fe.json"}}, {"family": "Tawari", "given": "Nilesh", "initials": "N", "orcid": "0000-0002-1127-0765", "researcher": {"href": "https://publications.scilifelab.se/researcher/03aaffb62f14402a8bc51a9e00029188.json"}}, {"family": "Mane", "given": "Shrinivas", "initials": "S", "orcid": "0000-0003-4123-624X", "researcher": {"href": "https://publications.scilifelab.se/researcher/7434a83edf4a400a8bd52a84391edfbb.json"}}, {"family": "Hawkins", "given": "Troy", "initials": "T", "orcid": "0000-0002-6982-5014", "researcher": {"href": "https://publications.scilifelab.se/researcher/c649726ebbd14f93a19740206d26fd7f.json"}}, {"family": "Hedhammar", "given": "\u00c5ke", "initials": "\u00c5"}, {"family": "Gruet", "given": "Philippe", "initials": "P"}, {"family": "H\u00e4ggstr\u00f6m", "given": "Jens", "initials": "J", "orcid": "0000-0003-3402-023X", "researcher": {"href": "https://publications.scilifelab.se/researcher/5e1779188e20402294f12861a8232e71.json"}}, {"family": "Lindblad-Toh", "given": "Kerstin", "initials": "K"}], "type": "journal article", "published": "2021-09-00", "journal": {"title": "PLoS Genet.", "issn": "1553-7404", "volume": "17", "issue": "9", "pages": "e1009726", "issn-l": "1553-7390"}, "abstract": "Selective breeding for desirable traits in strictly controlled populations has generated an extraordinary diversity in canine morphology and behaviour, but has also led to loss of genetic variation and random entrapment of disease alleles. As a consequence, specific diseases are now prevalent in certain breeds, but whether the recent breeding practice led to an overall increase in genetic load remains unclear. Here we generate whole genome sequencing (WGS) data from 20 dogs per breed from eight breeds and document a ~10% rise in the number of derived alleles per genome at evolutionarily conserved sites in the heavily bottlenecked cavalier King Charles spaniel breed (cKCs) relative to in most breeds studied here. Our finding represents the first clear indication of a relative increase in levels of deleterious genetic variation in a specific breed, arguing that recent breeding practices probably were associated with an accumulation of genetic load in dogs. We then use the WGS data to identify candidate risk alleles for the most common cause for veterinary care in cKCs-the heart disease myxomatous mitral valve disease (MMVD). We verify a potential link to MMVD for candidate variants near the heart specific NEBL gene in a dachshund population and show that two of the NEBL candidate variants have regulatory potential in heart-derived cell lines and are associated with reduced NEBL isoform nebulette expression in papillary muscle (but not in mitral valve, nor in left ventricular wall). Alleles linked to reduced nebulette expression may hence predispose cKCs and other breeds to MMVD via loss of papillary muscle integrity.", "doi": "10.1371/journal.pgen.1009726", "pmid": "34473707", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "PGENETICS-D-21-00373"}, {"db": "pmc", "key": "PMC8412370"}], "notes": [], "created": "2021-09-13T06:41:47.658Z", "modified": "2024-01-16T13:48:38.576Z"}, {"entity": "publication", "iuid": "3f41da8f8fce4eea80f6148233aa9ae8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3f41da8f8fce4eea80f6148233aa9ae8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3f41da8f8fce4eea80f6148233aa9ae8"}}, "title": "Positive selection plays a major role in shaping signatures of differentiation across the genomic landscape of two independent Ficedula flycatcher species pairs.", "authors": [{"family": "Chase", "given": "Madeline A", "initials": "MA", "orcid": "0000-0002-7916-3560", "researcher": {"href": "https://publications.scilifelab.se/researcher/3053121df4b64418bc1dcc2d7e50d87c.json"}}, {"family": "Ellegren", "given": "Hans", "initials": "H"}, {"family": "Mugal", "given": "Carina F", "initials": "CF"}], "type": "journal article", "published": "2021-09-00", "journal": {"title": "Evolution", "issn": "1558-5646", "issn-l": "0014-3820", "volume": "75", "issue": "9", "pages": "2179-2196"}, "abstract": "A current debate within population genomics surrounds the relevance of patterns of genomic differentiation between closely related species for our understanding of adaptation and speciation. Mounting evidence across many taxa suggests that the same genomic regions repeatedly develop elevated differentiation in independent species pairs. These regions often coincide with high gene density and/or low recombination, leading to the hypothesis that the genomic differentiation landscape mostly reflects a history of background selection, and reveals little about adaptation or speciation. A comparative genomics approach with multiple independent species pairs at a timescale where gene flow and ILS are negligible permits investigating whether different evolutionary processes are responsible for generating lineage-specific versus shared patterns of species differentiation. We use whole-genome resequencing data of 195 individuals from four Ficedula flycatcher species comprising two independent species pairs: collared and pied flycatchers, and red-breasted and taiga flycatchers. We found that both shared and lineage-specific FST peaks could partially be explained by selective sweeps, with recurrent selection likely to underlie shared signatures of selection, whereas indirect evidence supports a role of recombination landscape evolution in driving lineage-specific signatures of selection. This work therefore provides evidence for an interplay of positive selection and recombination to genomic landscape evolution.", "doi": "10.1111/evo.14234", "pmid": "33851440", "labels": {"Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support and Infrastructure": "Service", "National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "Dryad", "key": "10.5061/dryad.n2z34tmw6"}], "notes": [], "created": "2021-12-02T14:05:48.724Z", "modified": "2024-01-16T13:48:38.584Z"}, {"entity": "publication", "iuid": "9e5836ea464143e5ba4a0f2b0cc29cb3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9e5836ea464143e5ba4a0f2b0cc29cb3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9e5836ea464143e5ba4a0f2b0cc29cb3"}}, "title": "Interaction between the STAT4 rs11889341(T) risk allele and smoking confers increased risk of myocardial infarction and nephritis in patients with systemic lupus erythematosus.", "authors": [{"family": "Reid", "given": "Sarah", "initials": "S", "orcid": "0000-0003-4065-6875", "researcher": {"href": "https://publications.scilifelab.se/researcher/689ab046bc19433483d502284d2c51c4.json"}}, {"family": "Hagberg", "given": "Niklas", "initials": "N", "orcid": "0000-0003-2064-2716", "researcher": {"href": "https://publications.scilifelab.se/researcher/0d0998bb419c424083b0978ebdbe8629.json"}}, {"family": "Sandling", "given": "Johanna K", "initials": "JK", "orcid": "0000-0003-1382-2321", "researcher": {"href": "https://publications.scilifelab.se/researcher/9c7bae5a05ac47eeac96547ca7336767.json"}}, {"family": "Alexsson", "given": "Andrei", "initials": "A"}, {"family": "Pucholt", "given": "Pascal", "initials": "P", "orcid": "0000-0003-3342-1373", "researcher": {"href": "https://publications.scilifelab.se/researcher/61a214ff2d494b568cb6da944e858acf.json"}}, {"family": "Sj\u00f6wall", "given": "Christopher", "initials": "C", "orcid": "0000-0003-0900-2048", "researcher": {"href": "https://publications.scilifelab.se/researcher/fe4dd47b8ca1436e8a26fdea33f5e7f6.json"}}, {"family": "Lerang", "given": "Karoline", "initials": "K"}, {"family": "J\u00f6nsen", "given": "Andreas", "initials": "A"}, {"family": "Gunnarsson", "given": "Iva", "initials": "I"}, {"family": "Syv\u00e4nen", "given": "Ann-Christine", "initials": "AC"}, {"family": "Troldborg", "given": "Anne Margrethe", "initials": "AM"}, {"family": "Voss", "given": "Anne", "initials": "A"}, {"family": "Bengtsson", "given": "Anders A", "initials": "AA"}, {"family": "Molberg", "given": "\u00d8yvind", "initials": "\u00d8"}, {"family": "Jacobsen", "given": "S\u00f8ren", "initials": "S"}, {"family": "Svenungsson", "given": "Elisabet", "initials": "E", "orcid": "0000-0003-3396-3244", "researcher": {"href": "https://publications.scilifelab.se/researcher/0ab5989c3c604a96bf42b1b6f90434a0.json"}}, {"family": "R\u00f6nnblom", "given": "Lars", "initials": "L", "orcid": "0000-0001-9403-6503", "researcher": {"href": "https://publications.scilifelab.se/researcher/053ed3b657124a1bab3a78dc685556e6.json"}}, {"family": "Leonard", "given": "Dag", "initials": "D"}], "type": "journal article", "published": "2021-09-00", "journal": {"title": "Ann. Rheum. Dis.", "issn": "1468-2060", "issn-l": "0003-4967", "volume": "80", "issue": "9", "pages": "1183-1189"}, "abstract": "To investigate how genetics influence the risk of smoking-related systemic lupus erythematosus (SLE) manifestations.\n\nPatients with SLE (ndiscovery cohort=776, nreplication cohort=836) were genotyped using the 200K Immunochip single nucleotide polymorphisms (SNP) Array (Illumina) and a custom array. Sixty SNPs with SLE association (p<5.0\u00d710-8) were analysed. Signal transducer and activator of transcription 4 (STAT4) activation was assessed in in vitro stimulated peripheral blood mononuclear cells from healthy controls (n=45).\n\nIn the discovery cohort, smoking was associated with myocardial infarction (MI) (OR 1.96 (95% CI 1.09 to 3.55)), with a greater effect in patients carrying any rs11889341 STAT4 risk allele (OR 2.72 (95% CI 1.24 to 6.00)) or two risk alleles (OR 8.27 (95% CI 1.48 to 46.27)).Smokers carrying the risk allele also displayed an increased risk of nephritis (OR 1.47 (95% CI 1.06 to 2.03)). In the replication cohort, the high risk of MI in smokers carrying the risk allele and the association between the STAT4 risk allele and nephritis in smokers were confirmed (OR 6.19 (95% CI 1.29 to 29.79) and 1.84 (95% CI 1.05 to 3.29), respectively).The interaction between smoking and the STAT4 risk allele resulted in further increase in the risk of MI (OR 2.14 (95% CI 1.01 to 4.62)) and nephritis (OR 1.53 (95% CI 1.08 to 2.17)), with 54% (MI) and 34% (nephritis) of the risk attributable to the interaction. Levels of interleukin-12-induced phosphorylation of STAT4 in CD8+ T cells were higher in smokers than in non-smokers (mean geometric fluorescence intensity 1063 vs 565, p=0.0063).Lastly, the IL12A rs564799 risk allele displayed association with MI in both cohorts (OR 1.53 (95% CI 1.01 to 2.31) and 2.15 (95% CI 1.08 to 4.26), respectively).\n\nSmoking in the presence of the STAT4 risk gene variant appears to increase the risk of MI and nephritis in SLE. Our results also highlight the role of the IL12-STAT4 pathway in SLE-cardiovascular morbidity.", "doi": "10.1136/annrheumdis-2020-219727", "pmid": "33766895", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "annrheumdis-2020-219727"}, {"db": "pmc", "key": "PMC8372395"}], "notes": [], "created": "2021-04-08T14:44:05.247Z", "modified": "2024-01-16T13:48:38.594Z"}, {"entity": "publication", "iuid": "fdb75d5c468f48ef8993915d18f13b5d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/fdb75d5c468f48ef8993915d18f13b5d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/fdb75d5c468f48ef8993915d18f13b5d"}}, "title": "Establishing community reference samples, data and call sets for benchmarking cancer mutation detection using whole-genome sequencing.", "authors": [{"family": "Fang", "given": "Li Tai", "initials": "LT", "orcid": "0000-0003-3201-5162", "researcher": {"href": "https://publications.scilifelab.se/researcher/b580a1ef08e04613adc5824605d9d442.json"}}, {"family": "Zhu", "given": "Bin", "initials": "B", "orcid": "0000-0003-0172-5516", "researcher": {"href": "https://publications.scilifelab.se/researcher/67eaeee64f3741c58132c76ba8d33d2b.json"}}, {"family": "Zhao", "given": "Yongmei", "initials": "Y", "orcid": "0000-0003-0800-4658", "researcher": {"href": "https://publications.scilifelab.se/researcher/3a5a787c429e416da061067ec701a3b1.json"}}, {"family": "Chen", "given": "Wanqiu", "initials": "W", "orcid": "0000-0003-3706-7834", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff236616beef483ea11661874e91b7d1.json"}}, {"family": "Yang", "given": "Zhaowei", "initials": "Z", "orcid": "0000-0002-1805-4360", "researcher": {"href": "https://publications.scilifelab.se/researcher/d44c90c628d545268666f92531fb66c4.json"}}, {"family": "Kerrigan", "given": "Liz", "initials": "L"}, {"family": "Langenbach", "given": "Kurt", "initials": "K"}, {"family": "de Mars", "given": "Maryellen", "initials": "M"}, {"family": "Lu", "given": "Charles", "initials": "C"}, {"family": "Idler", "given": "Kenneth", "initials": "K"}, {"family": "Jacob", "given": "Howard", "initials": "H"}, {"family": "Zheng", "given": "Yuanting", "initials": "Y"}, {"family": "Ren", "given": "Luyao", "initials": "L"}, {"family": "Yu", "given": "Ying", "initials": "Y"}, {"family": "Jaeger", "given": "Erich", "initials": "E"}, {"family": "Schroth", "given": "Gary P", "initials": "GP", "orcid": "0000-0002-3055-056X", "researcher": {"href": "https://publications.scilifelab.se/researcher/4bcf10fe362c4775a8e8e49fd189deaa.json"}}, {"family": "Abaan", "given": "Ogan D", "initials": "OD"}, {"family": "Talsania", "given": "Keyur", "initials": "K"}, {"family": "Lack", "given": "Justin", "initials": "J"}, {"family": "Shen", "given": "Tsai-Wei", "initials": "TW", "orcid": "0000-0001-9644-1748", "researcher": {"href": "https://publications.scilifelab.se/researcher/d4552cb624e84ab58bc6df541408c06e.json"}}, {"family": "Chen", "given": "Zhong", "initials": "Z", "orcid": "0000-0003-2444-8216", "researcher": {"href": "https://publications.scilifelab.se/researcher/32a2952ea73345708fb30f2fdb331030.json"}}, {"family": "Stanbouly", "given": "Seta", "initials": "S"}, {"family": "Tran", "given": "Bao", "initials": "B"}, {"family": "Shetty", "given": "Jyoti", "initials": "J"}, {"family": "Kriga", "given": "Yuliya", "initials": "Y"}, {"family": "Meerzaman", "given": "Daoud", "initials": "D"}, {"family": "Nguyen", "given": "Cu", "initials": "C"}, {"family": "Petitjean", "given": "Virginie", "initials": "V"}, {"family": "Sultan", "given": "Marc", "initials": "M"}, {"family": "Cam", "given": "Margaret", "initials": "M"}, {"family": "Mehta", "given": "Monika", "initials": "M", "orcid": "0000-0003-3928-3733", "researcher": {"href": "https://publications.scilifelab.se/researcher/ad52c831763d4e1c85e373918efd5b53.json"}}, {"family": "Hung", "given": "Tiffany", "initials": "T"}, {"family": "Peters", "given": "Eric", "initials": "E"}, {"family": "Kalamegham", "given": "Rasika", "initials": "R"}, {"family": "Sahraeian", "given": "Sayed Mohammad Ebrahim", "initials": "SME"}, {"family": "Mohiyuddin", "given": "Marghoob", "initials": "M"}, {"family": "Guo", "given": "Yunfei", "initials": "Y"}, {"family": "Yao", "given": "Lijing", "initials": "L"}, {"family": "Song", "given": "Lei", "initials": "L"}, {"family": "Lam", "given": "Hugo Y K", "initials": "HYK"}, {"family": "Drabek", "given": "Jiri", "initials": "J"}, {"family": "Vojta", "given": "Petr", "initials": "P", "orcid": "0000-0003-0036-1853", "researcher": {"href": "https://publications.scilifelab.se/researcher/ed2d113a90ca4afea526bedd0ca871c6.json"}}, {"family": "Maestro", "given": "Roberta", "initials": "R", "orcid": "0000-0002-6642-5592", "researcher": {"href": "https://publications.scilifelab.se/researcher/d722fdb372d748c3a4a0a5b9fea02b36.json"}}, {"family": "Gasparotto", "given": "Daniela", "initials": "D"}, {"family": "K\u00f5ks", "given": "Sulev", "initials": "S", "orcid": "0000-0001-6087-6643", "researcher": {"href": "https://publications.scilifelab.se/researcher/dea893f45b1b45a5a92890878fa044e5.json"}}, {"family": "Reimann", "given": "Ene", "initials": "E", "orcid": "0000-0002-5410-4433", "researcher": {"href": "https://publications.scilifelab.se/researcher/25325fa20b3940a6acd1ebd0a58629ef.json"}}, {"family": "Scherer", "given": "Andreas", "initials": "A", "orcid": "0000-0002-4254-7122", "researcher": {"href": "https://publications.scilifelab.se/researcher/a0fa00ba4b5a443ab92a281ba7ec897d.json"}}, {"family": "Nordlund", "given": "Jessica", "initials": "J"}, {"family": "Liljedahl", "given": "Ulrika", "initials": "U"}, {"family": "Jensen", "given": "Roderick V", "initials": "RV"}, {"family": "Pirooznia", "given": "Mehdi", "initials": "M", "orcid": "0000-0002-4210-6458", "researcher": {"href": "https://publications.scilifelab.se/researcher/1b65f2a816224c6f91b136a2a6e0ecc0.json"}}, {"family": "Li", "given": "Zhipan", "initials": "Z"}, {"family": "Xiao", "given": "Chunlin", "initials": "C", "orcid": "0000-0001-8702-4889", "researcher": {"href": "https://publications.scilifelab.se/researcher/8b1a63c56506470cba459c6e60378ba2.json"}}, {"family": "Sherry", "given": "Stephen T", "initials": "ST"}, {"family": "Kusko", "given": "Rebecca", "initials": "R", "orcid": "0000-0001-6730-5990", "researcher": {"href": "https://publications.scilifelab.se/researcher/a81dcb197b234869aeb588d5d6270224.json"}}, {"family": "Moos", "given": "Malcolm", "initials": "M"}, {"family": "Donaldson", "given": "Eric", "initials": "E"}, {"family": "Tezak", "given": "Zivana", "initials": "Z"}, {"family": "Ning", "given": "Baitang", "initials": "B"}, {"family": "Tong", "given": "Weida", "initials": "W"}, {"family": "Li", "given": "Jing", "initials": "J"}, {"family": "Duerken-Hughes", "given": "Penelope", "initials": "P"}, {"family": "Catalanotti", "given": "Claudia", "initials": "C"}, {"family": "Maheshwari", "given": "Shamoni", "initials": "S"}, {"family": "Shuga", "given": "Joe", "initials": "J"}, {"family": "Liang", "given": "Winnie S", "initials": "WS", "orcid": "0000-0002-5698-7735", "researcher": {"href": "https://publications.scilifelab.se/researcher/e186731d8a0448fc83c40a4a2603fb6e.json"}}, {"family": "Keats", "given": "Jonathan", "initials": "J", "orcid": "0000-0003-4375-7399", "researcher": {"href": "https://publications.scilifelab.se/researcher/92f1d1894d53401c9525117e2be662d5.json"}}, {"family": "Adkins", "given": "Jonathan", "initials": "J"}, {"family": "Tassone", "given": "Erica", "initials": "E"}, {"family": "Zismann", "given": "Victoria", "initials": "V"}, {"family": "McDaniel", "given": "Timothy", "initials": "T"}, {"family": "Trent", "given": "Jeffrey", "initials": "J", "orcid": "0000-0003-0183-4202", "researcher": {"href": "https://publications.scilifelab.se/researcher/09c95f8f34e345838dedabc47ac6f393.json"}}, {"family": "Foox", "given": "Jonathan", "initials": "J"}, {"family": "Butler", "given": "Daniel", "initials": "D"}, {"family": "Mason", "given": "Christopher E", "initials": "CE", "orcid": "0000-0002-1850-1642", "researcher": {"href": "https://publications.scilifelab.se/researcher/2af4cb8577d34907b22b030f9e79e90e.json"}}, {"family": "Hong", "given": "Huixiao", "initials": "H", "orcid": "0000-0001-8087-3968", "researcher": {"href": "https://publications.scilifelab.se/researcher/158916b8a0cc4a28b2dceb12514d4a88.json"}}, {"family": "Shi", "given": "Leming", "initials": "L", "orcid": "0000-0002-2981-4150", "researcher": {"href": "https://publications.scilifelab.se/researcher/7389ba41b5f449f6b2f2dc7311235f92.json"}}, {"family": "Wang", "given": "Charles", "initials": "C"}, {"family": "Xiao", "given": "Wenming", "initials": "W", "orcid": "0000-0003-4096-9724", "researcher": {"href": "https://publications.scilifelab.se/researcher/633df103f81f4142ace7a3763b56af54.json"}}, {"family": "Somatic Mutation Working Group of Sequencing Quality Control Phase II Consortium", "given": "", "initials": ""}], "type": "journal article", "published": "2021-09-00", "journal": {"title": "Nat. Biotechnol.", "issn": "1546-1696", "volume": "39", "issue": "9", "pages": "1151-1160", "issn-l": "1087-0156"}, "abstract": "The lack of samples for generating standardized DNA datasets for setting up a sequencing pipeline or benchmarking the performance of different algorithms limits the implementation and uptake of cancer genomics. Here, we describe reference call sets obtained from paired tumor-normal genomic DNA (gDNA) samples derived from a breast cancer cell line-which is highly heterogeneous, with an aneuploid genome, and enriched in somatic alterations-and a matched lymphoblastoid cell line. We partially validated both somatic mutations and germline variants in these call sets via whole-exome sequencing (WES) with different sequencing platforms and targeted sequencing with >2,000-fold coverage, spanning 82% of genomic regions with high confidence. Although the gDNA reference samples are not representative of primary cancer cells from a clinical sample, when setting up a sequencing pipeline, they not only minimize potential biases from technologies, assays and informatics but also provide a unique resource for benchmarking 'tumor-only' or 'matched tumor-normal' analyses.", "doi": "10.1038/s41587-021-00993-6", "pmid": "34504347", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Collaborative", "National Genomics Infrastructure": "Collaborative"}, "xrefs": [{"db": "mid", "key": "NIHMS1740806"}, {"db": "pmc", "key": "PMC8532138"}, {"db": "pii", "key": "10.1038/s41587-021-00993-6"}], "notes": [], "created": "2021-09-13T06:39:20.517Z", "modified": "2023-06-19T13:22:42.166Z"}, {"entity": "publication", "iuid": "5bda2a11b7db434eb59bf15b95416b79", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5bda2a11b7db434eb59bf15b95416b79.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5bda2a11b7db434eb59bf15b95416b79"}}, "title": "A genome-wide association study with 1,126,563 individuals identifies new risk loci for Alzheimer's disease.", "authors": [{"family": "Wightman", "given": "Douglas P", "initials": "DP", "orcid": "0000-0003-3377-4806", "researcher": {"href": "https://publications.scilifelab.se/researcher/13ef837e483c421ebf9e9a20c9c03704.json"}}, {"family": "Jansen", "given": "Iris E", "initials": "IE"}, {"family": "Savage", "given": "Jeanne E", "initials": "JE", "orcid": "0000-0002-2034-8341", "researcher": {"href": "https://publications.scilifelab.se/researcher/d8768341f7f44f449c2f70a493cc556d.json"}}, {"family": "Shadrin", "given": "Alexey A", "initials": "AA", "orcid": "0000-0002-7467-250X", "researcher": {"href": "https://publications.scilifelab.se/researcher/3fc77cdfdcc7428f9efa8dfb3d74f6b8.json"}}, {"family": "Bahrami", "given": "Shahram", "initials": "S"}, {"family": "Holland", "given": "Dominic", "initials": "D"}, {"family": "Rongve", "given": "Arvid", "initials": "A", "orcid": "0000-0002-0476-4134", "researcher": {"href": "https://publications.scilifelab.se/researcher/f9705ecf2a9c4153a56409c17236e71a.json"}}, {"family": "B\u00f8rte", "given": "Sigrid", "initials": "S", "orcid": "0000-0001-9540-3256", "researcher": {"href": "https://publications.scilifelab.se/researcher/b8ad5cab444b45e58e850f8e17ce8c57.json"}}, {"family": "Winsvold", "given": "Bendik S", "initials": "BS", "orcid": "0000-0003-4171-8919", "researcher": {"href": "https://publications.scilifelab.se/researcher/03c8e10afc604295a98f2a057c4179b5.json"}}, {"family": "Drange", "given": "Ole Kristian", "initials": "OK"}, {"family": "Martinsen", "given": "Amy E", "initials": "AE"}, {"family": "Skogholt", "given": "Anne Heidi", "initials": "AH"}, {"family": "Willer", "given": "Cristen", "initials": "C", "orcid": "0000-0001-5645-4966", "researcher": {"href": "https://publications.scilifelab.se/researcher/b3a8e1d33146452b87e7e21eb5339f80.json"}}, {"family": "Br\u00e5then", "given": "Geir", "initials": "G", "orcid": "0000-0003-3224-7983", "researcher": {"href": "https://publications.scilifelab.se/researcher/52e7ea4ab30548829139064396d7c044.json"}}, {"family": "Bosnes", "given": "Ingunn", "initials": "I"}, {"family": "Nielsen", "given": "Jonas Bille", "initials": "JB"}, {"family": "Fritsche", "given": "Lars G", "initials": "LG", "orcid": "0000-0002-2110-1690", "researcher": {"href": "https://publications.scilifelab.se/researcher/00bea312a34a4b8f8436d00fcf799ac3.json"}}, {"family": "Thomas", "given": "Laurent F", "initials": "LF", "orcid": "0000-0003-0548-2486", "researcher": {"href": "https://publications.scilifelab.se/researcher/75b15803ea4445c4b22eaee02e3f131b.json"}}, {"family": "Pedersen", "given": "Linda M", "initials": "LM", "orcid": "0000-0002-8448-983X", "researcher": {"href": "https://publications.scilifelab.se/researcher/e4533b5ba55a4b22ba3b9cf6229f4dd9.json"}}, {"family": "Gabrielsen", "given": "Maiken E", "initials": "ME"}, {"family": "Johnsen", "given": "Marianne Bakke", "initials": "MB"}, {"family": "Meisingset", "given": "Tore Wergeland", "initials": "TW"}, {"family": "Zhou", "given": "Wei", "initials": "W", "orcid": "0000-0001-7719-0859", "researcher": {"href": "https://publications.scilifelab.se/researcher/78c70f5da0ef414680693f1c41dcf99a.json"}}, {"family": "Proitsi", "given": "Petroula", "initials": "P", "orcid": "0000-0002-2553-6974", "researcher": {"href": "https://publications.scilifelab.se/researcher/724f31ac8bc746e7801728be49ab9cc2.json"}}, {"family": "Hodges", "given": "Angela", "initials": "A", "orcid": "0000-0002-5565-6678", "researcher": {"href": "https://publications.scilifelab.se/researcher/4d7d11a2c2dd433bbb7661083cba78b4.json"}}, {"family": "Dobson", "given": "Richard", "initials": "R", "orcid": "0000-0003-4224-9245", "researcher": {"href": "https://publications.scilifelab.se/researcher/098ba38a51a64ba89362ed2a2e51455f.json"}}, {"family": "Velayudhan", "given": "Latha", "initials": "L", "orcid": "0000-0002-7712-930X", "researcher": {"href": "https://publications.scilifelab.se/researcher/2094a9d79b25424692fd809268beb49c.json"}}, {"family": "Heilbron", "given": "Karl", "initials": "K"}, {"family": "Auton", "given": "Adam", "initials": "A"}, {"family": "23andMe Research Team", "given": "", "initials": ""}, {"family": "Sealock", "given": "Julia M", "initials": "JM", "orcid": "0000-0002-9346-3498", "researcher": {"href": "https://publications.scilifelab.se/researcher/9219887fe38b47d5975fd70fdeb83653.json"}}, {"family": "Davis", "given": "Lea K", "initials": "LK", "orcid": "0000-0001-5143-2282", "researcher": {"href": "https://publications.scilifelab.se/researcher/60132a034c8d412dbbb7fedbc9743d81.json"}}, {"family": "Pedersen", "given": "Nancy L", "initials": "NL"}, {"family": "Reynolds", "given": "Chandra A", "initials": "CA", "orcid": "0000-0001-6502-7173", "researcher": {"href": "https://publications.scilifelab.se/researcher/6b7cd2b82d81463c8dd3f13c4d75ab6f.json"}}, {"family": "Karlsson", "given": "Ida K", "initials": "IK"}, {"family": "Magnusson", "given": "Sigurdur", "initials": "S", "orcid": "0000-0001-6669-3071", "researcher": {"href": "https://publications.scilifelab.se/researcher/7fe6813ffc624ef7912596694c9a5475.json"}}, {"family": "Stefansson", "given": "Hreinn", "initials": "H", "orcid": "0000-0002-9331-6666", "researcher": {"href": "https://publications.scilifelab.se/researcher/f7063dc7b22a493c86eb0998366d8c1b.json"}}, {"family": "Thordardottir", "given": "Steinunn", "initials": "S"}, {"family": "Jonsson", "given": "Palmi V", "initials": "PV"}, {"family": "Snaedal", "given": "Jon", "initials": "J"}, {"family": "Zettergren", "given": "Anna", "initials": "A", "orcid": "0000-0002-7182-8417", "researcher": {"href": "https://publications.scilifelab.se/researcher/238188e1165e4de88918f024e3b1289e.json"}}, {"family": "Skoog", "given": "Ingmar", "initials": "I"}, {"family": "Kern", "given": "Silke", "initials": "S"}, {"family": "Waern", "given": "Margda", "initials": "M"}, {"family": "Zetterberg", "given": "Henrik", "initials": "H"}, {"family": "Blennow", "given": "Kaj", "initials": "K"}, {"family": "Stordal", "given": "Eystein", "initials": "E", "orcid": "0000-0002-2443-7923", "researcher": {"href": "https://publications.scilifelab.se/researcher/6eacc414991448c38cee92ac328eb4d3.json"}}, {"family": "Hveem", "given": "Kristian", "initials": "K"}, {"family": "Zwart", "given": "John-Anker", "initials": "JA", "orcid": "0000-0001-5721-0154", "researcher": {"href": "https://publications.scilifelab.se/researcher/d6ba64e625064349b7405b23439e1bfe.json"}}, {"family": "Athanasiu", "given": "Lavinia", "initials": "L"}, {"family": "Selnes", "given": "Per", "initials": "P"}, {"family": "Saltvedt", "given": "Ingvild", "initials": "I", "orcid": "0000-0002-7897-9808", "researcher": {"href": "https://publications.scilifelab.se/researcher/036815a19f424c5eacb62d47bd93f5f7.json"}}, {"family": "Sando", "given": "Sigrid B", "initials": "SB"}, {"family": "Ulstein", "given": "Ingun", "initials": "I"}, {"family": "Djurovic", "given": "Srdjan", "initials": "S", "orcid": "0000-0002-8140-8061", "researcher": {"href": "https://publications.scilifelab.se/researcher/906538321c8e4f38b6bb4a7b0bc18fa3.json"}}, {"family": "Fladby", "given": "Tormod", "initials": "T", "orcid": "0000-0002-9984-9797", "researcher": {"href": "https://publications.scilifelab.se/researcher/9a3bb37886ef42939d74038635209539.json"}}, {"family": "Aarsland", "given": "Dag", "initials": "D", "orcid": "0000-0001-6314-216X", "researcher": {"href": "https://publications.scilifelab.se/researcher/121af6702db54d68b1ca94e8c22a8688.json"}}, {"family": "Selb\u00e6k", "given": "Geir", "initials": "G", "orcid": "0000-0001-6511-8219", "researcher": {"href": "https://publications.scilifelab.se/researcher/c43c9a49c1ba453fbb1fb59f2da44662.json"}}, {"family": "Ripke", "given": "Stephan", "initials": "S", "orcid": "0000-0003-3622-835X", "researcher": {"href": "https://publications.scilifelab.se/researcher/e2b56c2c5f534130b7fdc2b14d6b7f15.json"}}, {"family": "Stefansson", "given": "Kari", "initials": "K", "orcid": "0000-0003-1676-864X", "researcher": {"href": "https://publications.scilifelab.se/researcher/679465193fba4887a68e2aec34ccfd8e.json"}}, {"family": "Andreassen", "given": "Ole A", "initials": "OA", "orcid": "0000-0002-4461-3568", "researcher": {"href": "https://publications.scilifelab.se/researcher/56f384e8e2fd4a7383c7b26e88a828b2.json"}}, {"family": "Posthuma", "given": "Danielle", "initials": "D", "orcid": "0000-0001-7582-2365", "researcher": {"href": "https://publications.scilifelab.se/researcher/406e98180d174e8ca087f50074c025c9.json"}}], "type": "journal article", "published": "2021-09-00", "journal": {"title": "Nat. Genet.", "issn": "1546-1718", "volume": "53", "issue": "9", "pages": "1276-1282", "issn-l": "1061-4036"}, "abstract": "Late-onset Alzheimer's disease is a prevalent age-related polygenic disease that accounts for 50-70% of dementia cases. Currently, only a fraction of the genetic variants underlying Alzheimer's disease have been identified. Here we show that increased sample sizes allowed identification of seven previously unidentified genetic loci contributing to Alzheimer's disease. This study highlights microglia, immune cells and protein catabolism as relevant to late-onset Alzheimer's disease, while identifying and prioritizing previously unidentified genes of potential interest. We anticipate that these results can be included in larger meta-analyses of Alzheimer's disease to identify further genetic variants that contribute to Alzheimer's pathology.", "doi": "10.1038/s41588-021-00921-z", "pmid": "34493870", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41588-021-00921-z"}], "notes": [], "created": "2021-12-22T19:40:03.174Z", "modified": "2023-06-20T15:55:43.752Z"}, {"entity": "publication", "iuid": "c0b22b8488e949e984ce8d0398e5ef9b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c0b22b8488e949e984ce8d0398e5ef9b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c0b22b8488e949e984ce8d0398e5ef9b"}}, "title": "A genome-wide association study of the frailty index highlights brain pathways in ageing.", "authors": [{"family": "Atkins", "given": "Janice L", "initials": "JL", "orcid": "0000-0003-4919-9068", "researcher": {"href": "https://publications.scilifelab.se/researcher/3d251cfaba844c7d866ad2cd624e25ce.json"}}, {"family": "Jylh\u00e4v\u00e4", "given": "Juulia", "initials": "J"}, {"family": "Pedersen", "given": "Nancy L", "initials": "NL"}, {"family": "Magnusson", "given": "Patrik K", "initials": "PK"}, {"family": "Lu", "given": "Yi", "initials": "Y"}, {"family": "Wang", "given": "Yunzhang", "initials": "Y"}, {"family": "H\u00e4gg", "given": "Sara", "initials": "S", "orcid": "0000-0002-2452-1500", "researcher": {"href": "https://publications.scilifelab.se/researcher/e1d010dfe5d84a33b6a6c7ec815ca3dc.json"}}, {"family": "Melzer", "given": "David", "initials": "D"}, {"family": "Williams", "given": "Dylan M", "initials": "DM"}, {"family": "Pilling", "given": "Luke C", "initials": "LC", "orcid": "0000-0002-3332-8454", "researcher": {"href": "https://publications.scilifelab.se/researcher/aadea4e5796940d88b315b83530162e4.json"}}], "type": "journal article", "published": "2021-09-00", "journal": {"title": "Aging Cell", "issn": "1474-9726", "issn-l": "1474-9718", "volume": "20", "issue": "9", "pages": "e13459"}, "abstract": "Frailty is a common geriatric syndrome and strongly associated with disability, mortality and hospitalization. Frailty is commonly measured using the frailty index (FI), based on the accumulation of a number of health deficits during the life course. The mechanisms underlying FI are multifactorial and not well understood, but a genetic basis has been suggested with heritability estimates between 30 and 45%. Understanding the genetic determinants and biological mechanisms underpinning FI may help to delay or even prevent frailty. We performed a genome-wide association study (GWAS) meta-analysis of a frailty index in European descent UK Biobank participants (n = 164,610, 60-70 years) and Swedish TwinGene participants (n = 10,616, 41-87 years). FI calculation was based on 49 or 44 self-reported items on symptoms, disabilities and diagnosed diseases for UK Biobank and TwinGene, respectively. 14 loci were associated with the FI (p < 5*10-8 ). Many FI-associated loci have established associations with traits such as body mass index, cardiovascular disease, smoking, HLA proteins, depression and neuroticism; however, one appears to be novel. The estimated single nucleotide polymorphism (SNP) heritability of the FI was 11% (0.11, SE 0.005). In enrichment analysis, genes expressed in the frontal cortex and hippocampus were significantly downregulated (adjusted p < 0.05). We also used Mendelian randomization to identify modifiable traits and exposures that may affect frailty risk, with a higher educational attainment genetic risk score being associated with a lower degree of frailty. Risk of frailty is influenced by many genetic factors, including well-known disease risk factors and mental health, with particular emphasis on pathways in the brain.", "doi": "10.1111/acel.13459", "pmid": "34431594", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC8441299"}], "notes": [], "created": "2021-09-07T11:11:44.764Z", "modified": "2021-12-07T07:30:15.087Z"}, {"entity": "publication", "iuid": "f4f2d21b7c8b4a61a312b996c70f1d51", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f4f2d21b7c8b4a61a312b996c70f1d51.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f4f2d21b7c8b4a61a312b996c70f1d51"}}, "title": "Consistent B Cell Receptor Immunoglobulin Features Between Siblings in Familial Chronic Lymphocytic Leukemia.", "authors": [{"family": "Kolijn", "given": "P Martijn", "initials": "PM"}, {"family": "Muggen", "given": "Alice F", "initials": "AF"}, {"family": "Ljungstr\u00f6m", "given": "Viktor", "initials": "V"}, {"family": "Agathangelidis", "given": "Andreas", "initials": "A"}, {"family": "Wolvers-Tettero", "given": "Ingrid L M", "initials": "ILM"}, {"family": "Beverloo", "given": "H Berna", "initials": "HB"}, {"family": "P\u00e1l", "given": "Karol", "initials": "K"}, {"family": "Hengeveld", "given": "Paul J", "initials": "PJ"}, {"family": "Darzentas", "given": "Nikos", "initials": "N"}, {"family": "Hendriks", "given": "Rudi W", "initials": "RW"}, {"family": "van Dongen", "given": "Jacques J M", "initials": "JJM"}, {"family": "Rosenquist", "given": "Richard", "initials": "R"}, {"family": "Langerak", "given": "Anton W", "initials": "AW"}], "type": "journal article", "published": "2021-08-26", "journal": {"title": "Front Oncol", "issn": "2234-943X", "volume": "11", "pages": "740083", "issn-l": "2234-943X"}, "abstract": "Key processes in the onset and evolution of chronic lymphocytic leukemia (CLL) are thought to include chronic (antigenic) activation of mature B cells through the B cell receptor (BcR), signals from the microenvironment, and acquisition of genetic alterations. Here we describe three families in which two or more siblings were affected by CLL. We investigated whether there are immunogenetic similarities in the leukemia-specific immunoglobulin heavy (IGH) and light (IGL/IGK) chain gene rearrangements of the siblings in each family. Furthermore, we performed array analysis to study if similarities in CLL-associated chromosomal aberrations are present within each family and screened for somatic mutations using paired tumor/normal whole-genome sequencing (WGS). In two families a consistent IGHV gene mutational status (one IGHV-unmutated, one IGHV-mutated) was observed. Intriguingly, the third family with four affected siblings was characterized by usage of the lambda IGLV3-21 gene, with the hallmark R110 mutation of the recently described clinically aggressive IGLV3-21R110 subset. In this family, the CLL-specific rearrangements in two siblings could be assigned to either stereotyped subset #2 or the immunogenetically related subset #169, both of which belong to the broader IGLV3-21R110 subgroup. Consistent patterns of cytogenetic aberrations were encountered in all three families. Furthermore, the CLL clones carried somatic mutations previously associated with IGHV mutational status, cytogenetic aberrations and stereotyped subsets, respectively. From these findings, we conclude that similarities in immunogenetic characteristics in familial CLL, in combination with genetic aberrations acquired, point towards shared underlying mechanisms behind CLL development within each family.", "doi": "10.3389/fonc.2021.740083", "pmid": "34513715", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC8427434"}], "notes": [], "created": "2021-12-08T13:53:22.649Z", "modified": "2021-12-08T13:53:22.655Z"}, {"entity": "publication", "iuid": "505018863a1d416d90c48d08477c6194", "links": {"self": {"href": "https://publications.scilifelab.se/publication/505018863a1d416d90c48d08477c6194.json"}, "display": {"href": "https://publications.scilifelab.se/publication/505018863a1d416d90c48d08477c6194"}}, "title": "Haplotype-Specific Expression Analysis of MHC Class II Genes in Healthy Individuals and Rheumatoid Arthritis Patients.", "authors": [{"family": "Houtman", "given": "Miranda", "initials": "M"}, {"family": "Hesselberg", "given": "Espen", "initials": "E"}, {"family": "R\u00f6nnblom", "given": "Lars", "initials": "L"}, {"family": "Klareskog", "given": "Lars", "initials": "L"}, {"family": "Malmstr\u00f6m", "given": "Vivianne", "initials": "V"}, {"family": "Padyukov", "given": "Leonid", "initials": "L"}], "type": "journal article", "published": "2021-08-17", "journal": {"title": "Front Immunol", "issn": "1664-3224", "volume": "12", "pages": "707217", "issn-l": "1664-3224"}, "abstract": "HLA-DRB1 alleles have been associated with several autoimmune diseases. For anti-citrullinated protein antibody positive rheumatoid arthritis (RA), HLA-DRB1 shared epitope (SE) alleles are the major genetic risk factors. In order to study the genetic regulation of major histocompatibility complex (MHC) Class II gene expression in immune cells, we investigated transcriptomic profiles of a variety of immune cells from healthy individuals carrying different HLA-DRB1 alleles. Sequencing libraries from peripheral blood mononuclear cells, CD4+ T cells, CD8+ T cells, and CD14+ monocytes of 32 genetically pre-selected healthy female individuals were generated, sequenced and reads were aligned to the standard reference. For the MHC region, reads were mapped to available MHC reference haplotypes and AltHapAlignR was used to estimate gene expression. Using this method, HLA-DRB and HLA-DQ were found to be differentially expressed in different immune cells of healthy individuals as well as in whole blood samples of RA patients carrying HLA-DRB1 SE-positive versus SE-negative alleles. In contrast, no genes outside the MHC region were differentially expressed between individuals carrying HLA-DRB1 SE-positive and SE-negative alleles, thus HLA-DRB1 SE alleles have a strong cis effect on gene expression. Altogether, our findings suggest that immune effects associated with different allelic forms of HLA-DR and HLA-DQ may be associated not only with differences in the structure of these proteins, but also with differences in their expression levels.", "doi": "10.3389/fimmu.2021.707217", "pmid": "34484204", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC8416041"}], "notes": [], "created": "2021-09-13T06:41:23.038Z", "modified": "2024-01-16T13:48:38.715Z"}, {"entity": "publication", "iuid": "6c278a1350574689b5be50dacebe33b7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6c278a1350574689b5be50dacebe33b7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6c278a1350574689b5be50dacebe33b7"}}, "title": "Association of Variants Near the Bradykinin Receptor B2 Gene With Angioedema in Patients Taking ACE Inhibitors.", "authors": [{"family": "Ghouse", "given": "Jonas", "initials": "J"}, {"family": "Ahlberg", "given": "Gustav", "initials": "G"}, {"family": "Andreasen", "given": "Laura", "initials": "L"}, {"family": "Banasik", "given": "Karina", "initials": "K"}, {"family": "Brunak", "given": "S\u00f8ren", "initials": "S"}, {"family": "Schwinn", "given": "Michael", "initials": "M"}, {"family": "Larsen", "given": "Ina Holst", "initials": "IH"}, {"family": "Petersen", "given": "Oscar", "initials": "O"}, {"family": "S\u00f8rensen", "given": "Erik", "initials": "E"}, {"family": "Ullum", "given": "Henrik", "initials": "H"}, {"family": "Rasmussen", "given": "Eva Rye", "initials": "ER"}, {"family": "Eriksson", "given": "Niclas", "initials": "N"}, {"family": "Hallberg", "given": "P\u00e4r", "initials": "P"}, {"family": "Wadelius", "given": "Mia", "initials": "M"}, {"family": "Bundgaard", "given": "Henning", "initials": "H"}, {"family": "Olesen", "given": "Morten S", "initials": "MS"}], "type": "journal article", "published": "2021-08-17", "journal": {"title": "J. Am. Coll. Cardiol.", "issn": "1558-3597", "issn-l": "0735-1097", "volume": "78", "issue": "7", "pages": "696-709"}, "abstract": "Angioedema is a rare but potentially life-threatening adverse reaction associated with angiotensin-converting enzyme (ACE) inhibitors. Identification of potential genetic factors related to this adverse event may help identify at-risk patients.\r\n\r\nThe aim of this study was to identify genetic factors associated with ACE inhibitor-associated angioedema.\r\n\r\nA genomewide association study involving patients of European descent, all taking ACE inhibitors, was conducted in a discovery cohort (Copenhagen Hospital Biobank), and associations were confirmed in a replication cohort (Swedegene). Cases were defined as subjects with angioedema events and filled prescriptions for ACE inhibitors \u2264180 days before the events. Control subjects were defined as those with continuous treatment with ACE inhibitors without any history of angioedema. Odds ratios (ORs) and 95% confidence intervals (CIs) were computed for angioedema risk using logistic mixed model regression analysis. Summary statistics from the discovery and replication cohorts were analyzed using a fixed-effects meta-analysis model.\r\n\r\nThe discovery cohort consisted of 462 cases and 53,391 ACE inhibitor-treated control subjects. The replication cohort consisted of 142 cases and 1,345 ACE inhibitor-treated control subjects. In the discovery cohort, 1 locus, residing at chromosome 14q32.2, was identified that associated with angioedema at the genomewide significance level of P <5 \u00d7 10-8. The lead variant at this locus, rs34485356, is an intergenic variant located 60 kb upstream of BDKRB2 (OR: 1.62; 95% CI: 1.38 to 1.90; P = 4.3 \u00d7 10-9). This variant was validated in our replication cohort with a similar direction and effect size (OR: 1.60; 95% CI: 1.13 to 2.25; P = 7.2 \u00d7 10-3). We found that carriers of the risk allele had significantly lower systolic (-0.46 mm Hg per T allele; 95% CI: -0.83 to -0.10; P = 0.013) and diastolic (-0.26 mm Hg per T allele; 95% CI: -0.46 to -0.05; P = 0.013) blood pressure.\r\n\r\nIn this genomewide association study involving individuals treated with ACE inhibitors, we found that common variants located in close proximity to the bradykinin receptor B2 gene were associated with increased risk for ACE inhibitor-related angioedema.", "doi": "10.1016/j.jacc.2021.05.054", "pmid": "34384552", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "S0735-1097(21)05394-8"}], "notes": [], "created": "2021-09-07T11:12:27.591Z", "modified": "2021-12-07T07:31:15.161Z"}, {"entity": "publication", "iuid": "19379a893e0b48ff9f84c9acbc2f7509", "links": {"self": {"href": "https://publications.scilifelab.se/publication/19379a893e0b48ff9f84c9acbc2f7509.json"}, "display": {"href": "https://publications.scilifelab.se/publication/19379a893e0b48ff9f84c9acbc2f7509"}}, "title": "Microbiological Surveillance of Biogas Plants: Targeting Acetogenic Community.", "authors": [{"family": "Singh", "given": "Abhijeet", "initials": "A"}, {"family": "Moestedt", "given": "Jan", "initials": "J"}, {"family": "Berg", "given": "Andreas", "initials": "A"}, {"family": "Schn\u00fcrer", "given": "Anna", "initials": "A"}], "type": "journal article", "published": "2021-08-16", "journal": {"title": "Front Microbiol", "issn": "1664-302X", "volume": "12", "pages": "700256", "issn-l": "1664-302X"}, "abstract": "Acetogens play a very important role in anaerobic digestion and are essential in ensuring process stability. Despite this, targeted studies of the acetogenic community in biogas processes remain limited. Some efforts have been made to identify and understand this community, but the lack of a reliable molecular analysis strategy makes the detection of acetogenic bacteria tedious. Recent studies suggest that screening of bacterial genetic material for formyltetrahydrofolate synthetase (FTHFS), a key marker enzyme in the Wood-Ljungdahl pathway, can give a strong indication of the presence of putative acetogens in biogas environments. In this study, we applied an acetogen-targeted analyses strategy developed previously by our research group for microbiological surveillance of commercial biogas plants. The surveillance comprised high-throughput sequencing of FTHFS gene amplicons and unsupervised data analysis with the AcetoScan pipeline. The results showed differences in the acetogenic community structure related to feed substrate and operating parameters. They also indicated that our surveillance method can be helpful in the detection of community changes before observed changes in physico-chemical profiles, and that frequent high-throughput surveillance can assist in management towards stable process operation, thus improving the economic viability of biogas plants. To our knowledge, this is the first study to apply a high-throughput microbiological surveillance approach to visualise the potential acetogenic population in commercial biogas digesters.", "doi": "10.3389/fmicb.2021.700256", "pmid": "34484143", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC8415747"}], "notes": [], "created": "2021-12-08T13:52:04.733Z", "modified": "2024-01-16T13:48:38.725Z"}, {"entity": "publication", "iuid": "626a62e0410d42a690604515e58e829b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/626a62e0410d42a690604515e58e829b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/626a62e0410d42a690604515e58e829b"}}, "title": "Characterization of Dynamic Regulatory Gene and Protein Networks in Wheat Roots Upon Perceiving Water Deficit Through Comparative Transcriptomics Survey.", "authors": [{"family": "Rahimi", "given": "Yousef", "initials": "Y"}, {"family": "Ingvarsson", "given": "P\u00e4r K", "initials": "PK"}, {"family": "Bihamta", "given": "Mohammad Reza", "initials": "MR"}, {"family": "Alipour", "given": "Hadi", "initials": "H"}, {"family": "Taleei", "given": "Alireza", "initials": "A"}, {"family": "Khoshnoodi Jabar Abadi", "given": "Shaghayegh", "initials": "S"}], "type": "journal article", "published": "2021-08-16", "journal": {"title": "Front Plant Sci", "issn": "1664-462X", "volume": "12", "pages": "710867", "issn-l": "1664-462X"}, "abstract": "A well-developed root system benefits host plants by optimizing water absorption and nutrient uptake and thereby increases plant productivity. In this study we have characterized the root transcriptome using RNA-seq and subsequential functional analysis in a set of drought tolerant and susceptible genotypes. The goal of the study was to elucidate and characterize water deficit-responsive genes in wheat landraces that had been through long-term field and biochemical screening for drought tolerance. The results confirm genotype differences in water-deficit tolerance in line with earlier results from field trials. The transcriptomics survey highlighted a total of 14,187 differentially expressed genes (DEGs) that responded to water deficit. The characterization of these genes shows that all chromosomes contribute to water-deficit tolerance, but to different degrees, and the B genome showed higher involvement than the A and D genomes. The DEGs were mainly mapped to flavonoid, phenylpropanoid, and diterpenoid biosynthesis pathways, as well as glutathione metabolism and hormone signaling. Furthermore, extracellular region, apoplast, cell periphery, and external encapsulating structure were the main water deficit-responsive cellular components in roots. A total of 1,377 DEGs were also predicted to function as transcription factors (TFs) from different families regulating downstream cascades. TFs from the AP2/ERF-ERF, MYB-related, B3, WRKY, Tify, and NAC families were the main genotype-specific regulatory factors. To further characterize the dynamic biosynthetic pathways, protein-protein interaction (PPI) networks were constructed using significant KEGG proteins and putative TFs. In PPIs, enzymes from the CYP450, TaABA8OH2, PAL, and GST families play important roles in water-deficit tolerance in connection with MYB13-1, MADS-box, and NAC transcription factors.", "doi": "10.3389/fpls.2021.710867", "pmid": "34484273", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC8415571"}], "notes": [], "created": "2022-01-16T21:08:45.935Z", "modified": "2024-01-16T13:48:38.732Z"}, {"entity": "publication", "iuid": "06e65b3fd65f4c00ac715731fc165702", "links": {"self": {"href": "https://publications.scilifelab.se/publication/06e65b3fd65f4c00ac715731fc165702.json"}, "display": {"href": "https://publications.scilifelab.se/publication/06e65b3fd65f4c00ac715731fc165702"}}, "title": "Transcriptome Analysis of Post-Mortem Brain Tissue Reveals Up-Regulation of the Complement Cascade in a Subgroup of Schizophrenia Patients.", "authors": [{"family": "Lindholm Carlstr\u00f6m", "given": "Eva", "initials": "E"}, {"family": "Niazi", "given": "Adnan", "initials": "A", "orcid": "0000-0003-0311-5279", "researcher": {"href": "https://publications.scilifelab.se/researcher/c9e07c9891804a60980eb07956a7cd0d.json"}}, {"family": "Etemadikhah", "given": "Mitra", "initials": "M", "orcid": "0000-0001-5795-9085", "researcher": {"href": "https://publications.scilifelab.se/researcher/7e68ca63254a4b5697188bb87087852f.json"}}, {"family": "Halvardson", "given": "Jonatan", "initials": "J"}, {"family": "Enroth", "given": "Stefan", "initials": "S", "orcid": "0000-0002-5056-9137", "researcher": {"href": "https://publications.scilifelab.se/researcher/16bb97ef16ee49f3ae0c7ea0495fd971.json"}}, {"family": "Stockmeier", "given": "Craig A", "initials": "CA", "orcid": "0000-0003-1861-1013", "researcher": {"href": "https://publications.scilifelab.se/researcher/89ebb5b73b9a42498192d35aea2d92c5.json"}}, {"family": "Rajkowska", "given": "Grazyna", "initials": "G"}, {"family": "Nilsson", "given": "Bo", "initials": "B"}, {"family": "Feuk", "given": "Lars", "initials": "L"}], "type": "journal article", "published": "2021-08-13", "journal": {"title": "Genes", "issn": "2073-4425", "issn-l": "2073-4425", "volume": "12", "issue": "8", "pages": null}, "abstract": "Schizophrenia is a genetically complex neuropsychiatric disorder with largely unresolved mechanisms of pathology. Identification of genes and pathways associated with schizophrenia is important for understanding the development, progression and treatment of schizophrenia. In this study, pathways associated with schizophrenia were explored at the level of gene expression. The study included post-mortem brain tissue samples from 68 schizophrenia patients and 44 age and sex-matched control subjects. Whole transcriptome poly-A selected paired-end RNA sequencing was performed on tissue from the prefrontal cortex and orbitofrontal cortex. RNA expression differences were detected between case and control individuals, focusing both on single genes and pathways. The results were validated with RT-qPCR. Significant differential expression between patient and controls groups was found for 71 genes. Gene ontology analysis of differentially expressed genes revealed an up-regulation of multiple genes in immune response among the patients (corrected p-value = 0.004). Several genes in the category belong to the complement system, including C1R, C1S, C7, FCN3, SERPING1, C4A and CFI. The increased complement expression is primarily driven by a subgroup of patients with increased expression of immune/inflammatory response genes, pointing to important differences in disease etiology within the patient group. Weighted gene co-expression network analysis highlighted networks associated with both synaptic transmission and activation of the immune response. Our results demonstrate the importance of immune-related pathways in schizophrenia and provide evidence for elevated expression of the complement cascade as an important pathway in schizophrenia pathology.", "doi": "10.3390/genes12081242", "pmid": "34440415", "labels": {"NGI Uppsala (Uppsala Genome Center)": "Service", "National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "genes12081242"}, {"db": "pmc", "key": "PMC8393670"}], "notes": [], "created": "2021-11-24T13:25:18.239Z", "modified": "2024-01-16T13:48:38.753Z"}, {"entity": "publication", "iuid": "4fc47fbead1f4a22811bb59baaed3383", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4fc47fbead1f4a22811bb59baaed3383.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4fc47fbead1f4a22811bb59baaed3383"}}, "title": "Mutational patterns and clonal evolution from diagnosis to relapse in pediatric acute lymphoblastic leukemia.", "authors": [{"family": "Sayyab", "given": "Shumaila", "initials": "S"}, {"family": "Lundmark", "given": "Anders", "initials": "A"}, {"family": "Larsson", "given": "Malin", "initials": "M"}, {"family": "Ringn\u00e9r", "given": "Markus", "initials": "M"}, {"family": "Nystedt", "given": "Sara", "initials": "S"}, {"family": "Marincevic-Zuniga", "given": "Yanara", "initials": "Y"}, {"family": "Tamm", "given": "Katja Pokrovskaja", "initials": "KP"}, {"family": "Abrahamsson", "given": "Jonas", "initials": "J"}, {"family": "Fogelstrand", "given": "Linda", "initials": "L"}, {"family": "Heyman", "given": "Mats", "initials": "M"}, {"family": "Nor\u00e9n-Nystr\u00f6m", "given": "Ulrika", "initials": "U"}, {"family": "L\u00f6nnerholm", "given": "Gudmar", "initials": "G"}, {"family": "Harila-Saari", "given": "Arja", "initials": "A"}, {"family": "Berglund", "given": "Eva C", "initials": "EC"}, {"family": "Nordlund", "given": "Jessica", "initials": "J"}, {"family": "Syv\u00e4nen", "given": "Ann-Christine", "initials": "A"}], "type": "journal article", "published": "2021-08-06", "journal": {"title": "Sci Rep", "issn": "2045-2322", "issn-l": "2045-2322", "volume": "11", "issue": "1", "pages": "15988"}, "abstract": "The mechanisms driving clonal heterogeneity and evolution in relapsed pediatric acute lymphoblastic leukemia (ALL) are not fully understood. We performed whole genome sequencing of samples collected at diagnosis, relapse(s) and remission from 29 Nordic patients. Somatic point mutations and large-scale structural variants were called using individually matched remission samples as controls, and allelic expression of the mutations was assessed in ALL cells using RNA-sequencing. We observed an increased burden of somatic mutations at relapse, compared to diagnosis, and at second relapse compared to first relapse. In addition to 29 known ALL driver genes, of which nine genes carried recurrent protein-coding mutations in our sample set, we identified putative non-protein coding mutations in regulatory regions of seven additional genes that have not previously been described in ALL. Cluster analysis of hundreds of somatic mutations per sample revealed three distinct evolutionary trajectories during ALL progression from diagnosis to relapse. The evolutionary trajectories provide insight into the mutational mechanisms leading relapse in ALL and could offer biomarkers for improved risk prediction in individual patients.", "doi": "10.1038/s41598-021-95109-0", "pmid": "34362951", "labels": {"Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-021-95109-0"}, {"db": "pmc", "key": "PMC8346595"}], "notes": [], "created": "2021-08-09T12:21:51.023Z", "modified": "2024-01-16T13:48:38.827Z"}, {"entity": "publication", "iuid": "58eb7a843c0344258c15ea9349bdbe5a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/58eb7a843c0344258c15ea9349bdbe5a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/58eb7a843c0344258c15ea9349bdbe5a"}}, "title": "Single-cell multimodal analysis in a case with reduced penetrance of Progranulin-Frontotemporal Dementia.", "authors": [{"family": "Natarajan", "given": "Karthick", "initials": "K", "orcid": "0000-0001-5335-875X", "researcher": {"href": "https://publications.scilifelab.se/researcher/389c50cf68cc43c2bd154addeafe768a.json"}}, {"family": "Eisfeldt", "given": "Jesper", "initials": "J"}, {"family": "Hammond", "given": "Maria", "initials": "M"}, {"family": "Laffita-Mesa", "given": "Jos\u00e9 Miguel", "initials": "JM"}, {"family": "Patra", "given": "Kalicharan", "initials": "K"}, {"family": "Khoshnood", "given": "Behzad", "initials": "B"}, {"family": "\u00d6ijerstedt", "given": "Linn", "initials": "L"}, {"family": "Graff", "given": "Caroline", "initials": "C"}], "type": "journal article", "published": "2021-08-03", "journal": {"title": "Acta Neuropathol Commun", "issn": "2051-5960", "issn-l": "2051-5960", "volume": "9", "issue": "1", "pages": "132"}, "abstract": "We identified an autosomal dominant progranulin mutation carrier without symptoms of dementia in her lifetime (Reduced Penetrance Mutation Carrier, RedPenMC). This resistance to develop expected pathology presents a unique opportunity to interrogate neurodegenerative mechanisms. We performed multimodal single-nuclei analyses of post-mortem frontal cortex from RedPenMC, including transcriptomics and global levels of chromatin marks. RedPenMC had an increased ratio of GRN-expressing microglia, higher levels of activating histone mark H3k4me3 in microglia and lower levels of the repressive chromatin marks H3k9me1 and H3k9me3 in the frontal cortex than her affected mutation carrier son and evidence of higher protein levels of progranulin in both plasma and brain homogenates. Although the study is limited to one case, the results support that restoring brain progranulin levels may be sufficient to escape neurodegeneration and FTD. In addition to previously identified modifier genes, it is possible that epigenetic marks may contribute to the increased progranulin expression in cases of reduced penetrance. These findings may stimulate similar follow-up studies and new therapeutic approaches.", "doi": "10.1186/s40478-021-01234-2", "pmid": "34344473", "labels": {"Bioinformatics Support and Infrastructure": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "Affinity Proteomics Uppsala": "Technology development", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1186/s40478-021-01234-2"}, {"db": "pmc", "key": "PMC8336016"}], "notes": [], "created": "2021-08-25T09:08:35.655Z", "modified": "2024-01-16T13:48:38.876Z"}, {"entity": "publication", "iuid": "c627962c4fb849df853d4ce183c38491", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c627962c4fb849df853d4ce183c38491.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c627962c4fb849df853d4ce183c38491"}}, "title": "Long- and short-read metabarcoding technologies reveal similar spatiotemporal structures in fungal communities.", "authors": [{"family": "Furneaux", "given": "Brendan", "initials": "B", "orcid": "0000-0003-3522-7363", "researcher": {"href": "https://publications.scilifelab.se/researcher/df196c994b3c4086b4f94eacf4e57239.json"}}, {"family": "Bahram", "given": "Mohammad", "initials": "M", "orcid": "0000-0002-9539-3307", "researcher": {"href": "https://publications.scilifelab.se/researcher/26b5310cd872405aa2716c09a3f9d4bf.json"}}, {"family": "Rosling", "given": "Anna", "initials": "A", "orcid": "0000-0002-7003-5941", "researcher": {"href": "https://publications.scilifelab.se/researcher/c4c4bbb9e6c343808e8fa9345b7c05b2.json"}}, {"family": "Yorou", "given": "Nourou S", "initials": "NS", "orcid": "0000-0001-6997-811X", "researcher": {"href": "https://publications.scilifelab.se/researcher/a56781052962486cb78d1b4462a52fcb.json"}}, {"family": "Ryberg", "given": "Martin", "initials": "M", "orcid": "0000-0002-6795-4349", "researcher": {"href": "https://publications.scilifelab.se/researcher/c0a8578a1ace4105be91ec8116c84365.json"}}], "type": "journal article", "published": "2021-08-00", "journal": {"title": "Mol Ecol Resour", "issn": "1755-0998", "issn-l": "1755-098X", "volume": "21", "issue": "6", "pages": "1833-1849"}, "abstract": "Fungi form diverse communities and play essential roles in many terrestrial ecosystems, yet there are methodological challenges in taxonomic and phylogenetic placement of fungi from environmental sequences. To address such challenges, we investigated spatiotemporal structure of a fungal community using soil metabarcoding with four different sequencing strategies: short-amplicon sequencing of the ITS2 region (300-400 bp) with Illumina MiSeq, Ion Torrent Ion S5 and PacBio RS II, all from the same PCR library, as well as long-amplicon sequencing of the full ITS and partial LSU regions (1200-1600 bp) with PacBio RS II. Resulting community structure and diversity depended more on statistical method than sequencing technology. The use of long-amplicon sequencing enables construction of a phylogenetic tree from metabarcoding reads, which facilitates taxonomic identification of sequences. However, long reads present issues for denoising algorithms in diverse communities. We present a solution that splits the reads into shorter homologous regions prior to denoising, and then reconstructs the full denoised reads. In the choice between short and long amplicons, we suggest a hybrid approach using short amplicons for sampling breadth and depth, and long amplicons to characterize the local species pool for improved identification and phylogenetic analyses.", "doi": "10.1111/1755-0998.13387", "pmid": "33811446", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2021-08-23T06:33:39.481Z", "modified": "2024-01-16T13:48:38.968Z"}, {"entity": "publication", "iuid": "84cea954e35f463d9145c008e1921ca1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/84cea954e35f463d9145c008e1921ca1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/84cea954e35f463d9145c008e1921ca1"}}, "title": "Genomic inference of contemporary effective population size in a large island population of collared flycatchers (Ficedula albicollis).", "authors": [{"family": "Nadachowska-Brzyska", "given": "Krystyna", "initials": "K", "orcid": "0000-0002-8457-310X", "researcher": {"href": "https://publications.scilifelab.se/researcher/fc84301b6f3943058c16d3f644713078.json"}}, {"family": "Dutoit", "given": "Ludovic", "initials": "L", "orcid": "0000-0002-0164-9878", "researcher": {"href": "https://publications.scilifelab.se/researcher/32e987a37c504d9eb3069525bbca54ad.json"}}, {"family": "Smeds", "given": "Linn\u00e9a", "initials": "L", "orcid": "0000-0002-8415-9259", "researcher": {"href": "https://publications.scilifelab.se/researcher/b46a4a275c954de8bb969ef4cda9e33b.json"}}, {"family": "Kardos", "given": "Martin", "initials": "M"}, {"family": "Gustafsson", "given": "Lars", "initials": "L", "orcid": "0000-0001-6566-2863", "researcher": {"href": "https://publications.scilifelab.se/researcher/e04fef54f3f5431f86062e52aaf00748.json"}}, {"family": "Ellegren", "given": "Hans", "initials": "H", "orcid": "0000-0002-5035-1736", "researcher": {"href": "https://publications.scilifelab.se/researcher/819e68cc7125446baec6165aabd2d19c.json"}}], "type": "journal article", "published": "2021-08-00", "journal": {"title": "Mol. Ecol.", "issn": "1365-294X", "volume": "30", "issue": "16", "pages": "3965-3973", "issn-l": "0962-1083"}, "abstract": "Due to its central importance to many aspects of evolutionary biology and population genetics, the long-term effective population size (Ne ) has been estimated for numerous species and populations. However, estimating contemporary Ne is difficult and in practice this parameter is often unknown. In principle, contemporary Ne can be estimated using either analyses of temporal changes in allele frequencies, or the extent of linkage disequilibrium (LD) between unlinked markers. We applied these approaches to estimate contemporary Ne of a relatively recently founded island population of collared flycatchers (Ficedula albicollis). We sequenced the genomes of 85 birds sampled in 1993 and 2015, and applied several temporal methods to estimate Ne at a few thousand (4000-7000). The approach based on LD provided higher estimates of Ne (20,000-32,000) and was associated with high variance, often resulting in infinite Ne . We conclude that whole-genome sequencing data offers new possibilities to estimate high (>1000) contemporary Ne , but also note that such estimates remain challenging, in particular for LD-based methods for contemporary Ne estimation.", "doi": "10.1111/mec.16025", "pmid": "34145933", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "RefSeq", "key": "GCA_000247815.2"}], "notes": [], "created": "2021-12-07T21:36:36.159Z", "modified": "2024-01-16T13:48:38.980Z"}, {"entity": "publication", "iuid": "c50d34ea5add4ae7a33885a5325c5863", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c50d34ea5add4ae7a33885a5325c5863.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c50d34ea5add4ae7a33885a5325c5863"}}, "title": "Genetic insights into biological mechanisms governing human ovarian ageing.", "authors": [{"family": "Ruth", "given": "Katherine S", "initials": "KS"}, {"family": "Day", "given": "Felix R", "initials": "FR"}, {"family": "Hussain", "given": "Jazib", "initials": "J"}, {"family": "Mart\u00ednez-Marchal", "given": "Ana", "initials": "A"}, {"family": "Aiken", "given": "Catherine E", "initials": "CE"}, {"family": "Azad", "given": "Ajuna", "initials": "A"}, {"family": "Thompson", "given": "Deborah J", "initials": "DJ"}, {"family": "Knoblochova", "given": "Lucie", "initials": "L"}, {"family": "Abe", "given": "Hironori", "initials": "H"}, {"family": "Tarry-Adkins", "given": "Jane L", "initials": "JL"}, {"family": "Gonzalez", "given": "Javier Martin", "initials": "JM"}, {"family": "Fontanillas", "given": "Pierre", "initials": "P"}, {"family": "Claringbould", "given": "Annique", "initials": "A"}, {"family": "Bakker", "given": "Olivier B", "initials": "OB"}, {"family": "Sulem", "given": "Patrick", "initials": "P"}, {"family": "Walters", "given": "Robin G", "initials": "RG"}, {"family": "Terao", "given": "Chikashi", "initials": "C"}, {"family": "Turon", "given": "Sandra", "initials": "S"}, {"family": "Horikoshi", "given": "Momoko", "initials": "M"}, {"family": "Lin", "given": "Kuang", "initials": "K"}, {"family": "Onland-Moret", "given": "N Charlotte", "initials": "NC"}, {"family": "Sankar", "given": "Aditya", "initials": "A"}, {"family": "Hertz", "given": "Emil Peter Thrane", "initials": "EPT"}, {"family": "Timshel", "given": "Pascal N", "initials": "PN"}, {"family": "Shukla", "given": "Vallari", "initials": "V"}, {"family": "Borup", "given": "Rehannah", "initials": "R"}, {"family": "Olsen", "given": "Kristina W", "initials": "KW"}, {"family": "Aguilera", "given": "Paula", "initials": "P"}, {"family": "Ferrer-Roda", "given": "M\u00f2nica", "initials": "M"}, {"family": "Huang", "given": "Yan", "initials": "Y"}, {"family": "Stankovic", "given": "Stasa", "initials": "S"}, {"family": "Timmers", "given": "Paul R H J", "initials": "PRHJ"}, {"family": "Ahearn", "given": "Thomas U", "initials": "TU"}, {"family": "Alizadeh", "given": "Behrooz Z", "initials": "BZ"}, {"family": "Naderi", "given": "Elnaz", "initials": "E"}, {"family": "Andrulis", "given": "Irene L", "initials": "IL"}, {"family": "Arnold", "given": "Alice M", "initials": "AM"}, {"family": "Aronson", "given": "Kristan J", "initials": "KJ"}, {"family": "Augustinsson", "given": "Annelie", "initials": "A"}, {"family": "Bandinelli", "given": "Stefania", "initials": "S"}, {"family": "Barbieri", "given": "Caterina M", "initials": "CM"}, {"family": "Beaumont", "given": "Robin N", "initials": "RN"}, {"family": "Becher", "given": "Heiko", "initials": "H"}, {"family": "Beckmann", "given": "Matthias W", "initials": "MW"}, {"family": "Benonisdottir", "given": "Stefania", "initials": "S"}, {"family": "Bergmann", "given": "Sven", "initials": "S"}, {"family": "Bochud", "given": "Murielle", "initials": "M"}, {"family": "Boerwinkle", "given": "Eric", "initials": "E"}, {"family": "Bojesen", "given": "Stig E", "initials": "SE"}, {"family": "Bolla", "given": "Manjeet K", "initials": "MK"}, {"family": "Boomsma", "given": "Dorret I", "initials": "DI"}, {"family": "Bowker", "given": "Nicholas", "initials": "N"}, {"family": "Brody", "given": "Jennifer A", "initials": "JA"}, {"family": "Broer", "given": "Linda", "initials": "L"}, {"family": "Buring", "given": "Julie E", "initials": "JE"}, {"family": "Campbell", "given": "Archie", "initials": "A"}, {"family": "Campbell", "given": "Harry", "initials": "H"}, {"family": "Castelao", "given": "Jose E", "initials": "JE"}, {"family": "Catamo", "given": "Eulalia", "initials": "E"}, {"family": "Chanock", "given": "Stephen J", "initials": "SJ"}, {"family": "Chenevix-Trench", "given": "Georgia", "initials": "G"}, {"family": "Ciullo", "given": "Marina", "initials": "M"}, {"family": "Corre", "given": "Tanguy", "initials": "T"}, {"family": "Couch", "given": "Fergus J", "initials": "FJ"}, {"family": "Cox", "given": "Angela", "initials": "A"}, {"family": "Crisponi", "given": "Laura", "initials": "L"}, {"family": "Cross", "given": "Simon S", "initials": "SS"}, {"family": "Cucca", "given": "Francesco", "initials": "F"}, {"family": "Czene", "given": "Kamila", "initials": "K"}, {"family": "Smith", "given": "George Davey", "initials": "GD"}, {"family": "de Geus", "given": "Eco J C N", "initials": "EJCN"}, {"family": "de Mutsert", "given": "Ren\u00e9e", "initials": "R"}, {"family": "De Vivo", "given": "Immaculata", "initials": "I"}, {"family": "Demerath", "given": "Ellen W", "initials": "EW"}, {"family": "Dennis", "given": "Joe", "initials": "J"}, {"family": "Dunning", "given": "Alison M", "initials": "AM"}, {"family": "Dwek", "given": "Miriam", "initials": "M"}, {"family": "Eriksson", "given": "Mikael", "initials": "M"}, {"family": "Esko", "given": "T\u00f5nu", "initials": "T"}, {"family": "Fasching", "given": "Peter A", "initials": "PA"}, {"family": "Faul", "given": "Jessica D", "initials": "JD"}, {"family": "Ferrucci", "given": "Luigi", "initials": "L"}, {"family": "Franceschini", "given": "Nora", "initials": "N"}, {"family": "Frayling", "given": "Timothy M", "initials": "TM"}, {"family": "Gago-Dominguez", "given": "Manuela", "initials": "M"}, {"family": "Mezzavilla", "given": "Massimo", "initials": "M"}, {"family": "Garc\u00eda-Closas", "given": "Montserrat", "initials": "M"}, {"family": "Gieger", "given": "Christian", "initials": "C"}, {"family": "Giles", "given": "Graham G", "initials": "GG"}, {"family": "Grallert", "given": "Harald", "initials": "H"}, {"family": "Gudbjartsson", "given": "Daniel F", "initials": "DF"}, {"family": "Gudnason", "given": "Vilmundur", "initials": "V"}, {"family": "Gu\u00e9nel", "given": "Pascal", "initials": "P"}, {"family": "Haiman", "given": "Christopher A", "initials": "CA"}, {"family": "H\u00e5kansson", "given": "Niclas", "initials": "N"}, {"family": "Hall", "given": "Per", "initials": "P"}, {"family": "Hayward", "given": "Caroline", "initials": "C"}, {"family": "He", "given": "Chunyan", "initials": "C"}, {"family": "He", "given": "Wei", "initials": "W"}, {"family": "Heiss", "given": "Gerardo", "initials": "G"}, {"family": "H\u00f8ffding", "given": "Miya K", "initials": "MK"}, {"family": "Hopper", "given": "John L", "initials": "JL"}, {"family": "Hottenga", "given": "Jouke J", "initials": "JJ"}, {"family": "Hu", "given": "Frank", "initials": "F"}, {"family": "Hunter", "given": "David", "initials": "D"}, {"family": "Ikram", "given": "Mohammad A", "initials": "MA"}, {"family": "Jackson", "given": "Rebecca D", "initials": "RD"}, {"family": "Joaquim", "given": "Micaella D R", "initials": "MDR"}, {"family": "John", "given": "Esther M", "initials": "EM"}, {"family": "Joshi", "given": "Peter K", "initials": "PK"}, {"family": "Karasik", "given": "David", "initials": "D"}, {"family": "Kardia", "given": "Sharon L R", "initials": "SLR"}, {"family": "Kartsonaki", "given": "Christiana", "initials": "C"}, {"family": "Karlsson", "given": "Robert", "initials": 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"given": "Tricia", "initials": "T"}, {"family": "Linet", "given": "Martha", "initials": "M"}, {"family": "Liu", "given": "YongMei", "initials": "Y"}, {"family": "Liu", "given": "Simin", "initials": "S"}, {"family": "Luan", "given": "Jian'an", "initials": "J"}, {"family": "M\u00e4gi", "given": "Reedik", "initials": "R"}, {"family": "Magnusson", "given": "Patrik K E", "initials": "PKE"}, {"family": "Mangino", "given": "Massimo", "initials": "M"}, {"family": "Mannermaa", "given": "Arto", "initials": "A"}, {"family": "Marco", "given": "Brumat", "initials": "B"}, {"family": "Marten", "given": "Jonathan", "initials": "J"}, {"family": "Martin", "given": "Nicholas G", "initials": "NG"}, {"family": "Mbarek", "given": "Hamdi", "initials": "H"}, {"family": "McKnight", "given": "Barbara", "initials": "B"}, {"family": "Medland", "given": "Sarah E", "initials": "SE"}, {"family": "Meisinger", "given": "Christa", "initials": "C"}, {"family": "Meitinger", "given": "Thomas", "initials": "T"}, {"family": 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{"family": "Lopez-Contreras", "given": "Andres J", "initials": "AJ"}, {"family": "Daniel", "given": "Jeremy A", "initials": "JA"}, {"family": "Stefansson", "given": "Kari", "initials": "K"}, {"family": "Chang-Claude", "given": "Jenny", "initials": "J"}, {"family": "van der Schouw", "given": "Yvonne T", "initials": "YT"}, {"family": "Lunetta", "given": "Kathryn L", "initials": "KL"}, {"family": "Chasman", "given": "Daniel I", "initials": "DI"}, {"family": "Easton", "given": "Douglas F", "initials": "DF"}, {"family": "Visser", "given": "Jenny A", "initials": "JA"}, {"family": "Ozanne", "given": "Susan E", "initials": "SE"}, {"family": "Namekawa", "given": "Satoshi H", "initials": "SH"}, {"family": "Solc", "given": "Petr", "initials": "P"}, {"family": "Murabito", "given": "Joanne M", "initials": "JM"}, {"family": "Ong", "given": "Ken K", "initials": "KK"}, {"family": "Hoffmann", "given": "Eva R", "initials": "ER", "orcid": "0000-0002-2588-0652", "researcher": {"href": "https://publications.scilifelab.se/researcher/4d5725300d8449e18c06581c63f36807.json"}}, {"family": "Murray", "given": "Anna", "initials": "A", "orcid": "0000-0002-2351-2522", "researcher": {"href": "https://publications.scilifelab.se/researcher/f13e8be561b94eff8130199fe499c965.json"}}, {"family": "Roig", "given": "Ignasi", "initials": "I", "orcid": "0000-0003-0313-3581", "researcher": {"href": "https://publications.scilifelab.se/researcher/138805893cb940d39e98c8347f909260.json"}}, {"family": "Perry", "given": "John R B", "initials": "JRB", "orcid": "0000-0001-6483-3771", "researcher": {"href": "https://publications.scilifelab.se/researcher/39d95b143f6849b1b914bca9563218c8.json"}}], "type": "journal article", "published": "2021-08-00", "journal": {"title": "Nature", "issn": "1476-4687", "issn-l": "0028-0836", "volume": "596", "issue": "7872", "pages": "393-397"}, "abstract": "Reproductive longevity is essential for fertility and influences healthy ageing in women1,2, but insights into its underlying biological mechanisms and treatments to preserve it are limited. Here we identify 290 genetic determinants of ovarian ageing, assessed using normal variation in age at natural menopause (ANM) in about 200,000 women of European ancestry. These common alleles were associated with clinical extremes of ANM; women in the top 1% of genetic susceptibility have an equivalent risk of premature ovarian insufficiency to those carrying monogenic FMR1 premutations3. The identified loci implicate a broad range of DNA damage response (DDR) processes and include loss-of-function variants in key DDR-associated genes. Integration with experimental models demonstrates that these DDR processes act across the life-course to shape the ovarian reserve and its rate of depletion. Furthermore, we demonstrate that experimental manipulation of DDR pathways highlighted by human genetics increases fertility and extends reproductive life in mice. Causal inference analyses using the identified genetic variants indicate that extending reproductive life in women improves bone health and reduces risk of type 2 diabetes, but increases the risk of hormone-sensitive cancers. These findings provide insight into the mechanisms that govern ovarian ageing, when they act, and how they might be targeted by therapeutic approaches to extend fertility and prevent disease.", "doi": "10.1038/s41586-021-03779-7", "pmid": "34349265", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41586-021-03779-7"}, {"db": "pmc", "key": "PMC7611832"}, {"db": "mid", "key": "EMS136340"}], "notes": [], "created": "2021-08-19T13:41:39.539Z", "modified": "2021-12-07T07:32:53.556Z"}, {"entity": "publication", "iuid": "5321d052b82a493991baf82d30627863", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5321d052b82a493991baf82d30627863.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5321d052b82a493991baf82d30627863"}}, "title": "Genetic association study of childhood aggression across raters, instruments, and age.", "authors": 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"https://publications.scilifelab.se/researcher/d5cfdc61a13f46589373c8c4b5a15a47.json"}}, {"family": "Bolhuis", "given": "Koen", "initials": "K"}, {"family": "Palviainen", "given": "Teemu", "initials": "T", "orcid": "0000-0002-7847-8384", "researcher": {"href": "https://publications.scilifelab.se/researcher/bcbc4c92052b4819b5d7d821c0c421b0.json"}}, {"family": "Zafarmand", "given": "Hadi", "initials": "H"}, {"family": "Colodro-Conde", "given": "Luc\u00eda", "initials": "L", "orcid": "0000-0002-9004-364X", "researcher": {"href": "https://publications.scilifelab.se/researcher/a3d04cc447a34470a5063ae581eb9030.json"}}, {"family": "Gordon", "given": "Scott", "initials": "S", "orcid": "0000-0001-7623-328X", "researcher": {"href": "https://publications.scilifelab.se/researcher/8815739662214e75b60f71f0b1ca58a6.json"}}, {"family": "Zayats", "given": "Tetyana", "initials": "T"}, {"family": "Aliev", "given": "Fazil", "initials": "F", "orcid": "0000-0001-8357-4699", "researcher": {"href": "https://publications.scilifelab.se/researcher/85556629452a4054bf7228b5f7049811.json"}}, {"family": "Jiang", "given": "Chang", "initials": "C"}, {"family": "Wang", "given": "Carol A", "initials": "CA"}, {"family": "Saunders", "given": "Gretchen", "initials": "G"}, {"family": "Karhunen", "given": "Ville", "initials": "V", "orcid": "0000-0001-6064-1588", "researcher": {"href": "https://publications.scilifelab.se/researcher/219a89cb373447218073a1f58fb77864.json"}}, {"family": "Hammerschlag", "given": "Anke R", "initials": "AR"}, {"family": "Adkins", "given": "Daniel E", "initials": "DE"}, {"family": "Border", "given": "Richard", "initials": "R", "orcid": "0000-0002-6293-2968", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a0382c1a2bb4c0ca9e9c2256b0ce00b.json"}}, {"family": "Peterson", "given": "Roseann E", "initials": "RE"}, {"family": "Prinz", "given": "Joseph A", "initials": "JA"}, {"family": "Thiering", "given": "Elisabeth", "initials": "E"}, {"family": 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"Robin", "initials": "R"}, {"family": "Evans", "given": "Luke M", "initials": "LM", "orcid": "0000-0002-7458-1720", "researcher": {"href": "https://publications.scilifelab.se/researcher/ac3c651e69a9455d9e8cb7921afb05d9.json"}}, {"family": "Sugden", "given": "Karen", "initials": "K"}, {"family": "Alemany", "given": "Silvia", "initials": "S", "orcid": "0000-0002-7925-6767", "researcher": {"href": "https://publications.scilifelab.se/researcher/da641b351c9f48fcbd54a186d28806e5.json"}}, {"family": "Sass", "given": "L\u00e6rke", "initials": "L", "orcid": "0000-0002-5217-7014", "researcher": {"href": "https://publications.scilifelab.se/researcher/950b17ef41394606b8023743f86aba1c.json"}}, {"family": "Vinding", "given": "Rebecca", "initials": "R"}, {"family": "Ruth", "given": "Kate", "initials": "K", "orcid": "0000-0003-4966-9170", "researcher": {"href": "https://publications.scilifelab.se/researcher/e5569a5bc7384a75a5a98c2bf04ded7b.json"}}, {"family": "Tyrrell", "given": "Jess", "initials": "J"}, {"family": "Davies", "given": "Gareth E", "initials": "GE"}, {"family": "Ehli", "given": "Erik A", "initials": "EA", "orcid": "0000-0002-7865-3015", "researcher": {"href": "https://publications.scilifelab.se/researcher/16c7ee4d9b20410ba4975ffa49c4b03e.json"}}, {"family": "Hagenbeek", "given": "Fiona A", "initials": "FA", "orcid": "0000-0002-8773-0430", "researcher": {"href": "https://publications.scilifelab.se/researcher/1874bbcb93ed4633879199558ae54877.json"}}, {"family": "De Zeeuw", "given": "Eveline", "initials": "E"}, {"family": "Van Beijsterveldt", "given": "Toos C E M", "initials": "TCEM"}, {"family": "Larsson", "given": "Henrik", "initials": "H"}, {"family": "Snieder", "given": "Harold", "initials": "H", "orcid": "0000-0003-1949-2298", "researcher": {"href": "https://publications.scilifelab.se/researcher/e9276827839a4f3cb50dcaa2ad4708a5.json"}}, {"family": "Verhulst", "given": "Frank C", "initials": "FC"}, {"family": "Amin", "given": "Najaf", "initials": "N"}, {"family": "Whipp", "given": "Alyce M", "initials": "AM"}, {"family": "Korhonen", "given": "Tellervo", "initials": "T"}, {"family": "Vuoksimaa", "given": "Eero", "initials": "E"}, {"family": "Rose", "given": "Richard J", "initials": "RJ"}, {"family": "Uitterlinden", "given": "Andr\u00e9 G", "initials": "AG", "orcid": "0000-0002-7276-3387", "researcher": {"href": "https://publications.scilifelab.se/researcher/273577b238854023a9dffe34dabc3551.json"}}, {"family": "Heath", "given": "Andrew C", "initials": "AC"}, {"family": "Madden", "given": "Pamela", "initials": "P"}, {"family": "Haavik", "given": "Jan", "initials": "J", "orcid": "0000-0001-7865-2808", "researcher": {"href": "https://publications.scilifelab.se/researcher/68db11f9f0c246bdb7cd7943fbdb2af0.json"}}, {"family": "Harris", "given": "Jennifer R", "initials": "JR"}, {"family": "Helgeland", "given": "\u00d8yvind", "initials": "\u00d8"}, {"family": "Johansson", "given": "Stefan", "initials": "S", "orcid": "0000-0002-2298-7008", "researcher": {"href": "https://publications.scilifelab.se/researcher/1b957ea589b342fb9def8ce13ef3bd7e.json"}}, {"family": "Knudsen", "given": "Gun Peggy S", "initials": "GPS", "orcid": "0000-0002-6193-4291", "researcher": {"href": "https://publications.scilifelab.se/researcher/1d14dc1ad847447789b7d9b2176cd972.json"}}, {"family": "Njolstad", "given": "Pal Rasmus", "initials": "PR", "orcid": "0000-0003-0304-6728", "researcher": {"href": "https://publications.scilifelab.se/researcher/7369f0ad21d9406cadc53eec4b05a71b.json"}}, {"family": "Lu", "given": "Qing", "initials": "Q"}, {"family": "Rodriguez", "given": "Alina", "initials": "A", "orcid": "0000-0003-1209-8802", "researcher": {"href": "https://publications.scilifelab.se/researcher/3b887eeb21fe4ebd8e9ab58c409b052a.json"}}, {"family": "Henders", "given": "Anjali K", "initials": "AK"}, {"family": "Mamun", "given": "Abdullah", "initials": "A"}, {"family": "Najman", "given": "Jackob M", "initials": "JM"}, {"family": "Brown", "given": "Sandy", "initials": "S", "orcid": "0000-0001-8780-0323", "researcher": {"href": "https://publications.scilifelab.se/researcher/b7595d4595284a879786dedad90c490b.json"}}, {"family": "Hopfer", "given": "Christian", "initials": "C"}, {"family": "Krauter", "given": "Kenneth", "initials": "K"}, {"family": "Reynolds", "given": "Chandra", "initials": "C"}, {"family": "Smolen", "given": "Andrew", "initials": "A"}, {"family": "Stallings", "given": "Michael", "initials": "M"}, {"family": "Wadsworth", "given": "Sally", "initials": "S"}, {"family": "Wall", "given": "Tamara L", "initials": "TL"}, {"family": "Silberg", "given": "Judy L", "initials": "JL"}, {"family": "Miller", "given": "Allison", "initials": "A", "orcid": "0000-0003-3816-2251", "researcher": {"href": "https://publications.scilifelab.se/researcher/e6311431d086475abc6b2842984202be.json"}}, {"family": "Keltikangas-J\u00e4rvinen", "given": "Liisa", "initials": "L", "orcid": "0000-0002-7977-3852", "researcher": {"href": "https://publications.scilifelab.se/researcher/070ce33c4a654544beaccf943345ef6c.json"}}, {"family": "Hakulinen", "given": "Christian", "initials": "C"}, {"family": "Pulkki-R\u00e5back", "given": "Laura", "initials": "L"}, {"family": "Havdahl", "given": "Alexandra", "initials": "A", "orcid": "0000-0002-9268-0423", "researcher": {"href": "https://publications.scilifelab.se/researcher/27ff8da085f7404c920bad58b6b907a3.json"}}, {"family": "Magnus", "given": "Per", "initials": "P"}, {"family": "Raitakari", "given": "Olli T", "initials": "OT"}, {"family": "Perry", "given": "John R B", "initials": "JRB", "orcid": "0000-0001-6483-3771", "researcher": {"href": "https://publications.scilifelab.se/researcher/39d95b143f6849b1b914bca9563218c8.json"}}, {"family": "Llop", "given": "Sabrina", "initials": "S"}, {"family": "Lopez-Espinosa", "given": "Maria-Jose", "initials": "M"}, {"family": "B\u00f8nnelykke", "given": "Klaus", "initials": "K"}, {"family": "Bisgaard", "given": "Hans", "initials": "H"}, {"family": "Sunyer", "given": "Jordi", "initials": "J"}, {"family": "Lehtim\u00e4ki", "given": "Terho", "initials": "T", "orcid": "0000-0002-2555-4427", "researcher": {"href": "https://publications.scilifelab.se/researcher/03ed59707dae4c8fb9e63ac1f7c398e3.json"}}, {"family": "Arseneault", "given": "Louise", "initials": "L", "orcid": "0000-0002-2938-2191", "researcher": {"href": "https://publications.scilifelab.se/researcher/0664e4afe7de4354924a1b39b87cf570.json"}}, {"family": "Standl", "given": "Marie", "initials": "M"}, {"family": "Heinrich", "given": "Joachim", "initials": "J"}, {"family": "Boden", "given": "Joseph", "initials": "J", "orcid": "0000-0003-1502-1608", "researcher": {"href": "https://publications.scilifelab.se/researcher/3543b6fb1f8e415ebff77901d4f25cbe.json"}}, {"family": "Pearson", "given": "John", "initials": "J", "orcid": "0000-0001-5607-4517", "researcher": {"href": "https://publications.scilifelab.se/researcher/ab30b4696c52461a8b8632d9bf5d0e2d.json"}}, {"family": "Horwood", "given": "L John", "initials": "LJ"}, {"family": "Kennedy", "given": "Martin", "initials": "M", "orcid": "0000-0002-6445-8526", "researcher": {"href": "https://publications.scilifelab.se/researcher/b3ca738758034d28ad823bde5256ffd9.json"}}, {"family": "Poulton", "given": "Richie", "initials": "R", "orcid": "0000-0002-1052-4583", "researcher": {"href": "https://publications.scilifelab.se/researcher/8f61fd90a9804126b169485da8cf65a1.json"}}, {"family": "Eaves", "given": "Lindon J", "initials": "LJ"}, {"family": "Maes", "given": "Hermine H", "initials": "HH"}, {"family": "Hewitt", "given": "John", "initials": "J"}, {"family": "Copeland", "given": "William E", "initials": "WE", "orcid": "0000-0002-1348-7781", "researcher": {"href": "https://publications.scilifelab.se/researcher/751b7c2a826748168fa3eab48fd71bc6.json"}}, {"family": "Costello", "given": "Elizabeth J", "initials": "EJ"}, {"family": "Williams", "given": "Gail M", "initials": "GM"}, {"family": "Wray", "given": "Naomi", "initials": "N", "orcid": "0000-0001-7421-3357", "researcher": {"href": "https://publications.scilifelab.se/researcher/15a175036d9f44f9b4090d7d431f78d7.json"}}, {"family": "J\u00e4rvelin", "given": "Marjo-Riitta", "initials": "M"}, {"family": "McGue", "given": "Matt", "initials": "M", "orcid": "0000-0002-5580-1433", "researcher": {"href": "https://publications.scilifelab.se/researcher/8e55e07667274620b817abebddcbede5.json"}}, {"family": "Iacono", "given": "William", "initials": "W"}, {"family": "Caspi", "given": "Avshalom", "initials": "A"}, {"family": "Moffitt", "given": "Terrie E", "initials": "TE"}, {"family": "Whitehouse", "given": "Andrew", "initials": "A"}, {"family": "Pennell", "given": "Craig E", "initials": "CE", "orcid": "0000-0002-0937-6165", "researcher": {"href": "https://publications.scilifelab.se/researcher/9e35a98141ce4350b6775593f87e40a5.json"}}, {"family": "Klump", "given": "Kelly L", "initials": "KL"}, {"family": "Burt", "given": "S Alexandra", "initials": "SA"}, {"family": "Dick", "given": "Danielle M", "initials": "DM", "orcid": "0000-0002-1636-893X", "researcher": {"href": "https://publications.scilifelab.se/researcher/4b2567011fc84f32a0a1f17c277dbefe.json"}}, {"family": "Reichborn-Kjennerud", "given": "Ted", "initials": "T"}, {"family": "Martin", "given": "Nicholas G", "initials": "NG", "orcid": "0000-0003-4069-8020", "researcher": {"href": "https://publications.scilifelab.se/researcher/1b445e5935f74fd6a71b2e92a9dac176.json"}}, {"family": "Medland", "given": "Sarah E", "initials": "SE", "orcid": "0000-0003-1382-380X", "researcher": {"href": "https://publications.scilifelab.se/researcher/da1f0230a912425c9237830be85aa642.json"}}, {"family": "Vrijkotte", "given": "Tanja", "initials": "T"}, {"family": "Kaprio", "given": "Jaakko", "initials": "J", "orcid": "0000-0002-3716-2455", "researcher": {"href": "https://publications.scilifelab.se/researcher/814d362333844b72a70cba9ebcf61e6f.json"}}, {"family": "Tiemeier", "given": "Henning", "initials": "H", "orcid": "0000-0002-4395-1397", "researcher": {"href": "https://publications.scilifelab.se/researcher/73e05bd74af344ba8d963463f49bb242.json"}}, {"family": "Davey Smith", "given": "George", "initials": "G", "orcid": "0000-0002-1407-8314", "researcher": {"href": "https://publications.scilifelab.se/researcher/0790d5850377432087ad3900af0044e0.json"}}, {"family": "Hartman", "given": "Catharina A", "initials": "CA"}, {"family": "Oldehinkel", "given": "Albertine J", "initials": "AJ", "orcid": "0000-0003-3925-3913", "researcher": {"href": "https://publications.scilifelab.se/researcher/65ee5f9938f547bcbe51cbaf5fd7a9ba.json"}}, {"family": "Casas", "given": "Miquel", "initials": "M"}, {"family": "Ribas\u00e9s", "given": "Marta", "initials": "M", "orcid": "0000-0003-1039-1116", "researcher": {"href": "https://publications.scilifelab.se/researcher/643ddd67f10547c3a68ab3c5cd9ee627.json"}}, {"family": "Lichtenstein", "given": "Paul", "initials": "P", "orcid": "0000-0003-3037-5287", "researcher": {"href": "https://publications.scilifelab.se/researcher/4db67c51837b4cdfa18cacbc3fca1173.json"}}, {"family": "Lundstr\u00f6m", "given": "Sebastian", "initials": "S"}, {"family": "Plomin", "given": "Robert", "initials": "R", "orcid": "0000-0002-0756-3629", "researcher": {"href": "https://publications.scilifelab.se/researcher/26e3ca0c39ff4a5087146d5125e0190f.json"}}, {"family": "Bartels", "given": "Meike", "initials": "M", "orcid": "0000-0002-9667-7555", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a91c095e993411b99e81e21f40d8597.json"}}, {"family": "Nivard", "given": "Michel G", "initials": "MG", "orcid": "0000-0003-2015-1888", "researcher": {"href": "https://publications.scilifelab.se/researcher/0d65d2277e7344a3a13f0d2193c6813b.json"}}, {"family": "Boomsma", "given": "Dorret I", "initials": "DI", "orcid": "0000-0002-7099-7972", "researcher": {"href": "https://publications.scilifelab.se/researcher/4b66ab2525fd4a468e7a4ad14c955cb4.json"}}], "type": "journal article", "published": "2021-07-30", "journal": {"title": "Transl Psychiatry", "issn": "2158-3188", "issn-l": "2158-3188", "volume": "11", "issue": "1", "pages": "413"}, "abstract": "Childhood aggressive behavior (AGG) has a substantial heritability of around 50%. Here we present a genome-wide association meta-analysis (GWAMA) of childhood AGG, in which all phenotype measures across childhood ages from multiple assessors were included. We analyzed phenotype assessments for a total of 328 935 observations from 87 485 children aged between 1.5 and 18 years, while accounting for sample overlap. We also meta-analyzed within subsets of the data, i.e., within rater, instrument and age. SNP-heritability for the overall meta-analysis (AGGoverall) was 3.31% (SE = 0.0038). We found no genome-wide significant SNPs for AGGoverall. The gene-based analysis returned three significant genes: ST3GAL3 (P = 1.6E-06), PCDH7 (P = 2.0E-06), and IPO13 (P = 2.5E-06). All three genes have previously been associated with educational traits. Polygenic scores based on our GWAMA significantly predicted aggression in a holdout sample of children (variance explained = 0.44%) and in retrospectively assessed childhood aggression (variance explained = 0.20%). Genetic correlations (rg) among rater-specific assessment of AGG ranged from rg = 0.46 between self- and teacher-assessment to rg = 0.81 between mother- and teacher-assessment. We obtained moderate-to-strong rgs with selected phenotypes from multiple domains, but hardly with any of the classical biomarkers thought to be associated with AGG. Significant genetic correlations were observed with most psychiatric and psychological traits (range [Formula: see text]: 0.19-1.00), except for obsessive-compulsive disorder. Aggression had a negative genetic correlation (rg = ~-0.5) with cognitive traits and age at first birth. Aggression was strongly genetically correlated with smoking phenotypes (range [Formula: see text]: 0.46-0.60). The genetic correlations between aggression and psychiatric disorders were weaker for teacher-reported AGG than for mother- and self-reported AGG. The current GWAMA of childhood aggression provides a powerful tool to interrogate the rater-specific genetic etiology of AGG.", "doi": "10.1038/s41398-021-01480-x", "pmid": "34330890", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41398-021-01480-x"}, {"db": "pmc", "key": "PMC8324785"}], "notes": [], "created": "2021-08-19T13:42:02.005Z", "modified": "2021-12-07T13:20:40.961Z"}, {"entity": "publication", "iuid": "0e967e9b60494dd292eadc8c4e0724ce", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0e967e9b60494dd292eadc8c4e0724ce.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0e967e9b60494dd292eadc8c4e0724ce"}}, "title": "Leukocytes with chromosome Y loss have reduced abundance of the cell surface immunoprotein CD99.", "authors": [{"family": "Mattisson", "given": "Jonas", "initials": "J"}, {"family": "Danielsson", "given": "Marcus", "initials": "M"}, {"family": "Hammond", "given": "Maria", "initials": "M"}, {"family": "Davies", "given": "Hanna", "initials": "H"}, {"family": "Gallant", "given": "Caroline J", "initials": "CJ"}, {"family": "Nordlund", "given": "Jessica", "initials": "J"}, {"family": "Raine", "given": "Amanda", "initials": "A"}, {"family": "Ed\u00e9n", "given": "Malin", "initials": "M"}, {"family": "Kilander", "given": "Lena", "initials": "L"}, {"family": "Ingelsson", "given": "Martin", "initials": "M"}, {"family": "Dumanski", "given": "Jan P", "initials": "JP"}, {"family": "Halvardson", "given": "Jonatan", "initials": "J"}, {"family": "Forsberg", "given": "Lars A", "initials": "LA"}], "type": "journal article", "published": "2021-07-26", "journal": {"title": "Sci Rep", "issn": "2045-2322", "issn-l": "2045-2322", "volume": "11", "issue": "1", "pages": "15160"}, "abstract": "Mosaic loss of chromosome Y (LOY) in immune cells is a male-specific mutation associated with increased risk for morbidity and mortality. The CD99 gene, positioned in the pseudoautosomal regions of chromosomes X and Y, encodes a cell surface protein essential for several key properties of leukocytes and immune system functions. Here we used CITE-seq for simultaneous quantification of CD99 derived mRNA and cell surface CD99 protein abundance in relation to LOY in single cells. The abundance of CD99 molecules was lower on the surfaces of LOY cells compared with cells without this aneuploidy in all six types of leukocytes studied, while the abundance of CD proteins encoded by genes located on autosomal chromosomes were independent from LOY. These results connect LOY in single cells with immune related cellular properties at the protein level, providing mechanistic insight regarding disease vulnerability in men affected with mosaic chromosome Y loss in blood leukocytes.", "doi": "10.1038/s41598-021-94588-5", "pmid": "34312421", "labels": {"Affinity Proteomics Uppsala": "Technology development", "NGI Uppsala (SNP&SEQ Technology Platform)": "Collaborative", "National Genomics Infrastructure": "Collaborative", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-021-94588-5"}, {"db": "pmc", "key": "PMC8313698"}], "notes": [], "created": "2021-08-27T13:32:48.686Z", "modified": "2024-01-16T13:48:39.087Z"}, {"entity": "publication", "iuid": "7da26c536ad8449498fb9c9cf3193a48", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7da26c536ad8449498fb9c9cf3193a48.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7da26c536ad8449498fb9c9cf3193a48"}}, "title": "Genome of Pe\u015ftera Muierii skull shows high diversity and low mutational load in pre-glacial Europe.", "authors": [{"family": "Svensson", "given": "Emma", "initials": "E"}, {"family": "G\u00fcnther", "given": "Torsten", "initials": "T"}, {"family": "Hoischen", "given": "Alexander", "initials": "A"}, {"family": "Hervella", "given": "Montserrat", "initials": "M"}, {"family": "Munters", "given": "Arielle R", "initials": "AR"}, {"family": "Ioana", "given": "Mihai", "initials": "M"}, {"family": "Ridiche", "given": "Florin", "initials": "F"}, {"family": "Edlund", "given": "Hanna", "initials": "H"}, {"family": "van Deuren", "given": "Rosanne C", "initials": "RC"}, {"family": "Soficaru", "given": "Andrei", "initials": "A"}, {"family": "de-la-Rua", "given": "Concepci\u00f3n", "initials": "C"}, {"family": "Netea", "given": "Mihai G", "initials": "MG"}, {"family": "Jakobsson", "given": "Mattias", "initials": "M", "orcid": "0000-0001-7840-7853", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a4abe0fcb20492d9ec849c9fbf58a71.json"}}], "type": "journal article", "published": "2021-07-26", "journal": {"title": "Curr. Biol.", "issn": "1879-0445", "volume": "31", "issue": "14", "pages": "2973-2983.e9", "issn-l": "0960-9822"}, "abstract": "Few complete human genomes from the European Early Upper Palaeolithic (EUP) have been sequenced. Using novel sampling and DNA extraction approaches, we sequenced the genome of a woman from \"Pe\u015ftera Muierii,\" Romania who lived \u223c34,000 years ago to 13.5\u00d7 coverage. The genome shows similarities to modern-day Europeans, but she is not a direct ancestor. Although her cranium exhibits both modern human and Neanderthal features, the genome shows similar levels of Neanderthal admixture (\u223c3.1%) to most EUP humans but only half compared to the \u223c40,000-year-old Pe\u015ftera Oase 1. All EUP European hunter-gatherers display high genetic diversity, demonstrating that the severe loss of diversity occurred during and after the Last Glacial Maximum (LGM) rather than just during the out-of-Africa migration. The prevalence of genetic diseases is expected to increase with low diversity; however, pathogenic variant load was relatively constant from EUP to modern times, despite post-LGM hunter-gatherers having the lowest diversity ever observed among Europeans.", "doi": "10.1016/j.cub.2021.04.045", "pmid": "34010592", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "S0960-9822(21)00592-3"}], "notes": [], "created": "2021-05-25T06:50:37.310Z", "modified": "2024-01-16T13:48:39.094Z"}, {"entity": "publication", "iuid": "567f1e445eab4cdc987f086685d0350b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/567f1e445eab4cdc987f086685d0350b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/567f1e445eab4cdc987f086685d0350b"}}, "title": "A search for modifying genetic factors in CHEK2:c.1100delC breast cancer patients.", "authors": [{"family": "Wendt", "given": "Camilla", "initials": "C"}, {"family": "Muranen", "given": "Taru A", "initials": "TA"}, {"family": "Mielik\u00e4inen", "given": "Lotta", "initials": "L"}, {"family": "Thutkawkorapin", "given": "Jessada", "initials": "J"}, {"family": "Blomqvist", "given": "Carl", "initials": "C"}, {"family": "Jiao", "given": "Xiang", "initials": "X"}, {"family": "Ehrencrona", "given": "Hans", "initials": "H"}, {"family": "Tham", "given": "Emma", "initials": "E"}, {"family": "Arver", "given": "Brita", "initials": "B"}, {"family": "Melin", "given": "Beatrice", "initials": "B"}, {"family": "Kuchinskaya", "given": "Ekaterina", "initials": "E"}, {"family": "Stenmark Askmalm", "given": "Marie", "initials": "M"}, {"family": "Paulsson-Karlsson", "given": "Ylva", "initials": "Y"}, {"family": "Einbeigi", "given": "Zakaria", "initials": "Z"}, {"family": "von Wachenfeldt V\u00e4ppling", "given": "Anna", "initials": "A"}, {"family": "Kalso", "given": "Eija", "initials": "E"}, {"family": "Tasmuth", "given": "Tiina", "initials": "T"}, {"family": "Kallioniemi", "given": "Anne", "initials": "A"}, {"family": "Aittom\u00e4ki", "given": "Kristiina", "initials": "K"}, {"family": "Nevanlinna", "given": "Heli", "initials": "H"}, {"family": "Borg", "given": "\u00c5ke", "initials": "\u00c5"}, {"family": "Lindblom", "given": "Annika", "initials": "A"}], "type": "journal article", "published": "2021-07-20", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "11", "issue": "1", "pages": "14763", "issn-l": "2045-2322"}, "abstract": "The risk of breast cancer associated with CHEK2:c.1100delC is 2-threefold but higher in carriers with a family history of breast cancer than without, suggesting that other genetic loci in combination with CHEK2:c.1100delC confer an increased risk in a polygenic model. Part of the excess familial risk has been associated with common low-penetrance variants. This study aimed to identify genetic loci that modify CHEK2:c.1100delC-associated breast cancer risk by searching for candidate risk alleles that are overrepresented in CHEK2:c.1100delC carriers with breast cancer compared with controls. We performed whole-exome sequencing in 28 breast cancer cases with germline CHEK2:c.1100delC, 28 familial breast cancer cases and 70 controls. Candidate alleles were selected for validation in larger cohorts. One recessive synonymous variant, rs16897117, was suggested, but no overrepresentation of homozygous CHEK2:c.1100delC carriers was found in the following validation. Furthermore, 11 non-synonymous candidate alleles were suggested for further testing, but no significant difference in allele frequency could be detected in the validation in CHEK2:c.1100delC cases compared with familial breast cancer, sporadic breast cancer and controls. With this method, we found no support for a CHEK2:c.1100delC-specific genetic modifier. Further studies of CHEK2:c.1100delC genetic modifiers are warranted to improve risk assessment in clinical practice.", "doi": "10.1038/s41598-021-93926-x", "pmid": "34285278", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-021-93926-x"}, {"db": "pmc", "key": "PMC8292481"}], "notes": [], "created": "2021-09-13T06:42:16.025Z", "modified": "2024-01-16T13:48:39.103Z"}, {"entity": "publication", "iuid": "9e727294e08a4ca59f254d6dc320f817", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9e727294e08a4ca59f254d6dc320f817.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9e727294e08a4ca59f254d6dc320f817"}}, "title": "DNA Methylation-Based Interferon Scores Associate With Sub-Phenotypes in Primary Sj\u00f6gren's Syndrome.", "authors": [{"family": "Imgenberg-Kreuz", "given": "Juliana", "initials": "J"}, {"family": "Sandling", "given": "Johanna K", "initials": "JK"}, {"family": "Norheim", "given": "Katrine Br\u00e6kke", "initials": "KB"}, {"family": "Johnsen", "given": "Svein Joar Augl\u00e6nd", "initials": "SJA"}, {"family": "Omdal", "given": "Roald", "initials": "R"}, {"family": "Syv\u00e4nen", "given": "Ann-Christine", "initials": "AC"}, {"family": "Svenungsson", "given": "Elisabet", "initials": "E"}, {"family": "R\u00f6nnblom", "given": "Lars", "initials": "L"}, {"family": "Eloranta", "given": "Maija-Leena", "initials": "ML"}, {"family": "Nordmark", "given": "Gunnel", "initials": "G"}], "type": "journal article", "published": "2021-07-16", "journal": {"title": "Front Immunol", "issn": "1664-3224", "issn-l": "1664-3224", "volume": "12", "issue": null, "pages": "702037"}, "abstract": "Primary Sj\u00f6gren's syndrome (pSS) is an autoimmune inflammatory disease with profound clinical heterogeneity, where excessive activation of the type I interferon (IFN) system is considered one of the key mechanisms in disease pathogenesis. Here we present a DNA methylation-based IFN system activation score (DNAm IFN score) and investigate its potential associations with sub-phenotypes of pSS. The study comprised 100 Swedish patients with pSS and 587 Swedish controls. For replication, 48 patients with pSS from Stavanger, Norway, were included. IFN scores were calculated from DNA methylation levels at the IFN-induced genes RSAD2, IFIT1 and IFI44L. A high DNAm IFN score, defined as > meancontrols +2SDcontrols (IFN score >4.4), was observed in 59% of pSS patients and in 4% of controls (p=1.3x10-35). Patients with a high DNAm IFN score were on average seven years younger at symptom onset (p=0.017) and at diagnosis (p=3x10-3). The DNAm IFN score levels were significantly higher in pSS positive for both SSA and SSB antibodies compared to SSA/SSB negative patients (pdiscovery=1.9x10-8, preplication=7.8x10-4). In patients positive for both SSA subtypes Ro52 and Ro60, an increased score was identified compared to single positive patients (p=0.022). Analyzing the discovery and replication cohorts together, elevated DNAm IFN scores were observed in pSS with hypergammaglobulinemia (p=2x10-8) and low C4 (p=1.5x10-3) compared to patients without these manifestations. Patients < 70 years with ongoing lymphoma at DNA sampling or lymphoma at follow-up (n=7), presented an increased DNAm IFN score compared to pSS without lymphoma (p=0.025). In conclusion, the DNAm-based IFN score is a promising alternative to mRNA-based scores for identification of patients with activation of the IFN system and may be applied for patient stratification guiding treatment decisions, monitoring and inclusion in clinical trials.", "doi": "10.3389/fimmu.2021.702037", "pmid": "34335613", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Collaborative", "National Genomics Infrastructure": "Collaborative", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC8322981"}], "notes": [], "created": "2021-08-19T13:41:29.169Z", "modified": "2024-01-16T13:48:39.110Z"}, {"entity": "publication", "iuid": "8971713f42574a95affd0b83410a3a23", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8971713f42574a95affd0b83410a3a23.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8971713f42574a95affd0b83410a3a23"}}, "title": "Single-cell RNAseq and longitudinal proteomic analysis of a novel semi-spontaneous urothelial cancer model reveals tumor cell heterogeneity and pretumoral urine protein alterations.", "authors": [{"family": "Kerzeli", "given": "Iliana K", "initials": "IK"}, {"family": "Lord", "given": "Martin", "initials": "M"}, {"family": "Doroszko", "given": "Milena", "initials": "M"}, {"family": "Elgendy", "given": "Ramy", "initials": "R", "orcid": "0000-0002-2592-3448", "researcher": {"href": "https://publications.scilifelab.se/researcher/0a5ce4db4317446bb1ef113f7c6e8eb5.json"}}, {"family": "Chourlia", "given": "Aikaterini", "initials": "A"}, {"family": "Stepanek", "given": "Ivan", "initials": "I"}, {"family": "Larsson", "given": "Elinor", "initials": "E"}, {"family": "van Hooren", "given": "Luuk", "initials": "L"}, {"family": "Nelander", "given": "Sven", "initials": "S"}, {"family": "Malmstrom", "given": "Per-Uno", "initials": "PU"}, {"family": "Dragomir", "given": "Anca", "initials": "A"}, {"family": "Segersten", "given": "Ulrika", "initials": "U"}, {"family": "Mangsbo", "given": "Sara M", "initials": "SM", "orcid": "0000-0002-1355-2678", "researcher": {"href": "https://publications.scilifelab.se/researcher/c743bbcad6554f049c8fc5f64a6801bc.json"}}], "type": "journal article", "published": "2021-07-07", "journal": {"title": "PLoS ONE", "issn": "1932-6203", "volume": "16", "issue": "7", "pages": "e0253178", "issn-l": "1932-6203"}, "abstract": "Bladder cancer, one of the most prevalent malignancies worldwide, remains hard to classify due to a staggering molecular complexity. Despite a plethora of diagnostic tools and therapies, it is hard to outline the key steps leading up to the transition from high-risk non-muscle-invasive bladder cancer (NMIBC) to muscle-invasive bladder cancer (MIBC). Carcinogen-induced murine models can recapitulate urothelial carcinogenesis and natural anti-tumor immunity. Herein, we have developed and profiled a novel model of progressive NMIBC based on 10 weeks of OH-BBN exposure in hepatocyte growth factor/cyclin dependent kinase 4 (R24C) (Hgf-Cdk4R24C) mice. The profiling of the model was performed by histology grading, single cell transcriptomic and proteomic analysis, while the derivation of a tumorigenic cell line was validated and used to assess in vivo anti-tumor effects in response to immunotherapy. Established NMIBC was present in females at 10 weeks post OH-BBN exposure while neoplasia was not as advanced in male mice, however all mice progressed to MIBC. Single cell RNA sequencing analysis revealed an intratumoral heterogeneity also described in the human disease trajectory. Moreover, although immune activation biomarkers were elevated in urine during carcinogen exposure, anti-programmed cell death protein 1 (anti-PD1) monotherapy did not prevent tumor progression. Furthermore, anti-PD1 immunotherapy did not control the growth of subcutaneous tumors formed by the newly derived urothelial cancer cell line. However, treatment with CpG-oligodeoxynucleotides (ODN) significantly decreased tumor volume, but only in females. In conclusion, the molecular map of this novel preclinical model of bladder cancer provides an opportunity to further investigate pharmacological therapies ahead with regards to both targeted drugs and immunotherapies to improve the strategies of how we should tackle the heterogeneous tumor microenvironment in urothelial bladder cancer to improve responses rates in the clinic.", "doi": "10.1371/journal.pone.0253178", "pmid": "34232958", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Affinity Proteomics Uppsala": "Service"}, "xrefs": [{"db": "pii", "key": "PONE-D-20-39368"}, {"db": "pmc", "key": "PMC8262791"}], "notes": [], "created": "2021-12-07T21:40:24.842Z", "modified": "2021-12-10T15:10:01.474Z"}, {"entity": "publication", "iuid": "42bc4acdfb2e4d4a8906a7407100584a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/42bc4acdfb2e4d4a8906a7407100584a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/42bc4acdfb2e4d4a8906a7407100584a"}}, "title": "Common and mutation specific phenotypes of KRAS and BRAF mutations in colorectal cancer cells revealed by integrative -omics analysis.", "authors": [{"family": "Kundu", "given": "Snehangshu", "initials": "S"}, {"family": "Ali", "given": "Muhammad Akhtar", "initials": "MA"}, {"family": "Handin", "given": "Niklas", "initials": "N"}, {"family": "Conway", "given": "Louis P", "initials": "LP"}, {"family": "Rendo", "given": "Veronica", "initials": "V"}, {"family": "Artursson", "given": "Per", "initials": "P"}, {"family": "He", "given": "Liqun", "initials": "L"}, {"family": "Globisch", "given": "Daniel", "initials": "D"}, {"family": "Sj\u00f6blom", "given": "Tobias", "initials": "T"}], "type": "journal article", "published": "2021-07-07", "journal": {"title": "J. Exp. Clin. Cancer Res.", "issn": "1756-9966", "volume": "40", "issue": "1", "pages": "225", "issn-l": "1756-9966"}, "abstract": "Genes in the Ras pathway have somatic mutations in at least 60 % of colorectal cancers. Despite activating the same pathway, the BRAF V600E mutation and the prevalent mutations in codon 12 and 13 of KRAS have all been linked to different clinical outcomes, but the molecular mechanisms behind these differences largely remain to be clarified.\n\nTo characterize the similarities and differences between common activating KRAS mutations and between KRAS and BRAF mutations, we used genome editing to engineer KRAS G12C/D/V and G13D mutations in colorectal cancer cells that had their mutant BRAF V600E allele removed and subjected them to transcriptome sequencing, global proteomics and metabolomics analyses.\n\nBy intersecting differentially expressed genes, proteins and metabolites, we uncovered (i) two-fold more regulated genes and proteins when comparing KRAS to BRAF mutant cells to those lacking Ras pathway mutation, (ii) five differentially expressed proteins in KRAS mutants compared to cells lacking Ras pathway mutation (IFI16, S100A10, CD44, GLRX and AHNAK2) and 6 (CRABP2, FLNA, NXN, LCP1, S100A10 and S100A2) compared to BRAF mutant cells, (iii) 19 proteins expressed differentially in a KRAS mutation specific manner versus BRAF V600E cells, (iv) regulation of the Integrin Linked Kinase pathway by KRAS but not BRAF mutation, (v) regulation of amino acid metabolism, particularly of the tyrosine, histidine, arginine and proline pathways, the urea cycle and purine metabolism by Ras pathway mutations, (vi) increased free carnitine in KRAS and BRAF mutant RKO cells.\n\nThis comprehensive integrative -omics analysis confirms known and adds novel genes, proteins and metabolic pathways regulated by mutant KRAS and BRAF signaling in colorectal cancer. The results from the new model systems presented here can inform future development of diagnostic and therapeutic approaches targeting tumors with KRAS and BRAF mutations.", "doi": "10.1186/s13046-021-02025-2", "pmid": "34233735", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1186/s13046-021-02025-2"}, {"db": "pmc", "key": "PMC8265010"}], "notes": [], "created": "2021-12-07T21:36:43.108Z", "modified": "2024-01-16T13:48:39.137Z"}, {"entity": "publication", "iuid": "ed820a56d6594ec48ebf8d5d78c801d1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ed820a56d6594ec48ebf8d5d78c801d1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ed820a56d6594ec48ebf8d5d78c801d1"}}, "title": "Comparative analyses of the Hymenoscyphus fraxineus and Hymenoscyphus albidus genomes reveals potentially adaptive differences in secondary metabolite and transposable element repertoires.", "authors": [{"family": "Elfstrand", "given": "Malin", "initials": "M"}, {"family": "Chen", "given": "Jun", "initials": "J"}, {"family": "Cleary", "given": "Michelle", "initials": "M"}, {"family": "Halecker", "given": "Sandra", "initials": "S"}, {"family": "Ihrmark", "given": "Katarina", "initials": "K"}, {"family": "Karlsson", "given": "Magnus", "initials": "M"}, {"family": "Davydenko", "given": "Kateryna", "initials": "K"}, {"family": "Stenlid", "given": "Jan", "initials": "J"}, {"family": "Stadler", "given": "Marc", "initials": "M"}, {"family": "Durling", "given": "Mikael Brandstr\u00f6m", "initials": "MB"}], "type": "journal article", "published": "2021-07-04", "journal": {"title": "BMC Genomics", "issn": "1471-2164", "volume": "22", "issue": "1", "pages": "503", "issn-l": "1471-2164"}, "abstract": "The dieback epidemic decimating common ash (Fraxinus excelsior) in Europe is caused by the invasive fungus Hymenoscyphus fraxineus. In this study we analyzed the genomes of H. fraxineus and H. albidus, its native but, now essentially displaced, non-pathogenic sister species, and compared them with several other members of Helotiales. The focus of the analyses was to identify signals in the genome that may explain the rapid establishment of H. fraxineus and displacement of H. albidus.\n\nThe genomes of H. fraxineus and H. albidus showed a high level of synteny and identity. The assembly of H. fraxineus is 13 Mb longer than that of H. albidus', most of this difference can be attributed to higher dispersed repeat content (i.e. transposable elements [TEs]) in H. fraxineus. In general, TE families in H. fraxineus showed more signals of repeat-induced point mutations (RIP) than in H. albidus, especially in Long-terminal repeat (LTR)/Copia and LTR/Gypsy elements. Comparing gene family expansions and 1:1 orthologs, relatively few genes show signs of positive selection between species. However, several of those did appeared to be associated with secondary metabolite genes families, including gene families containing two of the genes in the H. fraxineus-specific, hymenosetin biosynthetic gene cluster (BGC).\n\nThe genomes of H. fraxineus and H. albidus show a high degree of synteny, and are rich in both TEs and BGCs, but the genomic signatures also indicated that H. albidus may be less well equipped to adapt and maintain its ecological niche in a rapidly changing environment.", "doi": "10.1186/s12864-021-07837-2", "pmid": "34217229", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1186/s12864-021-07837-2"}, {"db": "pmc", "key": "PMC8254937"}], "notes": [], "created": "2021-12-07T21:36:40.820Z", "modified": "2021-12-07T21:36:40.833Z"}, {"entity": "publication", "iuid": "ed26a59be0924ddea2f556caaa4136c5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ed26a59be0924ddea2f556caaa4136c5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ed26a59be0924ddea2f556caaa4136c5"}}, "title": "Whole genome sequencing reveals high differentiation, low levels of genetic diversity and short runs of homozygosity among Swedish wels catfish.", "authors": [{"family": "Jensen", "given": "Axel", "initials": "A", "orcid": "0000-0003-1766-560X", "researcher": {"href": "https://publications.scilifelab.se/researcher/7f139b7f3dac49e28ef6430637d88592.json"}}, {"family": "Lillie", "given": "Mette", "initials": "M", "orcid": "0000-0001-8714-0812", "researcher": {"href": "https://publications.scilifelab.se/researcher/3ce02b2116c0417e8a4dcd578f45983b.json"}}, {"family": "Bergstr\u00f6m", "given": "Kristofer", "initials": "K", "orcid": "0000-0002-6570-5525", "researcher": {"href": "https://publications.scilifelab.se/researcher/8bcd7d3b7b47405185ba0d0062111a13.json"}}, {"family": "Larsson", "given": "Per", "initials": "P", "orcid": "0000-0003-0344-1939", "researcher": {"href": "https://publications.scilifelab.se/researcher/c4aa4fd680f64fe294f8bdd91218581a.json"}}, {"family": "H\u00f6glund", "given": "Jacob", "initials": "J", "orcid": "0000-0002-5840-779X", "researcher": {"href": "https://publications.scilifelab.se/researcher/8e1eb3c1903f4a97a4c585a2dee3b05f.json"}}], "type": "journal article", "published": "2021-07-00", "journal": {"title": "Heredity (Edinb)", "issn": "1365-2540", "volume": "127", "issue": "1", "pages": "79-91", "issn-l": "0018-067X"}, "abstract": "The use of genetic markers in the context of conservation is largely being outcompeted by whole-genome data. Comparative studies between the two are sparse, and the knowledge about potential effects of this methodology shift is limited. Here, we used whole-genome sequencing data to assess the genetic status of peripheral populations of the wels catfish (Silurus glanis), and discuss the results in light of a recent microsatellite study of the same populations. The Swedish populations of the wels catfish have suffered from severe declines during the last centuries and persists in only a few isolated water systems. Fragmented populations generally are at greater risk of extinction, for example due to loss of genetic diversity, and may thus require conservation actions. We sequenced individuals from the three remaining native populations (B\u00e5ven, Em\u00e5n, and M\u00f6ckeln) and one reintroduced population of admixed origin (Helge \u00e5), and found that genetic diversity was highest in Em\u00e5n but low overall, with strong differentiation among the populations. No signature of recent inbreeding was found, but a considerable number of short runs of homozygosity were present in all populations, likely linked to historically small population sizes and bottleneck events. Genetic substructure within any of the native populations was at best weak. Individuals from the admixed population Helge \u00e5 shared most genetic ancestry with the B\u00e5ven population (72%). Our results are largely in agreement with the microsatellite study, and stresses the need to protect these isolated populations at the northern edge of the distribution of the species.", "doi": "10.1038/s41437-021-00438-5", "pmid": "33963302", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41437-021-00438-5"}, {"db": "pmc", "key": "PMC8249479"}], "notes": [], "created": "2021-12-07T21:26:42.688Z", "modified": "2024-01-16T13:48:39.185Z"}, {"entity": "publication", "iuid": "2ed7430a7f8f40e986cd3c251f8e8353", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2ed7430a7f8f40e986cd3c251f8e8353.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2ed7430a7f8f40e986cd3c251f8e8353"}}, "title": "Variants in BANK1 are associated with lupus nephritis of European ancestry.", "authors": [{"family": "Bolin", "given": "Karin", "initials": "K"}, {"family": "Imgenberg-Kreuz", "given": "Juliana", "initials": "J"}, {"family": "Leonard", "given": "Dag", "initials": "D"}, {"family": "Sandling", "given": "Johanna K", "initials": "JK"}, {"family": "Alexsson", "given": "Andrei", "initials": "A"}, {"family": "Pucholt", "given": "Pascal", "initials": "P", "orcid": "0000-0003-3342-1373", "researcher": {"href": "https://publications.scilifelab.se/researcher/61a214ff2d494b568cb6da944e858acf.json"}}, {"family": "Haarhaus", "given": "Malena Loberg", "initials": "ML"}, {"family": "Alml\u00f6f", "given": "Jonas Carlsson", "initials": "JC"}, {"family": "Nititham", "given": "Joanne", "initials": "J"}, {"family": "J\u00f6nsen", "given": "Andreas", "initials": "A"}, {"family": "Sj\u00f6wall", "given": "Christopher", "initials": "C", "orcid": "0000-0003-0900-2048", "researcher": {"href": "https://publications.scilifelab.se/researcher/fe4dd47b8ca1436e8a26fdea33f5e7f6.json"}}, {"family": "Bengtsson", "given": "Anders A", "initials": "AA"}, {"family": "Rantap\u00e4\u00e4-Dahlqvist", "given": "Solbritt", "initials": "S"}, {"family": "Svenungsson", "given": "Elisabet", "initials": "E"}, {"family": "Gunnarsson", "given": "Iva", "initials": "I"}, {"family": "Syv\u00e4nen", "given": "Ann-Christine", "initials": "AC"}, {"family": "Lerang", "given": "Karoline", "initials": "K"}, {"family": "Troldborg", "given": "Anne", "initials": "A"}, {"family": "Voss", "given": "Anne", "initials": "A"}, {"family": "Molberg", "given": "\u00d8yvind", "initials": "\u00d8"}, {"family": "Jacobsen", "given": "S\u00f8ren", "initials": "S"}, {"family": "Criswell", "given": "Lindsey", "initials": "L"}, {"family": "R\u00f6nnblom", "given": "Lars", "initials": "L", "orcid": "0000-0001-9403-6503", "researcher": {"href": "https://publications.scilifelab.se/researcher/053ed3b657124a1bab3a78dc685556e6.json"}}, {"family": "Nordmark", "given": "Gunnel", "initials": "G", "orcid": "0000-0002-3829-7431", "researcher": {"href": "https://publications.scilifelab.se/researcher/188fda53498740dbb007441cc94bb1ad.json"}}], "type": "journal article", "published": "2021-07-00", "journal": {"title": "Genes Immun.", "issn": "1476-5470", "issn-l": "1466-4879", "volume": "22", "issue": "3", "pages": "194-202"}, "abstract": "The genetic background of lupus nephritis (LN) has not been completely elucidated. We performed a case-only study of 2886 SLE patients, including 947 (33%) with LN. Renal biopsies were available from 396 patients. The discovery cohort (Sweden, n = 1091) and replication cohort 1 (US, n = 962) were genotyped on the Immunochip and replication cohort 2 (Denmark/Norway, n = 833) on a custom array. Patients with LN, proliferative nephritis, or LN with end-stage renal disease were compared with SLE without nephritis. Six loci were associated with LN (p < 1 \u00d7 10-4, NFKBIA, CACNA1S, ITGA1, BANK1, OR2Y, and ACER3) in the discovery cohort. Variants in BANK1 showed the strongest association with LN in replication cohort 1 (p = 9.5 \u00d7 10-4) and proliferative nephritis in a meta-analysis of discovery and replication cohort 1. There was a weak association between BANK1 and LN in replication cohort 2 (p = 0.052), and in the meta-analysis of all three cohorts the association was strengthened (p = 2.2 \u00d7 10-7). DNA methylation data in 180 LN patients demonstrated methylation quantitative trait loci (meQTL) effects between a CpG site and BANK1 variants. To conclude, we describe genetic variations in BANK1 associated with LN and evidence for genetic regulation of DNA methylation within the BANK1 locus. This indicates a role for BANK1 in LN pathogenesis.", "doi": "10.1038/s41435-021-00142-8", "pmid": "34127828", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Collaborative", "National Genomics Infrastructure": "Collaborative", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41435-021-00142-8"}, {"db": "pmc", "key": "PMC8277572"}], "notes": [], "created": "2021-08-19T13:41:28.034Z", "modified": "2024-01-16T13:48:39.193Z"}, {"entity": "publication", "iuid": "ddf03b5f1f1c47209a97f015b429d9c4", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ddf03b5f1f1c47209a97f015b429d9c4.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ddf03b5f1f1c47209a97f015b429d9c4"}}, "title": "On the origin of the widespread self-compatible allotetraploid Capsella bursa-pastoris (Brassicaceae).", "authors": [{"family": "Bachmann", "given": "J\u00f6rg A", "initials": "JA", "orcid": "0000-0002-7212-813X", "researcher": {"href": "https://publications.scilifelab.se/researcher/7dadd1300e85443d8ee98a2d58d08a4b.json"}}, {"family": "Tedder", "given": "Andrew", "initials": "A", "orcid": "0000-0002-7378-4673", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a29b3c1160f46bf8b21e331268eb4b1.json"}}, {"family": "Fracassetti", "given": "Marco", "initials": "M", "orcid": "0000-0002-2962-2669", "researcher": {"href": "https://publications.scilifelab.se/researcher/695213cdd1a645cbbf10d44122237b18.json"}}, {"family": "Steige", "given": "Kim A", "initials": "KA"}, {"family": "Lafon-Placette", "given": "Cl\u00e9ment", "initials": "C"}, {"family": "K\u00f6hler", "given": "Claudia", "initials": "C", "orcid": "0000-0002-2619-4857", "researcher": {"href": "https://publications.scilifelab.se/researcher/accd3f9307614c8ab67154dd5e50cdac.json"}}, {"family": "Slotte", "given": "Tanja", "initials": "T"}], "type": "journal article", "published": "2021-07-00", "journal": {"title": "Heredity (Edinb)", "issn": "1365-2540", "issn-l": "0018-067X", "volume": "127", "issue": "1", "pages": "124-134"}, "abstract": "Polyploidy, or whole-genome duplication, is a common speciation mechanism in plants. An important barrier to polyploid establishment is a lack of compatible mates. Because self-compatibility alleviates this problem, it has long been hypothesized that there should be an association between polyploidy and self-compatibility (SC), but empirical support for this prediction is mixed. Here, we investigate whether the molecular makeup of the Brassicaceae self-incompatibility (SI) system, and specifically dominance relationships among S-haplotypes mediated by small RNAs, could facilitate loss of SI in allopolyploid crucifers. We focus on the allotetraploid species Capsella bursa-pastoris, which formed ~300 kya by hybridization and whole-genome duplication involving progenitors from the lineages of Capsella orientalis and Capsella grandiflora. We conduct targeted long-read sequencing to assemble and analyze eight full-length S-locus haplotypes, representing both homeologous subgenomes of C. bursa-pastoris. We further analyze small RNA (sRNA) sequencing data from flower buds to identify candidate dominance modifiers. We find that C. orientalis-derived S-haplotypes of C. bursa-pastoris harbor truncated versions of the male SI specificity gene SCR and express a conserved sRNA-based candidate dominance modifier with a target in the C. grandiflora-derived S-haplotype. These results suggest that pollen-level dominance may have facilitated loss of SI in C. bursa-pastoris. Finally, we demonstrate that spontaneous somatic tetraploidization after a wide cross between C. orientalis and C. grandiflora can result in production of self-compatible tetraploid offspring. We discuss the implications of this finding on the mode of formation of this widespread weed.", "doi": "10.1038/s41437-021-00434-9", "pmid": "33875831", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41437-021-00434-9"}, {"db": "pmc", "key": "PMC8249383"}], "notes": [], "created": "2021-09-02T09:52:09.038Z", "modified": "2024-01-16T13:48:39.247Z"}, {"entity": "publication", "iuid": "21bd29fecb7746a989295e2f8dbf5bc1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/21bd29fecb7746a989295e2f8dbf5bc1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/21bd29fecb7746a989295e2f8dbf5bc1"}}, "title": "Insights into the multitrophic interactions between the biocontrol agent Bacillus subtilis MBI 600, the pathogen Botrytis cinerea and their plant host.", "authors": [{"family": "Samaras", "given": "Anastasios", "initials": "A"}, {"family": "Karaoglanidis", "given": "George S", "initials": "GS"}, {"family": "Tzelepis", "given": "Georgios", "initials": "G"}], "type": "evaluation study", "published": "2021-07-00", "journal": {"title": "Microbiol Res", "issn": "1618-0623", "volume": "248", "pages": "126752", "issn-l": null}, "abstract": "Botrytis cinerea is a plant pathogen causing the gray mold disease in a plethora of host plants. The control of the disease is based mostly on chemical pesticides, which are responsible for environmental pollution, while they also pose risks for human health. Furthermore, B. cinerea resistant isolates have been identified against many fungicide groups, making the control of this disease challenging. The application of biocontrol agents can be a possible solution, but requires deep understanding of the molecular mechanisms in order to be effective. In this study, we investigated the multitrophic interactions between the biocontrol agent Bacillus subtilis MBI 600, a new commercialized biopesticide, the pathogen B. cinerea and their plant host. Our analysis showed that this biocontrol agent reduced B. cinerea mycelial growth in vitro, and was able to suppress the disease incidence on cucumber plants. Moreover, treatment with B. subtilis led to induction of genes involved in plant immunity. RNA-seq analysis of B. cinerea transcriptome upon exposure to bacterial secretome, showed that genes coding for MFS and ABC transporters were highly induced. Deletion of the Bcmfs1 MFS transporter gene, using a CRISP/Cas9 editing method, affected its virulence and the tolerance of B. cinerea to bacterial secondary metabolites. These findings suggest that specific detoxification transporters are involved in these interactions, with crucial role in different aspects of B. cinerea physiology.", "doi": "10.1016/j.micres.2021.126752", "pmid": "33839506", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pii", "key": "S0944-5013(21)00058-6"}], "notes": [], "created": "2022-01-16T21:32:37.830Z", "modified": "2022-01-16T21:32:37.859Z"}, {"entity": "publication", "iuid": "f2d82122377a4bd19678ec33ef4e5761", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f2d82122377a4bd19678ec33ef4e5761.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f2d82122377a4bd19678ec33ef4e5761"}}, "title": "Extreme Y chromosome polymorphism corresponds to five male reproductive morphs of a freshwater fish.", "authors": [{"family": "Sandkam", "given": "Benjamin A", "initials": "BA", "orcid": "0000-0002-5043-9295", "researcher": {"href": "https://publications.scilifelab.se/researcher/f002e335e3d34b93b84cfc886defd6e3.json"}}, {"family": "Almeida", "given": "Pedro", "initials": "P", "orcid": "0000-0001-6790-8687", "researcher": {"href": "https://publications.scilifelab.se/researcher/bb2e2881fe7449659d89e9beb407e0a4.json"}}, {"family": "Darolti", "given": "Iulia", "initials": "I"}, {"family": "Furman", "given": "Benjamin L S", "initials": "BLS"}, {"family": "van der Bijl", "given": "Wouter", "initials": "W", "orcid": "0000-0002-7366-1868", "researcher": {"href": "https://publications.scilifelab.se/researcher/88e29dfbe1a746c8bd87596c3df7d50e.json"}}, {"family": "Morris", "given": "Jake", "initials": "J", "orcid": "0000-0002-0137-2610", "researcher": {"href": "https://publications.scilifelab.se/researcher/e5c8a8618c7a4144b6620da18f923f19.json"}}, {"family": "Bourne", "given": "Godfrey R", "initials": "GR"}, {"family": "Breden", "given": "Felix", "initials": "F"}, {"family": "Mank", "given": "Judith E", "initials": "JE"}], "type": "journal article", "published": "2021-07-00", "journal": {"title": "Nat Ecol Evol", "issn": "2397-334X", "volume": "5", "issue": "7", "pages": "939-948", "issn-l": "2397-334X"}, "abstract": "Loss of recombination between sex chromosomes often depletes Y chromosomes of functional content and genetic variation, which might limit their potential to generate adaptive diversity. Males of the freshwater fish Poecilia parae occur as one of five discrete morphs, all of which shoal together in natural populations where morph frequency has been stable for over 50 years. Each morph uses a different complex reproductive strategy and morphs differ dramatically in colour, body size and mating behaviour. Morph phenotype is passed perfectly from father to son, indicating there are five Y haplotypes segregating in the species, which encode the complex male morph characteristics. Here, we examine Y diversity in natural populations of P. parae. Using linked-read sequencing on multiple P. parae females and males of all five morphs, we find that the genetic architecture of the male morphs evolved on the Y chromosome after recombination suppression had occurred with the X. Comparing Y chromosomes between each of the morphs, we show that, although the Ys of the three minor morphs that differ in colour are highly similar, there are substantial amounts of unique genetic material and divergence between the Ys of the three major morphs that differ in reproductive strategy, body size and mating behaviour. Altogether, our results suggest that the Y chromosome is able to overcome the constraints of recombination loss to generate extreme diversity, resulting in five discrete Y chromosomes that control complex reproductive strategies.", "doi": "10.1038/s41559-021-01452-w", "pmid": "33958755", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41559-021-01452-w"}], "notes": [], "created": "2021-12-07T21:28:20.241Z", "modified": "2021-12-07T21:28:20.334Z"}, {"entity": "publication", "iuid": "beb46404be78423ebb108a8aed3fceee", "links": {"self": {"href": "https://publications.scilifelab.se/publication/beb46404be78423ebb108a8aed3fceee.json"}, "display": {"href": "https://publications.scilifelab.se/publication/beb46404be78423ebb108a8aed3fceee"}}, "title": "Combined prenatal Lactobacillus reuteri and \u03c9-3 supplementation synergistically modulates DNA methylation in neonatal T helper cells.", "authors": [{"family": "Huoman", "given": "Johanna", "initials": "J", "orcid": "0000-0003-2509-2418", "researcher": {"href": "https://publications.scilifelab.se/researcher/471444d05e834a9b86a5a6d187da2c04.json"}}, {"family": "Mart\u00ednez-Enguita", "given": "David", "initials": "D"}, {"family": "Olsson", "given": "Elin", "initials": "E"}, {"family": "Ernerudh", "given": "Jan", "initials": "J"}, {"family": "Nilsson", "given": "Lennart", "initials": "L"}, {"family": "Duch\u00e9n", "given": "Karel", "initials": "K"}, {"family": "Gustafsson", "given": "Mika", "initials": "M"}, {"family": "Jenmalm", "given": "Maria C", "initials": "MC"}], "type": "journal article", "published": "2021-06-30", "journal": {"title": "Clin Epigenetics", "issn": "1868-7083", "issn-l": "1868-7075", "volume": "13", "issue": "1", "pages": "135"}, "abstract": "Environmental exposures may alter DNA methylation patterns of T helper cells. As T helper cells are instrumental for allergy development, changes in methylation patterns may constitute a mechanism of action for allergy preventive interventions. While epigenetic effects of separate perinatal probiotic or \u03c9-3 fatty acid supplementation have been studied previously, the combined treatment has not been assessed. We aimed to investigate epigenome-wide DNA methylation patterns from a sub-group of children in an on-going randomised double-blind placebo-controlled allergy prevention trial using pre- and postnatal combined Lactobacillus reuteri and \u03c9-3 fatty acid treatment. To this end, > 866000 CpG sites (MethylationEPIC 850K array) in cord blood CD4+ T cells were examined in samples from all four study arms (double-treatment: n = 18, single treatments: probiotics n = 16, \u03c9-3 n = 15, and double placebo: n = 14). Statistical and bioinformatic analyses identified treatment-associated differentially methylated CpGs and genes, which were used to identify putatively treatment-induced network modules. Pathway analyses inferred biological relevance, and comparisons were made to an independent allergy data set.\r\n\r\nComparing the active treatments to the double placebo group, most differentially methylated CpGs and genes were hypermethylated, possibly suggesting induction of transcriptional inhibition. The double-treated group showed the largest number of differentially methylated CpGs, of which many were unique, suggesting synergy between interventions. Clusters within the double-treated network module consisted of immune-related pathways, including T cell receptor signalling, and antigen processing and presentation, with similar pathways revealed for the single-treatment modules. CpGs derived from differential methylation and network module analyses were enriched in an independent allergy data set, particularly in the double-treatment group, proposing treatment-induced DNA methylation changes as relevant for allergy development.\r\n\r\nPrenatal L. reuteri and/or \u03c9-3 fatty acid treatment results in hypermethylation and affects immune- and allergy-related pathways in neonatal T helper cells, with potentially synergistic effects between the interventions and relevance for allergic disease. Further studies need to address these findings on a transcriptional level, and whether the results associate to allergy development in the children. Understanding the role of DNA methylation in regulating effects of perinatal probiotic and \u03c9-3 interventions may provide essential knowledge in the development of efficacious allergy preventive strategies. Trial registration ClinicalTrials.gov, ClinicalTrials.gov-ID: NCT01542970. Registered 27th of February 2012-Retrospectively registered, https://clinicaltrials.gov/ct2/show/NCT01542970 .", "doi": "10.1186/s13148-021-01115-4", "pmid": "34193262", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pii", "key": "10.1186/s13148-021-01115-4"}, {"db": "pmc", "key": "PMC8247185"}, {"db": "ClinicalTrials.gov", "key": "NCT01542970"}], "notes": [], "created": "2021-08-19T13:41:37.013Z", "modified": "2021-12-07T13:21:25.193Z"}, {"entity": "publication", "iuid": "ee600cff45c440d3a228c2c95aace408", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ee600cff45c440d3a228c2c95aace408.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ee600cff45c440d3a228c2c95aace408"}}, "title": "Genome-wide association studies identify 137 genetic loci for DNA methylation biomarkers of aging.", "authors": [{"family": "McCartney", "given": "Daniel L", "initials": "DL"}, {"family": "Min", "given": "Josine L", "initials": "JL"}, {"family": "Richmond", "given": "Rebecca C", "initials": "RC"}, {"family": "Lu", "given": "Ake T", "initials": "AT"}, {"family": "Sobczyk", "given": "Maria K", "initials": "MK"}, {"family": "Davies", "given": "Gail", "initials": "G"}, {"family": "Broer", "given": "Linda", "initials": "L"}, {"family": "Guo", "given": "Xiuqing", "initials": "X"}, {"family": "Jeong", "given": "Ayoung", "initials": "A"}, {"family": "Jung", "given": "Jeesun", "initials": "J"}, {"family": "Kasela", "given": "Silva", "initials": "S"}, {"family": "Katrinli", "given": "Seyma", "initials": "S"}, {"family": "Kuo", "given": "Pei-Lun", "initials": "P"}, {"family": "Matias-Garcia", "given": "Pamela R", "initials": "PR"}, {"family": "Mishra", "given": "Pashupati P", "initials": "PP"}, {"family": "Nygaard", "given": "Marianne", "initials": "M"}, {"family": "Palviainen", "given": "Teemu", "initials": "T"}, {"family": "Patki", "given": "Amit", "initials": "A"}, {"family": "Raffield", "given": "Laura M", "initials": "LM"}, {"family": "Ratliff", "given": "Scott M", "initials": "SM"}, {"family": "Richardson", "given": "Tom G", "initials": "TG"}, {"family": "Robinson", "given": "Oliver", "initials": "O"}, {"family": "Soerensen", "given": "Mette", "initials": "M"}, {"family": "Sun", "given": "Dianjianyi", "initials": "D"}, {"family": "Tsai", "given": "Pei-Chien", "initials": "P"}, {"family": "van der Zee", "given": "Matthijs D", "initials": "MD"}, {"family": "Walker", "given": "Rosie M", "initials": "RM"}, {"family": "Wang", "given": "Xiaochuan", "initials": "X"}, {"family": "Wang", "given": "Yunzhang", "initials": "Y"}, {"family": "Xia", "given": "Rui", "initials": "R"}, {"family": "Xu", "given": "Zongli", "initials": "Z"}, {"family": "Yao", "given": "Jie", "initials": "J"}, {"family": "Zhao", "given": "Wei", "initials": "W"}, {"family": "Correa", "given": "Adolfo", "initials": "A"}, {"family": "Boerwinkle", "given": "Eric", "initials": "E"}, {"family": "Dugu\u00e9", "given": "Pierre-Antoine", "initials": "P"}, {"family": "Durda", "given": "Peter", "initials": "P"}, {"family": "Elliott", "given": "Hannah R", "initials": "HR"}, {"family": "Gieger", "given": "Christian", "initials": "C"}, {"family": "Genetics of DNA Methylation Consortium", "given": "", "initials": ""}, {"family": "de Geus", "given": "Eco J C", "initials": "EJC"}, {"family": "Harris", "given": "Sarah E", "initials": "SE"}, {"family": "Hemani", "given": "Gibran", "initials": "G"}, {"family": "Imboden", "given": "Medea", "initials": "M"}, {"family": "K\u00e4h\u00f6nen", "given": "Mika", "initials": "M"}, {"family": "Kardia", "given": "Sharon L R", "initials": "SLR"}, {"family": "Kresovich", "given": "Jacob K", "initials": "JK"}, {"family": "Li", "given": "Shengxu", "initials": "S"}, {"family": "Lunetta", "given": "Kathryn L", "initials": "KL"}, {"family": "Mangino", "given": "Massimo", "initials": "M"}, {"family": "Mason", "given": "Dan", "initials": "D"}, {"family": "McIntosh", "given": "Andrew M", "initials": "AM"}, {"family": "Mengel-From", "given": "Jonas", "initials": "J"}, {"family": "Moore", "given": "Ann Zenobia", "initials": "AZ"}, {"family": "Murabito", "given": "Joanne M", "initials": "JM"}, {"family": "NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium", "given": "", "initials": ""}, {"family": "Ollikainen", "given": "Miina", "initials": "M"}, {"family": "Pankow", "given": "James S", "initials": "JS"}, {"family": "Pedersen", "given": "Nancy L", "initials": "NL"}, {"family": "Peters", "given": "Annette", "initials": "A"}, {"family": "Polidoro", "given": "Silvia", "initials": "S"}, {"family": "Porteous", "given": "David J", "initials": "DJ"}, {"family": "Raitakari", "given": "Olli", "initials": "O"}, {"family": "Rich", "given": "Stephen S", "initials": "SS"}, {"family": "Sandler", "given": "Dale P", "initials": "DP"}, {"family": "Sillanp\u00e4\u00e4", "given": "Elina", "initials": "E"}, {"family": "Smith", "given": "Alicia K", "initials": "AK"}, {"family": "Southey", "given": "Melissa C", "initials": "MC"}, {"family": "Strauch", "given": "Konstantin", "initials": "K"}, {"family": "Tiwari", "given": "Hemant", "initials": "H"}, {"family": "Tanaka", "given": "Toshiko", "initials": "T"}, {"family": "Tillin", "given": "Therese", "initials": "T"}, {"family": "Uitterlinden", "given": "Andre G", "initials": "AG"}, {"family": "Van Den Berg", "given": "David J", "initials": "DJ"}, {"family": "van Dongen", "given": "Jenny", "initials": "J"}, {"family": "Wilson", "given": "James G", "initials": "JG"}, {"family": "Wright", "given": "John", "initials": "J"}, {"family": "Yet", "given": "Idil", "initials": "I"}, {"family": "Arnett", "given": "Donna", "initials": "D"}, {"family": "Bandinelli", "given": "Stefania", "initials": "S"}, {"family": "Bell", "given": "Jordana T", "initials": "JT"}, {"family": "Binder", "given": "Alexandra M", "initials": "AM"}, {"family": "Boomsma", "given": "Dorret I", "initials": "DI"}, {"family": "Chen", "given": "Wei", "initials": "W"}, {"family": "Christensen", "given": "Kaare", "initials": "K"}, {"family": "Conneely", "given": "Karen N", "initials": "KN"}, {"family": "Elliott", "given": "Paul", "initials": "P"}, {"family": "Ferrucci", "given": "Luigi", "initials": "L"}, {"family": "Fornage", "given": "Myriam", "initials": "M"}, {"family": "H\u00e4gg", "given": "Sara", "initials": "S"}, {"family": "Hayward", "given": "Caroline", "initials": "C"}, {"family": "Irvin", "given": "Marguerite", "initials": "M"}, {"family": "Kaprio", "given": "Jaakko", "initials": "J"}, {"family": "Lawlor", "given": "Deborah A", "initials": "DA"}, {"family": "Lehtim\u00e4ki", "given": "Terho", "initials": "T"}, {"family": "Lohoff", "given": "Falk W", "initials": "FW"}, {"family": "Milani", "given": "Lili", "initials": "L"}, {"family": "Milne", "given": "Roger L", "initials": "RL"}, {"family": "Probst-Hensch", "given": "Nicole", "initials": "N"}, {"family": "Reiner", "given": "Alex P", "initials": "AP"}, {"family": "Ritz", "given": "Beate", "initials": "B"}, {"family": "Rotter", "given": "Jerome I", "initials": "JI"}, {"family": "Smith", "given": "Jennifer A", "initials": "JA"}, {"family": "Taylor", "given": "Jack A", "initials": "JA"}, {"family": "van Meurs", "given": "Joyce B J", "initials": "JBJ"}, {"family": "Vineis", "given": "Paolo", "initials": "P"}, {"family": "Waldenberger", "given": "Melanie", "initials": "M"}, {"family": "Deary", "given": "Ian J", "initials": "IJ"}, {"family": "Relton", "given": "Caroline L", "initials": "CL"}, {"family": "Horvath", "given": "Steve", "initials": "S"}, {"family": "Marioni", "given": "Riccardo E", "initials": "RE", "orcid": "0000-0003-4430-4260", "researcher": {"href": "https://publications.scilifelab.se/researcher/de00275009694c829f00754ee739f70c.json"}}], "type": "journal article", "published": "2021-06-29", "journal": {"title": "Genome Biol.", "issn": "1474-760X", "issn-l": "1474-7596", "volume": "22", "issue": "1", "pages": "194"}, "abstract": "Biological aging estimators derived from DNA methylation data are heritable and correlate with morbidity and mortality. Consequently, identification of genetic and environmental contributors to the variation in these measures in populations has become a major goal in the field.\r\n\r\nLeveraging DNA methylation and SNP data from more than 40,000 individuals, we identify 137 genome-wide significant loci, of which 113 are novel, from genome-wide association study (GWAS) meta-analyses of four epigenetic clocks and epigenetic surrogate markers for granulocyte proportions and plasminogen activator inhibitor 1 levels, respectively. We find evidence for shared genetic loci associated with the Horvath clock and expression of transcripts encoding genes linked to lipid metabolism and immune function. Notably, these loci are independent of those reported to regulate DNA methylation levels at constituent clock CpGs. A polygenic score for GrimAge acceleration showed strong associations with adiposity-related traits, educational attainment, parental longevity, and C-reactive protein levels.\r\n\r\nThis study illuminates the genetic architecture underlying epigenetic aging and its shared genetic contributions with lifestyle factors and longevity.", "doi": "10.1186/s13059-021-02398-9", "pmid": "34187551", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pii", "key": "10.1186/s13059-021-02398-9"}, {"db": "pmc", "key": "PMC8243879"}], "notes": [], "created": "2021-08-19T13:42:05.680Z", "modified": "2021-12-07T13:41:12.538Z"}, {"entity": "publication", "iuid": "0f41cddd0a724aad8eebbd2eee4e75e2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0f41cddd0a724aad8eebbd2eee4e75e2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0f41cddd0a724aad8eebbd2eee4e75e2"}}, "title": "A multi-ethnic epigenome-wide association study of leukocyte DNA methylation and blood lipids.", "authors": [{"family": "Jhun", "given": "Min-A", "initials": "M"}, {"family": "Mendelson", "given": "Michael", "initials": "M", "orcid": "0000-0001-7590-3958", "researcher": {"href": "https://publications.scilifelab.se/researcher/d30230bbef094ca6831089c8e4afc846.json"}}, {"family": "Wilson", "given": "Rory", "initials": "R", "orcid": "0000-0001-6135-3764", "researcher": {"href": "https://publications.scilifelab.se/researcher/9c107a0ec79f4672b6ec73ff4273c338.json"}}, {"family": "Gondalia", "given": "Rahul", "initials": "R"}, {"family": "Joehanes", "given": "Roby", "initials": "R", "orcid": "0000-0001-5549-9054", "researcher": {"href": "https://publications.scilifelab.se/researcher/28dc0f841c0148c59291a83c4ffe1a78.json"}}, {"family": "Salfati", "given": "Elias", "initials": "E"}, {"family": "Zhao", "given": "Xiaoping", "initials": "X"}, {"family": "Braun", "given": "Kim Valeska Emilie", "initials": "KVE", "orcid": "0000-0001-8738-4139", "researcher": {"href": "https://publications.scilifelab.se/researcher/b0966cb600ed4c749be09388bb798d8d.json"}}, {"family": "Do", "given": "Anh Nguyet", "initials": "AN"}, {"family": "Hedman", "given": "\u00c5sa K", "initials": "\u00c5K", "orcid": "0000-0001-5413-204X", "researcher": {"href": "https://publications.scilifelab.se/researcher/2b9eaa6a5dfc4ecf8bf82ece793cd457.json"}}, {"family": "Zhang", "given": "Tao", "initials": "T"}, {"family": "Carnero-Montoro", "given": "Elena", "initials": "E", "orcid": "0000-0002-1947-9627", "researcher": {"href": "https://publications.scilifelab.se/researcher/87403846db104d3c9e4283dd00065da3.json"}}, {"family": "Shen", "given": "Jincheng", "initials": "J"}, {"family": "Bartz", "given": "Traci M", "initials": "TM"}, {"family": "Brody", "given": "Jennifer A", "initials": "JA", "orcid": "0000-0001-8509-148X", "researcher": {"href": "https://publications.scilifelab.se/researcher/7e137fc0192e4fa295a88589d57e3498.json"}}, {"family": "Montasser", "given": "May E", "initials": "ME"}, {"family": "O'Connell", "given": "Jeff R", "initials": "JR"}, {"family": "Yao", "given": "Chen", "initials": "C", "orcid": "0000-0002-3944-7788", "researcher": {"href": "https://publications.scilifelab.se/researcher/8d1a3603e21e4d52a4648eef4b86d3f8.json"}}, {"family": "Xia", "given": "Rui", "initials": "R"}, {"family": "Boerwinkle", "given": "Eric", "initials": "E"}, {"family": "Grove", "given": "Megan", "initials": "M"}, {"family": "Guan", "given": "Weihua", "initials": "W"}, {"family": "Liliane", "given": "Pfeiffer", "initials": "P"}, {"family": "Singmann", "given": "Paula", "initials": "P", "orcid": "0000-0003-2109-9970", "researcher": {"href": "https://publications.scilifelab.se/researcher/db716a10b55f4e57af04c01c5e8007d7.json"}}, {"family": "M\u00fcller-Nurasyid", "given": "Martina", "initials": "M", "orcid": "0000-0003-3793-5910", "researcher": {"href": "https://publications.scilifelab.se/researcher/4d21299bb41343f88142255e64a9da57.json"}}, {"family": "Meitinger", "given": "Thomas", "initials": "T"}, {"family": "Gieger", "given": "Christian", "initials": "C"}, {"family": "Peters", "given": "Annette", "initials": "A", "orcid": "0000-0001-6645-0985", "researcher": {"href": "https://publications.scilifelab.se/researcher/05465e52a0f6412e81752d2249af30de.json"}}, {"family": "Zhao", "given": "Wei", "initials": "W", "orcid": "0000-0001-7388-0692", "researcher": {"href": "https://publications.scilifelab.se/researcher/a0c2246e69494086bab7ead8e6f1f717.json"}}, {"family": "Ware", "given": "Erin B", "initials": "EB", "orcid": "0000-0003-4731-8158", "researcher": {"href": "https://publications.scilifelab.se/researcher/675e10a2b27a4f4b9de0ee766c4907dc.json"}}, {"family": "Smith", "given": "Jennifer A", "initials": "JA", "orcid": "0000-0002-3575-5468", "researcher": {"href": "https://publications.scilifelab.se/researcher/311c7381092b4143bcd2e4ef93250526.json"}}, {"family": "Dhana", "given": "Klodian", "initials": "K"}, {"family": "van Meurs", "given": "Joyce", "initials": "J"}, {"family": "Uitterlinden", "given": "Andre", "initials": "A", "orcid": "0000-0002-7276-3387", "researcher": {"href": "https://publications.scilifelab.se/researcher/273577b238854023a9dffe34dabc3551.json"}}, {"family": "Ikram", "given": "Mohammad Arfan", "initials": "MA", "orcid": "0000-0003-0372-8585", "researcher": {"href": "https://publications.scilifelab.se/researcher/2ec81571f4a94af682b4e23526f87385.json"}}, {"family": "Ghanbari", "given": "Mohsen", "initials": "M", "orcid": "0000-0002-9476-7143", "researcher": {"href": "https://publications.scilifelab.se/researcher/52ef9606de1144c994e0e854c5a85569.json"}}, {"family": "Zhi", "given": "Deugi", "initials": "D"}, {"family": "Gustafsson", "given": "Stefan", "initials": "S", "orcid": "0000-0001-5894-0351", "researcher": {"href": "https://publications.scilifelab.se/researcher/9a0552f8a6514baa9bdb6809148aaddc.json"}}, {"family": "Lind", "given": "Lars", "initials": "L"}, {"family": "Li", "given": "Shengxu", "initials": "S"}, {"family": "Sun", "given": "Dianjianyi", "initials": "D"}, {"family": "Spector", "given": "Tim D", "initials": "TD", "orcid": "0000-0002-9795-0365", "researcher": {"href": "https://publications.scilifelab.se/researcher/9b3b149961364ccbb448a8cc3cdd6687.json"}}, {"family": "Chen", "given": "Yii-der Ida", "initials": "YI"}, {"family": "Damcott", "given": "Coleen", "initials": "C", "orcid": "0000-0001-6233-7395", "researcher": {"href": "https://publications.scilifelab.se/researcher/234acf5657cd4ede95641ee045cb23cd.json"}}, {"family": "Shuldiner", "given": "Alan R", "initials": "AR"}, {"family": "Absher", "given": "Devin M", "initials": "DM"}, {"family": "Horvath", "given": "Steve", "initials": "S", "orcid": "0000-0002-4110-3589", "researcher": {"href": "https://publications.scilifelab.se/researcher/d9fd917cfb8e43329e4dadb4e14e32ef.json"}}, {"family": "Tsao", "given": "Philip S", "initials": "PS", "orcid": "0000-0001-7274-9318", "researcher": {"href": "https://publications.scilifelab.se/researcher/1520706d352e454688b0a737b5d590ef.json"}}, {"family": "Kardia", "given": "Sharon", "initials": "S"}, {"family": "Psaty", "given": "Bruce M", "initials": "BM"}, {"family": "Sotoodehnia", "given": "Nona", "initials": "N"}, {"family": "Bell", "given": "Jordana T", "initials": "JT", "orcid": "0000-0002-3858-5986", "researcher": {"href": "https://publications.scilifelab.se/researcher/078c46640d7946ed9ed4e08e9f9a71fa.json"}}, {"family": "Ingelsson", "given": "Erik", "initials": "E"}, {"family": "Chen", "given": "Wei", "initials": "W", "orcid": "0000-0003-1566-7943", "researcher": {"href": "https://publications.scilifelab.se/researcher/905609ccc3704af9afccd0b9ab0553bf.json"}}, {"family": "Dehghan", "given": "Abbas", "initials": "A"}, {"family": "Arnett", "given": "Donna K", "initials": "DK", "orcid": "0000-0003-2219-657X", "researcher": {"href": "https://publications.scilifelab.se/researcher/e1d283344e5c4e7daf4ff1a3709ba492.json"}}, {"family": "Waldenberger", "given": "Melanie", "initials": "M", "orcid": "0000-0003-0583-5093", "researcher": {"href": "https://publications.scilifelab.se/researcher/c8de22214f2448c6a7f86fc1040d0104.json"}}, {"family": "Hou", "given": "Lifang", "initials": "L"}, {"family": "Whitsel", "given": "Eric A", "initials": "EA"}, {"family": "Baccarelli", "given": "Andrea", "initials": "A"}, {"family": "Levy", "given": "Daniel", "initials": "D"}, {"family": "Fornage", "given": "Myriam", "initials": "M", "orcid": "0000-0003-0677-8158", "researcher": {"href": "https://publications.scilifelab.se/researcher/b5de431c325e40f4adfe13c06cf1e0b9.json"}}, {"family": "Irvin", "given": "Marguerite R", "initials": "MR"}, {"family": "Assimes", "given": "Themistocles L", "initials": "TL", "orcid": "0000-0003-2349-0009", "researcher": {"href": "https://publications.scilifelab.se/researcher/9e155ca3dd01486580be888d1ded405c.json"}}], "type": "journal article", "published": "2021-06-28", "journal": {"title": "Nat Commun", "issn": "2041-1723", "issn-l": "2041-1723", "volume": "12", "issue": "1", "pages": "3987"}, "abstract": "Here we examine the association between DNA methylation in circulating leukocytes and blood lipids in a multi-ethnic sample of 16,265 subjects. We identify 148, 35, and 4 novel associations among Europeans, African Americans, and Hispanics, respectively, and an additional 186 novel associations through a trans-ethnic meta-analysis. We observe a high concordance in the direction of effects across racial/ethnic groups, a high correlation of effect sizes between high-density lipoprotein and triglycerides, a modest overlap of associations with epigenome-wide association studies of other cardio-metabolic traits, and a largely non-overlap with lipid loci identified to date through genome-wide association studies. Thirty CpGs reached significance in at least 2 racial/ethnic groups including 7 that showed association with the expression of an annotated gene. CpGs annotated to CPT1A showed evidence of being influenced by triglycerides levels. DNA methylation levels of circulating leukocytes show robust and consistent association with blood lipid levels across multiple racial/ethnic groups.", "doi": "10.1038/s41467-021-23899-y", "pmid": "34183656", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-021-23899-y"}, {"db": "pmc", "key": "PMC8238961"}, {"db": "Dryad", "key": "10.5061/dryad.qfttdz0d8"}], "notes": [], "created": "2021-08-19T13:41:35.464Z", "modified": "2021-12-07T13:25:44.149Z"}, {"entity": "publication", "iuid": "47e2059a8c6d4ea5aefb39c53bc5c234", "links": {"self": {"href": "https://publications.scilifelab.se/publication/47e2059a8c6d4ea5aefb39c53bc5c234.json"}, "display": {"href": "https://publications.scilifelab.se/publication/47e2059a8c6d4ea5aefb39c53bc5c234"}}, "title": "Functional differences between TSHR alleles associate with variation in spawning season in Atlantic herring.", "authors": [{"family": "Chen", "given": "Junfeng", "initials": "J", "orcid": "0000-0001-6155-411X", "researcher": {"href": "https://publications.scilifelab.se/researcher/270488419b56484993472f518ba1d286.json"}}, {"family": "Bi", "given": "Huijuan", "initials": "H"}, {"family": "Pettersson", "given": "Mats E", "initials": "ME", "orcid": "0000-0002-7372-9076", "researcher": {"href": "https://publications.scilifelab.se/researcher/27011c7fbb8a44dda536a4fc876675b0.json"}}, {"family": "Sato", "given": "Daiki X", "initials": "DX", "orcid": "0000-0002-9527-8253", "researcher": {"href": "https://publications.scilifelab.se/researcher/7ad2eafb0bce4d2ba7c4f9cf7ed05eac.json"}}, {"family": "Fuentes-Pardo", "given": "Angela P", "initials": "AP", "orcid": "0000-0002-5734-9030", "researcher": {"href": "https://publications.scilifelab.se/researcher/f08a3b9b781b4ef9971a667a40b62d93.json"}}, {"family": "Mo", "given": "Chunheng", "initials": "C"}, {"family": "Younis", "given": "Shady", "initials": "S", "orcid": "0000-0002-4319-1738", "researcher": {"href": "https://publications.scilifelab.se/researcher/39b77c6e3ed14b9ba2e10132f89ef781.json"}}, {"family": "Wallerman", "given": "Ola", "initials": "O"}, {"family": "Jern", "given": "Patric", "initials": "P", "orcid": "0000-0003-3393-5825", "researcher": {"href": "https://publications.scilifelab.se/researcher/8baed28572fd470ba1e7b18fccd2e275.json"}}, {"family": "Mol\u00e9s", "given": "Gregorio", "initials": "G", "orcid": "0000-0001-5762-6993", "researcher": {"href": "https://publications.scilifelab.se/researcher/26c43e28a3fa49ccad6c77ae61f87777.json"}}, {"family": "G\u00f3mez", "given": "Ana", "initials": "A"}, {"family": "Kleinau", "given": "Gunnar", "initials": "G"}, {"family": "Scheerer", "given": "Patrick", "initials": "P", "orcid": "0000-0001-5028-2075", "researcher": {"href": "https://publications.scilifelab.se/researcher/50350a6ed93442f38ea62edb86eaa99b.json"}}, {"family": "Andersson", "given": "Leif", "initials": "L", "orcid": "0000-0002-4085-6968", "researcher": {"href": "https://publications.scilifelab.se/researcher/bd3343c12f994b1fabcae23027d3a76d.json"}}], "type": "journal article", "published": "2021-06-25", "journal": {"title": "Commun Biol", "issn": "2399-3642", "volume": "4", "issue": "1", "pages": "795", "issn-l": "2399-3642"}, "abstract": "The underlying molecular mechanisms that determine long day versus short day breeders remain unknown in any organism. Atlantic herring provides a unique opportunity to examine the molecular mechanisms involved in reproduction timing, because both spring and autumn spawners exist within the same species. Although our previous whole genome comparisons revealed a strong association of TSHR alleles with spawning seasons, the functional consequences of these variants remain unknown. Here we examined the functional significance of six candidate TSHR mutations strongly associated with herring reproductive seasonality. We show that the L471M missense mutation in the spring-allele causes enhanced cAMP signaling. The best candidate non-coding mutation is a 5.2 kb retrotransposon insertion upstream of the TSHR transcription start site, near an open chromatin region, which is likely to affect TSHR expression. The insertion occurred prior to the split between Pacific and Atlantic herring and was lost in the autumn-allele. Our study shows that strongly associated coding and non-coding variants at the TSHR locus may both contribute to the regulation of seasonal reproduction in herring.", "doi": "10.1038/s42003-021-02307-7", "pmid": "34172814", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s42003-021-02307-7"}, {"db": "pmc", "key": "PMC8233318"}, {"db": "Dryad", "key": "10.5061/dryad.pnvx0k6kr"}], "notes": [], "created": "2021-12-07T21:41:02.372Z", "modified": "2024-01-16T13:48:39.437Z"}, {"entity": "publication", "iuid": "e0711f8e6d244b13b40907137a87996f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e0711f8e6d244b13b40907137a87996f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e0711f8e6d244b13b40907137a87996f"}}, "title": "Toll-like receptor 4 methylation grade is linked to depressive symptom severity.", "authors": [{"family": "Rasmusson", "given": "Annica J", "initials": "AJ", "orcid": "0000-0002-7228-7755", "researcher": {"href": "https://publications.scilifelab.se/researcher/7ef833f6dd204c189586fba5c33d1d58.json"}}, {"family": "Gallwitz", "given": "Maike", "initials": "M"}, {"family": "Soltanabadi", "given": "Bardia", "initials": "B", "orcid": "0000-0003-4827-5268", "researcher": {"href": "https://publications.scilifelab.se/researcher/5018ceb09cc8462bb8df7b6cad75d615.json"}}, {"family": "Ciuculete", "given": "Diana M", "initials": "DM"}, {"family": "Mengel-From", "given": "Jonas", "initials": "J"}, {"family": "Christensen", "given": "Kaare", "initials": "K", "orcid": "0000-0002-5429-5292", "researcher": {"href": "https://publications.scilifelab.se/researcher/e79ea43d09544efc95351b52ac682910.json"}}, {"family": "Nygaard", "given": "Marianne", "initials": "M", "orcid": "0000-0003-0703-2665", "researcher": {"href": "https://publications.scilifelab.se/researcher/1d68eda16735460d81993dc39006d5a5.json"}}, {"family": "Soerensen", "given": "Mette", "initials": "M", "orcid": "0000-0001-5268-3366", "researcher": {"href": "https://publications.scilifelab.se/researcher/712cb1928fdf429ca777a8209b31090d.json"}}, {"family": "Bostr\u00f6m", "given": "Adrian E", "initials": "AE"}, {"family": "Fredriksson", "given": "Robert", "initials": "R"}, {"family": "Freyhult", "given": "Eva", "initials": "E"}, {"family": "Mwinyi", "given": "Jessica", "initials": "J"}, {"family": "Czamara", "given": "Darina", "initials": "D", "orcid": "0000-0001-7381-904X", "researcher": {"href": "https://publications.scilifelab.se/researcher/0e9a8a7d605d4f63a311fc8a211422a6.json"}}, {"family": "Binder", "given": "Elisabeth B", "initials": "EB", "orcid": "0000-0001-7088-6618", "researcher": {"href": "https://publications.scilifelab.se/researcher/0cfb2bf09e9d49ad922bb5c3c252c716.json"}}, {"family": "Schi\u00f6th", "given": "Helgi B", "initials": "HB"}, {"family": "Cunningham", "given": "Janet L", "initials": "JL", "orcid": "0000-0001-7876-7779", "researcher": {"href": "https://publications.scilifelab.se/researcher/3ab30dd6c6874bc7a227a8699c4a7085.json"}}], "type": "journal article", "published": "2021-06-24", "journal": {"title": "Transl Psychiatry", "issn": "2158-3188", "issn-l": "2158-3188", "volume": "11", "issue": "1", "pages": "371"}, "abstract": "This study explores potential associations between the methylation of promoter-associated CpG sites of the toll-like receptor (TLR)-family, plasma levels of pro-inflammatory proteins and depressive symptoms in young female psychiatric patients. Ratings of depressive symptoms and blood samples were obtained from 92 young women seeking psychiatric care. Methylation of 32 promoter-associated CpG sites in TLR1 to TLR10 was analysed using the Illumina Infinium Methylation EPIC BeadChip. Expression levels of 91 inflammatory proteins were determined by proximity extension assay. Statistical correlations between depressive state, TLR1-10 methylation and inflammatory proteins were investigated. Four additional cohorts were studied to evaluate the generalizability of the findings. In the discovery cohort, methylation grade of cg05429895 (TLR4) in blood was inversely correlated with depressive symptoms score in young adults. After correction for multiple testing, plasma levels of macrophage inflammatory protein 1\u03b2 (MIP-1\u03b2/CCL4) were associated with both TLR4 methylation and depressive symptom severity. A similar inverse association between TLR4 methylation in blood and affective symptoms score was also found in a cohort of 148 both males and females (<40 years of age) from the Danish Twin Registry. These findings were not, however, replicated in three other external cohorts; which differed from the first two cohorts by a higher age and mixed ethnicities, thus limiting the generalizability of our findings. However, TLR4 methylation inversely correlated with TLR4 mRNA expression in the Danish Twin Study indicating a functional significance of methylation at this particular CpG. Higher depression scores in young Scandinavian adults was associated with decreased methylation of TLR4 in blood.", "doi": "10.1038/s41398-021-01481-w", "pmid": "34226490", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Affinity Proteomics Uppsala": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC8257733"}, {"db": "pii", "key": "10.1038/s41398-021-01481-w"}], "notes": [], "created": "2021-08-19T13:41:38.152Z", "modified": "2024-01-16T13:48:39.445Z"}, {"entity": "publication", "iuid": "d16d934635db4fd4bc7a958e5c3f71a7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d16d934635db4fd4bc7a958e5c3f71a7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d16d934635db4fd4bc7a958e5c3f71a7"}}, "title": "Profiling temporal dynamics of acetogenic communities in anaerobic digesters using next-generation sequencing and T-RFLP.", "authors": [{"family": "Singh", "given": "Abhijeet", "initials": "A"}, {"family": "M\u00fcller", "given": "Bettina", "initials": "B"}, {"family": "Schn\u00fcrer", "given": "Anna", "initials": "A"}], "type": "journal article", "published": "2021-06-24", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "11", "issue": "1", "pages": "13298", "issn-l": "2045-2322"}, "abstract": "Acetogens play a key role in anaerobic degradation of organic material and in maintaining biogas process efficiency. Profiling this community and its temporal changes can help evaluate process stability and function, especially under disturbance/stress conditions, and avoid complete process failure. The formyltetrahydrofolate synthetase (FTHFS) gene can be used as a marker for acetogenic community profiling in diverse environments. In this study, we developed a new high-throughput FTHFS gene sequencing method for acetogenic community profiling and compared it with conventional terminal restriction fragment length polymorphism of the FTHFS gene, 16S rRNA gene-based profiling of the whole bacterial community, and indirect analysis via 16S rRNA profiling of the FTHFS gene-harbouring community. Analyses and method comparisons were made using samples from two laboratory-scale biogas processes, one operated under stable control and one exposed to controlled overloading disturbance. Comparative analysis revealed satisfactory detection of the bacterial community and its changes for all methods, but with some differences in resolution and taxonomic identification. FTHFS gene sequencing was found to be the most suitable and reliable method to study acetogenic communities. These results pave the way for community profiling in various biogas processes and in other environments where the dynamics of acetogenic bacteria have not been well studied.", "doi": "10.1038/s41598-021-92658-2", "pmid": "34168213", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-021-92658-2"}, {"db": "pmc", "key": "PMC8225771"}], "notes": [], "created": "2021-12-07T21:36:38.543Z", "modified": "2024-01-16T13:48:39.463Z"}, {"entity": "publication", "iuid": "588c74de2d17433bb685094ea5947079", "links": {"self": {"href": "https://publications.scilifelab.se/publication/588c74de2d17433bb685094ea5947079.json"}, "display": {"href": "https://publications.scilifelab.se/publication/588c74de2d17433bb685094ea5947079"}}, "title": "The \u03b3-tubulin meshwork assists in the recruitment of PCNA to chromatin in mammalian cells.", "authors": [{"family": "Corvaisier", "given": "Matthieu", "initials": "M"}, {"family": "Zhou", "given": "Jingkai", "initials": "J"}, {"family": "Malycheva", "given": "Darina", "initials": "D"}, {"family": "Cornella", "given": "Nicola", "initials": "N"}, {"family": "Chioureas", "given": "Dimitrios", "initials": "D"}, {"family": "Gustafsson", "given": "Nina M S", "initials": "NMS", "orcid": "0000-0001-6401-0548", "researcher": {"href": "https://publications.scilifelab.se/researcher/4484176c6d67435d9564a5fb65319e24.json"}}, {"family": "Rossell\u00f3", "given": "Catalina Ana", "initials": "CA", "orcid": "0000-0002-8977-607X", "researcher": {"href": "https://publications.scilifelab.se/researcher/e30f3fde2ced4d9aad8810029b7fc68e.json"}}, {"family": "Ayora", "given": "Silvia", "initials": "S", "orcid": "0000-0003-3121-1786", "researcher": {"href": "https://publications.scilifelab.se/researcher/40a4fa4ad7b244faa96b5b9460fea933.json"}}, {"family": "Li", "given": "Tongbin", "initials": "T"}, {"family": "Ekstr\u00f6m-Holka", "given": "Kristina", "initials": "K"}, {"family": "Jirstr\u00f6m", "given": "Karin", "initials": "K"}, {"family": "Lindstr\u00f6m", "given": "Lisa", "initials": "L"}, {"family": "Alvarado-Kristensson", "given": "Maria", "initials": "M", "orcid": "0000-0003-0598-7986", "researcher": {"href": "https://publications.scilifelab.se/researcher/70ee81797eff452fa037821f293d8673.json"}}], "type": "journal article", "published": "2021-06-22", "journal": {"title": "Commun Biol", "issn": "2399-3642", "volume": "4", "issue": "1", "pages": "767", "issn-l": "2399-3642"}, "abstract": "Changes in the location of \u03b3-tubulin ensure cell survival and preserve genome integrity. We investigated whether the nuclear accumulation of \u03b3-tubulin facilitates the transport of proliferating cell nuclear antigen (PCNA) between the cytosolic and the nuclear compartment in mammalian cells. We found that the \u03b3-tubulin meshwork assists in the recruitment of PCNA to chromatin. Also, decreased levels of \u03b3-tubulin reduce the nuclear pool of PCNA. In addition, the \u03b3-tubulin C terminus encodes a PCNA-interacting peptide (PIP) motif, and a \u03b3-tubulin-PIP-mutant affects the nuclear accumulation of PCNA. In a cell-free system, PCNA and \u03b3-tubulin formed a complex. In tumors, there is a significant positive correlation between TUBG1 and PCNA expression. Thus, we report a novel mechanism that constitutes the basis for tumor growth by which the \u03b3-tubulin meshwork maintains indefinite proliferation by acting as an opportune scaffold for the transport of PCNA from the cytosol to the chromatin.", "doi": "10.1038/s42003-021-02280-1", "pmid": "34158617", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s42003-021-02280-1"}, {"db": "pmc", "key": "PMC8219688"}], "notes": [], "created": "2021-11-03T15:39:48.182Z", "modified": "2021-11-10T12:23:58.806Z"}, {"entity": "publication", "iuid": "d3c1fc3c5f9745f084124f801a23a6c5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d3c1fc3c5f9745f084124f801a23a6c5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d3c1fc3c5f9745f084124f801a23a6c5"}}, "title": "Differential DNA Methylation of the Genes for Amyloid Precursor Protein, Tau, and Neurofilaments in Human Traumatic Brain Injury.", "authors": [{"family": "Abu Hamdeh", "given": "Sami", "initials": "S"}, {"family": "Ciuculete", "given": "Diana-Maria", "initials": "DM"}, {"family": "Sarkisyan", "given": "Daniil", "initials": "D"}, {"family": "Bakalkin", "given": "Georgy", "initials": "G"}, {"family": "Ingelsson", "given": "Martin", "initials": "M"}, {"family": "Schi\u00f6th", "given": "Helgi B", "initials": "HB"}, {"family": "Marklund", "given": "Niklas", "initials": "N"}], "type": "journal article", "published": "2021-06-15", "journal": {"title": "J. Neurotrauma", "issn": "1557-9042", "issn-l": "0897-7151", "volume": "38", "issue": "12", "pages": "1679-1688"}, "abstract": "Traumatic brain injury (TBI) is an established risk factor for neurodegenerative disorders and dementias. Epigenetic modifications, such as DNA methylation, may alter the expression of genes without altering the DNA sequence in response to environmental factors. We hypothesized that DNA methylation changes may occur in the injured human brain and be implicated in the neurodegenerative aftermath of TBI. The DNA methylation status of genes related to neurodegeneration; for example, amyloid beta precursor protein (APP), microtubule associated protein tau (MAPT), neurofilament heavy (NEFH), neurofilament medium (NEFM), and neurofilament light (NEFL), was analyzed in fresh, surgically resected human brain tissue from 17 severe TBI patients and compared with brain biopsy samples from 19 patients with idiopathic normal pressure hydrocephalus (iNPH). We also performed an epigenome-wide association study (EWAS) comparing TBI patients with iNPH controls. Thirty-eight CpG sites in the APP, MAPT, NEFH, and NEFL genes were differentially methylated by TBI. Among the top 20 differentially methylated CpG sites, 11 were in the APP gene. In addition, the EWAS evaluating 828,888 CpG sites revealed 308 differentially methylated CpG sites in genes related to cellular/anatomical structure development, cell differentiation, and anatomical morphogenesis. These preliminary findings provide the first evidence of an altered DNA methylome in the injured human brain, and may have implications for the neurodegenerative disorders associated with TBI.", "doi": "10.1089/neu.2020.7283", "pmid": "33191850", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2020-12-08T08:34:08.638Z", "modified": "2024-01-16T13:48:39.486Z"}, {"entity": "publication", "iuid": "e5624263d0d14df6b34de42bcd14cc12", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e5624263d0d14df6b34de42bcd14cc12.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e5624263d0d14df6b34de42bcd14cc12"}}, "title": "DNA Methylation Signatures Predict Cytogenetic Subtype and Outcome in Pediatric Acute Myeloid Leukemia (AML).", "authors": [{"family": "Krali", "given": "Olga", "initials": "O", "orcid": "0000-0002-6436-9531", "researcher": {"href": "https://publications.scilifelab.se/researcher/14a6e2f99d3b4758a10af78b93777779.json"}}, {"family": "Palle", "given": "Josefine", "initials": "J"}, {"family": "B\u00e4cklin", "given": "Christofer L", "initials": "CL"}, {"family": "Abrahamsson", "given": "Jonas", "initials": "J", "orcid": "0000-0002-9240-3522", "researcher": {"href": "https://publications.scilifelab.se/researcher/0f3199957bd147ec91bbdc04413f1dba.json"}}, {"family": "Nor\u00e9n-Nystr\u00f6m", "given": "Ulrika", "initials": "U"}, {"family": "Hasle", "given": "Henrik", "initials": "H", "orcid": "0000-0003-3976-9231", "researcher": {"href": "https://publications.scilifelab.se/researcher/4bd29fb163f9461d92b50157101bf384.json"}}, {"family": "Jahnukainen", "given": "Kirsi", "initials": "K"}, {"family": "J\u00f3nsson", "given": "\u00d3lafur G\u00edsli", "initials": "\u00d3G"}, {"family": "Hovland", "given": "Randi", "initials": "R"}, {"family": "Lausen", "given": "Birgitte", "initials": "B"}, {"family": "Larsson", "given": "Rolf", "initials": "R"}, {"family": "Palmqvist", "given": "Lars", "initials": "L", "orcid": "0000-0001-9274-360X", "researcher": {"href": "https://publications.scilifelab.se/researcher/7e50c0057dcb47f39e085b16580806c2.json"}}, {"family": "Staffas", "given": "Anna", "initials": "A"}, {"family": "Zeller", "given": "Bernward", "initials": "B"}, {"family": "Nordlund", "given": "Jessica", "initials": "J", "orcid": "0000-0001-8699-9959", "researcher": {"href": "https://publications.scilifelab.se/researcher/ddf48c9262134821bcc6ce1180049753.json"}}], "type": "journal article", "published": "2021-06-10", "journal": {"title": "Genes", "issn": "2073-4425", "issn-l": "2073-4425", "volume": "12", "issue": "6", "pages": "895"}, "abstract": "Pediatric acute myeloid leukemia (AML) is a heterogeneous disease composed of clinically relevant subtypes defined by recurrent cytogenetic aberrations. The majority of the aberrations used in risk grouping for treatment decisions are extensively studied, but still a large proportion of pediatric AML patients remain cytogenetically undefined and would therefore benefit from additional molecular investigation. As aberrant epigenetic regulation has been widely observed during leukemogenesis, we hypothesized that DNA methylation signatures could be used to predict molecular subtypes and identify signatures with prognostic impact in AML. To study genome-wide DNA methylation, we analyzed 123 diagnostic and 19 relapse AML samples on Illumina 450k DNA methylation arrays. We designed and validated DNA methylation-based classifiers for AML cytogenetic subtype, resulting in an overall test accuracy of 91%. Furthermore, we identified methylation signatures associated with outcome in t(8;21)/RUNX1-RUNX1T1, normal karyotype, and MLL/KMT2A-rearranged subgroups (p < 0.01). Overall, these results further underscore the clinical value of DNA methylation analysis in AML.", "doi": "10.3390/genes12060895", "pmid": "34200630", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Collaborative", "National Genomics Infrastructure": "Collaborative", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "genes12060895"}, {"db": "pmc", "key": "PMC8229099"}], "notes": [], "created": "2021-08-19T13:41:59.691Z", "modified": "2024-01-16T13:48:39.519Z"}, {"entity": "publication", "iuid": "b70be864396f40b68d30939cc4e01962", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b70be864396f40b68d30939cc4e01962.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b70be864396f40b68d30939cc4e01962"}}, "title": "Common variants in Alzheimer's disease and risk stratification by polygenic risk scores.", "authors": [{"family": "de Rojas", "given": "Itziar", "initials": "I", "orcid": 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"https://publications.scilifelab.se/researcher/5e646be026ce42ecbfd4d62eca3f9bce.json"}}, {"family": "Huisman", "given": "Martijn", "initials": "M"}, {"family": "Andreassen", "given": "Ole A", "initials": "OA", "orcid": "0000-0002-4461-3568", "researcher": {"href": "https://publications.scilifelab.se/researcher/56f384e8e2fd4a7383c7b26e88a828b2.json"}}, {"family": "Posthuma", "given": "Danielle", "initials": "D"}, {"family": "Clarim\u00f3n", "given": "Jordi", "initials": "J"}, {"family": "Boada", "given": "Merc\u00e8", "initials": "M", "orcid": "0000-0003-2617-3009", "researcher": {"href": "https://publications.scilifelab.se/researcher/c8d00c33569e41b481cf5cdc99cd96e9.json"}}, {"family": "van der Flier", "given": "Wiesje M", "initials": "WM", "orcid": "0000-0001-8766-6224", "researcher": {"href": "https://publications.scilifelab.se/researcher/0b32776a9e524f299765506b6dbe9768.json"}}, {"family": "Ramirez", "given": "Alfredo", "initials": "A", "orcid": "0000-0003-4991-763X", "researcher": {"href": "https://publications.scilifelab.se/researcher/a8995a57e82f4f479ab8251175aeb8d6.json"}}, {"family": "Lambert", "given": "Jean-Charles", "initials": "JC", "orcid": "0000-0003-0829-7817", "researcher": {"href": "https://publications.scilifelab.se/researcher/a0ec452344144906b7e8be95eb8c62d6.json"}}, {"family": "van der Lee", "given": "Sven J", "initials": "SJ", "orcid": "0000-0003-1606-8643", "researcher": {"href": "https://publications.scilifelab.se/researcher/9a34a1b7b98b4360b48dafe3f0d5dcb2.json"}}, {"family": "Ruiz", "given": "Agust\u00edn", "initials": "A", "orcid": "0000-0003-2633-2495", "researcher": {"href": "https://publications.scilifelab.se/researcher/33a263bd6bd24ca897c988d4fcbcaca1.json"}}], "type": "journal article", "published": "2021-06-07", "journal": {"title": "Nat Commun", "issn": "2041-1723", "issn-l": "2041-1723", "volume": "12", "issue": "1", "pages": "3417"}, "abstract": "Genetic discoveries of Alzheimer's disease are the drivers of our understanding, and together with polygenetic risk stratification can contribute towards planning of feasible and efficient preventive and curative clinical trials. We first perform a large genetic association study by merging all available case-control datasets and by-proxy study results (discovery n = 409,435 and validation size n = 58,190). Here, we add six variants associated with Alzheimer's disease risk (near APP, CHRNE, PRKD3/NDUFAF7, PLCG2 and two exonic variants in the SHARPIN gene). Assessment of the polygenic risk score and stratifying by APOE reveal a 4 to 5.5 years difference in median age at onset of Alzheimer's disease patients in APOE \u025b4 carriers. Because of this study, the underlying mechanisms of APP can be studied to refine the amyloid cascade and the polygenic risk score provides a tool to select individuals at high risk of Alzheimer's disease.", "doi": "10.1038/s41467-021-22491-8", "pmid": "34099642", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC8184987"}, {"db": "pii", "key": "10.1038/s41467-021-22491-8"}], "notes": [], "created": "2021-08-19T13:41:32.762Z", "modified": "2023-06-20T15:56:47.699Z"}, {"entity": "publication", "iuid": "b4b5d9a6dd4a476893c092bfc5e56f5c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b4b5d9a6dd4a476893c092bfc5e56f5c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b4b5d9a6dd4a476893c092bfc5e56f5c"}}, "title": "Variation in the SERPINA6/SERPINA1 locus alters morning plasma cortisol, hepatic corticosteroid binding globulin expression, gene expression in peripheral tissues, and risk of cardiovascular disease.", "authors": [{"family": "Crawford", "given": "Andrew A", "initials": "AA"}, {"family": "Bankier", "given": "Sean", "initials": "S"}, {"family": "Altmaier", "given": "Elisabeth", "initials": "E"}, {"family": "Barnes", "given": "Catriona L K", "initials": "CLK"}, {"family": "Clark", "given": "David W", "initials": "DW"}, {"family": "Ermel", "given": "Raili", "initials": "R"}, {"family": "Friedrich", "given": "Nele", "initials": "N"}, {"family": "van der Harst", "given": "Pim", "initials": "P"}, {"family": "Joshi", "given": "Peter K", "initials": "PK"}, {"family": "Karhunen", "given": "Ville", "initials": "V"}, {"family": "Lahti", "given": "Jari", "initials": "J", "orcid": "0000-0002-4310-5297", "researcher": {"href": "https://publications.scilifelab.se/researcher/09e0eb71fa6241449afef2b0542a738f.json"}}, {"family": "Mahajan", "given": "Anubha", "initials": "A"}, {"family": "Mangino", "given": "Massimo", "initials": "M", "orcid": "0000-0002-2167-7470", "researcher": {"href": "https://publications.scilifelab.se/researcher/65f456a10f394f1294b60158c3fb9f04.json"}}, {"family": "Nethander", "given": "Maria", "initials": "M"}, {"family": "Neumann", "given": "Alexander", "initials": "A", "orcid": "0000-0001-6653-3203", "researcher": {"href": "https://publications.scilifelab.se/researcher/e51ca6c997164410957bb8cac445d3e4.json"}}, {"family": "Pietzner", "given": "Maik", "initials": "M"}, {"family": "Sukhavasi", "given": "Katyayani", "initials": "K"}, {"family": "Wang", "given": "Carol A", "initials": "CA"}, {"family": "Bakker", "given": "Stephan J L", "initials": "SJL", "orcid": "0000-0003-3356-6791", "researcher": {"href": "https://publications.scilifelab.se/researcher/80180035048c45bf90b2e5f4460d1fe7.json"}}, {"family": "Bjorkegren", "given": "Johan L M", "initials": "JLM"}, {"family": "Campbell", "given": "Harry", "initials": "H"}, {"family": "Eriksson", "given": "Johan", "initials": "J"}, {"family": "Gieger", "given": "Christian", "initials": "C"}, {"family": "Hayward", "given": "Caroline", "initials": "C", "orcid": "0000-0002-9405-9550", "researcher": {"href": "https://publications.scilifelab.se/researcher/cd49e9ad5a024c7ca2f1aa97d9e58eba.json"}}, {"family": "Jarvelin", "given": "Marjo-Riitta", "initials": "M"}, {"family": "McLachlan", "given": "Stela", "initials": "S"}, {"family": "Morris", "given": "Andrew P", "initials": "AP"}, {"family": "Ohlsson", "given": "Claes", "initials": "C"}, {"family": "Pennell", "given": "Craig E", "initials": "CE"}, {"family": "Price", "given": "Jackie", "initials": "J"}, {"family": "Rudan", "given": "Igor", "initials": "I"}, {"family": "Ruusalepp", "given": "Arno", "initials": "A"}, {"family": "Spector", "given": "Tim", "initials": "T"}, {"family": "Tiemeier", "given": "Henning", "initials": "H", "orcid": "0000-0002-4395-1397", "researcher": {"href": "https://publications.scilifelab.se/researcher/73e05bd74af344ba8d963463f49bb242.json"}}, {"family": "V\u00f6lzke", "given": "Henry", "initials": "H"}, {"family": "Wilson", "given": "James F", "initials": "JF", "orcid": "0000-0001-5751-9178", "researcher": {"href": "https://publications.scilifelab.se/researcher/b39e6e0f7210494cb4f80be0f7413b6f.json"}}, {"family": "Michoel", "given": "Tom", "initials": "T"}, {"family": "Timpson", "given": "Nicolas J", "initials": "NJ"}, {"family": "Smith", "given": "George Davey", "initials": "GD"}, {"family": "Walker", "given": "Brian R", "initials": "BR"}, {"family": "CORtisol NETwork (CORNET) consortium", "given": "", "initials": ""}], "type": "journal article", "published": "2021-06-00", "journal": {"title": "J. Hum. Genet.", "issn": "1435-232X", "issn-l": "1434-5161", "volume": "66", "issue": "6", "pages": "625-636"}, "abstract": "The stress hormone cortisol modulates fuel metabolism, cardiovascular homoeostasis, mood, inflammation and cognition. The CORtisol NETwork (CORNET) consortium previously identified a single locus associated with morning plasma cortisol. Identifying additional genetic variants that explain more of the variance in cortisol could provide new insights into cortisol biology and provide statistical power to test the causative role of cortisol in common diseases. The CORNET consortium extended its genome-wide association meta-analysis for morning plasma cortisol from 12,597 to 25,314 subjects and from ~2.2 M to ~7 M SNPs, in 17 population-based cohorts of European ancestries. We confirmed the genetic association with SERPINA6/SERPINA1. This locus contains genes encoding corticosteroid binding globulin (CBG) and \u03b11-antitrypsin. Expression quantitative trait loci (eQTL) analyses undertaken in the STARNET cohort of 600 individuals showed that specific genetic variants within the SERPINA6/SERPINA1 locus influence expression of SERPINA6 rather than SERPINA1 in the liver. Moreover, trans-eQTL analysis demonstrated effects on adipose tissue gene expression, suggesting that variations in CBG levels have an effect on delivery of cortisol to peripheral tissues. Two-sample Mendelian randomisation analyses provided evidence that each genetically-determined standard deviation (SD) increase in morning plasma cortisol was associated with increased odds of chronic ischaemic heart disease (0.32, 95% CI 0.06-0.59) and myocardial infarction (0.21, 95% CI 0.00-0.43) in UK Biobank and similarly in CARDIoGRAMplusC4D. These findings reveal a causative pathway for CBG in determining cortisol action in peripheral tissues and thereby contributing to the aetiology of cardiovascular disease.", "doi": "10.1038/s10038-020-00895-6", "pmid": "33469137", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s10038-020-00895-6"}, {"db": "pmc", "key": "PMC8144017"}, {"db": "mid", "key": "EMS114696"}], "notes": [], "created": "2021-01-22T13:55:11.822Z", "modified": "2021-12-07T13:32:19.642Z"}, {"entity": "publication", "iuid": "a0ae22c4d617489f89a2c9fc6c709d7d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a0ae22c4d617489f89a2c9fc6c709d7d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a0ae22c4d617489f89a2c9fc6c709d7d"}}, "title": "The trans-ancestral genomic architecture of glycemic traits.", "authors": [{"family": "Chen", "given": "Ji", "initials": "J"}, 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{"family": "Kim", "given": "Young Jin", "initials": "YJ"}, {"family": "Kleber", "given": "Marcus E", "initials": "ME"}, {"family": "Kooner", "given": "Ishminder K", "initials": "IK"}, {"family": "Lai", "given": "Shuiqing", "initials": "S"}, {"family": "Lange", "given": "Leslie A", "initials": "LA"}, {"family": "Langefeld", "given": "Carl D", "initials": "CD"}, {"family": "Lauzon", "given": "Marie", "initials": "M"}, {"family": "Li", "given": "Man", "initials": "M"}, {"family": "Ligthart", "given": "Symen", "initials": "S"}, {"family": "Liu", "given": "Jun", "initials": "J"}, {"family": "Loh", "given": "Marie", "initials": "M"}, {"family": "Long", "given": "Jirong", "initials": "J"}, {"family": "Lyssenko", "given": "Valeriya", "initials": "V"}, {"family": "Mangino", "given": "Massimo", "initials": "M"}, {"family": "Marzi", "given": "Carola", "initials": "C"}, {"family": "Montasser", "given": "May E", "initials": "ME"}, {"family": "Nag", "given": "Abhishek", "initials": "A"}, {"family": 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{"family": "Hicks", "given": "Andrew A", "initials": "AA"}, {"family": "Hsieh", "given": "Chang-Hsun", "initials": "C"}, {"family": "Hsueh", "given": "Willa A", "initials": "WA"}, {"family": "Ichihara", "given": "Sahoko", "initials": "S"}, {"family": "Igase", "given": "Michiya", "initials": "M"}, {"family": "Ikram", "given": "M Arfan", "initials": "MA"}, {"family": "Johnson", "given": "W Craig", "initials": "WC"}, {"family": "J\u00f8rgensen", "given": "Marit E", "initials": "ME"}, {"family": "Joshi", "given": "Peter K", "initials": "PK"}, {"family": "Kalyani", "given": "Rita R", "initials": "RR"}, {"family": "Kandeel", "given": "Fouad R", "initials": "FR"}, {"family": "Katsuya", "given": "Tomohiro", "initials": "T"}, {"family": "Khor", "given": "Chiea Chuen", "initials": "CC"}, {"family": "Kiess", "given": "Wieland", "initials": "W"}, {"family": "Kolcic", "given": "Ivana", "initials": "I"}, {"family": "Kuulasmaa", "given": "Teemu", "initials": "T"}, {"family": "Kuusisto", "given": 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{"family": "Moon", "given": "Sanghoon", "initials": "S"}, {"family": "Nabika", "given": "Toru", "initials": "T"}, {"family": "Nadkarni", "given": "Girish N", "initials": "GN"}, {"family": "Nadler", "given": "Jerry L", "initials": "JL"}, {"family": "Nelis", "given": "Mari", "initials": "M"}, {"family": "Neville", "given": "Matt J", "initials": "MJ"}, {"family": "Norris", "given": "Jill M", "initials": "JM"}, {"family": "Ohyagi", "given": "Yasumasa", "initials": "Y"}, {"family": "Peters", "given": "Annette", "initials": "A"}, {"family": "Peyser", "given": "Patricia A", "initials": "PA"}, {"family": "Polasek", "given": "Ozren", "initials": "O"}, {"family": "Qi", "given": "Qibin", "initials": "Q"}, {"family": "Raven", "given": "Dennis", "initials": "D"}, {"family": "Reilly", "given": "Dermot F", "initials": "DF"}, {"family": "Reiner", "given": "Alex", "initials": "A"}, {"family": "Rivideneira", "given": "Fernando", "initials": "F"}, {"family": "Roll", "given": "Kathryn", "initials": "K"}, {"family": "Rudan", "given": "Igor", "initials": "I"}, {"family": "Sabanayagam", "given": "Charumathi", "initials": "C"}, {"family": "Sandow", "given": "Kevin", "initials": "K"}, {"family": "Sattar", "given": "Naveed", "initials": "N"}, {"family": "Sch\u00fcrmann", "given": "Annette", "initials": "A"}, {"family": "Shi", "given": "Jinxiu", "initials": "J"}, {"family": "Stringham", "given": "Heather M", "initials": "HM"}, {"family": "Taylor", "given": "Kent D", "initials": "KD"}, {"family": "Teslovich", "given": "Tanya M", "initials": "TM"}, {"family": "Thuesen", "given": "Betina", "initials": "B"}, {"family": "Timmers", "given": "Paul R H J", "initials": "PRHJ"}, {"family": "Tremoli", "given": "Elena", "initials": "E"}, {"family": "Tsai", "given": "Michael Y", "initials": "MY"}, {"family": "Uitterlinden", "given": "Andre", "initials": "A"}, {"family": "van Dam", "given": "Rob M", "initials": "RM"}, {"family": "van Heemst", "given": "Diana", "initials": "D"}, {"family": "van Hylckama Vlieg", "given": "Astrid", "initials": "A"}, {"family": "van Vliet-Ostaptchouk", "given": "Jana V", "initials": "JV"}, {"family": "Vangipurapu", "given": "Jagadish", "initials": "J"}, {"family": "Vestergaard", "given": "Henrik", "initials": "H"}, {"family": "Wang", "given": "Tao", "initials": "T"}, {"family": "Willems van Dijk", "given": "Ko", "initials": "K"}, {"family": "Zemunik", "given": "Tatijana", "initials": "T"}, {"family": "Abecasis", "given": "Gon\u00e7alo R", "initials": "GR"}, {"family": "Adair", "given": "Linda S", "initials": "LS"}, {"family": "Aguilar-Salinas", "given": "Carlos Alberto", "initials": "CA"}, {"family": "Alarc\u00f3n-Riquelme", "given": "Marta E", "initials": "ME"}, {"family": "An", "given": "Ping", "initials": "P"}, {"family": "Aviles-Santa", "given": "Larissa", "initials": "L"}, {"family": "Becker", "given": "Diane M", "initials": "DM"}, {"family": "Beilin", "given": "Lawrence J", "initials": "LJ"}, {"family": "Bergmann", "given": "Sven", "initials": "S"}, {"family": "Bisgaard", "given": "Hans", "initials": "H"}, {"family": "Black", "given": "Corri", "initials": "C"}, {"family": "Boehnke", "given": "Michael", "initials": "M"}, {"family": "Boerwinkle", "given": "Eric", "initials": "E"}, {"family": "B\u00f6hm", "given": "Bernhard O", "initials": "BO"}, {"family": "B\u00f8nnelykke", "given": "Klaus", "initials": "K"}, {"family": "Boomsma", "given": "D I", "initials": "DI"}, {"family": "Bottinger", "given": "Erwin P", "initials": "EP"}, {"family": "Buchanan", "given": "Thomas A", "initials": "TA"}, {"family": "Canouil", "given": "Micka\u00ebl", "initials": "M"}, {"family": "Caulfield", "given": "Mark J", "initials": "MJ"}, {"family": "Chambers", "given": "John C", "initials": "JC"}, {"family": "Chasman", "given": "Daniel I", "initials": "DI"}, {"family": "Chen", "given": "Yii-Der Ida", "initials": "YI"}, {"family": "Cheng", "given": "Ching-Yu", "initials": "C"}, {"family": "Collins", "given": "Francis S", "initials": "FS"}, {"family": "Correa", "given": "Adolfo", "initials": "A"}, {"family": "Cucca", "given": "Francesco", "initials": "F"}, {"family": "de Silva", "given": "H Janaka", "initials": "HJ"}, {"family": "Dedoussis", "given": "George", "initials": "G"}, {"family": "Elmst\u00e5hl", "given": "S\u00f6lve", "initials": "S"}, {"family": "Evans", "given": "Michele K", "initials": "MK"}, {"family": "Ferrannini", "given": "Ele", "initials": "E"}, {"family": "Ferrucci", "given": "Luigi", "initials": "L"}, {"family": "Florez", "given": "Jose C", "initials": "JC"}, {"family": "Franks", "given": "Paul W", "initials": "PW"}, {"family": "Frayling", "given": "Timothy M", "initials": "TM"}, {"family": "Froguel", "given": "Philippe", "initials": "P"}, {"family": "Gigante", "given": "Bruna", "initials": "B"}, {"family": "Goodarzi", "given": "Mark O", "initials": "MO"}, {"family": "Gordon-Larsen", "given": "Penny", "initials": "P"}, {"family": "Grallert", "given": "Harald", "initials": "H"}, {"family": "Grarup", "given": "Niels", "initials": "N"}, {"family": "Grimsgaard", "given": "Sameline", "initials": "S"}, {"family": "Groop", "given": "Leif", "initials": "L"}, {"family": "Gudnason", "given": "Vilmundur", "initials": "V"}, {"family": "Guo", "given": "Xiuqing", "initials": "X"}, {"family": "Hamsten", "given": "Anders", "initials": "A"}, {"family": "Hansen", "given": "Torben", "initials": "T"}, {"family": "Hayward", "given": "Caroline", "initials": "C"}, {"family": "Heckbert", "given": "Susan R", "initials": "SR"}, {"family": "Horta", "given": "Bernardo L", "initials": "BL"}, {"family": "Huang", "given": "Wei", "initials": "W"}, {"family": "Ingelsson", "given": "Erik", "initials": "E"}, {"family": "James", "given": "Pankow S", "initials": "PS"}, {"family": "Jarvelin", "given": "Marjo-Ritta", "initials": "M"}, {"family": "Jonas", "given": "Jost B", "initials": "JB"}, {"family": "Jukema", "given": "J Wouter", "initials": "JW"}, {"family": "Kaleebu", "given": "Pontiano", "initials": "P"}, {"family": "Kaplan", "given": "Robert", "initials": "R"}, {"family": "Kardia", "given": "Sharon L R", "initials": "SLR"}, {"family": "Kato", "given": "Norihiro", "initials": "N"}, {"family": "Keinanen-Kiukaanniemi", "given": "Sirkka M", "initials": "SM"}, {"family": "Kim", "given": "Bong-Jo", "initials": "B"}, {"family": "Kivimaki", "given": "Mika", "initials": "M"}, {"family": "Koistinen", "given": "Heikki A", "initials": "HA"}, {"family": "Kooner", "given": "Jaspal S", "initials": "JS"}, {"family": "K\u00f6rner", "given": "Antje", "initials": "A"}, {"family": "Kovacs", "given": "Peter", "initials": "P"}, {"family": "Kuh", "given": "Diana", "initials": "D"}, {"family": "Kumari", "given": "Meena", "initials": "M"}, {"family": "Kutalik", "given": "Zoltan", "initials": "Z"}, {"family": "Laakso", "given": "Markku", "initials": "M"}, {"family": "Lakka", "given": "Timo A", "initials": "TA"}, {"family": "Launer", "given": "Lenore J", "initials": "LJ"}, {"family": "Leander", "given": "Karin", "initials": "K"}, {"family": "Li", "given": "Huaixing", "initials": "H"}, {"family": "Lin", "given": "Xu", "initials": "X"}, {"family": "Lind", "given": "Lars", "initials": "L"}, {"family": "Lindgren", "given": "Cecilia", "initials": "C"}, {"family": "Liu", "given": "Simin", "initials": "S"}, {"family": "Loos", "given": "Ruth J F", "initials": "RJF"}, {"family": "Magnusson", "given": "Patrik K E", "initials": "PKE"}, {"family": "Mahajan", "given": "Anubha", "initials": "A"}, {"family": "Metspalu", "given": "Andres", "initials": "A"}, {"family": "Mook-Kanamori", "given": "Dennis O", "initials": "DO"}, {"family": "Mori", "given": "Trevor A", "initials": "TA"}, {"family": "Munroe", "given": "Patricia B", "initials": "PB"}, {"family": "Nj\u00f8lstad", "given": "Inger", "initials": "I"}, {"family": "O'Connell", "given": "Jeffrey R", "initials": "JR"}, {"family": "Oldehinkel", "given": "Albertine J", "initials": "AJ"}, {"family": "Ong", "given": "Ken K", "initials": "KK"}, {"family": "Padmanabhan", "given": "Sandosh", "initials": "S"}, {"family": "Palmer", "given": "Colin N A", "initials": "CNA"}, {"family": "Palmer", "given": "Nicholette D", "initials": "ND"}, {"family": "Pedersen", "given": "Oluf", "initials": "O"}, {"family": "Pennell", "given": "Craig E", "initials": "CE"}, {"family": "Porteous", "given": "David J", "initials": "DJ"}, {"family": "Pramstaller", "given": "Peter P", "initials": "PP"}, {"family": "Province", "given": "Michael A", "initials": "MA"}, {"family": "Psaty", "given": "Bruce M", "initials": "BM"}, {"family": "Qi", "given": "Lu", "initials": "L"}, {"family": "Raffel", "given": "Leslie J", "initials": "LJ"}, {"family": "Rauramaa", "given": "Rainer", "initials": "R"}, {"family": "Redline", "given": "Susan", "initials": "S"}, {"family": "Ridker", "given": "Paul M", "initials": "PM"}, {"family": "Rosendaal", "given": "Frits R", "initials": "FR"}, {"family": "Saaristo", "given": "Timo E", "initials": "TE"}, {"family": "Sandhu", "given": "Manjinder", "initials": "M"}, {"family": "Saramies", "given": "Jouko", "initials": "J"}, {"family": "Schneiderman", "given": "Neil", "initials": "N"}, {"family": "Schwarz", "given": "Peter", "initials": "P"}, {"family": "Scott", "given": "Laura J", "initials": "LJ"}, {"family": "Selvin", "given": "Elizabeth", "initials": "E"}, {"family": "Sever", "given": "Peter", "initials": "P"}, {"family": "Shu", "given": "Xiao-Ou", "initials": "X"}, {"family": "Slagboom", "given": "P Eline", "initials": "PE"}, {"family": "Small", "given": "Kerrin S", "initials": "KS"}, {"family": "Smith", "given": "Blair H", "initials": "BH"}, {"family": "Snieder", "given": "Harold", "initials": "H"}, {"family": "Sofer", "given": "Tamar", "initials": "T"}, {"family": "S\u00f8rensen", "given": "Thorkild I A", "initials": "TIA"}, {"family": "Spector", "given": "Tim D", "initials": "TD"}, {"family": "Stanton", "given": "Alice", "initials": "A"}, {"family": "Steves", "given": "Claire J", "initials": "CJ"}, {"family": "Stumvoll", "given": "Michael", "initials": "M"}, {"family": "Sun", "given": "Liang", "initials": "L"}, {"family": "Tabara", "given": "Yasuharu", "initials": "Y"}, {"family": "Tai", "given": "E Shyong", "initials": "ES"}, {"family": "Timpson", "given": "Nicholas J", "initials": "NJ"}, {"family": "T\u00f6njes", "given": "Anke", "initials": "A"}, {"family": "Tuomilehto", "given": "Jaakko", "initials": "J"}, {"family": "Tusie", "given": "Teresa", "initials": "T"}, {"family": "Uusitupa", "given": "Matti", "initials": "M"}, {"family": "van der Harst", "given": "Pim", "initials": "P"}, {"family": "van Duijn", "given": "Cornelia", "initials": "C"}, {"family": "Vitart", "given": "Veronique", "initials": "V"}, {"family": "Vollenweider", "given": "Peter", "initials": "P"}, {"family": "Vrijkotte", "given": "Tanja G M", "initials": "TGM"}, {"family": "Wagenknecht", "given": "Lynne E", "initials": "LE"}, {"family": "Walker", "given": "Mark", "initials": "M"}, {"family": "Wang", "given": "Ya X", "initials": "YX"}, {"family": "Wareham", "given": "Nick J", "initials": "NJ"}, {"family": "Watanabe", "given": "Richard M", "initials": "RM"}, {"family": "Watkins", "given": "Hugh", "initials": "H"}, {"family": "Wei", "given": "Wen B", "initials": "WB"}, {"family": "Wickremasinghe", "given": "Ananda R", "initials": "AR"}, {"family": "Willemsen", "given": "Gonneke", "initials": "G"}, {"family": "Wilson", "given": "James F", "initials": "JF"}, {"family": "Wong", "given": "Tien-Yin", "initials": "T"}, {"family": "Wu", "given": "Jer-Yuarn", "initials": "J"}, {"family": "Xiang", "given": "Anny H", "initials": "AH"}, {"family": "Yanek", "given": "Lisa R", "initials": "LR"}, {"family": "Yengo", "given": "Lo\u00efc", "initials": "L"}, {"family": "Yokota", "given": "Mitsuhiro", "initials": "M"}, {"family": "Zeggini", "given": "Eleftheria", "initials": "E"}, {"family": "Zheng", "given": "Wei", "initials": "W"}, {"family": "Zonderman", "given": "Alan B", "initials": "AB"}, {"family": "Rotter", "given": "Jerome I", "initials": "JI"}, {"family": "Gloyn", "given": "Anna L", "initials": "AL"}, {"family": "McCarthy", "given": "Mark I", "initials": "MI"}, {"family": "Dupuis", "given": "Jos\u00e9e", "initials": "J"}, {"family": "Meigs", "given": "James B", "initials": "JB"}, {"family": "Scott", "given": "Robert A", "initials": "RA"}, {"family": "Prokopenko", "given": "Inga", "initials": "I"}, {"family": "Leong", "given": "Aaron", "initials": "A"}, {"family": "Liu", "given": "Ching-Ti", "initials": "C"}, {"family": "Parker", "given": "Stephen C J", "initials": "SCJ", "orcid": "0000-0001-8122-0117", "researcher": {"href": "https://publications.scilifelab.se/researcher/eb44567679f44b0abc7798897b2cf1fc.json"}}, {"family": "Mohlke", "given": "Karen L", "initials": "KL"}, {"family": "Langenberg", "given": "Claudia", "initials": "C", "orcid": "0000-0002-5017-7344", "researcher": {"href": "https://publications.scilifelab.se/researcher/ca19370bb4d6437aa9df3905db9d3dd2.json"}}, {"family": "Wheeler", "given": "Eleanor", "initials": "E", "orcid": "0000-0002-8616-6444", "researcher": {"href": "https://publications.scilifelab.se/researcher/f7ed362ab4ba4b76b0ee743de84370c4.json"}}, {"family": "Morris", "given": "Andrew P", "initials": "AP", "orcid": "0000-0002-6805-6014", "researcher": {"href": "https://publications.scilifelab.se/researcher/991fd686a4a040a1a197c1f32d5b731b.json"}}, {"family": "Barroso", "given": "In\u00eas", "initials": "I", "orcid": "0000-0001-5800-4520", "researcher": {"href": "https://publications.scilifelab.se/researcher/c2dc6be9aa194bdc9a161e551d5e6747.json"}}, {"family": "Meta-Analysis of Glucose and Insulin-related Traits Consortium (MAGIC)", "given": "", "initials": ""}], "type": "journal article", "published": "2021-06-00", "journal": {"title": "Nat. Genet.", "issn": "1546-1718", "issn-l": "1061-4036", "volume": "53", "issue": "6", "pages": "840-860"}, "abstract": "Glycemic traits are used to diagnose and monitor type 2 diabetes and cardiometabolic health. To date, most genetic studies of glycemic traits have focused on individuals of European ancestry. Here we aggregated genome-wide association studies comprising up to 281,416 individuals without diabetes (30% non-European ancestry) for whom fasting glucose, 2-h glucose after an oral glucose challenge, glycated hemoglobin and fasting insulin data were available. Trans-ancestry and single-ancestry meta-analyses identified 242 loci (99 novel; P < 5 \u00d7 10-8), 80% of which had no significant evidence of between-ancestry heterogeneity. Analyses restricted to individuals of European ancestry with equivalent sample size would have led to 24 fewer new loci. Compared with single-ancestry analyses, equivalent-sized trans-ancestry fine-mapping reduced the number of estimated variants in 99% credible sets by a median of 37.5%. Genomic-feature, gene-expression and gene-set analyses revealed distinct biological signatures for each trait, highlighting different underlying biological pathways. Our results increase our understanding of diabetes pathophysiology by using trans-ancestry studies for improved power and resolution.", "doi": "10.1038/s41588-021-00852-9", "pmid": "34059833", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41588-021-00852-9"}, {"db": "pmc", "key": "PMC7610958"}, {"db": "mid", "key": "EMS120610"}], "notes": [], "created": "2021-06-02T14:41:54.348Z", "modified": "2021-12-07T13:34:42.616Z"}, {"entity": "publication", "iuid": "6fafb3fb4a434a16b201f782bf40b3a4", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6fafb3fb4a434a16b201f782bf40b3a4.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6fafb3fb4a434a16b201f782bf40b3a4"}}, "title": "RAG1 co-expression signature identifies ETV6-RUNX1-like B-cell precursor acute lymphoblastic leukemia in children.", "authors": [{"family": "Chen", "given": "Dongfeng", "initials": "D"}, {"family": "Camponeschi", "given": "Alessandro", "initials": "A"}, {"family": "Nordlund", "given": "Jessica", "initials": "J"}, {"family": "Marincevic-Zuniga", "given": "Yanara", "initials": "Y"}, {"family": "Abrahamsson", "given": "Jonas", "initials": "J"}, {"family": "L\u00f6nnerholm", "given": "Gudmar", "initials": "G"}, {"family": "Fogelstrand", "given": "Linda", "initials": "L"}, {"family": "M\u00e5rtensson", "given": "Inga-Lill", "initials": "IL", "orcid": "0000-0003-3415-0560", "researcher": {"href": "https://publications.scilifelab.se/researcher/c4f5cf8b693a4915b71a58e700768d6f.json"}}], "type": "journal article", "published": "2021-06-00", "journal": {"title": "Cancer Med", "issn": "2045-7634", "volume": "10", "issue": "12", "pages": "3997-4003", "issn-l": "2045-7634"}, "abstract": "B-cell precursor acute lymphoblastic leukemia (BCP-ALL) can be classified into subtypes according to the genetic aberrations they display. For instance, the translocation t(12;21)(p13;q22), representing the ETV6-RUNX1 fusion gene (ER), is present in a quarter of BCP-ALL cases. However, around 10% of the cases lack classifying chromosomal abnormalities (B-other). In pediatric ER BCP-ALL, rearrangement mediated by RAG (recombination-activating genes) has been proposed as the predominant driver of oncogenic rearrangement. Herein we analyzed almost 1600 pediatric BCP-ALL samples to determine which subtypes express RAG. We demonstrate that RAG1 mRNA levels are especially high in the ETV6-RUNX1 (ER) subtype and in a subset of B-other samples. We also define 31 genes that are co-expressed with RAG1 (RAG1-signature) in the ER subtype, a signature that also identifies this subset of B-other samples. Moreover, this subset also shares leukemia and pro-B gene expression signatures as well as high levels of the ETV6 target genes (BIRC7, WBP1L, CLIC5, ANGPTL2) with the ER subtype, indicating that these B-other cases are the recently identified ER-like subtype. We validated our results in a cohort where ER-like has been defined, which confirmed expression of the RAG1-signature in this recently described subtype. Taken together, our results demonstrate that the RAG1-signature identifies the ER-like subtype. As there are no definitive genetic markers to identify this novel subtype, the RAG1-signature represents a means to screen for this leukemia in children.", "doi": "10.1002/cam4.3928", "pmid": "33987955", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": null, "National Genomics Infrastructure": null}, "xrefs": [{"db": "pmc", "key": "PMC8209579"}], "notes": [], "created": "2021-12-10T10:40:15.529Z", "modified": "2021-12-10T10:40:15.575Z"}, {"entity": "publication", "iuid": "f6997001cfa5411e8dc27796e94d03c4", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f6997001cfa5411e8dc27796e94d03c4.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f6997001cfa5411e8dc27796e94d03c4"}}, "title": "Methylome and transcriptome signature of bronchoalveolar cells from multiple sclerosis patients in relation to smoking.", "authors": [{"family": "Ringh", "given": "Mikael V", "initials": "MV", "orcid": "0000-0001-9127-1284", "researcher": {"href": "https://publications.scilifelab.se/researcher/774da51e36434af882ef21ee3fda2b97.json"}}, {"family": "Hagemann-Jensen", "given": "Michael", "initials": "M", "orcid": "0000-0002-6423-8216", "researcher": {"href": "https://publications.scilifelab.se/researcher/26cb45960bd042c498f4914a342312a0.json"}}, {"family": "Needhamsen", "given": "Maria", "initials": "M"}, {"family": "Kullberg", "given": "Susanna", "initials": "S"}, {"family": "Wahlstr\u00f6m", "given": "Jan", "initials": "J"}, {"family": "Grunewald", "given": "Johan", "initials": "J"}, {"family": "Brynedal", "given": "Boel", "initials": "B"}, {"family": "Jagodic", "given": "Maja", "initials": "M"}, {"family": "Ekstr\u00f6m", "given": "Tomas J", "initials": "TJ"}, {"family": "\u00d6ckinger", "given": "Johan", "initials": "J"}, {"family": "Kular", "given": "Lara", "initials": "L"}], "type": "journal article", "published": "2021-06-00", "journal": {"title": "Mult. Scler.", "issn": "1477-0970", "issn-l": "1352-4585", "volume": "27", "issue": "7", "pages": "1014-1026"}, "abstract": "Despite compelling evidence that cigarette smoking impacts the risk of developing multiple sclerosis (MS), little is known about smoking-associated changes in the primary exposed lung cells of patients.\n\nWe aimed to examine molecular changes occurring in bronchoalveolar lavage (BAL) cells from MS patients in relation to smoking and in comparison to healthy controls (HCs).\n\nWe profiled DNA methylation in BAL cells from female MS (n = 17) and HC (n = 22) individuals, using Illumina Infinium EPIC and performed RNA-sequencing in non-smokers.\n\nThe most prominent changes were found in relation to smoking, with 1376 CpG sites (adjusted P < 0.05) differing between MS smokers and non-smokers. Approximately 30% of the affected genes overlapped with smoking-associated changes in HC, leading to a strong common smoking signature in both MS and HC after gene ontology analysis. Smoking in MS patients resulted in additional discrete changes related to neuronal processes. Methylome and transcriptome analyses in non-smokers suggest that BAL cells from MS patients display very subtle (not reaching adjusted P < 0.05) but concordant changes in genes connected to reduced transcriptional/translational processes and enhanced cellular motility.\n\nOur study provides insights into the impact of smoking on lung inflammation and immunopathogenesis of MS.", "doi": "10.1177/1352458520943768", "pmid": "32729352", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC8145441"}], "notes": [], "created": "2020-08-04T14:50:08.452Z", "modified": "2024-01-16T13:48:39.587Z"}, {"entity": "publication", "iuid": "e34ef08163944754a2a4a119c7fdfafa", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e34ef08163944754a2a4a119c7fdfafa.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e34ef08163944754a2a4a119c7fdfafa"}}, "title": "Gene-educational attainment interactions in a multi-ancestry genome-wide meta-analysis identify novel blood pressure loci.", "authors": [{"family": "de Las Fuentes", "given": "Lisa", "initials": "L", "orcid": "0000-0002-4689-325X", "researcher": {"href": "https://publications.scilifelab.se/researcher/87256c304d2f400d99b5a080aeed9185.json"}}, {"family": "Sung", "given": "Yun Ju", "initials": "YJ"}, {"family": "Noordam", "given": "Raymond", "initials": "R"}, {"family": "Winkler", "given": "Thomas", "initials": "T"}, {"family": "Feitosa", "given": "Mary F", "initials": "MF", "orcid": "0000-0002-0933-2410", "researcher": {"href": "https://publications.scilifelab.se/researcher/6e386c235834430eafaaca06e312aeb8.json"}}, {"family": "Schwander", "given": "Karen", "initials": "K"}, {"family": "Bentley", "given": "Amy R", "initials": "AR", "orcid": "0000-0002-0827-9101", "researcher": {"href": 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"BL", "orcid": "0000-0001-9843-412X", "researcher": {"href": "https://publications.scilifelab.se/researcher/1394a447fd314f05878d67dbc170f1ec.json"}}, {"family": "Kelly", "given": "Tanika N", "initials": "TN"}, {"family": "Kritchevsky", "given": "Stephen B", "initials": "SB"}, {"family": "Levy", "given": "Daniel", "initials": "D"}, {"family": "Palmas", "given": "Walter R", "initials": "WR"}, {"family": "Pereira", "given": "A C", "initials": "AC"}, {"family": "Province", "given": "Michael M", "initials": "MM"}, {"family": "Psaty", "given": "Bruce M", "initials": "BM"}, {"family": "Ridker", "given": "Paul M", "initials": "PM"}, {"family": "Rotimi", "given": "Charles N", "initials": "CN"}, {"family": "Tai", "given": "E Shyong", "initials": "ES"}, {"family": "van Dam", "given": "Rob M", "initials": "RM"}, {"family": "van Duijn", "given": "Cornelia M", "initials": "CM"}, {"family": "Wong", "given": "Tien Yin", "initials": "TY"}, {"family": "Rice", "given": "Kenneth", "initials": "K"}, {"family": "Gauderman", "given": "W James", "initials": "WJ"}, {"family": "Morrison", "given": "Alanna C", "initials": "AC"}, {"family": "North", "given": "Kari E", "initials": "KE"}, {"family": "Kardia", "given": "Sharon L R", "initials": "SLR"}, {"family": "Caulfield", "given": "Mark J", "initials": "MJ", "orcid": "0000-0001-9295-3594", "researcher": {"href": "https://publications.scilifelab.se/researcher/cc848c0cb6904712ad6b48c2058770f5.json"}}, {"family": "Elliott", "given": "Paul", "initials": "P"}, {"family": "Munroe", "given": "Patricia B", "initials": "PB"}, {"family": "Franks", "given": "Paul W", "initials": "PW"}, {"family": "Rao", "given": "Dabeeru C", "initials": "DC"}, {"family": "Fornage", "given": "Myriam", "initials": "M"}], "type": "journal article", "published": "2021-06-00", "journal": {"title": "Mol. Psychiatry", "issn": "1476-5578", "issn-l": "1359-4184", "volume": "26", "issue": "6", "pages": "2111-2125"}, "abstract": "Educational attainment is widely used as a surrogate for socioeconomic status (SES). Low SES is a risk factor for hypertension and high blood pressure (BP). To identify novel BP loci, we performed multi-ancestry meta-analyses accounting for gene-educational attainment interactions using two variables, \"Some College\" (yes/no) and \"Graduated College\" (yes/no). Interactions were evaluated using both a 1 degree of freedom (DF) interaction term and a 2DF joint test of genetic and interaction effects. Analyses were performed for systolic BP, diastolic BP, mean arterial pressure, and pulse pressure. We pursued genome-wide interrogation in Stage 1 studies (N = 117 438) and follow-up on promising variants in Stage 2 studies (N = 293 787) in five ancestry groups. Through combined meta-analyses of Stages 1 and 2, we identified 84 known and 18 novel BP loci at genome-wide significance level (P < 5 \u00d7 10-8). Two novel loci were identified based on the 1DF test of interaction with educational attainment, while the remaining 16 loci were identified through the 2DF joint test of genetic and interaction effects. Ten novel loci were identified in individuals of African ancestry. Several novel loci show strong biological plausibility since they involve physiologic systems implicated in BP regulation. They include genes involved in the central nervous system-adrenal signaling axis (ZDHHC17, CADPS, PIK3C2G), vascular structure and function (GNB3, CDON), and renal function (HAS2 and HAS2-AS1, SLIT3). Collectively, these findings suggest a role of educational attainment or SES in further dissection of the genetic architecture of BP.", "doi": "10.1038/s41380-020-0719-3", "pmid": "32372009", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41380-020-0719-3"}, {"db": "pmc", "key": "PMC7641978"}, {"db": "mid", "key": "NIHMS1579455"}], "notes": [], "created": "2021-01-07T17:01:46.378Z", "modified": "2021-12-07T13:40:35.407Z"}, {"entity": "publication", "iuid": "3781a12ed3544fa9b3e1a2daa02dc54b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3781a12ed3544fa9b3e1a2daa02dc54b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3781a12ed3544fa9b3e1a2daa02dc54b"}}, "title": "DNA methylation signatures of aggression and closely related constructs: A meta-analysis of epigenome-wide studies across the lifespan.", "authors": [{"family": "van Dongen", "given": "Jenny", "initials": "J", "orcid": "0000-0003-2063-8741", "researcher": {"href": "https://publications.scilifelab.se/researcher/fc28125d1b68438ea1a419437ad335c9.json"}}, {"family": "Hagenbeek", "given": "Fiona A", "initials": "FA", "orcid": "0000-0002-8773-0430", "researcher": {"href": "https://publications.scilifelab.se/researcher/1874bbcb93ed4633879199558ae54877.json"}}, {"family": "Suderman", "given": "Matthew", "initials": "M"}, {"family": "Roetman", "given": "Peter J", "initials": "PJ", "orcid": "0000-0002-6495-962X", "researcher": {"href": "https://publications.scilifelab.se/researcher/bd0b47e8144d4b0ab0c3bad505a1636f.json"}}, {"family": "Sugden", "given": "Karen", "initials": "K"}, {"family": "Chiocchetti", "given": "Andreas G", "initials": "AG", "orcid": "0000-0002-7329-9985", "researcher": {"href": "https://publications.scilifelab.se/researcher/b90b3aecf61a44f090e0511a52b0ebec.json"}}, {"family": "Ismail", "given": "Khadeeja", "initials": "K", "orcid": "0000-0003-0334-6480", "researcher": {"href": "https://publications.scilifelab.se/researcher/414de7510f734abb89a46dee9b50e708.json"}}, {"family": "Mulder", "given": "Rosa H", "initials": "RH"}, {"family": "Hafferty", "given": "Jonathan D", "initials": "JD"}, {"family": "Adams", "given": "Mark J", "initials": "MJ", "orcid": "0000-0002-3599-6018", "researcher": {"href": "https://publications.scilifelab.se/researcher/c669a6fd44e642429518845e37908dad.json"}}, {"family": "Walker", "given": "Rosie M", "initials": "RM", "orcid": "0000-0002-1060-4479", "researcher": {"href": "https://publications.scilifelab.se/researcher/79a65025d1a64ed2b383e69c803df0a4.json"}}, {"family": "Morris", "given": "Stewart W", "initials": "SW"}, {"family": "Lahti", "given": "Jari", "initials": "J", "orcid": "0000-0002-4310-5297", "researcher": {"href": "https://publications.scilifelab.se/researcher/09e0eb71fa6241449afef2b0542a738f.json"}}, {"family": "K\u00fcpers", "given": "Leanne K", "initials": "LK", "orcid": "0000-0001-9850-5215", "researcher": {"href": "https://publications.scilifelab.se/researcher/0a7f65b1431144afaba1acee5eea8fb6.json"}}, {"family": "Escaramis", "given": "Georgia", "initials": "G", "orcid": "0000-0002-5416-3177", "researcher": {"href": "https://publications.scilifelab.se/researcher/f1dcce4d1f2b4d4990c089441f6f2783.json"}}, {"family": "Alemany", "given": "Silvia", "initials": "S", "orcid": "0000-0002-7925-6767", "researcher": {"href": "https://publications.scilifelab.se/researcher/da641b351c9f48fcbd54a186d28806e5.json"}}, {"family": "Jan Bonder", "given": "Marc", "initials": "M", "orcid": "0000-0002-8431-3180", "researcher": {"href": "https://publications.scilifelab.se/researcher/a18167251318437c8eee87953b99e135.json"}}, {"family": "Meijer", "given": "Mandy", "initials": "M", "orcid": "0000-0002-9307-0643", "researcher": {"href": "https://publications.scilifelab.se/researcher/5964fc675db64b5ea17e02ed35999449.json"}}, {"family": "Ip", "given": "Hill F", "initials": "HF", "orcid": "0000-0003-1991-5019", "researcher": {"href": "https://publications.scilifelab.se/researcher/b04deeb54c174ad5aaed5247d9303dd2.json"}}, {"family": "Jansen", "given": "Rick", "initials": "R", "orcid": "0000-0002-3333-6737", "researcher": {"href": "https://publications.scilifelab.se/researcher/bcd392c9b9784ebe8c8730e05463377a.json"}}, {"family": "Baselmans", "given": "Bart M L", "initials": "BML"}, {"family": "Parmar", "given": "Priyanka", "initials": "P"}, {"family": "Lowry", "given": "Estelle", "initials": "E", "orcid": "0000-0002-4655-416X", "researcher": {"href": "https://publications.scilifelab.se/researcher/c7b0c07b3d19434f8f99de3e6ece921d.json"}}, {"family": "Streit", "given": "Fabian", "initials": "F", "orcid": "0000-0003-1080-4339", "researcher": {"href": "https://publications.scilifelab.se/researcher/faf42f4a84df4b3193cf59884ec8661b.json"}}, {"family": "Sirignano", "given": "Lea", "initials": "L", "orcid": "0000-0002-7989-5833", "researcher": {"href": "https://publications.scilifelab.se/researcher/b3e25818ffe646f8a843b8fea4fa1eee.json"}}, {"family": "Send", "given": "Tabea S", "initials": "TS"}, {"family": "Frank", "given": "Josef", "initials": "J", "orcid": "0000-0003-4867-9465", "researcher": {"href": "https://publications.scilifelab.se/researcher/041d6a59ba7d4c2dab9706861964bce1.json"}}, {"family": "Jylh\u00e4v\u00e4", "given": "Juulia", "initials": "J"}, {"family": "Wang", "given": "Yunzhang", "initials": "Y"}, {"family": "Mishra", "given": "Pashupati Prasad", "initials": "PP"}, {"family": "Colins", "given": "Olivier F", "initials": "OF", "orcid": "0000-0001-9532-2544", "researcher": {"href": "https://publications.scilifelab.se/researcher/ec63c561cea24f0bb78e8b92c6c5a82d.json"}}, {"family": "Corcoran", "given": "David L", "initials": "DL", "orcid": "0000-0001-7460-9247", "researcher": {"href": "https://publications.scilifelab.se/researcher/30eb6bb04e7846b58c7fa33a75cf3a51.json"}}, {"family": "Poulton", "given": "Richie", "initials": "R", "orcid": "0000-0002-1052-4583", "researcher": {"href": "https://publications.scilifelab.se/researcher/8f61fd90a9804126b169485da8cf65a1.json"}}, {"family": "Mill", "given": "Jonathan", "initials": "J", "orcid": "0000-0003-1115-3224", "researcher": {"href": "https://publications.scilifelab.se/researcher/480aff443bbd4605b3dd65736c08932e.json"}}, {"family": "Hannon", "given": "Eilis", "initials": "E", "orcid": "0000-0001-6840-072X", "researcher": {"href": "https://publications.scilifelab.se/researcher/2e059e0c152744da96bbfa7a26b4741f.json"}}, {"family": "Arseneault", "given": "Louise", "initials": "L", "orcid": "0000-0002-2938-2191", "researcher": {"href": "https://publications.scilifelab.se/researcher/0664e4afe7de4354924a1b39b87cf570.json"}}, {"family": "Korhonen", "given": "Tellervo", "initials": "T"}, {"family": "Vuoksimaa", "given": "Eero", "initials": "E"}, {"family": "Felix", "given": "Janine F", "initials": "JF", "orcid": "0000-0002-9801-5774", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a4482378cb24a9f832729f7004a41bf.json"}}, {"family": "Bakermans-Kranenburg", "given": "Marian J", "initials": "MJ", "orcid": "0000-0001-7763-0711", "researcher": {"href": "https://publications.scilifelab.se/researcher/11233b4bc1be47ca8248ac062f859e81.json"}}, {"family": "Campbell", "given": "Archie", "initials": "A", "orcid": "0000-0003-0198-5078", "researcher": {"href": "https://publications.scilifelab.se/researcher/89d6b9cb975246e5aa97c60035e2fdcc.json"}}, {"family": "Czamara", "given": "Darina", "initials": "D", "orcid": "0000-0001-7381-904X", "researcher": {"href": "https://publications.scilifelab.se/researcher/0e9a8a7d605d4f63a311fc8a211422a6.json"}}, {"family": "Binder", "given": "Elisabeth", "initials": "E", "orcid": "0000-0001-7088-6618", "researcher": {"href": "https://publications.scilifelab.se/researcher/0cfb2bf09e9d49ad922bb5c3c252c716.json"}}, {"family": "Corpeleijn", "given": "Eva", "initials": "E"}, {"family": "Gonzalez", "given": "Juan R", "initials": "JR", "orcid": "0000-0003-3267-2146", "researcher": {"href": "https://publications.scilifelab.se/researcher/0898265a25ee4d14b875e14d7ff09479.json"}}, {"family": "Grazuleviciene", "given": "Regina", "initials": "R", "orcid": "0000-0002-0210-8053", "researcher": {"href": "https://publications.scilifelab.se/researcher/223bfb218f2e49bf999bd1521369ba83.json"}}, {"family": "Gutzkow", "given": "Kristine B", "initials": "KB"}, {"family": "Evandt", "given": "Jorunn", "initials": "J"}, {"family": "Vafeiadi", "given": "Marina", "initials": "M", "orcid": "0000-0002-6143-7172", "researcher": {"href": "https://publications.scilifelab.se/researcher/eb8527777ad8409c89344e0b455365e7.json"}}, {"family": "Klein", "given": "Marieke", "initials": "M", "orcid": "0000-0001-8784-5679", "researcher": {"href": "https://publications.scilifelab.se/researcher/a7481a7b70b6411b98c77e27e0de9b2f.json"}}, {"family": "van der Meer", "given": "Dennis", "initials": "D", "orcid": "0000-0002-0466-386X", "researcher": {"href": "https://publications.scilifelab.se/researcher/77320b76a77b4045af6228ee5258f41e.json"}}, {"family": "Ligthart", "given": "Lannie", "initials": "L", "orcid": "0000-0002-6570-3319", "researcher": {"href": "https://publications.scilifelab.se/researcher/c352ff3a891d4eb5bfe9c0260238ef79.json"}}, {"family": "BIOS Consortium", "given": "", "initials": ""}, {"family": "Kluft", "given": "Cornelis", "initials": "C"}, {"family": "Davies", "given": "Gareth E", "initials": "GE"}, {"family": "Hakulinen", "given": "Christian", "initials": "C"}, {"family": "Keltikangas-J\u00e4rvinen", "given": "Liisa", "initials": "L"}, {"family": "Franke", "given": "Barbara", "initials": "B", "orcid": "0000-0003-4375-6572", "researcher": {"href": "https://publications.scilifelab.se/researcher/105f0131cfc34a668ed840e622e4f902.json"}}, {"family": "Freitag", "given": "Christine M", "initials": "CM", "orcid": "0000-0001-9676-4782", "researcher": {"href": "https://publications.scilifelab.se/researcher/5d9f9f97c28b4919b09be5c1292a806b.json"}}, {"family": "Konrad", "given": "Kerstin", "initials": "K", "orcid": "0000-0001-9039-2615", "researcher": {"href": "https://publications.scilifelab.se/researcher/4b063642dc3d425a8037e2cc0ff3a067.json"}}, {"family": "Hervas", "given": "Amaia", "initials": "A"}, {"family": "Fern\u00e1ndez-Rivas", "given": "Aranzazu", "initials": "A"}, {"family": "Vetro", "given": "Agnes", "initials": "A"}, {"family": "Raitakari", "given": "Olli", "initials": "O"}, {"family": "Lehtim\u00e4ki", "given": "Terho", "initials": "T", "orcid": "0000-0002-2555-4427", "researcher": {"href": "https://publications.scilifelab.se/researcher/03ed59707dae4c8fb9e63ac1f7c398e3.json"}}, {"family": "Vermeiren", "given": "Robert", "initials": "R"}, {"family": "Strandberg", "given": "Timo", "initials": "T"}, {"family": "R\u00e4ikk\u00f6nen", "given": "Katri", "initials": "K"}, {"family": "Snieder", "given": "Harold", "initials": "H", "orcid": "0000-0003-1949-2298", "researcher": {"href": "https://publications.scilifelab.se/researcher/e9276827839a4f3cb50dcaa2ad4708a5.json"}}, {"family": "Witt", "given": "Stephanie H", "initials": "SH", "orcid": "0000-0002-1571-1468", "researcher": {"href": "https://publications.scilifelab.se/researcher/88c8da59196f4adb8a57509e5e9e85ef.json"}}, {"family": "Deuschle", "given": "Michael", "initials": "M"}, {"family": "Pedersen", "given": "Nancy L", "initials": "NL"}, {"family": "H\u00e4gg", "given": "Sara", "initials": "S", "orcid": "0000-0002-2452-1500", "researcher": {"href": "https://publications.scilifelab.se/researcher/e1d010dfe5d84a33b6a6c7ec815ca3dc.json"}}, {"family": "Sunyer", "given": "Jordi", "initials": "J"}, {"family": "Franke", "given": "Lude", "initials": "L"}, {"family": "Kaprio", "given": "Jaakko", "initials": "J", "orcid": "0000-0002-3716-2455", "researcher": {"href": "https://publications.scilifelab.se/researcher/814d362333844b72a70cba9ebcf61e6f.json"}}, {"family": "Ollikainen", "given": "Miina", "initials": "M", "orcid": "0000-0003-3661-7400", "researcher": {"href": "https://publications.scilifelab.se/researcher/0cda8a90eedd4d179a230bc5377d3989.json"}}, {"family": "Moffitt", "given": "Terrie E", "initials": "TE"}, {"family": "Tiemeier", "given": "Henning", "initials": "H", "orcid": "0000-0002-4395-1397", "researcher": {"href": "https://publications.scilifelab.se/researcher/73e05bd74af344ba8d963463f49bb242.json"}}, {"family": "van IJzendoorn", "given": "Marinus H", "initials": "MH", "orcid": "0000-0003-1144-454X", "researcher": {"href": "https://publications.scilifelab.se/researcher/d8ae6deb331f4c52b835210f42c65abe.json"}}, {"family": "Relton", "given": "Caroline", "initials": "C"}, {"family": "Vrijheid", "given": "Martine", "initials": "M", "orcid": "0000-0002-7090-1758", "researcher": {"href": "https://publications.scilifelab.se/researcher/ccf0ebb5d1664b99bbb460c194d2f361.json"}}, {"family": "Sebert", "given": "Sylvain", "initials": "S", "orcid": "0000-0001-6681-6983", "researcher": {"href": "https://publications.scilifelab.se/researcher/c007e85f69d4421bb6cf76dc52a01eb8.json"}}, {"family": "Jarvelin", "given": "Marjo-Riitta", "initials": "M"}, {"family": "Caspi", "given": "Avshalom", "initials": "A"}, {"family": "Evans", "given": "Kathryn L", "initials": "KL", "orcid": "0000-0002-7884-5877", "researcher": {"href": "https://publications.scilifelab.se/researcher/2985078354be4ab19f96d66fa9b2c8cc.json"}}, {"family": "McIntosh", "given": "Andrew M", "initials": "AM", "orcid": "0000-0002-0198-4588", "researcher": {"href": "https://publications.scilifelab.se/researcher/cbac1cee97084746b97442ec39efe91b.json"}}, {"family": "Bartels", "given": "Meike", "initials": "M", "orcid": "0000-0002-9667-7555", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a91c095e993411b99e81e21f40d8597.json"}}, {"family": "Boomsma", "given": "Dorret I", "initials": "DI", "orcid": "0000-0002-7099-7972", "researcher": {"href": "https://publications.scilifelab.se/researcher/4b66ab2525fd4a468e7a4ad14c955cb4.json"}}], "type": "journal article", "published": "2021-06-00", "journal": {"title": "Mol. Psychiatry", "issn": "1476-5578", "issn-l": "1359-4184", "volume": "26", "issue": "6", "pages": "2148-2162"}, "abstract": "DNA methylation profiles of aggressive behavior may capture lifetime cumulative effects of genetic, stochastic, and environmental influences associated with aggression. Here, we report the first large meta-analysis of epigenome-wide association studies (EWAS) of aggressive behavior (N = 15,324 participants). In peripheral blood samples of 14,434 participants from 18 cohorts with mean ages ranging from 7 to 68 years, 13 methylation sites were significantly associated with aggression (alpha = 1.2 \u00d7 10-7; Bonferroni correction). In cord blood samples of 2425 children from five cohorts with aggression assessed at mean ages ranging from 4 to 7 years, 83% of these sites showed the same direction of association with childhood aggression (r = 0.74, p = 0.006) but no epigenome-wide significant sites were found. Top-sites (48 at a false discovery rate of 5% in the peripheral blood meta-analysis or in a combined meta-analysis of peripheral blood and cord blood) have been associated with chemical exposures, smoking, cognition, metabolic traits, and genetic variation (mQTLs). Three genes whose expression levels were associated with top-sites were previously linked to schizophrenia and general risk tolerance. At six CpGs, DNA methylation variation in blood mirrors variation in the brain. On average 44% (range = 3-82%) of the aggression-methylation association was explained by current and former smoking and BMI. These findings point at loci that are sensitive to chemical exposures with potential implications for neuronal functions. We hope these results to be a starting point for studies leading to applications as peripheral biomarkers and to reveal causal relationships with aggression and related traits.", "doi": "10.1038/s41380-020-00987-x", "pmid": "33420481", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41380-020-00987-x"}, {"db": "pmc", "key": "PMC8263810"}, {"db": "mid", "key": "EMS114691"}], "notes": [], "created": "2021-01-14T11:58:55.708Z", "modified": "2021-12-07T13:43:00.672Z"}, {"entity": "publication", "iuid": "df0dbc510b754682bfdebf127ba2393e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/df0dbc510b754682bfdebf127ba2393e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/df0dbc510b754682bfdebf127ba2393e"}}, "title": "Genomic basis of parallel adaptation varies with divergence in Arabidopsis and its relatives.", "authors": [{"family": "Bohut\u00ednsk\u00e1", "given": "Magdalena", "initials": "M"}, {"family": "Vl\u010dek", "given": "Jakub", "initials": "J", "orcid": "0000-0002-2174-9374", "researcher": {"href": "https://publications.scilifelab.se/researcher/26fabad020684e8296458cc3589813c0.json"}}, {"family": "Yair", "given": "Sivan", "initials": "S", "orcid": "0000-0001-5806-6895", "researcher": {"href": "https://publications.scilifelab.se/researcher/117c0e3537664adfbb1fbd8a3eb6ca71.json"}}, {"family": "Laenen", "given": "Benjamin", "initials": "B"}, {"family": "Kone\u010dn\u00e1", "given": "Veronika", "initials": "V"}, {"family": "Fracassetti", "given": "Marco", "initials": "M"}, {"family": "Slotte", "given": "Tanja", "initials": "T", "orcid": "0000-0001-6020-5102", "researcher": {"href": "https://publications.scilifelab.se/researcher/67c69ee78bae41478465a7e5fa63b946.json"}}, {"family": "Kol\u00e1\u0159", "given": "Filip", "initials": "F", "orcid": "0000-0002-8793-7992", "researcher": {"href": "https://publications.scilifelab.se/researcher/6bfaa4ec7256437badb1ad8c41dff51b.json"}}], "type": "journal article", "published": "2021-05-25", "journal": {"title": "Proc. Natl. Acad. Sci. U.S.A.", "issn": "1091-6490", "volume": "118", "issue": "21", "issn-l": "0027-8424"}, "abstract": "Parallel adaptation provides valuable insight into the predictability of evolutionary change through replicated natural experiments. A steadily increasing number of studies have demonstrated genomic parallelism, yet the magnitude of this parallelism varies depending on whether populations, species, or genera are compared. This led us to hypothesize that the magnitude of genomic parallelism scales with genetic divergence between lineages, but whether this is the case and the underlying evolutionary processes remain unknown. Here, we resequenced seven parallel lineages of two Arabidopsis species, which repeatedly adapted to challenging alpine environments. By combining genome-wide divergence scans with model-based approaches, we detected a suite of 151 genes that show parallel signatures of positive selection associated with alpine colonization, involved in response to cold, high radiation, short season, herbivores, and pathogens. We complemented these parallel candidates with published gene lists from five additional alpine Brassicaceae and tested our hypothesis on a broad scale spanning \u223c0.02 to 18 My of divergence. Indeed, we found quantitatively variable genomic parallelism whose extent significantly decreased with increasing divergence between the compared lineages. We further modeled parallel evolution over the Arabidopsis candidate genes and showed that a decreasing probability of repeated selection on the same standing or introgressed alleles drives the observed pattern of divergence-dependent parallelism. We therefore conclude that genetic divergence between populations, species, and genera, affecting the pool of shared variants, is an important factor in the predictability of genome evolution.", "doi": "10.1073/pnas.2022713118", "pmid": "34001609", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pii", "key": "2022713118"}, {"db": "pmc", "key": "PMC8166048"}], "notes": [], "created": "2021-12-10T15:14:38.311Z", "modified": "2021-12-10T15:14:38.443Z"}, {"entity": "publication", "iuid": "d6a88ec152fc41aa9cd664708fc3c565", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d6a88ec152fc41aa9cd664708fc3c565.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d6a88ec152fc41aa9cd664708fc3c565"}}, "title": "A combined approach for single-cell mRNA and intracellular protein expression analysis.", "authors": [{"family": "Reimeg\u00e5rd", "given": "Johan", "initials": "J"}, {"family": "Tarbier", "given": "Marcel", "initials": "M"}, {"family": "Danielsson", "given": "Marcus", "initials": "M", "orcid": "0000-0003-4418-0165", "researcher": {"href": "https://publications.scilifelab.se/researcher/d6b237ce613e4ef8a6d7ab2654c2c41e.json"}}, {"family": "Schuster", "given": "Jens", "initials": "J", "orcid": "0000-0002-4383-9880", "researcher": {"href": "https://publications.scilifelab.se/researcher/a194d037b21c47a2926b082e9e79de31.json"}}, {"family": "Baskaran", "given": "Sathishkumar", "initials": "S"}, {"family": "Panagiotou", "given": "Styliani", "initials": "S"}, {"family": "Dahl", "given": "Niklas", "initials": "N", "orcid": "0000-0002-8122-0800", "researcher": {"href": "https://publications.scilifelab.se/researcher/689e06ddc001490a8cb891050ba5a732.json"}}, {"family": "Friedl\u00e4nder", "given": "Marc R", "initials": "MR"}, {"family": "Gallant", "given": "Caroline J", "initials": "CJ", "orcid": "0000-0002-1499-8444", "researcher": {"href": "https://publications.scilifelab.se/researcher/b11c1c853309426faed0af716f1288cd.json"}}], "type": "journal article", "published": "2021-05-25", "journal": {"title": "Commun Biol", "issn": "2399-3642", "issn-l": "2399-3642", "volume": "4", "issue": "1", "pages": "624"}, "abstract": "Combined measurements of mRNA and protein expression in single cells enable in-depth analysis of cellular states. We present SPARC, an approach that combines single-cell RNA-sequencing with proximity extension essays to simultaneously measure global mRNA and 89 intracellular proteins in individual cells. We show that mRNA expression fails to accurately reflect protein abundance at the time of measurement, although the direction of changes is in agreement during neuronal differentiation. Moreover, protein levels of transcription factors better predict their downstream effects than do their corresponding transcripts. Finally, we highlight that protein expression variation is overall lower than mRNA variation, but relative protein variation does not reflect the mRNA level. Our results demonstrate that mRNA and protein measurements in single cells provide different and complementary information regarding cell states. SPARC presents a state-of-the-art co-profiling method that overcomes current limitations in throughput and protein localization, including removing the need for cell fixation.", "doi": "10.1038/s42003-021-02142-w", "pmid": "34035432", "labels": {"Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Affinity Proteomics Uppsala": "Technology development", "National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1038/s42003-021-02142-w"}, {"db": "pmc", "key": "PMC8149646"}], "notes": [], "created": "2021-06-02T12:38:48.106Z", "modified": "2024-01-16T13:48:39.677Z"}, {"entity": "publication", "iuid": "a399c8ea3f8f4803ac4af20a48121956", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a399c8ea3f8f4803ac4af20a48121956.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a399c8ea3f8f4803ac4af20a48121956"}}, "title": "Size Variation of the Nonrecombining Region on the Mating-Type Chromosomes in the Fungal Podospora anserina Species Complex.", "authors": [{"family": "Hartmann", "given": "Fanny E", "initials": "FE", "orcid": "0000-0002-9365-4008", "researcher": {"href": "https://publications.scilifelab.se/researcher/ac8e717031aa4621925ab90684adecdc.json"}}, {"family": "Ament-Vel\u00e1squez", "given": "Sandra Lorena", "initials": "SL"}, {"family": "Vogan", "given": "Aaron A", "initials": "AA"}, {"family": "Gautier", "given": "Val\u00e9rie", "initials": "V"}, {"family": "Le Prieur", "given": "Stephanie", "initials": "S"}, {"family": "Berramdane", "given": "Myriam", "initials": "M"}, {"family": "Snirc", "given": "Alodie", "initials": "A"}, {"family": "Johannesson", "given": "Hanna", "initials": "H"}, {"family": "Grognet", "given": "Pierre", "initials": "P"}, {"family": "Malagnac", "given": "Fabienne", "initials": "F"}, {"family": "Silar", "given": "Philippe", "initials": "P"}, {"family": "Giraud", "given": "Tatiana", "initials": "T"}], "type": "journal article", "published": "2021-05-19", "journal": {"title": "Mol. Biol. Evol.", "issn": "1537-1719", "volume": "38", "issue": "6", "pages": "2475-2492", "issn-l": "0737-4038"}, "abstract": "Sex chromosomes often carry large nonrecombining regions that can extend progressively over time, generating evolutionary strata of sequence divergence. However, some sex chromosomes display an incomplete suppression of recombination. Large genomic regions without recombination and evolutionary strata have also been documented around fungal mating-type loci, but have been studied in only a few fungal systems. In the model fungus Podospora anserina (Ascomycota, Sordariomycetes), the reference S strain lacks recombination across a 0.8-Mb region around the mating-type locus. The lack of recombination in this region ensures that nuclei of opposite mating types are packaged into a single ascospore (pseudohomothallic lifecycle). We found evidence for a lack of recombination around the mating-type locus in the genomes of ten P. anserina strains and six closely related pseudohomothallic Podospora species. Importantly, the size of the nonrecombining region differed between strains and species, as indicated by the heterozygosity levels around the mating-type locus and experimental selfing. The nonrecombining region is probably labile and polymorphic, differing in size and precise location within and between species, resulting in occasional, but infrequent, recombination at a given base pair. This view is also supported by the low divergence between mating types, and the lack of strong linkage disequilibrium, chromosomal rearrangements, transspecific polymorphism and genomic degeneration. We found a pattern suggestive of evolutionary strata in P. pseudocomata. The observed heterozygosity levels indicate low but nonnull outcrossing rates in nature in these pseudohomothallic fungi. This study adds to our understanding of mating-type chromosome evolution and its relationship to mating systems.", "doi": "10.1093/molbev/msab040", "pmid": "33555341", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "6130827"}, {"db": "pmc", "key": "PMC8136517"}], "notes": [], "created": "2021-12-08T14:00:24.674Z", "modified": "2024-01-16T13:48:39.711Z"}, {"entity": "publication", "iuid": "eac7874ed8294cfabb98f904d734dc74", "links": {"self": {"href": "https://publications.scilifelab.se/publication/eac7874ed8294cfabb98f904d734dc74.json"}, "display": {"href": "https://publications.scilifelab.se/publication/eac7874ed8294cfabb98f904d734dc74"}}, "title": "Comprehensive dataset of shotgun metagenomes from oxygen stratified freshwater lakes and ponds.", "authors": [{"family": "Buck", "given": "Moritz", "initials": "M"}, {"family": "Garcia", "given": "Sarahi L", "initials": "SL", "orcid": "0000-0002-8622-0308", "researcher": {"href": "https://publications.scilifelab.se/researcher/8aabc8c17d5b4ad7872c7380301d4562.json"}}, {"family": "Fernandez", "given": "Leyden", "initials": "L"}, {"family": "Martin", "given": "Ga\u00ebtan", "initials": "G", "orcid": "0000-0002-5289-6131", "researcher": {"href": "https://publications.scilifelab.se/researcher/3fa7c61072034af188ed3685ce83ca3c.json"}}, {"family": "Martinez-Rodriguez", "given": "Gustavo A", "initials": "GA"}, {"family": "Saarenheimo", "given": "Jatta", "initials": "J"}, {"family": "Zopfi", "given": "Jakob", "initials": "J", "orcid": "0000-0002-8437-7344", "researcher": {"href": "https://publications.scilifelab.se/researcher/fea1eab419af4e60b1455c0221a5b6e7.json"}}, {"family": "Bertilsson", "given": "Stefan", "initials": "S", "orcid": "0000-0002-4265-1835", "researcher": {"href": "https://publications.scilifelab.se/researcher/2c17765c2a9f4383b5383138d11ae93f.json"}}, {"family": "Peura", "given": "Sari", "initials": "S", "orcid": "0000-0003-3892-8157", "researcher": {"href": "https://publications.scilifelab.se/researcher/c430ad5c3bd14387b768c588a9b12ce0.json"}}], "type": "dataset", "published": "2021-05-14", "journal": {"title": "Sci Data", "issn": "2052-4463", "volume": "8", "issue": "1", "pages": "131", "issn-l": "2052-4463"}, "abstract": "Stratified lakes and ponds featuring steep oxygen gradients are significant net sources of greenhouse gases and hotspots in the carbon cycle. Despite their significant biogeochemical roles, the microbial communities, especially in the oxygen depleted compartments, are poorly known. Here, we present a comprehensive dataset including 267 shotgun metagenomes from 41 stratified lakes and ponds mainly located in the boreal and subarctic regions, but also including one tropical reservoir and one temperate lake. For most lakes and ponds, the data includes a vertical sample set spanning from the oxic surface to the anoxic bottom layer. The majority of the samples were collected during the open water period, but also a total of 29 samples were collected from under the ice. In addition to the metagenomic sequences, the dataset includes environmental variables for the samples, such as oxygen, nutrient and organic carbon concentrations. The dataset is ideal for further exploring the microbial taxonomic and functional diversity in freshwater environments and potential climate change impacts on the functioning of these ecosystems.", "doi": "10.1038/s41597-021-00910-1", "pmid": "33990618", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41597-021-00910-1"}, {"db": "pmc", "key": "PMC8121793"}], "notes": [], "created": "2021-06-01T20:55:20.891Z", "modified": "2024-01-16T13:48:39.756Z"}, {"entity": "publication", "iuid": "8cce79d935434ebf8878720309fe8b5b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8cce79d935434ebf8878720309fe8b5b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8cce79d935434ebf8878720309fe8b5b"}}, "title": "Freshwater Chlorobia Exhibit Metabolic Specialization among Cosmopolitan and Endemic Populations.", "authors": [{"family": "Garcia", "given": "Sarahi L", "initials": "SL", "orcid": "0000-0002-8622-0308", "researcher": {"href": "https://publications.scilifelab.se/researcher/8aabc8c17d5b4ad7872c7380301d4562.json"}}, {"family": "Mehrshad", "given": "Maliheh", "initials": "M"}, {"family": "Buck", "given": "Moritz", "initials": "M"}, {"family": "Tsuji", "given": "Jackson M", "initials": "JM"}, {"family": "Neufeld", "given": "Josh D", "initials": "JD", "orcid": "0000-0002-8722-8571", "researcher": {"href": "https://publications.scilifelab.se/researcher/fea734cbc1ad4f33bdc1da72d3a34c35.json"}}, {"family": "McMahon", "given": "Katherine D", "initials": "KD", "orcid": "0000-0002-7038-026X", "researcher": {"href": "https://publications.scilifelab.se/researcher/84f48c9a667f4b1d80d85ad7bc2694e2.json"}}, {"family": "Bertilsson", "given": "Stefan", "initials": "S"}, {"family": "Greening", "given": "Chris", "initials": "C", "orcid": "0000-0001-7616-0594", "researcher": {"href": "https://publications.scilifelab.se/researcher/48e65b0eddca4d029e24ac3b6bcbb965.json"}}, {"family": "Peura", "given": "Sari", "initials": "S", "orcid": "0000-0003-3892-8157", "researcher": {"href": "https://publications.scilifelab.se/researcher/c430ad5c3bd14387b768c588a9b12ce0.json"}}], "type": "journal article", "published": "2021-05-11", "journal": {"title": "mSystems", "issn": "2379-5077", "volume": "6", "issue": "3", "pages": null, "issn-l": "2379-5077"}, "abstract": "Photosynthetic bacteria from the class Chlorobia (formerly phylum Chlorobi) sustain carbon fixation in anoxic water columns. They harvest light at extremely low intensities and use various inorganic electron donors to fix carbon dioxide into biomass. Until now, most information on the functional ecology and local adaptations of Chlorobia members came from isolates and merely 26 sequenced genomes that may not adequately represent natural populations. To address these limitations, we analyzed global metagenomes to profile planktonic Chlorobia cells from the oxyclines of 42 freshwater bodies, spanning subarctic to tropical regions and encompassing all four seasons. We assembled and compiled over 500 genomes, including metagenome-assembled genomes (MAGs), single-amplified genomes (SAGs), and reference genomes from cultures, clustering them into 71 metagenomic operational taxonomic units (mOTUs or \"species\"). Of the 71 mOTUs, 57 were classified within the genus Chlorobium, and these mOTUs represented up to \u223c60% of the microbial communities in the sampled anoxic waters. Several Chlorobium-associated mOTUs were globally distributed, whereas others were endemic to individual lakes. Although most clades encoded the ability to oxidize hydrogen, many lacked genes for the oxidation of specific sulfur and iron substrates. Surprisingly, one globally distributed Scandinavian clade encoded the ability to oxidize hydrogen, sulfur, and iron, suggesting that metabolic versatility facilitated such widespread colonization. Overall, these findings provide new insight into the biogeography of the Chlorobia and the metabolic traits that facilitate niche specialization within lake ecosystems.IMPORTANCE The reconstruction of genomes from metagenomes has helped explore the ecology and evolution of environmental microbiota. We applied this approach to 274 metagenomes collected from diverse freshwater habitats that spanned oxic and anoxic zones, sampling seasons, and latitudes. We demonstrate widespread and abundant distributions of planktonic Chlorobia-associated bacteria in hypolimnetic waters of stratified freshwater ecosystems and show they vary in their capacities to use different electron donors. Having photoautotrophic potential, these Chlorobia members could serve as carbon sources that support metalimnetic and hypolimnetic food webs.", "doi": "10.1128/mSystems.01196-20", "pmid": "33975970", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "6/3/e01196-20"}, {"db": "pmc", "key": "PMC8125076"}], "notes": [], "created": "2021-06-01T20:56:01.234Z", "modified": "2024-01-16T13:48:39.770Z"}, {"entity": "publication", "iuid": "84feaff577c540c8a2808e4f594e2b8d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/84feaff577c540c8a2808e4f594e2b8d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/84feaff577c540c8a2808e4f594e2b8d"}}, "title": "INT-Hi-C reveals distinct chromatin architecture in endosperm and leaf tissues of Arabidopsis.", "authors": [{"family": "Yadav", "given": "Vikash Kumar", "initials": "VK", "orcid": "0000-0002-9581-5127", "researcher": {"href": "https://publications.scilifelab.se/researcher/258e8aeb778045e6b8e48c0f8639e0c3.json"}}, {"family": "Santos-Gonz\u00e1lez", "given": "Juan", "initials": "J", "orcid": "0000-0002-8712-9776", "researcher": {"href": "https://publications.scilifelab.se/researcher/d26cc8b837e64875aa2226cb9a8b8da3.json"}}, {"family": "K\u00f6hler", "given": "Claudia", "initials": "C", "orcid": "0000-0002-2619-4857", "researcher": {"href": "https://publications.scilifelab.se/researcher/accd3f9307614c8ab67154dd5e50cdac.json"}}], "type": "journal article", "published": "2021-05-07", "journal": {"title": "Nucleic Acids Res.", "issn": "1362-4962", "volume": "49", "issue": "8", "pages": "4371-4385", "issn-l": "0305-1048"}, "abstract": "Higher-order chromatin structure undergoes striking changes in response to various developmental and environmental signals, causing distinct cell types to adopt specific chromatin organization. High throughput chromatin conformation capture (Hi-C) allows studying higher-order chromatin structure; however, this technique requires substantial amounts of starting material, which has limited the establishment of cell type-specific higher-order chromatin structure in plants. To overcome this limitation, we established a protocol that is applicable to a limited amount of nuclei by combining the INTACT (isolation of nuclei tagged in specific cell types) method and Hi-C (INT-Hi-C). Using this INT-Hi-C protocol, we generated Hi-C data from INTACT purified endosperm and leaf nuclei. Our INT-Hi-C data from leaf accurately reiterated chromatin interaction patterns derived from conventional leaf Hi-C data. We found that the higher-order chromatin organization of mixed leaf tissues and endosperm differs and that DNA methylation and repressive histone marks positively correlate with the chromatin compaction level. We furthermore found that self-looped interacting genes have increased expression in leaves and endosperm and that interacting intergenic regions negatively impact on gene expression in the endosperm. Last, we identified several imprinted genes involved in long-range and trans interactions exclusively in endosperm. Our study provides evidence that the endosperm adopts a distinct higher-order chromatin structure that differs from other cell types in plants and that chromatin interactions influence transcriptional activity.", "doi": "10.1093/nar/gkab191", "pmid": "33744975", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "6179351"}, {"db": "pmc", "key": "PMC8096224"}], "notes": [], "created": "2021-12-07T21:42:00.584Z", "modified": "2021-12-07T21:42:00.660Z"}, {"entity": "publication", "iuid": "6cab2cbebcc34f5e8cc965eb5955fdca", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6cab2cbebcc34f5e8cc965eb5955fdca.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6cab2cbebcc34f5e8cc965eb5955fdca"}}, "title": "Genetically determined NLRP3 inflammasome activation associates with systemic inflammation and cardiovascular mortality.", "authors": [{"family": "Schunk", "given": "Stefan J", "initials": "SJ"}, {"family": "Kleber", "given": "Marcus E", "initials": "ME", "orcid": "0000-0003-0663-7275", "researcher": {"href": "https://publications.scilifelab.se/researcher/a51175112cfb4721b8c9fbfdc71c4307.json"}}, {"family": "M\u00e4rz", "given": "Winfried", "initials": "W"}, {"family": "Pang", "given": "Shichao", "initials": "S", "orcid": "0000-0002-4111-2864", "researcher": {"href": "https://publications.scilifelab.se/researcher/9839ca383ecb432dafae190a3a5b583a.json"}}, {"family": "Zewinger", "given": "Stephen", "initials": "S"}, {"family": "Triem", "given": "Sarah", "initials": "S"}, {"family": "Ege", "given": "Philipp", "initials": "P"}, {"family": "Reichert", "given": "Matthias C", "initials": "MC", "orcid": "0000-0002-8192-0575", "researcher": {"href": "https://publications.scilifelab.se/researcher/a12ee4f4194f4f9c8cfecd585aa92fe9.json"}}, {"family": "Krawczyk", "given": "Marcin", "initials": "M"}, {"family": "Weber", "given": "Susanne N", "initials": "SN"}, {"family": "Jaumann", "given": "Isabella", "initials": "I"}, {"family": "Schmit", "given": "David", "initials": "D"}, {"family": "Sarakpi", "given": "Tamim", "initials": "T"}, {"family": "Wagenpfeil", "given": "Stefan", "initials": "S", "orcid": "0000-0002-4558-4041", "researcher": {"href": "https://publications.scilifelab.se/researcher/9587116dd42d44d9b5a1cc33af1d6623.json"}}, {"family": "Kramann", "given": "Rafael", "initials": "R", "orcid": "0000-0003-4048-6351", "researcher": {"href": "https://publications.scilifelab.se/researcher/d5994a0ef0594c55a01e0886f3288b3b.json"}}, {"family": "Boerwinkle", "given": "Eric", "initials": "E"}, {"family": "Ballantyne", "given": "Christie M", "initials": "CM"}, {"family": "Grove", "given": "Megan L", "initials": "ML"}, {"family": "Tragante", "given": "Vinicius", "initials": "V", "orcid": "0000-0002-8223-8957", "researcher": {"href": "https://publications.scilifelab.se/researcher/eb83d260bc8546edba9e3e2ed2d2c752.json"}}, {"family": "Pilbrow", "given": "Anna P", "initials": "AP", "orcid": "0000-0003-1949-9449", "researcher": {"href": "https://publications.scilifelab.se/researcher/b86a1225a68e403e806a07b42e96c991.json"}}, {"family": "Richards", "given": "A Mark", "initials": "AM", "orcid": "0000-0002-2023-8177", "researcher": {"href": "https://publications.scilifelab.se/researcher/305e1cdb095145fab591d41542b578dd.json"}}, {"family": "Cameron", "given": "Vicky A", "initials": "VA", "orcid": "0000-0003-3147-683X", "researcher": {"href": "https://publications.scilifelab.se/researcher/72d115e749a34e239c336c16e35fdd64.json"}}, {"family": "Doughty", "given": "Robert N", "initials": "RN"}, {"family": "Dub\u00e9", "given": "Marie-Pierre", "initials": "M"}, {"family": "Tardif", "given": "Jean-Claude", "initials": "J"}, {"family": "Feroz-Zada", "given": "Yassamin", "initials": "Y"}, {"family": "Sun", "given": "Maxine", "initials": "M"}, {"family": "Liu", "given": "Chang", "initials": "C", "orcid": "0000-0002-8918-7224", "researcher": {"href": "https://publications.scilifelab.se/researcher/994fa918eb6142fca1897858b7b56a06.json"}}, {"family": "Ko", "given": "Yi-An", "initials": "Y"}, {"family": "Quyyumi", "given": "Arshed A", "initials": "AA"}, {"family": "Hartiala", "given": "Jaana A", "initials": "JA", "orcid": "0000-0003-4883-9318", "researcher": {"href": "https://publications.scilifelab.se/researcher/f39400df71774cf8ae408eccbe34d981.json"}}, {"family": "Tang", "given": "W H Wilson", "initials": "WHW", "orcid": "0000-0002-8335-735X", "researcher": {"href": "https://publications.scilifelab.se/researcher/5aab6a5657004a79aeda81c22a077268.json"}}, {"family": "Hazen", "given": "Stanley L", "initials": "SL", "orcid": "0000-0001-7124-6639", "researcher": {"href": "https://publications.scilifelab.se/researcher/abce9cd916c94667a73bc348ede57a01.json"}}, {"family": "Allayee", "given": "Hooman", "initials": "H", "orcid": "0000-0002-2384-5239", "researcher": {"href": 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"https://publications.scilifelab.se/researcher/abe3ddd140b3478485f44119d18926b7.json"}}, {"family": "Martinsson", "given": "Andreas", "initials": "A"}, {"family": "Smith", "given": "J Gustav", "initials": "JG"}, {"family": "Wallentin", "given": "Lars", "initials": "L", "orcid": "0000-0003-0378-6531", "researcher": {"href": "https://publications.scilifelab.se/researcher/388a76db2e4d423882d1cf2bf6b7d985.json"}}, {"family": "James", "given": "Stefan K", "initials": "SK"}, {"family": "Eriksson", "given": "Niclas", "initials": "N", "orcid": "0000-0002-2152-4343", "researcher": {"href": "https://publications.scilifelab.se/researcher/64611a83caba46d597f45371b77de26b.json"}}, {"family": "White", "given": "Harvey", "initials": "H", "orcid": "0000-0001-7712-6750", "researcher": {"href": "https://publications.scilifelab.se/researcher/3fe685eeba0d411f8d275e3ecbf4bb3c.json"}}, {"family": "Held", "given": "Claes", "initials": "C", "orcid": "0000-0001-9402-7404", "researcher": {"href": "https://publications.scilifelab.se/researcher/88c69f319fce4852aab37e02a75ed525.json"}}, {"family": "Waterworth", "given": "Dawn", "initials": "D", "orcid": "0000-0002-9226-1317", "researcher": {"href": "https://publications.scilifelab.se/researcher/9e78b8890897424abea48058cd4c77d2.json"}}, {"family": "Trompet", "given": "Stella", "initials": "S"}, {"family": "Jukema", "given": "J Wouter", "initials": "JW", "orcid": "0000-0002-3246-8359", "researcher": {"href": "https://publications.scilifelab.se/researcher/0479b794031d4df7bed96340b3470c19.json"}}, {"family": "Ford", "given": "Ian", "initials": "I", "orcid": "0000-0001-5927-1823", "researcher": {"href": "https://publications.scilifelab.se/researcher/317610dc46d14a2ebea4a1fc4e9cecc7.json"}}, {"family": "Stott", "given": "David J", "initials": "DJ", "orcid": "0000-0002-3110-7746", "researcher": {"href": "https://publications.scilifelab.se/researcher/c7e647358616409f9d8983f342485014.json"}}, {"family": "Sattar", "given": "Naveed", "initials": "N", "orcid": "0000-0002-1604-2593", "researcher": {"href": "https://publications.scilifelab.se/researcher/80fbc7cdcfc444acb066449f80f87181.json"}}, {"family": "Cresci", "given": "Sharon", "initials": "S", "orcid": "0000-0002-5417-1054", "researcher": {"href": "https://publications.scilifelab.se/researcher/e134fd37d561443eb2bd8c23c3aa6df9.json"}}, {"family": "Spertus", "given": "John A", "initials": "JA", "orcid": "0000-0002-2839-2611", "researcher": {"href": "https://publications.scilifelab.se/researcher/58934381001f467fa9c8ed53787956bb.json"}}, {"family": "Campbell", "given": "Hannah", "initials": "H"}, {"family": "Tierling", "given": "Sascha", "initials": "S"}, {"family": "Walter", "given": "J\u00f6rn", "initials": "J", "orcid": "0000-0003-0563-7417", "researcher": {"href": "https://publications.scilifelab.se/researcher/3ea3e512691b4aa39c5b7c7fdcdb585d.json"}}, {"family": "Ampofo", "given": "Emmanuel", "initials": "E"}, {"family": "Niemeyer", "given": "Barbara A", "initials": "BA", "orcid": "0000-0002-6963-0575", "researcher": {"href": "https://publications.scilifelab.se/researcher/f5261a56f977404b894cd4a5bad1bbc3.json"}}, {"family": "Lipp", "given": "Peter", "initials": "P", "orcid": "0000-0003-4728-9174", "researcher": {"href": "https://publications.scilifelab.se/researcher/b96abc30cbf54fc1917b2976308c12b3.json"}}, {"family": "Schunkert", "given": "Heribert", "initials": "H"}, {"family": "B\u00f6hm", "given": "Michael", "initials": "M"}, {"family": "Koenig", "given": "Wolfgang", "initials": "W", "orcid": "0000-0002-2064-9603", "researcher": {"href": "https://publications.scilifelab.se/researcher/b358f3d797814a07a05a63364ae37d27.json"}}, {"family": "Fliser", "given": "Danilo", "initials": "D"}, {"family": "Laufs", "given": "Ulrich", "initials": "U", "orcid": "0000-0003-2620-9323", "researcher": {"href": "https://publications.scilifelab.se/researcher/3d7b26e6a8964ce2b76be17eddf2c7ac.json"}}, {"family": "Speer", "given": "Thimoteus", "initials": "T", "orcid": "0000-0002-2491-6393", "researcher": {"href": "https://publications.scilifelab.se/researcher/4c3bc32b3f144c6080853bae7094d681.json"}}, {"family": "eQTLGen consortium", "given": "", "initials": ""}, {"family": "BIOS consortium", "given": "", "initials": ""}], "type": "journal article", "published": "2021-05-07", "journal": {"title": "Eur. Heart J.", "issn": "1522-9645", "issn-l": "0195-668X", "volume": "42", "issue": "18", "pages": "1742-1756"}, "abstract": "Inflammation plays an important role in cardiovascular disease (CVD) development. The NOD-like receptor protein-3 (NLRP3) inflammasome contributes to the development of atherosclerosis in animal models. Components of the NLRP3 inflammasome pathway such as interleukin-1\u03b2 can therapeutically be targeted. Associations of genetically determined inflammasome-mediated systemic inflammation with CVD and mortality in humans are unknown.\r\n\r\nWe explored the association of genetic NLRP3 variants with prevalent CVD and cardiovascular mortality in 538 167 subjects on the individual participant level in an explorative gene-centric approach without performing multiple testing. Functional relevance of single-nucleotide polymorphisms on NLRP3 inflammasome activation has been evaluated in monocyte-enriched peripheral blood mononuclear cells (PBMCs). Genetic analyses identified the highly prevalent (minor allele frequency 39.9%) intronic NLRP3 variant rs10754555 to affect NLRP3 gene expression. rs10754555 carriers showed significantly higher C-reactive protein and serum amyloid A plasma levels. Carriers of the G allele showed higher NLRP3 inflammasome activation in isolated human PBMCs. In carriers of the rs10754555 variant, the prevalence of coronary artery disease was significantly higher as compared to non-carriers with a significant interaction between rs10754555 and age. Importantly, rs10754555 carriers had significantly higher risk for cardiovascular mortality during follow-up. Inflammasome inducers (e.g. urate, triglycerides, apolipoprotein C3) modulated the association between rs10754555 and mortality.\r\n\r\nThe NLRP3 intronic variant rs10754555 is associated with increased systemic inflammation, inflammasome activation, prevalent coronary artery disease, and mortality. This study provides evidence for a substantial role of genetically driven systemic inflammation in CVD and highlights the NLRP3 inflammasome as a therapeutic target.", "doi": "10.1093/eurheartj/ehab107", "pmid": "33748830", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pii", "key": "6179517"}, {"db": "pmc", "key": "PMC8244638"}], "notes": [], "created": "2021-08-19T13:42:03.904Z", "modified": "2021-12-07T13:39:27.736Z"}, {"entity": "publication", "iuid": "deff2c719d7a42779cbc1bc349308d01", "links": {"self": {"href": "https://publications.scilifelab.se/publication/deff2c719d7a42779cbc1bc349308d01.json"}, "display": {"href": "https://publications.scilifelab.se/publication/deff2c719d7a42779cbc1bc349308d01"}}, "title": "How to Make a Rodent Giant: Genomic Basis and Tradeoffs of Gigantism in the Capybara, the World's Largest Rodent.", "authors": [{"family": "Herrera-\u00c1lvarez", "given": "Santiago", "initials": "S"}, {"family": "Karlsson", "given": "Elinor", "initials": "E"}, {"family": "Ryder", "given": "Oliver A", "initials": "OA"}, {"family": "Lindblad-Toh", "given": "Kerstin", "initials": "K", "orcid": "0000-0001-8338-0253", "researcher": {"href": "https://publications.scilifelab.se/researcher/e0063145f7d6476f80ab42f94833f4cf.json"}}, {"family": "Crawford", "given": "Andrew J", "initials": "AJ"}], "type": "journal article", "published": "2021-05-04", "journal": {"title": "Mol. Biol. Evol.", "issn": "1537-1719", "volume": "38", "issue": "5", "pages": "1715-1730", "issn-l": "0737-4038"}, "abstract": "Gigantism results when one lineage within a clade evolves extremely large body size relative to its small-bodied ancestors, a common phenomenon in animals. Theory predicts that the evolution of giants should be constrained by two tradeoffs. First, because body size is negatively correlated with population size, purifying selection is expected to be less efficient in species of large body size, leading to increased mutational load. Second, gigantism is achieved through generating a higher number of cells along with higher rates of cell proliferation, thus increasing the likelihood of cancer. To explore the genetic basis of gigantism in rodents and uncover genomic signatures of gigantism-related tradeoffs, we assembled a draft genome of the capybara (Hydrochoerus hydrochaeris), the world's largest living rodent. We found that the genome-wide ratio of nonsynonymous to synonymous mutations (\u03c9) is elevated in the capybara relative to other rodents, likely caused by a generation-time effect and consistent with a nearly neutral model of molecular evolution. A genome-wide scan for adaptive protein evolution in the capybara highlighted several genes controlling postnatal bone growth regulation and musculoskeletal development, which are relevant to anatomical and developmental modifications for an increase in overall body size. Capybara-specific gene-family expansions included a putative novel anticancer adaptation that involves T-cell-mediated tumor suppression, offering a potential resolution to the increased cancer risk in this lineage. Our comparative genomic results uncovered the signature of an intragenomic conflict where the evolution of gigantism in the capybara involved selection on genes and pathways that are directly linked to cancer.", "doi": "10.1093/molbev/msaa285", "pmid": "33169792", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "5970469"}, {"db": "pmc", "key": "PMC8097284"}], "notes": [], "created": "2020-12-08T23:29:44.480Z", "modified": "2024-01-16T13:48:39.806Z"}, {"entity": "publication", "iuid": "9acd5d0b7f5e4a668d85581efffd3c1a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9acd5d0b7f5e4a668d85581efffd3c1a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9acd5d0b7f5e4a668d85581efffd3c1a"}}, "title": "The association between genetically determined ABO blood types and major depressive disorder.", "authors": [{"family": "Garvert", "given": "Linda", "initials": "L", "orcid": "0000-0001-9067-8170", "researcher": {"href": "https://publications.scilifelab.se/researcher/05b37721238e4e77840b66458f808478.json"}}, {"family": "Baune", "given": "Bernhard T", "initials": "BT"}, {"family": "Berger", "given": "Klaus", "initials": "K"}, {"family": "Boomsma", "given": "Dorret I", "initials": "DI"}, {"family": "Breen", "given": "Gerome", "initials": "G"}, {"family": "Greinacher", "given": "Andreas", "initials": "A"}, {"family": "Hamilton", "given": "Steven P", "initials": "SP"}, {"family": "Levinson", "given": "Douglas F", "initials": "DF", "orcid": "0000-0001-8223-1301", "researcher": {"href": "https://publications.scilifelab.se/researcher/2157b66dad64472fbbbf395ddfb5304b.json"}}, {"family": "Lewis", "given": "Cathryn M", "initials": "CM"}, {"family": "Lucae", "given": "Susanne", "initials": "S"}, {"family": "Magnusson", "given": "Patrik K E", "initials": "PKE"}, {"family": "Martin", "given": "Nicholas G", "initials": "NG"}, {"family": "McIntosh", "given": "Andrew M", "initials": "AM"}, {"family": "Mors", "given": "Ole", "initials": "O"}, {"family": "M\u00fcller-Myhsok", "given": "Bertram", "initials": "B"}, {"family": "Penninx", "given": "Brenda W J H", "initials": "BWJH"}, {"family": "Perlis", "given": "Roy H", "initials": "RH"}, {"family": "Pistis", "given": "Giorgio", "initials": "G", "orcid": "0000-0002-4525-4608", "researcher": {"href": "https://publications.scilifelab.se/researcher/4c068265d6244ffb9f7cea5837fd8b81.json"}}, {"family": "Potash", "given": "James B", "initials": "JB"}, {"family": "Preisig", "given": "Martin", "initials": "M"}, {"family": "Rietschel", "given": "Marcella", "initials": "M"}, {"family": "Shi", "given": "Jianxin", "initials": "J"}, {"family": "Smoller", "given": "Jordan W", "initials": "JW"}, {"family": "Tiemeier", "given": "Henning", "initials": "H"}, {"family": "Uher", "given": "Rudolf", "initials": "R"}, {"family": "V\u00f6lker", "given": "Uwe", "initials": "U", "orcid": "0000-0002-5689-3448", "researcher": {"href": "https://publications.scilifelab.se/researcher/e529a40052644d83bdef588a3e4f4e99.json"}}, {"family": "V\u00f6lzke", "given": "Henry", "initials": "H"}, {"family": "Weissman", "given": "Myrna M", "initials": "MM"}, {"family": "Major Depressive Disorder Working Group of the Psychiatric Genomics Consortium", "given": "", "initials": ""}, {"family": "Grabe", "given": "Hans J", "initials": "HJ"}, {"family": "Van der Auwera", "given": "Sandra", "initials": "S"}], "type": "journal article", "published": "2021-05-00", "journal": {"title": "Psychiatry Res", "issn": "1872-7123", "issn-l": "0165-1781", "volume": "299", "issue": null, "pages": "113837"}, "abstract": "ABO blood types and their corresponding antigens have long been assumed to be related to different human diseases. So far, smaller studies on the relationship between mental disorders and blood types yielded contradicting results. In this study we analyzed the association between ABO blood types and lifetime major depressive disorder (MDD). We performed a pooled analysis with data from 26 cohorts that are part of the MDD working group of the Psychiatric Genomics Consortium (PGC). The dataset included 37,208 individuals of largely European ancestry of which 41.6% were diagnosed with lifetime MDD. ABO blood types were identified using three single nucleotide polymorphisms in the ABO gene: rs505922, rs8176746 and rs8176747. Regression analyses were performed to assess associations between the individual ABO blood types and MDD diagnosis as well as putative interaction effects with sex. The models were adjusted for sex, cohort and the first ten genetic principal components. The percentage of blood type A was slightly lower in cases than controls while blood type O was more prominent in cases. However, these differences were not statistically significant. Our analyses found no evidence of an association between ABO blood types and major depressive disorder.", "doi": "10.1016/j.psychres.2021.113837", "pmid": "33721783", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "S0165-1781(21)00134-7"}, {"db": "pmc", "key": "PMC8071927"}, {"db": "mid", "key": "NIHMS1683126"}], "notes": [], "created": "2021-04-28T15:32:48.271Z", "modified": "2021-12-07T13:24:50.935Z"}, {"entity": "publication", "iuid": "5623f32746cb4b67a34293cad348214a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5623f32746cb4b67a34293cad348214a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5623f32746cb4b67a34293cad348214a"}}, "title": "The Enterprise, a massive transposon carrying Spok meiotic drive genes.", "authors": [{"family": "Vogan", "given": "Aaron A", "initials": "AA", "orcid": "0000-0003-2013-7445", "researcher": {"href": "https://publications.scilifelab.se/researcher/71c6d460e3b44712a1a9dc19066211a4.json"}}, {"family": "Ament-Vel\u00e1squez", "given": "S Lorena", "initials": "SL", "orcid": "0000-0003-3371-9292", "researcher": {"href": "https://publications.scilifelab.se/researcher/9d54ef94f91c4c1c85d5dc3a846023e5.json"}}, {"family": "Bastiaans", "given": "Eric", "initials": "E", "orcid": "0000-0003-1502-0947", "researcher": {"href": "https://publications.scilifelab.se/researcher/870bd6035e54489187ef1d5131d14108.json"}}, {"family": "Wallerman", "given": "Ola", "initials": "O"}, {"family": "Saupe", "given": "Sven J", "initials": "SJ"}, {"family": "Suh", "given": "Alexander", "initials": "A", "orcid": "0000-0002-8979-9992", "researcher": {"href": "https://publications.scilifelab.se/researcher/4e39e1313d894596a6c4ed949e43e019.json"}}, {"family": "Johannesson", "given": "Hanna", "initials": "H", "orcid": "0000-0001-6359-9856", "researcher": {"href": "https://publications.scilifelab.se/researcher/36e8fe278e01470e8cddaaccc5dad596.json"}}], "type": "journal article", "published": "2021-05-00", "journal": {"title": "Genome Res.", "issn": "1549-5469", "volume": "31", "issue": "5", "pages": "789-798", "issn-l": "1088-9051"}, "abstract": "The genomes of eukaryotes are full of parasitic sequences known as transposable elements (TEs). Here, we report the discovery of a putative giant tyrosine-recombinase-mobilized DNA transposon, Enterprise, from the model fungus Podospora anserina Previously, we described a large genomic feature called the Spok block which is notable due to the presence of meiotic drive genes of the Spok gene family. The Spok block ranges from 110 kb to 247 kb and can be present in at least four different genomic locations within P. anserina, despite what is an otherwise highly conserved genome structure. We propose that the reason for its varying positions is that the Spok block is not only capable of meiotic drive but is also capable of transposition. More precisely, the Spok block represents a unique case where the Enterprise has captured the Spoks, thereby parasitizing a resident genomic parasite to become a genomic hyperparasite. Furthermore, we demonstrate that Enterprise (without the Spoks) is found in other fungal lineages, where it can be as large as 70 kb. Lastly, we provide experimental evidence that the Spok block is deleterious, with detrimental effects on spore production in strains which carry it. This union of meiotic drivers and a transposon has created a selfish element of impressive size in Podospora, challenging our perception of how TEs influence genome evolution and broadening the horizons in terms of what the upper limit of transposition may be.", "doi": "10.1101/gr.267609.120", "pmid": "33875482", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "gr.267609.120"}, {"db": "pmc", "key": "PMC8092012"}], "notes": [], "created": "2021-06-01T20:57:51.352Z", "modified": "2024-01-16T13:48:39.850Z"}, {"entity": "publication", "iuid": "66c38388bcce41afa4006563a2e9e6f9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/66c38388bcce41afa4006563a2e9e6f9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/66c38388bcce41afa4006563a2e9e6f9"}}, "title": "Genetic basis of lacunar stroke: a pooled analysis of individual patient data and genome-wide association studies.", "authors": [{"family": "Traylor", "given": "Matthew", "initials": "M"}, {"family": "Persyn", "given": "Elodie", "initials": "E"}, {"family": "Tomppo", "given": "Liisa", "initials": "L"}, {"family": "Klasson", "given": "Sofia", "initials": "S"}, {"family": "Abedi", "given": "Vida", "initials": "V"}, {"family": "Bakker", "given": "Mark K", "initials": "MK"}, {"family": "Torres", "given": "Nuria", "initials": "N"}, {"family": "Li", "given": "Linxin", "initials": "L"}, {"family": "Bell", "given": "Steven", "initials": "S"}, {"family": "Rutten-Jacobs", "given": "Loes", "initials": "L"}, {"family": "Tozer", "given": "Daniel J", "initials": "DJ"}, {"family": "Griessenauer", "given": "Christoph J", "initials": "CJ"}, {"family": "Zhang", "given": "Yanfei", "initials": "Y"}, {"family": "Pedersen", "given": "Annie", "initials": "A"}, {"family": "Sharma", "given": "Pankaj", "initials": "P"}, {"family": "Jimenez-Conde", "given": "Jordi", "initials": "J"}, {"family": "Rundek", "given": "Tatjana", "initials": "T"}, {"family": "Grewal", "given": "Raji P", "initials": "RP"}, {"family": "Lindgren", "given": "Arne", "initials": "A"}, {"family": "Meschia", "given": "James F", "initials": "JF"}, {"family": "Salomaa", "given": "Veikko", "initials": "V"}, {"family": "Havulinna", "given": "Aki", "initials": "A"}, {"family": "Kourkoulis", "given": "Christina", "initials": "C"}, {"family": "Crawford", "given": "Katherine", "initials": "K"}, {"family": "Marini", "given": "Sandro", "initials": "S"}, {"family": "Mitchell", "given": "Braxton D", "initials": "BD"}, {"family": "Kittner", "given": "Steven J", "initials": "SJ"}, {"family": "Rosand", "given": "Jonathan", "initials": "J"}, {"family": "Dichgans", "given": "Martin", "initials": "M"}, {"family": "Jern", "given": "Christina", "initials": "C"}, {"family": "Strbian", "given": "Daniel", "initials": "D"}, {"family": "Fernandez-Cadenas", "given": "Israel", "initials": "I"}, {"family": "Zand", "given": "Ramin", "initials": "R"}, {"family": "Ruigrok", "given": "Ynte", "initials": "Y"}, {"family": "Rost", "given": "Natalia", "initials": "N"}, {"family": "Lemmens", "given": "Robin", "initials": "R"}, {"family": "Rothwell", "given": "Peter M", "initials": "PM"}, {"family": "Anderson", "given": "Christopher D", "initials": "CD"}, {"family": "Wardlaw", "given": "Joanna", "initials": "J"}, {"family": "Lewis", "given": "Cathryn M", "initials": "CM"}, {"family": "Markus", "given": "Hugh S", "initials": "HS"}, {"family": "Helsinki Stroke", "given": "Study Dutch Parelsnoer Institute-Cerebrovascular Accident (CVA) Study Group,", "initials": "SDPIA(SG"}, {"family": "National Institute of Neurological Disorders and Stroke (NINDS) Stroke Genetics Network", "given": "", "initials": ""}, {"family": "UK DNA Lacunar Stroke Study Investigators", "given": "", "initials": ""}, {"family": "International Stroke Genetics Consortium", "given": "", "initials": ""}], "type": "journal article", "published": "2021-05-00", "journal": {"title": "Lancet Neurol", "issn": "1474-4465", "issn-l": null, "volume": "20", "issue": "5", "pages": "351-361"}, "abstract": "The genetic basis of lacunar stroke is poorly understood, with a single locus on 16q24 identified to date. We sought to identify novel associations and provide mechanistic insights into the disease.\r\n\r\nWe did a pooled analysis of data from newly recruited patients with an MRI-confirmed diagnosis of lacunar stroke and existing genome-wide association studies (GWAS). Patients were recruited from hospitals in the UK as part of the UK DNA Lacunar Stroke studies 1 and 2 and from collaborators within the International Stroke Genetics Consortium. Cases and controls were stratified by ancestry and two meta-analyses were done: a European ancestry analysis, and a transethnic analysis that included all ancestry groups. We also did a multi-trait analysis of GWAS, in a joint analysis with a study of cerebral white matter hyperintensities (an aetiologically related radiological trait), to find additional genetic associations. We did a transcriptome-wide association study (TWAS) to detect genes for which expression is associated with lacunar stroke; identified significantly enriched pathways using multi-marker analysis of genomic annotation; and evaluated cardiovascular risk factors causally associated with the disease using mendelian randomisation.\r\n\r\nOur meta-analysis comprised studies from Europe, the USA, and Australia, including 7338 cases and 254 798 controls, of which 2987 cases (matched with 29 540 controls) were confirmed using MRI. Five loci (ICA1L-WDR12-CARF-NBEAL1, ULK4, SPI1-SLC39A13-PSMC3-RAPSN, ZCCHC14, ZBTB14-EPB41L3) were found to be associated with lacunar stroke in the European or transethnic meta-analyses. A further seven loci (SLC25A44-PMF1-BGLAP, LOX-ZNF474-LOC100505841, FOXF2-FOXQ1, VTA1-GPR126, SH3PXD2A, HTRA1-ARMS2, COL4A2) were found to be associated in the multi-trait analysis with cerebral white matter hyperintensities (n=42 310). Two of the identified loci contain genes (COL4A2 and HTRA1) that are involved in monogenic lacunar stroke. The TWAS identified associations between the expression of six genes (SCL25A44, ULK4, CARF, FAM117B, ICA1L, NBEAL1) and lacunar stroke. Pathway analyses implicated disruption of the extracellular matrix, phosphatidylinositol 5 phosphate binding, and roundabout binding (false discovery rate <0\u00b705). Mendelian randomisation analyses identified positive associations of elevated blood pressure, history of smoking, and type 2 diabetes with lacunar stroke.\r\n\r\nLacunar stroke has a substantial heritable component, with 12 loci now identified that could represent future treatment targets. These loci provide insights into lacunar stroke pathogenesis, highlighting disruption of the vascular extracellular matrix (COL4A2, LOX, SH3PXD2A, GPR126, HTRA1), pericyte differentiation (FOXF2, GPR126), TGF-\u03b2 signalling (HTRA1), and myelination (ULK4, GPR126) in disease risk.\r\n\r\nBritish Heart Foundation.", "doi": "10.1016/S1474-4422(21)00031-4", "pmid": "33773637", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "S1474-4422(21)00031-4"}, {"db": "pmc", "key": "PMC8062914"}], "notes": [], "created": "2021-05-07T14:20:33.285Z", "modified": "2021-12-07T13:44:21.308Z"}, {"entity": "publication", "iuid": "cb971709f76944139aa5a66027bd3da4", "links": {"self": {"href": "https://publications.scilifelab.se/publication/cb971709f76944139aa5a66027bd3da4.json"}, "display": {"href": "https://publications.scilifelab.se/publication/cb971709f76944139aa5a66027bd3da4"}}, "title": "Dual RNA-Seq transcriptome analysis of chicken macrophage-like cells (HD11) infected in vitro with Eimeria tenella.", "authors": [{"family": "Sandholt", "given": "Arnar K S", "initials": "AKS", "orcid": "0000-0001-8926-1052", "researcher": {"href": "https://publications.scilifelab.se/researcher/be881c7a0be44f878e9541b90899ea01.json"}}, {"family": "Xu", "given": "Feifei", "initials": "F"}, {"family": "S\u00f6derlund", "given": "Robert", "initials": "R"}, {"family": "Lund\u00e9n", "given": "Anna", "initials": "A"}, {"family": "Troell", "given": "Karin", "initials": "K"}, {"family": "Sv\u00e4rd", "given": "Staffan G", "initials": "SG"}, {"family": "Wattrang", "given": "Eva", "initials": "E", "orcid": "0000-0002-9804-169X", "researcher": {"href": "https://publications.scilifelab.se/researcher/8ef4e114ca144741a46f15eecde0f3ec.json"}}], "type": "journal article", "published": "2021-05-00", "journal": {"title": "Parasitology", "issn": "1469-8161", "volume": "148", "issue": "6", "pages": "712-725", "issn-l": null}, "abstract": "The study aimed to monitor parasite and host gene expression during the early stages of Eimeria tenella infection of chicken cells using dual RNA-Seq analysis. For this, we used chicken macrophage-like cell line HD11 cultures infected in vitro with purified E. tenella sporozoites. Cultures were harvested between 2 and 72 h post-infection and mRNA was extracted and sequenced. Dual RNA-Seq analysis showed clear patterns of altered expression for both parasite and host genes during infection. For example, genes in the chicken immune system showed upregulation early (2\u20134 h), a strong downregulation of genes across the immune system at 24 h and a repetition of early patterns at 72 h, indicating that invasion by a second generation of parasites was occurring. The observed downregulation may be due to immune self-regulation or to immune evasive mechanisms exerted by E. tenella. Results also suggested pathogen recognition receptors involved in E. tenella innate recognition, MRC2, TLR15 and NLRC5 and showed distinct chemokine and cytokine induction patterns. Moreover, the expression of several functional categories of Eimeria genes, such as rhoptry kinase genes and microneme genes, were also examined, showing distinctive differences which were expressed in sporozoites and merozoites.", "doi": "10.1017/S0031182021000111", "pmid": "33536090", "labels": {"NGI Stockholm (Genomics Production)": null, "NGI Stockholm (Genomics Applications)": null, "National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "S0031182021000111"}, {"db": "pmc", "key": "PMC8056837"}], "notes": [], "created": "2021-06-09T12:15:36.974Z", "modified": "2024-01-16T13:48:39.926Z"}, {"entity": "publication", "iuid": "86f05d7bca134d87b5dd15cffe3d55dd", "links": {"self": {"href": "https://publications.scilifelab.se/publication/86f05d7bca134d87b5dd15cffe3d55dd.json"}, "display": {"href": "https://publications.scilifelab.se/publication/86f05d7bca134d87b5dd15cffe3d55dd"}}, "title": "An introgressed gene causes meiotic drive in Neurospora sitophila.", "authors": [{"family": "Svedberg", "given": "Jesper", "initials": "J", "orcid": "0000-0002-0951-3019", "researcher": {"href": "https://publications.scilifelab.se/researcher/1d35216730c841d197a958bfa00a06a0.json"}}, {"family": "Vogan", "given": "Aaron A", "initials": "AA"}, {"family": "Rhoades", "given": "Nicholas A", "initials": "NA"}, {"family": "Sarmarajeewa", "given": "Dilini", "initials": "D"}, {"family": "Jacobson", "given": "David J", "initials": "DJ"}, {"family": "Lascoux", "given": "Martin", "initials": "M", "orcid": "0000-0003-1699-9042", "researcher": {"href": "https://publications.scilifelab.se/researcher/4ad3fadfb69448f397ad3bf55b2d2cb3.json"}}, {"family": "Hammond", "given": "Thomas M", "initials": "TM", "orcid": "0000-0002-0812-4759", "researcher": {"href": "https://publications.scilifelab.se/researcher/cdc694cc4c4749ca821feadf727fe77b.json"}}, {"family": "Johannesson", "given": "Hanna", "initials": "H", "orcid": "0000-0001-6359-9856", "researcher": {"href": "https://publications.scilifelab.se/researcher/36e8fe278e01470e8cddaaccc5dad596.json"}}], "type": "journal article", "published": "2021-04-27", "journal": {"title": "Proc. Natl. Acad. Sci. U.S.A.", "issn": "1091-6490", "volume": "118", "issue": "17", "pages": "e2026605118", "issn-l": "0027-8424"}, "abstract": "Meiotic drive elements cause their own preferential transmission following meiosis. In fungi, this phenomenon takes the shape of spore killing, and in the filamentous ascomycete Neurospora sitophila, the Sk-1 spore killer element is found in many natural populations. In this study, we identify the gene responsible for spore killing in Sk-1 by generating both long- and short-read genomic data and by using these data to perform a genome-wide association test. We name this gene Spk-1 Through molecular dissection, we show that a single 405-nt-long open reading frame generates a product that both acts as a poison capable of killing sibling spores and as an antidote that rescues spores that produce it. By phylogenetic analysis, we demonstrate that the gene has likely been introgressed from the closely related species Neurospora hispaniola, and we identify three subclades of N. sitophila, one where Sk-1 is fixed, another where Sk-1 is absent, and a third where both killer and sensitive strain are found. Finally, we show that spore killing can be suppressed through an RNA interference-based genome defense pathway known as meiotic silencing by unpaired DNA. Spk-1 is not related to other known meiotic drive genes, and similar sequences are only found within Neurospora These results shed light on the diversity of genes capable of causing meiotic drive, their origin and evolution, and their interaction with the host genome.", "doi": "10.1073/pnas.2026605118", "pmid": "33875604", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "2026605118"}, {"db": "pmc", "key": "PMC8092558"}, {"db": "figshare", "key": "10.6084/m9.figshare.c.5093585.v1"}], "notes": [], "created": "2021-06-01T20:57:22.667Z", "modified": "2024-01-16T13:48:39.983Z"}, {"entity": "publication", "iuid": "a4bc69e0882f4272ad5f75cd97457b73", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a4bc69e0882f4272ad5f75cd97457b73.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a4bc69e0882f4272ad5f75cd97457b73"}}, "title": "Epigenome-wide association study of level and change in cognitive abilities from midlife through late life.", "authors": [{"family": "Karlsson", "given": "Ida K", "initials": "IK", "orcid": "0000-0003-3605-7829", "researcher": {"href": "https://publications.scilifelab.se/researcher/b2c87ada82ae43df9753a891305ddb40.json"}}, {"family": "Ericsson", "given": "Malin", "initials": "M"}, {"family": "Wang", "given": "Yunzhang", "initials": "Y"}, {"family": "Jylh\u00e4v\u00e4", "given": "Juulia", "initials": "J"}, {"family": "H\u00e4gg", "given": "Sara", "initials": "S"}, {"family": "Dahl Aslan", "given": "Anna K", "initials": "AK"}, {"family": "Reynolds", "given": "Chandra A", "initials": "CA"}, {"family": "Pedersen", "given": "Nancy L", "initials": "NL"}], "type": "journal article", "published": "2021-04-21", "journal": {"title": "Clin Epigenetics", "issn": "1868-7083", "issn-l": "1868-7075", "volume": "13", "issue": "1", "pages": "85"}, "abstract": "Epigenetic mechanisms are important in aging and may be involved in late-life changes in cognitive abilities. We conducted an epigenome-wide association study of leukocyte DNA methylation in relation to level and change in cognitive abilities, from midlife through late life in 535 Swedish twins.\n\nMethylation levels were measured with the Infinium Human Methylation 450 K or Infinium MethylationEPIC array, and all sites passing quality control on both arrays were selected for analysis (n = 250,816). Empirical Bayes estimates of individual intercept (age 65), linear, and quadratic change were obtained from latent growth curve models of cognitive traits and used as outcomes in linear regression models. Significant sites (p < 2.4 \u00d7 10-7) were followed up in between-within twin pair models adjusting for familial confounding and full-growth modeling. We identified six significant associations between DNA methylation and level of cognitive abilities at age 65: cg18064256 (PPP1R13L) with processing speed and spatial ability; cg04549090 (NRXN3) with spatial ability; cg09988380 (POGZ), cg25651129 (-), and cg08011941 (ENTPD8) with working memory. The genes are involved in neuroinflammation, neuropsychiatric disorders, and ATP metabolism. Within-pair associations were approximately half that of between-pair associations across all sites. In full-growth curve models, associations between DNA methylation and cognitive level at age 65 were of small effect sizes, and associations between DNA methylation and longitudinal change in cognitive abilities of very small effect sizes.\n\nLeukocyte DNA methylation was associated with level, but not change in cognitive abilities. The associations were substantially attenuated in within-pair analyses, indicating they are influenced in part by genetic factors.", "doi": "10.1186/s13148-021-01075-9", "pmid": "33883019", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1186/s13148-021-01075-9"}, {"db": "pmc", "key": "PMC8061224"}], "notes": [], "created": "2021-04-28T15:32:47.179Z", "modified": "2024-01-16T13:48:40.037Z"}, {"entity": "publication", "iuid": "bd84e4b6289945fb90c07141e570869d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/bd84e4b6289945fb90c07141e570869d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/bd84e4b6289945fb90c07141e570869d"}}, "title": "smartPARE: An R Package for Efficient Identification of True mRNA Cleavage Sites.", "authors": [{"family": "Persson Hod\u00e9n", "given": "Kristian", "initials": "K", "orcid": "0000-0003-0354-0662", "researcher": {"href": "https://publications.scilifelab.se/researcher/e8b41e8e41574ee6bcb55df3b0d145d9.json"}}, {"family": "Hu", "given": "Xinyi", "initials": "X"}, {"family": "Martinez", "given": "German", "initials": "G"}, {"family": "Dixelius", "given": "Christina", "initials": "C", "orcid": "0000-0003-0150-0608", "researcher": {"href": "https://publications.scilifelab.se/researcher/197905a68ba24d429fc14a598dc22132.json"}}], "type": "journal article", "published": "2021-04-20", "journal": {"title": "Int J Mol Sci", "issn": "1422-0067", "volume": "22", "issue": "8", "pages": "4267", "issn-l": null}, "abstract": "Degradome sequencing is commonly used to generate high-throughput information on mRNA cleavage sites mediated by small RNAs (sRNA). In our datasets of potato (Solanum tuberosum, St) and Phytophthora infestans (Pi), initial predictions generated high numbers of cleavage site predictions, which highlighted the need of improved analytic tools. Here, we present an R package based on a deep learning convolutional neural network (CNN) in a machine learning environment to optimize discrimination of false from true cleavage sites. When applying smartPARE to our datasets on potato during the infection process by the late blight pathogen, 7.3% of all cleavage windows represented true cleavages distributed on 214 sites in P. infestans and 444 sites in potato. The sRNA landscape of the two organisms is complex with uneven sRNA production and cleavage regions widespread in the two genomes. Multiple targets and several cases of complex regulatory cascades, particularly in potato, was revealed. We conclude that our new analytic approach is useful for anyone working on complex biological systems and with the interest of identifying cleavage sites particularly inferred by sRNA classes beyond miRNAs.", "doi": "10.3390/ijms22084267", "pmid": "33924042", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "ijms22084267"}, {"db": "pmc", "key": "PMC8073297"}], "notes": [], "created": "2021-06-01T20:54:34.856Z", "modified": "2021-11-10T12:25:40.854Z"}, {"entity": "publication", "iuid": "20427cabf35d4505bd39ae01cd1bb3df", "links": {"self": {"href": "https://publications.scilifelab.se/publication/20427cabf35d4505bd39ae01cd1bb3df.json"}, "display": {"href": "https://publications.scilifelab.se/publication/20427cabf35d4505bd39ae01cd1bb3df"}}, "title": "The effects of drift and selection on latitudinal genetic variation in Scandinavian common toads (Bufo bufo) following postglacial recolonisation.", "authors": [{"family": "Th\u00f6rn", "given": "Filip", "initials": "F", "orcid": "0000-0002-8173-7877", "researcher": {"href": "https://publications.scilifelab.se/researcher/e272339ca04d4daf935b708b04c5c53e.json"}}, {"family": "R\u00f6din-M\u00f6rch", "given": "Patrik", "initials": "P", "orcid": "0000-0001-6737-1488", "researcher": {"href": "https://publications.scilifelab.se/researcher/9e6abe040b284d67b11f45db1e58540e.json"}}, {"family": "Cortazar-Chinarro", "given": "Maria", "initials": "M"}, {"family": "Richter-Boix", "given": "Alex", "initials": "A", "orcid": "0000-0002-8559-5191", "researcher": {"href": "https://publications.scilifelab.se/researcher/0eaa32ef12fb498eb13d0c6906d21375.json"}}, {"family": "Laurila", "given": "Anssi", "initials": "A"}, {"family": "H\u00f6glund", "given": "Jacob", "initials": "J"}], "type": "journal article", "published": "2021-04-00", "journal": {"title": "Heredity (Edinb)", "issn": "1365-2540", "volume": "126", "issue": "4", "pages": "656-667", "issn-l": "0018-067X"}, "abstract": "Clinal variation is paramount for understanding the factors shaping genetic diversity in space and time. During the last glacial maximum, northern Europe was covered by glacial ice that rendered the region uninhabitable for most taxa. Different evolutionary processes during and after the recolonisation of this area from different glacial refugia have affected the genetic landscape of the present day European flora and fauna. In this study, we focus on the common toad (Bufo bufo) in Sweden and present evidence suggesting that these processes have resulted in two separate lineages of common toad, which colonised Sweden from two directions. Using ddRAD sequencing data for demographic modelling, structure analyses, and analysis of molecular variance (AMOVA), we provide evidence of a contact zone located between Uppland and V\u00e4sterbotten in central Sweden. Genetic diversity was significantly higher in southern Sweden compared to the north, in accordance with a pattern of decreased genetic diversity with increasing distance from glacial refugia. Candidate genes under putative selection are identified through outlier detection and gene-environment association methods. We provide evidence of divergent selection related to stress response and developmental processes in these candidate genes. The colonisation of Sweden by two separate lineages may have implications for how future conservation efforts should be directed by identifying management units and putative local adaptations.", "doi": "10.1038/s41437-020-00400-x", "pmid": "33564181", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41437-020-00400-x"}, {"db": "pmc", "key": "PMC8115047"}], "notes": [], "created": "2021-12-08T13:58:44.714Z", "modified": "2024-01-16T13:48:40.206Z"}, {"entity": "publication", "iuid": "e80c590ff50e4d539845ffae17d694e5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e80c590ff50e4d539845ffae17d694e5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e80c590ff50e4d539845ffae17d694e5"}}, "title": "PD-L1 and IDO1 are potential targets for treatment in patients with primary diffuse large B-cell lymphoma of the CNS.", "authors": [{"family": "Abdulla", "given": "Maysaa", "initials": "M"}, {"family": "Alexsson", "given": "Andrei", "initials": "A"}, {"family": "Sundstr\u00f6m", "given": "Christer", "initials": "C"}, {"family": "Ladenvall", "given": "Claes", "initials": "C"}, {"family": "Mansouri", "given": "Larry", "initials": "L"}, {"family": "Lindskog", "given": "Cecilia", "initials": "C"}, {"family": "Berglund", "given": "Mattias", "initials": "M"}, {"family": "Cavelier", "given": "Lucia", "initials": "L"}, {"family": "Enblad", "given": "Gunilla", "initials": "G", "orcid": "0000-0002-0594-724X", "researcher": {"href": "https://publications.scilifelab.se/researcher/11313af3f4a241ecb93af23ab2652195.json"}}, {"family": "Hollander", "given": "Peter", "initials": "P"}, {"family": "Amini", "given": "Rose-Marie", "initials": "RM", "orcid": "0000-0003-0901-5252", "researcher": {"href": "https://publications.scilifelab.se/researcher/c157abcd61fa4900b5ad502b408d6d95.json"}}], "type": "journal article", "published": "2021-04-00", "journal": {"title": "Acta Oncol", "issn": "1651-226X", "issn-l": "0284-186X", "volume": "60", "issue": "4", "pages": "531-538"}, "abstract": "Programmed cell death 1 (PD-1) and its ligands PD-L1 and PD-L2, as well as Indoleamine 2,3-deoxygenase (IDO1) can be expressed both by tumor and microenvironmental cells and are crucial for tumor immune escape. We aimed to evaluate the role of PD-1, its ligands and IDO1 in a cohort of patients with primary diffuse large B-cell lymphoma of the CNS (PCNSL).\n\nTissue microarrays (TMAs) were constructed in 45 PCNSL cases. RNA extraction from whole tissue sections and RNA sequencing were successfully performed in 33 cases. Immunohistochemical stainings for PD-1, PD-L1/paired box protein 5 (PAX-5), PD-L2/PAX-5 and IDO1, and Epstein-Barr virus encoding RNA (EBER) in situ hybridization were analyzed.\n\nHigh proportions of PD-L1 and PD-L2 positive tumor cells were observed in 11% and 9% of cases, respectively. High proportions of PD-L1 and PD-L2 positive leukocytes were observed in 55% and 51% of cases, respectively. RNA sequencing revealed that gene expression of IDO1 was high in patients with high proportion of PD-L1 positive leukocytes (p = .01). Protein expression of IDO1 in leukocytes was detected in 14/45 cases, in 79% of these cases a high proportion of PD-L1 positive leukocytes was observed. Gene expression of IDO1 was high in EBER-positive cases (p = .0009) and protein expression of IDO1 was detected in five of six EBER-positive cases.\n\nOur study shows a significant association between gene and protein expression of IDO1 and protein expression of PD-L1 in the tumor microenvironment of PCNSL, possibly of importance for prediction of response to immunotherapies.", "doi": "10.1080/0284186X.2021.1881161", "pmid": "33579170", "labels": {"Clinical Genomics Uppsala": "Service", "National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Clinical Genomics": "Service"}, "xrefs": [], "notes": [], "created": "2021-12-06T08:28:38.570Z", "modified": "2023-06-20T15:58:18.800Z"}, {"entity": "publication", "iuid": "1709ae2a29f648c1b91bf3572239c1c9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1709ae2a29f648c1b91bf3572239c1c9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1709ae2a29f648c1b91bf3572239c1c9"}}, "title": "Meta-analysis uncovers genome-wide significant variants for rapid kidney function decline.", "authors": [{"family": "Gorski", "given": "Mathias", "initials": "M", "orcid": "0000-0003-2229-1120", "researcher": {"href": "https://publications.scilifelab.se/researcher/ebc59079554842ecb3512ef90249a2f2.json"}}, {"family": "Jung", "given": "Bettina", "initials": "B"}, {"family": "Li", "given": "Yong", "initials": "Y"}, {"family": "Matias-Garcia", "given": "Pamela R", "initials": "PR"}, {"family": "Wuttke", "given": "Matthias", "initials": "M"}, {"family": "Coassin", "given": "Stefan", "initials": "S"}, {"family": "Thio", "given": "Chris H L", "initials": "CHL"}, {"family": "Kleber", "given": "Marcus E", "initials": "ME"}, {"family": "Winkler", "given": "Thomas W", "initials": "TW"}, {"family": "Wanner", "given": "Veronika", "initials": "V"}, {"family": "Chai", "given": "Jin-Fang", "initials": "J"}, {"family": "Chu", "given": "Audrey Y", "initials": "AY"}, {"family": "Cocca", "given": "Massimiliano", "initials": "M"}, {"family": "Feitosa", "given": "Mary F", "initials": "MF"}, {"family": "Ghasemi", "given": "Sahar", "initials": "S"}, {"family": "Hoppmann", "given": "Anselm", "initials": "A"}, {"family": "Horn", "given": "Katrin", "initials": "K"}, {"family": "Li", "given": "Man", "initials": "M"}, {"family": "Nutile", "given": "Teresa", "initials": "T"}, {"family": "Scholz", "given": "Markus", "initials": "M"}, {"family": "Sieber", "given": "Karsten B", "initials": "KB"}, {"family": "Teumer", "given": "Alexander", "initials": "A"}, {"family": "Tin", "given": "Adrienne", "initials": "A"}, {"family": "Wang", "given": "Judy", "initials": "J"}, {"family": "Tayo", "given": "Bamidele O", "initials": "BO"}, {"family": "Ahluwalia", "given": "Tarunveer S", "initials": "TS"}, {"family": "Almgren", "given": "Peter", "initials": "P"}, {"family": "Bakker", "given": "Stephan J L", "initials": "SJL"}, {"family": "Banas", "given": "Bernhard", "initials": "B"}, {"family": "Bansal", "given": "Nisha", "initials": "N"}, {"family": "Biggs", "given": "Mary L", "initials": "ML"}, {"family": "Boerwinkle", "given": "Eric", "initials": "E"}, {"family": "Bottinger", "given": "Erwin P", "initials": "EP"}, {"family": "Brenner", "given": "Hermann", "initials": "H"}, {"family": "Carroll", "given": "Robert J", "initials": "RJ"}, {"family": "Chalmers", "given": "John", "initials": "J"}, {"family": "Chee", "given": "Miao-Li", "initials": "M"}, {"family": "Chee", "given": "Miao-Ling", "initials": "M"}, {"family": "Cheng", "given": "Ching-Yu", "initials": "C"}, {"family": "Coresh", "given": "Josef", "initials": "J"}, {"family": "de Borst", "given": "Martin H", "initials": "MH"}, {"family": "Degenhardt", "given": "Frauke", "initials": "F"}, {"family": "Eckardt", "given": "Kai-Uwe", "initials": "K"}, {"family": "Endlich", "given": "Karlhans", "initials": "K"}, {"family": "Franke", "given": "Andre", "initials": "A"}, {"family": "Freitag-Wolf", "given": "Sandra", "initials": "S"}, {"family": "Gampawar", "given": "Piyush", "initials": "P"}, {"family": "Gansevoort", "given": "Ron T", "initials": "RT"}, {"family": "Ghanbari", "given": "Mohsen", "initials": "M"}, {"family": "Gieger", "given": "Christian", "initials": "C"}, {"family": "Hamet", "given": "Pavel", "initials": "P"}, {"family": "Ho", "given": "Kevin", "initials": "K"}, {"family": "Hofer", "given": "Edith", "initials": "E"}, {"family": "Holleczek", "given": "Bernd", "initials": "B"}, {"family": "Xian Foo", "given": "Valencia Hui", "initials": "VH"}, {"family": "Hutri-K\u00e4h\u00f6nen", "given": "Nina", "initials": "N"}, {"family": "Hwang", "given": "Shih-Jen", "initials": "S"}, {"family": "Ikram", "given": "M Arfan", "initials": "MA"}, {"family": "Josyula", "given": "Navya Shilpa", "initials": "NS"}, {"family": "K\u00e4h\u00f6nen", "given": "Mika", "initials": "M"}, {"family": "Khor", "given": "Chiea-Chuen", "initials": "C"}, {"family": "Koenig", "given": "Wolfgang", "initials": "W"}, {"family": "Kramer", "given": "Holly", "initials": "H"}, {"family": "Kr\u00e4mer", "given": "Bernhard K", "initials": "BK"}, {"family": "K\u00fchnel", "given": "Brigitte", "initials": "B"}, {"family": "Lange", "given": "Leslie A", "initials": "LA"}, {"family": "Lehtim\u00e4ki", "given": "Terho", "initials": "T"}, {"family": "Lieb", "given": "Wolfgang", "initials": "W"}, {"family": "Lifelines Cohort Study", "given": "", "initials": ""}, {"family": "Regeneron Genetics Center", "given": "", "initials": ""}, {"family": "Loos", "given": "Ruth J F", "initials": "RJF"}, {"family": "Lukas", "given": "Mary Ann", "initials": "MA"}, {"family": "Lyytik\u00e4inen", "given": "Leo-Pekka", "initials": "L"}, {"family": "Meisinger", "given": "Christa", "initials": "C"}, {"family": "Meitinger", "given": "Thomas", "initials": "T"}, {"family": "Melander", "given": "Olle", "initials": "O"}, {"family": "Milaneschi", "given": "Yuri", "initials": "Y"}, {"family": "Mishra", "given": "Pashupati P", "initials": "PP"}, {"family": "Mononen", "given": "Nina", "initials": "N"}, {"family": "Mychaleckyj", "given": "Josyf C", "initials": "JC"}, {"family": "Nadkarni", "given": "Girish N", "initials": "GN"}, {"family": "Nauck", "given": "Matthias", "initials": "M"}, {"family": "Nikus", "given": "Kjell", "initials": "K"}, {"family": "Ning", "given": "Boting", "initials": "B"}, {"family": "Nolte", "given": "Ilja M", "initials": "IM"}, {"family": "O'Donoghue", "given": "Michelle L", "initials": "ML"}, {"family": "Orho-Melander", "given": "Marju", "initials": "M"}, {"family": "Pendergrass", "given": "Sarah A", "initials": "SA"}, {"family": "Penninx", "given": "Brenda W J H", "initials": "BWJH"}, {"family": "Preuss", "given": "Michael H", "initials": "MH"}, {"family": "Psaty", "given": "Bruce M", "initials": "BM"}, {"family": "Raffield", "given": "Laura M", "initials": "LM"}, {"family": "Raitakari", "given": "Olli T", "initials": "OT"}, {"family": "Rettig", "given": "Rainer", "initials": "R"}, {"family": "Rheinberger", "given": "Myriam", "initials": "M"}, {"family": "Rice", "given": "Kenneth M", "initials": "KM"}, {"family": "Rosenkranz", "given": "Alexander R", "initials": "AR"}, {"family": "Rossing", "given": "Peter", "initials": "P"}, {"family": "Rotter", "given": "Jerome I", "initials": "JI"}, {"family": "Sabanayagam", "given": "Charumathi", "initials": "C"}, {"family": "Schmidt", "given": "Helena", "initials": "H"}, {"family": "Schmidt", "given": "Reinhold", "initials": "R"}, {"family": "Sch\u00f6ttker", "given": "Ben", "initials": "B"}, {"family": "Schulz", "given": "Christina-Alexandra", "initials": "C"}, {"family": "Sedaghat", "given": "Sanaz", "initials": "S"}, {"family": "Shaffer", "given": "Christian M", "initials": "CM"}, {"family": "Strauch", "given": "Konstantin", "initials": "K"}, {"family": "Szymczak", "given": "Silke", "initials": "S"}, {"family": "Taylor", "given": "Kent D", "initials": "KD"}, {"family": "Tremblay", "given": "Johanne", "initials": "J"}, {"family": "Chaker", "given": "Layal", "initials": "L"}, {"family": "van der Harst", "given": "Pim", "initials": "P"}, {"family": "van der Most", "given": "Peter J", "initials": "PJ"}, {"family": "Verweij", "given": "Niek", "initials": "N"}, {"family": "V\u00f6lker", "given": "Uwe", "initials": "U"}, {"family": "Waldenberger", "given": "Melanie", "initials": "M"}, {"family": "Wallentin", "given": "Lars", "initials": "L"}, {"family": "Waterworth", "given": "Dawn M", "initials": "DM"}, {"family": "White", "given": "Harvey D", "initials": "HD"}, {"family": "Wilson", "given": "James G", "initials": "JG"}, {"family": "Wong", "given": "Tien-Yin", "initials": "T"}, {"family": "Woodward", "given": "Mark", "initials": "M"}, {"family": "Yang", "given": "Qiong", "initials": "Q"}, {"family": "Yasuda", "given": "Masayuki", "initials": "M"}, {"family": "Yerges-Armstrong", "given": "Laura M", "initials": "LM"}, {"family": "Zhang", "given": "Yan", "initials": "Y"}, {"family": "Snieder", "given": "Harold", "initials": "H"}, {"family": "Wanner", "given": "Christoph", "initials": "C"}, {"family": "B\u00f6ger", "given": "Carsten A", "initials": "CA"}, {"family": "K\u00f6ttgen", "given": "Anna", "initials": "A", "orcid": "0000-0002-4671-3714", "researcher": {"href": "https://publications.scilifelab.se/researcher/fe4cb85a14da4db6bc932a8bc4148efb.json"}}, {"family": "Kronenberg", "given": "Florian", "initials": "F"}, {"family": "Pattaro", "given": "Cristian", "initials": "C"}, {"family": "Heid", "given": "Iris M", "initials": "IM"}], "type": "journal article", "published": "2021-04-00", "journal": {"title": "Kidney Int.", "issn": "1523-1755", "issn-l": "0085-2538", "volume": "99", "issue": "4", "pages": "926-939"}, "abstract": "Rapid decline of glomerular filtration rate estimated from creatinine (eGFRcrea) is associated with severe clinical endpoints. In contrast to cross-sectionally assessed eGFRcrea, the genetic basis for rapid eGFRcrea decline is largely unknown. To help define this, we meta-analyzed 42 genome-wide association studies from the Chronic Kidney Diseases Genetics Consortium and United Kingdom Biobank to identify genetic loci for rapid eGFRcrea decline. Two definitions of eGFRcrea decline were used: 3 mL/min/1.73m2/year or more (\"Rapid3\"; encompassing 34,874 cases, 107,090 controls) and eGFRcrea decline 25% or more and eGFRcrea under 60 mL/min/1.73m2 at follow-up among those with eGFRcrea 60 mL/min/1.73m2 or more at baseline (\"CKDi25\"; encompassing 19,901 cases, 175,244 controls). Seven independent variants were identified across six loci for Rapid3 and/or CKDi25: consisting of five variants at four loci with genome-wide significance (near UMOD-PDILT (2), PRKAG2, WDR72, OR2S2) and two variants among 265 known eGFRcrea variants (near GATM, LARP4B). All these loci were novel for Rapid3 and/or CKDi25 and our bioinformatic follow-up prioritized variants and genes underneath these loci. The OR2S2 locus is novel for any eGFRcrea trait including interesting candidates. For the five genome-wide significant lead variants, we found supporting effects for annual change in blood urea nitrogen or cystatin-based eGFR, but not for GATM or LARP4B. Individuals at high compared to those at low genetic risk (8-14 vs. 0-5 adverse alleles) had a 1.20-fold increased risk of acute kidney injury (95% confidence interval 1.08-1.33). Thus, our identified loci for rapid kidney function decline may help prioritize therapeutic targets and identify mechanisms and individuals at risk for sustained deterioration of kidney function.", "doi": "10.1016/j.kint.2020.09.030", "pmid": "33137338", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "S0085-2538(20)31239-4"}, {"db": "pmc", "key": "PMC8010357"}, {"db": "mid", "key": "NIHMS1677067"}], "notes": [], "created": "2020-11-05T14:07:50.074Z", "modified": "2021-12-07T13:33:16.249Z"}, {"entity": "publication", "iuid": "d406576e0299489da3a3ae80d552f37a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d406576e0299489da3a3ae80d552f37a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d406576e0299489da3a3ae80d552f37a"}}, "title": "Life-Time Covariation of Major Cardiovascular Diseases: A 40-Year Longitudinal Study and Genetic Studies.", "authors": [{"family": "Lind", "given": "Lars", "initials": "L", "orcid": "0000-0003-2335-8542", "researcher": {"href": "https://publications.scilifelab.se/researcher/4c517dacca7c4ec58a3e03b59ffb4044.json"}}, {"family": "Sundstr\u00f6m", "given": "Johan", "initials": "J", "orcid": "0000-0003-2247-8454", "researcher": {"href": "https://publications.scilifelab.se/researcher/91a40d3c138d43f2b0d38f66be4b71c7.json"}}, {"family": "\u00c4rnl\u00f6v", "given": "Johan", "initials": "J", "orcid": "0000-0002-6933-4637", "researcher": {"href": "https://publications.scilifelab.se/researcher/314de3900dec4c45b85943d72d4bd3e6.json"}}, {"family": "Ingelsson", "given": "Martin", "initials": "M"}, {"family": "Henry", "given": "Albert", "initials": "A", "orcid": "0000-0001-7422-2288", "researcher": {"href": "https://publications.scilifelab.se/researcher/9b1557b87fc542eb8e4d7b733e5b79dc.json"}}, {"family": "Lumbers", "given": "R Thomas", "initials": "RT", "orcid": "0000-0002-9077-4741", "researcher": {"href": "https://publications.scilifelab.se/researcher/a53e4d6591db481f881ec6046d54535b.json"}}, {"family": "Lampa", "given": "Erik", "initials": "E", "orcid": "0000-0002-3268-8810", "researcher": {"href": "https://publications.scilifelab.se/researcher/fb38398f7d3f41058d36d5b3f2a6d545.json"}}], "type": "journal article", "published": "2021-04-00", "journal": {"title": "Circ Genom Precis Med", "issn": "2574-8300", "issn-l": "2574-8300", "volume": "14", "issue": "2", "pages": "e002963"}, "abstract": "It is known that certain cardiovascular diseases (CVD) are associated, like atrial fibrillation and stroke. However, for other CVDs, the links and temporal trends are less studied. In this longitudinal study, we have investigated temporal epidemiological and genetic associations between different CVDs.\n\nThe ULSAM (Uppsala Longitudinal Study of Adult Men; 2322 men aged 50 years) has been followed for 40 years regarding 4 major CVDs (incident myocardial infarction, ischemic stroke, heart failure, and atrial fibrillation). For the genetic analyses, publicly available data were used.\n\nUsing multistate modeling, significant relationships were seen between pairs of all of the 4 investigated CVDs. However, the risk of obtaining one additional CVD differed substantially both between different CVDs and between their temporal order. The relationship between heart failure and atrial fibrillation showed a high risk ratio (risk ratios, 24-26) regardless of the temporal order. A consistent association was seen also for myocardial infarction and atrial fibrillation but with a lower relative risk (risk ratios, 4-5). In contrast, the risk of receiving a diagnosis of heart failure following a myocardial infarction was almost twice as high as for the reverse temporal order (risk ratios, 16 versus 9). Genetic loci linked to traditional risk factors could partly explain the observed associations between the CVDs, but pathway analyses disclosed also other pathophysiological links.\n\nDuring 40 years, all of the 4 investigated CVDs were pairwise associated with each other regardless of the temporal order of occurrence, but the risk magnitude differed between different CVDs and their temporal order. Genetic analyses disclosed new pathophysiological links between CVDs.", "doi": "10.1161/CIRCGEN.120.002963", "pmid": "33635119", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC8284356"}], "notes": [], "created": "2021-03-03T14:45:25.550Z", "modified": "2024-01-16T13:48:40.295Z"}, {"entity": "publication", "iuid": "a96b36a0cd1c4ae5a6c7bd698a64e2bf", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a96b36a0cd1c4ae5a6c7bd698a64e2bf.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a96b36a0cd1c4ae5a6c7bd698a64e2bf"}}, "title": "Later Stone Age human hair from Vaalkrans Shelter, Cape Floristic Region of South Africa, reveals genetic affinity to Khoe groups.", "authors": [{"family": "Coutinho", "given": "Alexandra", "initials": "A"}, {"family": "Malmstr\u00f6m", "given": "Helena", "initials": "H"}, {"family": "Edlund", "given": "Hanna", "initials": "H"}, {"family": "Henshilwood", "given": "Christopher S", "initials": "CS"}, {"family": "van Niekerk", "given": "Karen L", "initials": "KL"}, {"family": "Lombard", "given": "Marlize", "initials": "M"}, {"family": "Schlebusch", "given": "Carina M", "initials": "CM"}, {"family": "Jakobsson", "given": "Mattias", "initials": "M", "orcid": "0000-0001-7840-7853", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a4abe0fcb20492d9ec849c9fbf58a71.json"}}], "type": "historical article", "published": "2021-04-00", "journal": {"title": "Am. J. Phys. Anthropol.", "issn": "1096-8644", "volume": "174", "issue": "4", "pages": "701-713", "issn-l": "0002-9483"}, "abstract": "Previous studies show that the indigenous people of the southern Cape of South Africa were dramatically impacted by the arrival of European colonists starting ~400 years ago and their descendants are today mixed with Europeans and Asians. To gain insight on the occupants of the Vaalkrans Shelter located at the southernmost tip of Africa, we investigated the genetic make-up of an individual who lived there about 200 years ago. We further contextualize the genetic ancestry of this individual among prehistoric and current groups. From a hair sample excavated at the shelter, which was indirectly dated to about 200 years old, we sequenced the genome (1.01 times coverage) of a Later Stone Age individual. We analyzed the Vaalkrans genome together with genetic data from 10 ancient (pre-colonial) individuals from southern Africa spanning the last 2000 years. We show that the individual from Vaalkrans was a man who traced ~80% of his ancestry to local southern San hunter-gatherers and ~20% to a mixed East African-Eurasian source. This genetic make-up is similar to modern-day Khoekhoe individuals from the Northern Cape Province (South Africa) and Namibia, but in the southern Cape, the Vaalkrans man's descendants have likely been assimilated into mixed-ancestry \"Coloured\" groups. The Vaalkrans man's genome reveals that Khoekhoe pastoralist groups/individuals lived in the southern Cape as late as 200 years ago, without mixing with non-African colonists or Bantu-speaking farmers. Our findings are also consistent with the model of a Holocene pastoralist migration, originating in Eastern Africa, shaping the genomic landscape of historic and current southern African populations.", "doi": "10.1002/ajpa.24236", "pmid": "33539553", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [], "notes": [], "created": "2021-12-10T11:37:51.156Z", "modified": "2021-12-10T11:37:51.172Z"}, {"entity": "publication", "iuid": "5d1db6c9ab8c419a8e81f3e3f84d41dd", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5d1db6c9ab8c419a8e81f3e3f84d41dd.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5d1db6c9ab8c419a8e81f3e3f84d41dd"}}, "title": "Immune cells lacking Y chromosome show dysregulation of autosomal gene expression.", "authors": [{"family": "Dumanski", "given": "Jan P", "initials": "JP", "orcid": "0000-0002-1489-1452", "researcher": {"href": "https://publications.scilifelab.se/researcher/15b14282209342cfa9c82cdbf02999f6.json"}}, {"family": "Halvardson", "given": "Jonatan", "initials": "J"}, {"family": "Davies", "given": "Hanna", "initials": "H"}, {"family": "Rychlicka-Buniowska", "given": "Edyta", "initials": "E"}, {"family": "Mattisson", "given": "Jonas", "initials": "J"}, {"family": "Moghadam", "given": "Behrooz Torabi", "initials": "BT"}, {"family": "Nagy", "given": "Noemi", "initials": "N"}, {"family": "W\u0119glarczyk", "given": "Kazimierz", "initials": "K"}, {"family": "Bukowska-Strakova", "given": "Karolina", "initials": "K"}, {"family": "Danielsson", "given": "Marcus", "initials": "M"}, {"family": "Olszewski", "given": "Pawe\u0142", "initials": "P"}, {"family": "Piotrowski", "given": "Arkadiusz", "initials": "A"}, {"family": "Oerton", "given": "Erin", "initials": "E"}, {"family": "Ambicka", "given": "Aleksandra", "initials": "A"}, {"family": "Przewo\u017anik", "given": "Marcin", "initials": "M"}, {"family": "Be\u0142ch", "given": "\u0141ukasz", "initials": "\u0141"}, {"family": "Grodzicki", "given": "Tomasz", "initials": "T"}, {"family": "Ch\u0142osta", "given": "Piotr L", "initials": "PL"}, {"family": "Imreh", "given": "Stefan", "initials": "S"}, {"family": "Giedraitis", "given": "Vilmantas", "initials": "V"}, {"family": "Kilander", "given": "Lena", "initials": "L"}, {"family": "Nordlund", "given": "Jessica", "initials": "J", "orcid": "0000-0001-8699-9959", "researcher": {"href": "https://publications.scilifelab.se/researcher/ddf48c9262134821bcc6ce1180049753.json"}}, {"family": "Ameur", "given": "Adam", "initials": "A", "orcid": "0000-0001-6085-6749", "researcher": {"href": "https://publications.scilifelab.se/researcher/e960811513664a78b2804a00ee70f7c3.json"}}, {"family": "Gyllensten", "given": "Ulf", "initials": "U"}, {"family": "Johansson", "given": "\u00c5sa", "initials": "\u00c5"}, {"family": "J\u00f3zkowicz", "given": "Alicja", "initials": "A"}, {"family": "Siedlar", "given": "Maciej", "initials": "M"}, {"family": "Klich-R\u0105czka", "given": "Alicja", "initials": "A"}, {"family": "Jaszczy\u0144ski", "given": "Janusz", "initials": "J"}, {"family": "Enroth", "given": "Stefan", "initials": "S"}, {"family": "Baran", "given": "Jaros\u0142aw", "initials": "J"}, {"family": "Ingelsson", "given": "Martin", "initials": "M"}, {"family": "Perry", "given": "John R B", "initials": "JRB"}, {"family": "Ry\u015b", "given": "Janusz", "initials": "J"}, {"family": "Forsberg", "given": "Lars A", "initials": "LA", "orcid": "0000-0002-1701-755X", "researcher": {"href": "https://publications.scilifelab.se/researcher/9ac2d8e983764a82982118b6db84029e.json"}}], "type": "journal article", "published": "2021-04-00", "journal": {"title": "Cell. Mol. Life Sci.", "issn": "1420-9071", "issn-l": "1420-682X", "volume": "78", "issue": "8", "pages": "4019-4033"}, "abstract": "Epidemiological investigations show that mosaic loss of chromosome Y (LOY) in leukocytes is associated with earlier mortality and morbidity from many diseases in men. LOY is the most common acquired mutation and is associated with aberrant clonal expansion of cells, yet it remains unclear whether this mosaicism exerts a direct physiological effect. We studied DNA and RNA from leukocytes in sorted- and single-cells in vivo and in vitro. DNA analyses of sorted cells showed that men diagnosed with Alzheimer's disease was primarily affected with LOY in NK cells whereas prostate cancer patients more frequently displayed LOY in CD4 + T cells and granulocytes. Moreover, bulk and single-cell RNA sequencing in leukocytes allowed scoring of LOY from mRNA data and confirmed considerable variation in the rate of LOY across individuals and cell types. LOY-associated transcriptional effect (LATE) was observed in ~ 500 autosomal genes showing dysregulation in leukocytes with LOY. The fraction of LATE genes within specific cell types was substantially larger than the fraction of LATE genes shared between different subsets of leukocytes, suggesting that LOY might have pleiotropic effects. LATE genes are involved in immune functions but also encode proteins with roles in other diverse biological processes. Our findings highlight a surprisingly broad role for chromosome Y, challenging the view of it as a \"genetic wasteland\", and support the hypothesis that altered immune function in leukocytes could be a mechanism linking LOY to increased risk for disease.", "doi": "10.1007/s00018-021-03822-w", "pmid": "33837451", "labels": {"National Genomics Infrastructure": "Collaborative", "NGI Uppsala (Uppsala Genome Center)": "Collaborative", "NGI Uppsala (SNP&SEQ Technology Platform)": "Collaborative", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1007/s00018-021-03822-w"}, {"db": "pmc", "key": "PMC8106578"}], "notes": [], "created": "2021-04-12T09:32:05.156Z", "modified": "2024-01-16T13:48:40.302Z"}, {"entity": "publication", "iuid": "886b1418f40b4c32b01fd338e3302530", "links": {"self": {"href": "https://publications.scilifelab.se/publication/886b1418f40b4c32b01fd338e3302530.json"}, "display": {"href": "https://publications.scilifelab.se/publication/886b1418f40b4c32b01fd338e3302530"}}, "title": "Multiple migrations to the Philippines during the last 50,000 years.", "authors": [{"family": "Larena", "given": "Maximilian", "initials": "M", "orcid": "0000-0002-8799-7645", "researcher": {"href": "https://publications.scilifelab.se/researcher/5d580f1f3e584c809f5f22d7355f154f.json"}}, {"family": "Sanchez-Quinto", "given": "Federico", "initials": "F", "orcid": "0000-0002-0201-6204", "researcher": {"href": "https://publications.scilifelab.se/researcher/c554aeb35ee04ee1ac43c5291a8d7f3c.json"}}, {"family": "Sj\u00f6din", "given": "Per", "initials": "P"}, {"family": "McKenna", "given": "James", "initials": "J"}, {"family": "Ebeo", "given": "Carlo", "initials": "C"}, {"family": "Reyes", "given": "Rebecca", "initials": "R"}, {"family": "Casel", "given": "Ophelia", "initials": "O"}, {"family": "Huang", "given": "Jin-Yuan", "initials": "JY"}, {"family": "Hagada", "given": "Kim Pullupul", "initials": "KP", "orcid": "0000-0002-1272-4132", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a2728ede8ca453c8e8c2fe8a98344bd.json"}}, {"family": "Guilay", "given": "Dennis", "initials": "D"}, {"family": "Reyes", "given": "Jennelyn", "initials": "J", "orcid": "0000-0002-9879-582X", "researcher": {"href": "https://publications.scilifelab.se/researcher/3c1a796da8c44d178de38fab6109c132.json"}}, {"family": "Allian", "given": "Fatima Pir", "initials": "FP"}, {"family": "Mori", "given": "Virgilio", "initials": "V"}, {"family": "Azarcon", "given": "Lahaina Sue", "initials": "LS"}, {"family": "Manera", "given": "Alma", "initials": "A"}, {"family": "Terando", "given": "Celito", "initials": "C", "orcid": "0000-0002-4939-1802", "researcher": {"href": "https://publications.scilifelab.se/researcher/351d926e87094101bfba53fe7322680a.json"}}, {"family": "Jamero", "given": "Lucio", "initials": "L"}, {"family": "Sireg", "given": "Gauden", "initials": "G"}, {"family": "Manginsay-Tremedal", "given": "Renefe", "initials": "R"}, {"family": "Labos", "given": "Maria Shiela", "initials": "MS"}, {"family": "Vilar", "given": "Richard Dian", "initials": "RD"}, {"family": "Latiph", "given": "Acram", "initials": "A"}, {"family": "Saway", "given": "Rodelio Linsahay", "initials": "RL", "orcid": "0000-0003-2445-048X", "researcher": {"href": "https://publications.scilifelab.se/researcher/1c910747bc3f41369eaa95eafcb2f381.json"}}, {"family": "Marte", "given": "Erwin", "initials": "E"}, {"family": "Magbanua", "given": "Pablito", "initials": "P"}, {"family": "Morales", "given": "Amor", "initials": "A"}, {"family": "Java", "given": "Ismael", "initials": "I"}, {"family": "Reveche", "given": "Rudy", "initials": "R"}, {"family": "Barrios", "given": "Becky", "initials": "B"}, {"family": "Burton", "given": "Erlinda", "initials": "E"}, {"family": "Salon", "given": "Jesus Christopher", "initials": "JC"}, {"family": "Kels", "given": "Ma Junaliah Tuazon", "initials": "MJT"}, {"family": "Albano", "given": "Adrian", "initials": "A"}, {"family": "Cruz-Angeles", "given": "Rose Beatrix", "initials": "RB", "orcid": "0000-0003-3828-4929", "researcher": {"href": "https://publications.scilifelab.se/researcher/b6ac99916cbb41e2990452c0446e88f5.json"}}, {"family": "Molanida", "given": "Edison", "initials": "E"}, {"family": "Graneh\u00e4ll", "given": "Lena", "initials": "L", "orcid": "0000-0001-9970-4080", "researcher": {"href": "https://publications.scilifelab.se/researcher/1900cb5164304c70ab0f5aa19cf10564.json"}}, {"family": "Vicente", "given": "M\u00e1rio", "initials": "M", "orcid": "0000-0002-9122-4530", "researcher": {"href": "https://publications.scilifelab.se/researcher/603244b141da49dfa9ff3a8d17f42b70.json"}}, {"family": "Edlund", "given": "Hanna", "initials": "H"}, {"family": "Loo", "given": "Jun-Hun", "initials": "JH"}, {"family": "Trejaut", "given": "Jean", "initials": "J", "orcid": "0000-0002-4245-0814", "researcher": {"href": "https://publications.scilifelab.se/researcher/57eab8fc843743929a82453430b422dc.json"}}, {"family": "Ho", "given": "Simon Y W", "initials": "SYW", "orcid": "0000-0002-0361-2307", "researcher": {"href": "https://publications.scilifelab.se/researcher/00d59fd0713e440b8ddb35f58c53f19c.json"}}, {"family": "Reid", "given": "Lawrence", "initials": "L"}, {"family": "Malmstr\u00f6m", "given": "Helena", "initials": "H"}, {"family": "Schlebusch", "given": "Carina", "initials": "C", "orcid": "0000-0002-8160-9621", "researcher": {"href": "https://publications.scilifelab.se/researcher/682f10853c1145649b8c76680605dd9b.json"}}, {"family": "Lambeck", "given": "Kurt", "initials": "K"}, {"family": "Endicott", "given": "Phillip", "initials": "P", "orcid": "0000-0003-2452-8507", "researcher": {"href": "https://publications.scilifelab.se/researcher/de01eeca292648eaaf16fe9480923187.json"}}, {"family": "Jakobsson", "given": "Mattias", "initials": "M", "orcid": "0000-0001-7840-7853", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a4abe0fcb20492d9ec849c9fbf58a71.json"}}], "type": "historical article", "published": "2021-03-30", "journal": {"title": "Proc. Natl. Acad. Sci. U.S.A.", "issn": "1091-6490", "volume": "118", "issue": "13", "issn-l": "0027-8424"}, "abstract": "Island Southeast Asia has recently produced several surprises regarding human history, but the region's complex demography remains poorly understood. Here, we report \u223c2.3 million genotypes from 1,028 individuals representing 115 indigenous Philippine populations and genome-sequence data from two \u223c8,000-y-old individuals from Liangdao in the Taiwan Strait. We show that the Philippine islands were populated by at least five waves of human migration: initially by Northern and Southern Negritos (distantly related to Australian and Papuan groups), followed by Manobo, Sama, Papuan, and Cordilleran-related populations. The ancestors of Cordillerans diverged from indigenous peoples of Taiwan at least \u223c8,000 y ago, prior to the arrival of paddy field rice agriculture in the Philippines \u223c2,500 y ago, where some of their descendants remain to be the least admixed East Asian groups carrying an ancestry shared by all Austronesian-speaking populations. These observations contradict an exclusive \"out-of-Taiwan\" model of farming-language-people dispersal within the last four millennia for the Philippines and Island Southeast Asia. Sama-related ethnic groups of southwestern Philippines additionally experienced some minimal South Asian gene flow starting \u223c1,000 y ago. Lastly, only a few lowlanders, accounting for <1% of all individuals, presented a low level of West Eurasian admixture, indicating a limited genetic legacy of Spanish colonization in the Philippines. Altogether, our findings reveal a multilayered history of the Philippines, which served as a crucial gateway for the movement of people that ultimately changed the genetic landscape of the Asia-Pacific region.", "doi": "10.1073/pnas.2026132118", "pmid": "33753512", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "2026132118"}, {"db": "pmc", "key": "PMC8020671"}], "notes": [], "created": "2021-12-10T11:33:51.314Z", "modified": "2024-01-16T13:48:40.354Z"}, {"entity": "publication", "iuid": "a21d1190458948ae865690f8d44e833a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a21d1190458948ae865690f8d44e833a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a21d1190458948ae865690f8d44e833a"}}, "title": "Genotyping Strategies Using ddRAD Sequencing in Farmed Arctic Charr (Salvelinus alpinus).", "authors": [{"family": "Pappas", "given": "Fotis", "initials": "F"}, {"family": "Palaiokostas", "given": "Christos", "initials": "C"}], "type": "journal article", "published": "2021-03-21", "journal": {"title": "Animals (Basel)", "issn": "2076-2615", "volume": "11", "issue": "3", "issn-l": null}, "abstract": "Incorporation of genomic technologies into fish breeding programs is a modern reality, promising substantial advances regarding the accuracy of selection, monitoring the genetic diversity and pedigree record verification. Single nucleotide polymorphism (SNP) arrays are the most commonly used genomic tool, but the investments required make them unsustainable for emerging species, such as Arctic charr (Salvelinus alpinus), where production volume is low. The requirement to genotype a large number of animals for breeding practices necessitates cost effective genotyping approaches. In the current study, we used double digest restriction site-associated DNA (ddRAD) sequencing of either high or low coverage to genotype Arctic charr from the Swedish national breeding program and performed analytical procedures to assess their utility in a range of tasks. SNPs were identified and used for deciphering the genetic structure of the studied population, estimating genomic relationships and implementing an association study for growth-related traits. Missing information and underestimation of heterozygosity in the low coverage set were limiting factors in genetic diversity and genomic relationship analyses, where high coverage performed notably better. On the other hand, the high coverage dataset proved to be valuable when it comes to identifying loci that are associated with phenotypic traits of interest. In general, both genotyping strategies offer sustainable alternatives to hybridization-based genotyping platforms and show potential for applications in aquaculture selective breeding.", "doi": "10.3390/ani11030899", "pmid": "33801139", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pii", "key": "ani11030899"}, {"db": "pmc", "key": "PMC8004150"}], "notes": [], "created": "2021-12-08T13:59:01.983Z", "modified": "2021-12-08T13:59:02.021Z"}, {"entity": "publication", "iuid": "33b8258d3dae4c76bc38ea20958228dd", "links": {"self": {"href": "https://publications.scilifelab.se/publication/33b8258d3dae4c76bc38ea20958228dd.json"}, "display": {"href": "https://publications.scilifelab.se/publication/33b8258d3dae4c76bc38ea20958228dd"}}, "title": "Sperm Methylome Profiling Can Discern Fertility Levels in the Porcine Biomedical Model.", "authors": [{"family": "P\u00e9rtille", "given": "Fabio", "initials": "F", "orcid": "0000-0002-7214-9184", "researcher": {"href": "https://publications.scilifelab.se/researcher/2279c5ebf16f419bab7c3af87bac81d3.json"}}, {"family": "Alvarez-Rodriguez", "given": "Manuel", "initials": "M", "orcid": "0000-0003-0120-354X", "researcher": {"href": "https://publications.scilifelab.se/researcher/3a5fb294906a4207a70936f871a38835.json"}}, {"family": "da Silva", "given": "Arthur Nery", "initials": "AN", "orcid": "0000-0002-4668-9769", "researcher": {"href": "https://publications.scilifelab.se/researcher/728eb328ab4448bf98c4b81957bda020.json"}}, {"family": "Barranco", "given": "Isabel", "initials": "I", "orcid": "0000-0001-9873-814X", "researcher": {"href": "https://publications.scilifelab.se/researcher/ae7e0d86b5ee4056bf375d83e57b0f22.json"}}, {"family": "Roca", "given": "Jordi", "initials": "J", "orcid": "0000-0002-4213-3093", "researcher": {"href": "https://publications.scilifelab.se/researcher/de7704c544ae4dfb8789782bf33dcd24.json"}}, {"family": "Guerrero-Bosagna", "given": "Carlos", "initials": "C"}, {"family": "Rodriguez-Martinez", "given": "Heriberto", "initials": "H", "orcid": "0000-0002-5194-2124", "researcher": {"href": "https://publications.scilifelab.se/researcher/ebd20bf7b79844539931a1825391a3f7.json"}}], "type": "journal article", "published": "2021-03-06", "journal": {"title": "Int J Mol Sci", "issn": "1422-0067", "volume": "22", "issue": "5", "pages": "2679", "issn-l": null}, "abstract": "A combined Genotyping By Sequencing (GBS) and methylated DNA immunoprecipitation (MeDIP) protocol was used to identify-in parallel-genetic variation (Genomic-Wide Association Studies (GWAS) and epigenetic differences of Differentially Methylated Regions (DMR) in the genome of spermatozoa from the porcine animal model. Breeding boars with good semen quality (n = 11) and specific and well-documented differences in fertility (farrowing rate, FR) and prolificacy (litter size, LS) (n = 7) in artificial insemination programs, using combined FR and LS, were categorized as High Fertile (HF, n = 4) or Low Fertile (LF, n = 3), and boars with Unknown Fertility (UF, n = 4) were tested for eventual epigenetical similarity with those fertility-proven. We identified 165,944 Single Nucleotide Polymorphisms (SNPs) that explained 14-15% of variance among selection lines. Between HF and LF individuals (n = 7, 4 HF and 3 LF), we identified 169 SNPs with p \u2264 0.00015, which explained 58% of the variance. For the epigenetic analyses, we considered fertility and period of ejaculate collection (late-summer and mid-autumn). Approximately three times more DMRs were observed in HF than in LF boars across these periods. Interestingly, UF boars were clearly clustered with one of the other HF or LF groups. The highest differences in DMRs between HF and LF experimental groups across the pig genome were located in the chr 3, 9, 13, and 16, with most DMRs being hypermethylated in LF boars. In both HF and LF boars, DMRs were mostly hypermethylated in late-summer compared to mid-autumn. Three overlaps were detected between SNPs (p \u2264 0.0005, n = 1318) and CpG sites within DMRs. In conclusion, fertility levels in breeding males including FR and LS can be discerned using methylome analyses. The findings in this biomedical animal model ought to be applied besides sire selection for andrological diagnosis of idiopathic sub/infertility.", "doi": "10.3390/ijms22052679", "pmid": "33800945", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "ijms22052679"}, {"db": "pmc", "key": "PMC7961483"}], "notes": [], "created": "2021-06-01T20:54:03.647Z", "modified": "2021-11-10T12:26:27.950Z"}, {"entity": "publication", "iuid": "d2dcebf2618f40958e150ee74da1f65f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d2dcebf2618f40958e150ee74da1f65f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d2dcebf2618f40958e150ee74da1f65f"}}, "title": "Effluent solids recirculation to municipal sludge digesters enhances long-chain fatty acids degradation capacity.", "authors": [{"family": "Shakeri Yekta", "given": "Sepehr", "initials": "S"}, {"family": "Liu", "given": "Tong", "initials": "T"}, {"family": "Mendes Anacleto", "given": "Thuane", "initials": "T"}, {"family": "Axelsson Bjerg", "given": "Mette", "initials": "M"}, {"family": "\u0160afari\u010d", "given": "Luka", "initials": "L"}, {"family": "Goux", "given": "Xavier", "initials": "X"}, {"family": "Karlsson", "given": "Anna", "initials": "A"}, {"family": "Bj\u00f6rn", "given": "Annika", "initials": "A"}, {"family": "Schn\u00fcrer", "given": "Anna", "initials": "A"}], "type": "journal article", "published": "2021-03-04", "journal": {"title": "Biotechnol Biofuels", "issn": "1754-6834", "volume": "14", "issue": "1", "pages": "56", "issn-l": "1754-6834"}, "abstract": "Slow degradation kinetics of long-chain fatty acids (LCFA) and their accumulation in anaerobic digesters disrupt methanogenic activity and biogas production at high loads of waste lipids. In this study, we evaluated the effect of effluent solids recirculation on microbial LCFA (oleate) degradation capacity in continuous stirred-tank sludge digesters, with the overall aim of providing operating conditions for efficient co-digestion of waste lipids. Furthermore, the impacts of LCFA feeding frequency and sulfide on process performance and microbial community dynamics were investigated, as parameters that were previously shown to be influential on LCFA conversion to biogas.\n\nEffluent solids recirculation to municipal sludge digesters enabled biogas production of up to 78% of the theoretical potential from 1.0 g oleate l-1 day-1. In digesters without effluent recirculation, comparable conversion efficiency could only be reached at oleate loading rates up to 0.5 g l-1 day-1. Pulse feeding of oleate (supplementation of 2.0 g oleate l-1 every second day instead of 1.0 g oleate l-1 every day) did not have a substantial impact on the degree of oleate conversion to biogas in the digesters that operated with effluent recirculation, while it marginally enhanced oleate conversion to biogas in the digesters without effluent recirculation. Next-generation sequencing of 16S rRNA gene amplicons of bacteria and archaea revealed that pulse feeding resulted in prevalence of fatty acid-degrading Smithella when effluent recirculation was applied, whereas Candidatus Cloacimonas prevailed after pulse feeding of oleate in the digesters without effluent recirculation. Combined oleate pulse feeding and elevated sulfide level contributed to increased relative abundance of LCFA-degrading Syntrophomonas and enhanced conversion efficiency of oleate, but only in the digesters without effluent recirculation.\n\nEffluent solids recirculation improves microbial LCFA degradation capacity, providing possibilities for co-digestion of larger amounts of waste lipids with municipal sludge.", "doi": "10.1186/s13068-021-01913-1", "pmid": "33663594", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1186/s13068-021-01913-1"}, {"db": "pmc", "key": "PMC7934545"}], "notes": [], "created": "2021-03-07T08:25:36.140Z", "modified": "2024-01-16T13:48:40.547Z"}, {"entity": "publication", "iuid": "dee4fe6435e34f18a610e3cd2679205c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/dee4fe6435e34f18a610e3cd2679205c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/dee4fe6435e34f18a610e3cd2679205c"}}, "title": "Comparative analysis of targeted next-generation sequencing panels for the detection of gene mutations in chronic lymphocytic leukemia: an ERIC multi-center study.", "authors": [{"family": "Sutton", "given": "Lesley-Ann", "initials": "L"}, {"family": "Ljungstr\u00f6m", "given": "Viktor", "initials": "V"}, {"family": "Enjuanes", "given": "Anna", "initials": "A"}, {"family": "Cortese", "given": "Diego", "initials": "D"}, {"family": "Skaftason", "given": "Aron", "initials": "A"}, {"family": "Tausch", "given": "Eugen", "initials": "E"}, {"family": "Stano Kozubik", "given": "Katerina", "initials": "K"}, {"family": "Nadeu", "given": "Ferran", "initials": "F"}, {"family": "Armand", "given": "Marine", "initials": "M"}, {"family": "Malcikova", "given": "Jikta", "initials": "J"}, {"family": "Pandzic", "given": "Tatjana", "initials": "T"}, {"family": "Forster", "given": "Jade", "initials": "J"}, {"family": "Davis", "given": "Zadie", "initials": "Z"}, {"family": "Oscier", "given": "David", "initials": "D"}, {"family": "Rossi", "given": "Davide", "initials": "D"}, {"family": "Ghia", "given": "Paolo", "initials": "P"}, {"family": "Strefford", "given": "Jonathan C", "initials": "JC"}, {"family": "Pospisilova", "given": "Sarka", "initials": "S"}, {"family": "Stilgenbauer", "given": "Stephan", "initials": "S"}, {"family": "Davi", "given": "Frederic", "initials": "F"}, {"family": "Campo", "given": "Elias", "initials": "E"}, {"family": "Stamatopoulos", "given": "Kostas", "initials": "K"}, {"family": "Rosenquist", "given": "Richard", "initials": "R"}], "type": "journal article", "published": "2021-03-01", "journal": {"title": "Haematologica", "issn": "1592-8721", "issn-l": "0390-6078", "volume": "106", "issue": "3", "pages": "682-691"}, "abstract": "Next-generation sequencing (NGS) has transitioned from research toclinical routine, yet the comparability of different technologies formutation profiling remains an open question. We performed aEuropean multicenter (n=6) evaluation of three amplicon-based NGS assaystargeting 11 genes recurrently mutated in chronic lymphocytic leukemia.Each assay was assessed by two centers using 48 pre-characterized chroniclymphocytic leukemia samples; libraries were sequenced on the IlluminaMiSeq instrument and bioinformatics analyses were centralized. Across allcenters the median percentage of target reads \u2265100x ranged from 94.2-99.8%. In order to rule out assay-specific technical variability, we firstassessed variant calling at the individual assay level i.e., pairwise analysis ofvariants detected amongst partner centers. After filtering for variants presentin the paired normal sample and removal of PCR/sequencing artefacts, thepanels achieved 96.2% (Multiplicom), 97.7% (TruSeq) and 90% (HaloPlex)concordance at a variant allele frequency (VAF) >0.5%. Reproducibility wasassessed by looking at the inter-laboratory variation in detecting mutationsand 107 of 115 (93% concordance) mutations were detected by all six centers,while the remaining eight variants (7%) were undetected by a singlecenter. Notably, 6 of 8 of these variants concerned minor subclonal mutations(VAF <5%). We sought to investigate low-frequency mutations furtherby using a high-sensitivity assay containing unique molecular identifiers,which confirmed the presence of several minor subclonal mutations. Thus,while amplicon-based approaches can be adopted for somatic mutationdetection with VAF >5%, after rigorous validation, the use of unique molecularidentifiers may be necessary to reach a higher sensitivity and ensureconsistent and accurate detection of low-frequency variants.", "doi": "10.3324/haematol.2019.234716", "pmid": "32273480", "labels": {"Clinical Genomics Uppsala": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Clinical Genomics": "Service"}, "xrefs": [{"db": "pii", "key": "haematol.2019.234716"}, {"db": "pmc", "key": "PMC7927885"}], "notes": [], "created": "2020-12-08T15:43:49.578Z", "modified": "2021-12-27T14:44:36.161Z"}, {"entity": "publication", "iuid": "623279ebcab34ac7abee4d1296a1fd72", "links": {"self": {"href": "https://publications.scilifelab.se/publication/623279ebcab34ac7abee4d1296a1fd72.json"}, "display": {"href": "https://publications.scilifelab.se/publication/623279ebcab34ac7abee4d1296a1fd72"}}, "title": "Whole-genome analyses provide no evidence for dog introgression in Fennoscandian wolf populations.", "authors": [{"family": "Smeds", "given": "Linn\u00e9a", "initials": "L", "orcid": "0000-0002-8415-9259", "researcher": {"href": "https://publications.scilifelab.se/researcher/b46a4a275c954de8bb969ef4cda9e33b.json"}}, {"family": "Aspi", "given": "Jouni", "initials": "J"}, {"family": "Berglund", "given": "Jonas", "initials": "J"}, {"family": "Kojola", "given": "Ilpo", "initials": "I"}, {"family": "Tirronen", "given": "Konstantin", "initials": "K"}, {"family": "Ellegren", "given": "Hans", "initials": "H", "orcid": "0000-0002-5035-1736", "researcher": {"href": "https://publications.scilifelab.se/researcher/819e68cc7125446baec6165aabd2d19c.json"}}], "type": "journal article", "published": "2021-03-00", "journal": {"title": "Evol Appl", "issn": "1752-4571", "volume": "14", "issue": "3", "pages": "721-734", "issn-l": "1752-4571"}, "abstract": "Hybridization and admixture can threaten the genetic integrity of populations and be of particular concern to endangered species. Hybridization between grey wolves and dogs has been documented in many wolf populations worldwide and is a prominent example of human-mediated hybridization between a domesticated species and its wild relative. We analysed whole-genome sequences from >200 wolves and >100 dogs to study admixture in Fennoscandian wolf populations. A principal component analysis of genetic variation and admixture showed that wolves and dogs were well-separated, without evidence for introgression. Analyses of local ancestry revealed that wolves had <1% mixed ancestry, levels comparable to the degree of mixed ancestry in many dogs, and likely not resulting from recent wolf-dog hybridization. We also show that the founders of the Scandinavian wolf population were genetically inseparable from Finnish and Russian Karelian wolves, pointing at the geographical origin of contemporary Scandinavian wolves. Moreover, we found Scandinavian-born animals among wolves sampled in Finland, demonstrating bidirectional gene flow between the Scandinavian Peninsula and eastern countries. The low incidence of admixture between wolves and dogs in Fennoscandia may be explained by the fact that feral dogs are rare in this part of Europe and that careful monitoring and management act to remove hybrids before they backcross into wolf populations.", "doi": "10.1111/eva.13151", "pmid": "33767747", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "EVA13151"}, {"db": "pmc", "key": "PMC7980305"}, {"db": "Dryad", "key": "10.5061/dryad.8gtht76n6"}], "notes": [], "created": "2021-06-01T20:53:12.887Z", "modified": "2024-01-16T13:48:40.561Z"}, {"entity": "publication", "iuid": "6c457acdccf942f7ad5f2a040919b53a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6c457acdccf942f7ad5f2a040919b53a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6c457acdccf942f7ad5f2a040919b53a"}}, "title": "Abundantly expressed class of noncoding RNAs conserved through the multicellular evolution of dictyostelid social amoebas.", "authors": [{"family": "Kjellin", "given": "Jonas", "initials": "J", "orcid": "0000-0002-3830-7046", "researcher": {"href": "https://publications.scilifelab.se/researcher/daf9964b08fa498e9c0eb3540a0aa1fa.json"}}, {"family": "Avesson", "given": "Lotta", "initials": "L"}, {"family": "Reimeg\u00e5rd", "given": "Johan", "initials": "J"}, {"family": "Liao", "given": "Zhen", "initials": "Z"}, {"family": "Eichinger", "given": "Ludwig", "initials": "L"}, {"family": "Noegel", "given": "Angelika", "initials": "A"}, {"family": "Gl\u00f6ckner", "given": "Gernot", "initials": "G"}, {"family": "Schaap", "given": "Pauline", "initials": "P"}, {"family": "S\u00f6derbom", "given": "Fredrik", "initials": "F", "orcid": "0000-0003-3616-3509", "researcher": {"href": "https://publications.scilifelab.se/researcher/4952b493871a4970a089074117bb303f.json"}}], "type": "journal article", "published": "2021-03-00", "journal": {"title": "Genome Res.", "issn": "1549-5469", "volume": "31", "issue": "3", "pages": "436-447", "issn-l": "1088-9051"}, "abstract": "Aggregative multicellularity has evolved multiple times in diverse groups of eukaryotes, exemplified by the well-studied development of dictyostelid social amoebas, for example, Dictyostelium discoideum However, it is still poorly understood why multicellularity emerged in these amoebas while the majority of other members of Amoebozoa are unicellular. Previously, a novel type of noncoding RNA, Class I RNAs, was identified in D. discoideum and shown to be important for normal multicellular development. Here, we investigated Class I RNA evolution and its connection to multicellular development. We identified a large number of new Class I RNA genes by constructing a covariance model combined with a scoring system based on conserved upstream sequences. Multiple genes were predicted in representatives of each major group of Dictyostelia and expression analysis confirmed that our search approach identifies expressed Class I RNA genes with high accuracy and sensitivity and that the RNAs are developmentally regulated. Further studies showed that Class I RNAs are ubiquitous in Dictyostelia and share highly conserved structure and sequence motifs. In addition, Class I RNA genes appear to be unique to dictyostelid social amoebas because they could not be identified in outgroup genomes, including their closest known relatives. Our results show that Class I RNA is an ancient class of ncRNAs, likely to have been present in the last common ancestor of Dictyostelia dating back at least 600 million years. Based on previous functional analyses and the presented evolutionary investigation, we hypothesize that Class I RNAs were involved in evolution of multicellularity in Dictyostelia.", "doi": "10.1101/gr.272856.120", "pmid": "33479022", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pii", "key": "gr.272856.120"}, {"db": "pmc", "key": "PMC7919456"}], "notes": [], "created": "2021-12-10T10:43:43.443Z", "modified": "2021-12-10T10:43:43.527Z"}, {"entity": "publication", "iuid": "48ce3099225e4521962b6d5bc27cfb16", "links": {"self": {"href": "https://publications.scilifelab.se/publication/48ce3099225e4521962b6d5bc27cfb16.json"}, "display": {"href": "https://publications.scilifelab.se/publication/48ce3099225e4521962b6d5bc27cfb16"}}, "title": "Combined removal of organic micropollutants and ammonium in reactive barriers developed for managed aquifer recharge.", "authors": [{"family": "Modrzy\u0144ski", "given": "Jakub J", "initials": "JJ"}, {"family": "Aamand", "given": "Jens", "initials": "J"}, {"family": "Wittorf", "given": "Lea", "initials": "L", "orcid": "0000-0002-4478-7816", "researcher": {"href": "https://publications.scilifelab.se/researcher/3f3a73ebc63c41fe8f487e5c0e6e12ad.json"}}, {"family": "Badawi", "given": "Nora", "initials": "N"}, {"family": "Hubalek", "given": "Valerie", "initials": "V"}, {"family": "Canelles", "given": "Arnau", "initials": "A"}, {"family": "Hallin", "given": "Sara", "initials": "S", "orcid": "0000-0002-9069-9024", "researcher": {"href": "https://publications.scilifelab.se/researcher/6e3491aec8fe4fbf827e2448c898356e.json"}}, {"family": "Albers", "given": "Christian N", "initials": "CN", "orcid": "0000-0001-7253-3509", "researcher": {"href": "https://publications.scilifelab.se/researcher/46a3cc1da4454d5bb6f4a595d31c05c9.json"}}], "type": "journal article", "published": "2021-02-15", "journal": {"title": "Water Res.", "issn": "1879-2448", "issn-l": "0043-1354", "volume": "190", "issue": null, "pages": "116669"}, "abstract": "Groundwater is an important drinking water resource. To ensure clean drinking water, managed aquifer recharge (MAR) could be an attractive solution when recharging with treated wastewater. The installation of reactive barriers, e.g. with compost or other organic materials at MAR facilities, may improve pollutant removal. To link pollutant transformation processes and microbiology in reactive barriers, we simulated infiltration through different sand-compost mixtures using laboratory columns with depth-specific sampling of water and barrier material. We also evaluated the effect of inoculation with activated sludge. Our focus was on the simultaneous removal of organic micropollutants and nitrogen species, with parallel monitoring of the development of microbial communities. During 17 weeks of operation, the columns were fed with synthetic wastewater containing five organic micropollutants (1-2 \u00b5g/L each) and ammonium (2 mg N/L). Unique communities developed in the columns in relation to barrier material, with high effects of compost addition and minor effect of inoculation. Removal of the micropollutant paracetamol (acetaminophen) occurred in all columns, while sulfamethoxazole was only removed in columns with 50% compost. By contrast, limited removal was observed for sulfadiazine, carbamazepine and diuron, with the latter two displaying transient removal, attributed sorption. Oxygen was depleted within the top few cm of the columns when compost was present, but this was sufficient to remove all ammonium through nitrification. The fate of accumulated nitrate at deeper layers depended on the fraction of compost, with more compost leading to removal of nitrate by denitrification, but also by dissimilatory nitrate reduction to ammonium, hampering the overall nitrogen removal efficiency. Introducing compost as reactive barrier in MAR facilities has a large effect on the microbial communities and processes, but whether it will provide overall cleaner water to the underlying aquifer is uncertain and will depend very much on the type of pollutant.", "doi": "10.1016/j.watres.2020.116669", "pmid": "33279750", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "S0043-1354(20)31204-5"}], "notes": [], "created": "2020-12-08T23:21:56.772Z", "modified": "2024-01-16T13:48:40.698Z"}, {"entity": "publication", "iuid": "e5924e2e04a64152ac970d7f2353229e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e5924e2e04a64152ac970d7f2353229e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e5924e2e04a64152ac970d7f2353229e"}}, "title": "A novel canine reference genome resolves genomic architecture and uncovers transcript complexity.", "authors": [{"family": "Wang", "given": "Chao", "initials": "C", "orcid": "0000-0003-3936-4023", "researcher": {"href": "https://publications.scilifelab.se/researcher/202a8fd115e14824809a362a7cfc5a41.json"}}, {"family": "Wallerman", "given": "Ola", "initials": "O"}, {"family": "Arendt", "given": "Maja-Louise", "initials": "ML"}, {"family": "Sundstr\u00f6m", "given": "Elisabeth", "initials": "E", "orcid": "0000-0001-9526-8541", "researcher": {"href": "https://publications.scilifelab.se/researcher/20f87b64e71b4a00a9474ec4d898601d.json"}}, {"family": "Karlsson", "given": "\u00c5sa", "initials": "\u00c5"}, {"family": "Nordin", "given": "Jessika", "initials": "J", "orcid": "0000-0002-8414-2190", "researcher": {"href": "https://publications.scilifelab.se/researcher/2603df7f3ff84e6980605b9e8eef4c2f.json"}}, {"family": "M\u00e4kel\u00e4inen", "given": "Suvi", "initials": "S", "orcid": "0000-0001-7378-4991", "researcher": {"href": "https://publications.scilifelab.se/researcher/1b1f91bf7dcd466a9814effddf67976e.json"}}, {"family": "Pielberg", "given": "Gerli Rosengren", "initials": "GR"}, {"family": "Hanson", "given": "Jeanette", "initials": "J"}, {"family": "Ohlsson", "given": "\u00c5sa", "initials": "\u00c5"}, {"family": "Saellstr\u00f6m", "given": "Sara", "initials": "S", "orcid": "0000-0001-5253-5830", "researcher": {"href": "https://publications.scilifelab.se/researcher/aac98530437d4d6890dffcbd31eabde0.json"}}, {"family": "R\u00f6nnberg", "given": "Henrik", "initials": "H", "orcid": "0000-0001-6098-5364", "researcher": {"href": "https://publications.scilifelab.se/researcher/8f8783f23d664f4b98ef8f6ff03b6693.json"}}, {"family": "Ljungvall", "given": "Ingrid", "initials": "I"}, {"family": "H\u00e4ggstr\u00f6m", "given": "Jens", "initials": "J"}, {"family": "Bergstr\u00f6m", "given": "Tomas F", "initials": "TF", "orcid": "0000-0002-7480-2669", "researcher": {"href": "https://publications.scilifelab.se/researcher/b590797209ee4feab6302920621fc621.json"}}, {"family": "Hedhammar", "given": "\u00c5ke", "initials": "\u00c5"}, {"family": "Meadows", "given": "Jennifer R S", "initials": "JRS", "orcid": "0000-0002-0850-230X", "researcher": {"href": "https://publications.scilifelab.se/researcher/86acdca0104c4552880d5a7cb5ac6565.json"}}, {"family": "Lindblad-Toh", "given": "Kerstin", "initials": "K", "orcid": "0000-0001-8338-0253", "researcher": {"href": "https://publications.scilifelab.se/researcher/e0063145f7d6476f80ab42f94833f4cf.json"}}], "type": "comparative study", "published": "2021-02-10", "journal": {"title": "Commun Biol", "issn": "2399-3642", "issn-l": "2399-3642", "volume": "4", "issue": "1", "pages": "185"}, "abstract": "We present GSD_1.0, a high-quality domestic dog reference genome with chromosome length scaffolds and contiguity increased 55-fold over CanFam3.1. Annotation with generated and existing long and short read RNA-seq, miRNA-seq and ATAC-seq, revealed that 32.1% of lifted over CanFam3.1 gaps harboured previously hidden functional elements, including promoters, genes and miRNAs in GSD_1.0. A catalogue of canine \"dark\" regions was made to facilitate mapping rescue. Alignment in these regions is difficult, but we demonstrate that they harbour trait-associated variation. Key genomic regions were completed, including the Dog Leucocyte Antigen (DLA), T Cell Receptor (TCR) and 366 COSMIC cancer genes. 10x linked-read sequencing of 27 dogs (19 breeds) uncovered 22.1 million SNPs, indels and larger structural variants. Subsequent intersection with protein coding genes showed that 1.4% of these could directly influence gene products, and so provide a source of normal or aberrant phenotypic modifications.", "doi": "10.1038/s42003-021-01698-x", "pmid": "33568770", "labels": {"NGI Uppsala (Uppsala Genome Center)": "Service", "National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s42003-021-01698-x"}, {"db": "pmc", "key": "PMC7875987"}], "notes": [], "created": "2021-02-17T19:15:39.689Z", "modified": "2024-01-16T13:48:40.742Z"}, {"entity": "publication", "iuid": "70655a5870824411b3765f5eee576afe", "links": {"self": {"href": "https://publications.scilifelab.se/publication/70655a5870824411b3765f5eee576afe.json"}, "display": {"href": "https://publications.scilifelab.se/publication/70655a5870824411b3765f5eee576afe"}}, "title": "Genomic characterization of relapsed acute myeloid leukemia reveals novel putative therapeutic targets.", "authors": [{"family": "Stratmann", "given": "Svea", "initials": "S", "orcid": "0000-0002-7438-9093", "researcher": {"href": "https://publications.scilifelab.se/researcher/3927efe3aaf84399b26355d92c3a15cf.json"}}, {"family": "Yones", "given": "Sara A", "initials": "SA", "orcid": "0000-0002-7201-2604", "researcher": {"href": "https://publications.scilifelab.se/researcher/17817db9549947578bbe96ba93524cf5.json"}}, {"family": "Mayrhofer", "given": "Markus", "initials": "M"}, {"family": "Norgren", "given": "Nina", "initials": "N", "orcid": "0000-0002-3823-1555", "researcher": {"href": "https://publications.scilifelab.se/researcher/a14a423eff78442daffe57aff0130f33.json"}}, {"family": "Skaftason", "given": "Aron", "initials": "A"}, {"family": "Sun", "given": "Jitong", "initials": "J"}, {"family": "Smolinska", "given": "Karolina", "initials": "K", "orcid": "0000-0003-0907-5298", "researcher": {"href": "https://publications.scilifelab.se/researcher/5f60978d8a384de0a158c0579d8b0586.json"}}, {"family": "Komorowski", "given": "Jan", "initials": "J", "orcid": "0000-0002-0766-8789", "researcher": {"href": "https://publications.scilifelab.se/researcher/b2d1190dfa864e4089c58c864857b114.json"}}, {"family": "Herlin", "given": "Morten Krogh", "initials": "MK", "orcid": "0000-0001-7179-4643", "researcher": {"href": "https://publications.scilifelab.se/researcher/fc2efb7b874d46879e3f34e3d7a1b8ef.json"}}, {"family": "Sundstr\u00f6m", "given": "Christer", "initials": "C", "orcid": "0000-0002-8160-5647", "researcher": {"href": "https://publications.scilifelab.se/researcher/dfac750a70664f9986b3cc06334638cc.json"}}, {"family": "Eriksson", "given": "Anna", "initials": "A"}, {"family": "H\u00f6glund", "given": "Martin", "initials": "M", "orcid": "0000-0003-2468-0226", "researcher": {"href": "https://publications.scilifelab.se/researcher/8717164448ee4e2797fefd365103ddc8.json"}}, {"family": "Palle", "given": "Josefine", "initials": "J"}, {"family": "Abrahamsson", "given": "Jonas", "initials": "J"}, {"family": "Jahnukainen", "given": "Kirsi", "initials": "K"}, {"family": "Munthe-Kaas", "given": "Monica Cheng", "initials": "MC"}, {"family": "Zeller", "given": "Bernward", "initials": "B"}, {"family": "Tamm", "given": "Katja Pokrovskaja", "initials": "KP"}, {"family": "Cavelier", "given": "Lucia", "initials": "L", "orcid": "0009-0003-8195-370X", "researcher": {"href": "https://publications.scilifelab.se/researcher/f01226edb140436da0c9d166c1f5fe51.json"}}, {"family": "Holmfeldt", "given": "Linda", "initials": "L", "orcid": "0000-0003-4140-3423", "researcher": {"href": "https://publications.scilifelab.se/researcher/12b8b368e61e48d3b800516f006fbb7d.json"}}], "type": "journal article", "published": "2021-02-09", "journal": {"title": "Blood Adv", "issn": "2473-9537", "issn-l": "2473-9529", "volume": "5", "issue": "3", "pages": "900-912"}, "abstract": "Relapse is the leading cause of death of adult and pediatric patients with acute myeloid leukemia (AML). Numerous studies have helped to elucidate the complex mutational landscape at diagnosis of AML, leading to improved risk stratification and new therapeutic options. However, multi-whole-genome studies of adult and pediatric AML at relapse are necessary for further advances. To this end, we performed whole-genome and whole-exome sequencing analyses of longitudinal diagnosis, relapse, and/or primary resistant specimens from 48 adult and 25 pediatric patients with AML. We identified mutations recurrently gained at relapse in ARID1A and CSF1R, both of which represent potentially actionable therapeutic alternatives. Further, we report specific differences in the mutational spectrum between adult vs pediatric relapsed AML, with MGA and H3F3A p.Lys28Met mutations recurrently found at relapse in adults, whereas internal tandem duplications in UBTF were identified solely in children. Finally, our study revealed recurrent mutations in IKZF1, KANSL1, and NIPBL at relapse. All of the mentioned genes have either never been reported at diagnosis in de novo AML or have been reported at low frequency, suggesting important roles for these alterations predominantly in disease progression and/or resistance to therapy. Our findings shed further light on the complexity of relapsed AML and identified previously unappreciated alterations that may lead to improved outcomes through personalized medicine.", "doi": "10.1182/bloodadvances.2020003709", "pmid": "33560403", "labels": {"NGI Uppsala (Uppsala Genome Center)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Clinical Genomics Uppsala": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative", "Clinical Genomics": "Service"}, "xrefs": [{"db": "pii", "key": "S2473-9529(21)00115-4"}, {"db": "pmc", "key": "PMC7876890"}], "notes": [], "created": "2021-02-17T19:26:48.353Z", "modified": "2024-01-16T13:48:40.749Z"}, {"entity": "publication", "iuid": "627122d3b7f5410f829395df31d053e9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/627122d3b7f5410f829395df31d053e9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/627122d3b7f5410f829395df31d053e9"}}, "title": "Taste perception and lifestyle: insights from phenotype and genome data among Africans and Asians.", "authors": [{"family": "Sj\u00f6strand", "given": "Agn\u00e8s E", "initials": "AE"}, {"family": "Sj\u00f6din", "given": "Per", "initials": "P"}, {"family": "Hegay", "given": "Tatyana", "initials": "T"}, {"family": "Nikolaeva", "given": "Anna", "initials": "A"}, {"family": "Shayimkulov", "given": "Farhad", "initials": "F"}, {"family": "Blum", "given": "Michael G B", "initials": "MGB"}, {"family": "Heyer", "given": "Evelyne", "initials": "E", "orcid": "0000-0002-0266-3196", "researcher": {"href": "https://publications.scilifelab.se/researcher/aaa9ddd4afef4d28aa96f53bad9fc938.json"}}, {"family": "Jakobsson", "given": "Mattias", "initials": "M", "orcid": "0000-0001-7840-7853", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a4abe0fcb20492d9ec849c9fbf58a71.json"}}], "type": "journal article", "published": "2021-02-00", "journal": {"title": "Eur. J. Hum. Genet.", "issn": "1476-5438", "volume": "29", "issue": "2", "pages": "325-337", "issn-l": "1018-4813"}, "abstract": "Taste is essential for the interaction of animals with their food and has co-evolved with diet. Humans have peopled a large range of environments and present a wide range of diets, but little is known about the diversity and evolution of human taste perception. We measured taste recognition thresholds across populations differing in lifestyles (hunter gatherers and farmers from Central Africa, nomad herders, and farmers from Central Asia). We also generated genome-wide genotype data and performed association studies and selection scans in order to link the phenotypic variation in taste sensitivity with genetic variation. We found that hunter gatherers have lower overall sensitivity as well as lower sensitivity to quinine and fructose than their farming neighbors. In parallel, there is strong population divergence in genes associated with tongue morphogenesis and genes involved in the transduction pathway of taste signals in the African populations. We find signals of recent selection in bitter taste-receptor genes for all four populations. Enrichment analysis on association scans for the various tastes confirmed already documented associations and revealed novel GO terms that are good candidates for being involved in taste perception. Our framework permitted us to gain insight into the genetic basis of taste sensitivity variation across populations and lifestyles.", "doi": "10.1038/s41431-020-00736-2", "pmid": "33005019", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41431-020-00736-2"}, {"db": "pmc", "key": "PMC7868368"}], "notes": [], "created": "2020-10-20T06:59:23.977Z", "modified": "2024-01-16T13:48:40.806Z"}, {"entity": "publication", "iuid": "2267de4bdc2d49618a869e6329ab7d0c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2267de4bdc2d49618a869e6329ab7d0c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2267de4bdc2d49618a869e6329ab7d0c"}}, "title": "Small-scale population divergence is driven by local larval environment in a temperate amphibian.", "authors": [{"family": "R\u00f6din-M\u00f6rch", "given": "Patrik", "initials": "P", "orcid": "0000-0001-6737-1488", "researcher": {"href": "https://publications.scilifelab.se/researcher/9e6abe040b284d67b11f45db1e58540e.json"}}, {"family": "Palejowski", "given": "Hugo", "initials": "H"}, {"family": "Cortazar-Chinarro", "given": "Maria", "initials": "M"}, {"family": "K\u00e4rvemo", "given": "Simon", "initials": "S"}, {"family": "Richter-Boix", "given": "Alex", "initials": "A", "orcid": "0000-0002-8559-5191", "researcher": {"href": "https://publications.scilifelab.se/researcher/0eaa32ef12fb498eb13d0c6906d21375.json"}}, {"family": "H\u00f6glund", "given": "Jacob", "initials": "J"}, {"family": "Laurila", "given": "Anssi", "initials": "A"}], "type": "journal article", "published": "2021-02-00", "journal": {"title": "Heredity (Edinb)", "issn": "1365-2540", "volume": "126", "issue": "2", "pages": "279-292", "issn-l": "0018-067X"}, "abstract": "Genomic variation within and among populations is shaped by the interplay between natural selection and the effects of genetic drift and gene flow. Adaptive divergence can be found in small-scale natural systems even when population sizes are small, and the potential for gene flow is high, suggesting that local environments exert selection pressures strong enough to counteract the opposing effects of drift and gene flow. Here, we investigated genomic differentiation in nine moor frog (Rana arvalis) populations in a small-scale network of local wetlands using 16,707 ddRAD-seq SNPs, relating levels of differentiation with local environments, as well as with properties of the surrounding landscape. We characterized population structure and differentiation, and partitioned the effects of geographic distance, local larval environment, and landscape features on total genomic variation. We also conducted gene-environment association studies using univariate and multivariate approaches. We found small-scale population structure corresponding to 6-8 clusters. Local larval environment was the most influential component explaining 2.3% of the total genetic variation followed by landscape features (1.8%) and geographic distance (0.8%), indicative of isolation-by-environment, -by-landscape, and -by-distance, respectively. We identified 1000 potential candidate SNPs putatively under divergent selection mediated by the local larval environment. The candidate SNPs were involved in, among other biological functions, immune system function and development. Our results suggest that small-scale environmental differences can exert selection pressures strong enough to counteract homogenizing effects of gene flow and drift in this small-scale system, leading to observable population differentiation.", "doi": "10.1038/s41437-020-00371-z", "pmid": "32958927", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41437-020-00371-z"}, {"db": "pmc", "key": "PMC8027893"}], "notes": [], "created": "2020-12-08T23:38:10.164Z", "modified": "2024-01-16T13:48:40.813Z"}, {"entity": "publication", "iuid": "62ecd11c1f8b43f984f8802df9da6dbb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/62ecd11c1f8b43f984f8802df9da6dbb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/62ecd11c1f8b43f984f8802df9da6dbb"}}, "title": "Single nucleus transcriptomics data integration recapitulates the major cell types in human liver.", "authors": [{"family": "Diamanti", "given": "Klev", "initials": "K", "orcid": "0000-0002-4922-8415", "researcher": {"href": "https://publications.scilifelab.se/researcher/b71560391b294bb5a344b9c6cabfc956.json"}}, {"family": "Inda D\u00edaz", "given": "Juan Salvador", "initials": "JS", "orcid": "0000-0002-3735-8300", "researcher": {"href": "https://publications.scilifelab.se/researcher/40b6bd806d874198a7509500bddfd939.json"}}, {"family": "Raine", "given": "Amanda", "initials": "A", "orcid": "0000-0002-2775-6516", "researcher": {"href": "https://publications.scilifelab.se/researcher/a97b7df8379f42f0a412fb7c234a6c70.json"}}, {"family": "Pan", "given": "Gang", "initials": "G", "orcid": "0000-0003-4243-1821", "researcher": {"href": "https://publications.scilifelab.se/researcher/e956246a20aa4ed3a67c084a4c1e5289.json"}}, {"family": "Wadelius", "given": "Claes", "initials": "C", "orcid": "0000-0002-2033-7829", "researcher": {"href": "https://publications.scilifelab.se/researcher/2ec5ca1122024da4893b61e329a5ece5.json"}}, {"family": "Cavalli", "given": "Marco", "initials": "M", "orcid": "0000-0003-1143-1431", "researcher": {"href": "https://publications.scilifelab.se/researcher/e35211c06385459baee12101121d2a15.json"}}], "type": "journal article", "published": "2021-02-00", "journal": {"title": "Hepatol Res", "issn": "1386-6346", "issn-l": null, "volume": "51", "issue": "2", "pages": "233-238"}, "abstract": "The aim of this study was to explore the benefits of data integration from different platforms for single nucleus transcriptomics profiling to characterize cell populations in human liver.\n\nWe generated single-nucleus RNA sequencing data from Chromium 10X Genomics and Drop-seq for a human liver sample. We utilized state of the art bioinformatics tools to undertake a rigorous quality control and to integrate the data into a common space summarizing the gene expression variation from the respective platforms, while accounting for known and unknown confounding factors.\n\nAnalysis of single nuclei transcriptomes from both 10X and Drop-seq allowed identification of the major liver cell types, while the integrated set obtained enough statistical power to separate a small population of inactive hepatic stellate cells that was not characterized in either of the platforms.\n\nIntegration of droplet-based single nucleus transcriptomics data enabled identification of a small cluster of inactive hepatic stellate cells that highlights the potential of our approach. We suggest single-nucleus RNA sequencing integrative approaches could be utilized to design larger and cost-effective studies.", "doi": "10.1111/hepr.13585", "pmid": "33119937", "labels": {"National Genomics Infrastructure": "Collaborative", "NGI Uppsala (SNP&SEQ Technology Platform)": "Collaborative", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2020-12-08T23:37:37.148Z", "modified": "2024-01-16T13:48:40.820Z"}, {"entity": "publication", "iuid": "984a5218407a416aa006a0f62bb5521b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/984a5218407a416aa006a0f62bb5521b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/984a5218407a416aa006a0f62bb5521b"}}, "title": "Role of H1 and DNA methylation in selective regulation of transposable elements during heat stress.", "authors": [{"family": "Liu", "given": "Shujing", "initials": "S", "orcid": "0000-0002-5783-4204", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a1916bba339494f995b0a7a84428fcf.json"}}, {"family": "de Jonge", "given": "Jennifer", "initials": "J"}, {"family": "Trejo-Arellano", "given": "Minerva S", "initials": "MS", "orcid": "0000-0002-1982-3475", "researcher": {"href": "https://publications.scilifelab.se/researcher/0d1fc0e7004b41de889d2223941385c7.json"}}, {"family": "Santos-Gonz\u00e1lez", "given": "Juan", "initials": "J"}, {"family": "K\u00f6hler", "given": "Claudia", "initials": "C", "orcid": "0000-0002-2619-4857", "researcher": {"href": "https://publications.scilifelab.se/researcher/accd3f9307614c8ab67154dd5e50cdac.json"}}, {"family": "Hennig", "given": "Lars", "initials": "L", "orcid": "0000-0002-6645-1862", "researcher": {"href": "https://publications.scilifelab.se/researcher/9b350e5d9ba74c27bf1709ff0457e605.json"}}], "type": "journal article", "published": "2021-02-00", "journal": {"title": "New Phytol.", "issn": "1469-8137", "volume": "229", "issue": "4", "pages": "2238-2250", "issn-l": "0028-646X"}, "abstract": "Heat-stressed Arabidopsis plants release heterochromatin-associated transposable element (TE) silencing, yet it is not accompanied by major reductions of epigenetic repressive modifications. In this study, we explored the functional role of histone H1 in repressing heterochromatic TEs in response to heat stress. We generated and analyzed RNA and bisulfite-sequencing data of wild-type and h1 mutant seedlings before and after heat stress. Loss of H1 caused activation of pericentromeric Gypsy elements upon heat treatment, despite these elements remaining highly methylated. By contrast, nonpericentromeric Copia elements became activated concomitantly with loss of DNA methylation. The same Copia elements became activated in heat-treated chromomethylase 2 (cmt2) mutants, indicating that H1 represses Copia elements through maintaining DNA methylation under heat. We discovered that H1 is required for TE repression in response to heat stress, but its functional role differs depending on TE location. Strikingly, H1-deficient plants treated with the DNA methyltransferase inhibitor zebularine were highly tolerant to heat stress, suggesting that both H1 and DNA methylation redundantly suppress the plant response to heat stress.", "doi": "10.1111/nph.17018", "pmid": "33091182", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC7894476"}], "notes": [], "created": "2020-12-08T23:37:01.805Z", "modified": "2021-11-10T12:27:17.083Z"}, {"entity": "publication", "iuid": "5c1d6cec9af048a39ac813f6e0a4ce30", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5c1d6cec9af048a39ac813f6e0a4ce30.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5c1d6cec9af048a39ac813f6e0a4ce30"}}, "title": "Hybrid seed incompatibility in Capsella is connected to chromatin condensation defects in the endosperm.", "authors": [{"family": "Dziasek", "given": "Katarzyna", "initials": "K", "orcid": "0000-0002-7279-1417", "researcher": {"href": "https://publications.scilifelab.se/researcher/0376b8a4203a4ffba9f688227a8632a2.json"}}, {"family": "Simon", "given": "Lauriane", "initials": "L", "orcid": "0000-0001-7285-9437", "researcher": {"href": "https://publications.scilifelab.se/researcher/08c7a8b7df834ad7b1f905986eb1a99a.json"}}, {"family": "Lafon-Placette", "given": "Cl\u00e9ment", "initials": "C", "orcid": "0000-0001-6634-8104", "researcher": {"href": "https://publications.scilifelab.se/researcher/63262f71f9c54f438d6f08380d799d96.json"}}, {"family": "Laenen", "given": "Benjamin", "initials": "B"}, {"family": "W\u00e4rdig", "given": "Cecilia", "initials": "C"}, {"family": "Santos-Gonz\u00e1lez", "given": "Juan", "initials": "J", "orcid": "0000-0002-8712-9776", "researcher": {"href": "https://publications.scilifelab.se/researcher/d26cc8b837e64875aa2226cb9a8b8da3.json"}}, {"family": "Slotte", "given": "Tanja", "initials": "T", "orcid": "0000-0001-6020-5102", "researcher": {"href": "https://publications.scilifelab.se/researcher/67c69ee78bae41478465a7e5fa63b946.json"}}, {"family": "K\u00f6hler", "given": "Claudia", "initials": "C", "orcid": "0000-0002-2619-4857", "researcher": {"href": "https://publications.scilifelab.se/researcher/accd3f9307614c8ab67154dd5e50cdac.json"}}], "type": "journal article", "published": "2021-02-00", "journal": {"title": "PLoS Genet.", "issn": "1553-7404", "volume": "17", "issue": "2", "pages": "e1009370", "issn-l": "1553-7390"}, "abstract": "Hybridization of closely related plant species is frequently connected to endosperm arrest and seed failure, for reasons that remain to be identified. In this study, we investigated the molecular events accompanying seed failure in hybrids of the closely related species pair Capsella rubella and C. grandiflora. Mapping of QTL for the underlying cause of hybrid incompatibility in Capsella identified three QTL that were close to pericentromeric regions. We investigated whether there are specific changes in heterochromatin associated with interspecific hybridizations and found a strong reduction of chromatin condensation in the endosperm, connected with a strong loss of CHG and CHH methylation and random loss of a single chromosome. Consistent with reduced DNA methylation in the hybrid endosperm, we found a disproportionate deregulation of genes located close to pericentromeric regions, suggesting that reduced DNA methylation allows access of transcription factors to targets located in heterochromatic regions. Since the identified QTL were also associated with pericentromeric regions, we propose that relaxation of heterochromatin in response to interspecies hybridization exposes and activates loci leading to hybrid seed failure.", "doi": "10.1371/journal.pgen.1009370", "pmid": "33571184", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "PGENETICS-D-20-01346"}, {"db": "pmc", "key": "PMC7904229"}], "notes": [], "created": "2021-12-07T21:42:03.071Z", "modified": "2024-01-16T13:48:40.834Z"}, {"entity": "publication", "iuid": "630691e8978c4592989bc0837994eb1d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/630691e8978c4592989bc0837994eb1d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/630691e8978c4592989bc0837994eb1d"}}, "title": "Genome-wide single nucleotide polymorphism markers reveal population structure and dispersal direction of an expanding nuisance algal bloom species.", "authors": [{"family": "Rengefors", "given": "Karin", "initials": "K", "orcid": "0000-0001-6297-9734", "researcher": {"href": "https://publications.scilifelab.se/researcher/1c7353dd11fa445f9ff338db5ce8dadd.json"}}, {"family": "Gollnisch", "given": "Raphael", "initials": "R", "orcid": "0000-0001-6177-8877", "researcher": {"href": "https://publications.scilifelab.se/researcher/4f78f6e8cacf4eba9104fbfd2ab26f66.json"}}, {"family": "Sassenhagen", "given": "Ingrid", "initials": "I"}, {"family": "H\u00e4rnstr\u00f6m Aloisi", "given": "Karolina", "initials": "K"}, {"family": "Svensson", "given": "Marie", "initials": "M"}, {"family": "Lebret", "given": "Karen", "initials": "K"}, {"family": "\u010certnerov\u00e1", "given": "Dora", "initials": "D"}, {"family": "Cresko", "given": "William A", "initials": "WA", "orcid": "0000-0002-3496-8074", "researcher": {"href": "https://publications.scilifelab.se/researcher/5d5d9405a53046be86d108b7bd0a0850.json"}}, {"family": "Bassham", "given": "Susan", "initials": "S"}, {"family": "Ahr\u00e9n", "given": "Dag", "initials": "D", "orcid": "0000-0003-4713-0032", "researcher": {"href": "https://publications.scilifelab.se/researcher/d634886b77ad4331916bebc0a3b8b0e3.json"}}], "type": "journal article", "published": "2021-02-00", "journal": {"title": "Mol. Ecol.", "issn": "1365-294X", "issn-l": "0962-1083", "volume": "30", "issue": "4", "pages": "912-925"}, "abstract": "Species invasion and range expansion are currently under scrutiny due to increasing anthropogenic impact on the natural environment. This is also true for harmful algal blooms, which have been reported to have increased in frequency. However, this research is challenging due to the ephemeral nature, small size and mostly low concentrations of microalgae in the environment. One such species is the nuisance microalga Gonyostomum semen (Raphidophyceae), which has increased in occurrence in northern Europe in recent decades. The question of whether the species has expanded its habitat range or if it was already present in the lakes but was too rare to be detected remains unanswered. The aim of the present study was to determine the genetic structure and dispersal pathways of G. semen using RAD (restriction-site-associated DNA) tag sequencing. For G. semen, which has a huge genome (32 Gbp), we faced particular challenges, but were nevertheless able to recover over 1000 single nucleotide polymorphisms at high coverage. Our data revealed a distinct population genetic structure, demonstrating a divide of western and eastern populations that probably represent different lineages. Despite significant genetic differentiation among lakes, we found only limited isolation-by-distance. While we had expected a pattern of recent expansion northwards, the data demonstrated gene flow from the northeast/east towards the southwest/west. This genetic signature suggests that the observed gene flow may be due to dispersal by autumn migratory birds, which act as dispersal vectors of resistant resting propagules that form at the end of the G. semen blooms.", "doi": "10.1111/mec.15787", "pmid": "33386639", "labels": {"Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "RefSeq", "key": "PRJNA659541"}], "notes": [], "created": "2021-01-12T12:32:53.386Z", "modified": "2024-01-16T13:48:40.840Z"}, {"entity": "publication", "iuid": "5e532f9a568545aca2c58ed30c31853f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5e532f9a568545aca2c58ed30c31853f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5e532f9a568545aca2c58ed30c31853f"}}, "title": "Comparative genomics highlights the importance of drug efflux transporters during evolution of mycoparasitism in Clonostachys subgenus Bionectria (Fungi, Ascomycota, Hypocreales).", "authors": [{"family": "Broberg", "given": "Martin", "initials": "M"}, {"family": "Dubey", "given": "Mukesh", "initials": "M"}, {"family": "Iqbal", "given": "Mudassir", "initials": "M", "orcid": "0000-0003-4834-1587", "researcher": {"href": "https://publications.scilifelab.se/researcher/743e411d6e364b15ad5132d3b5f0bc2e.json"}}, {"family": "Gudmundssson", "given": "Mikael", "initials": "M"}, {"family": "Ihrmark", "given": "Katarina", "initials": "K"}, {"family": "Schroers", "given": "Hans-Josef", "initials": "HJ"}, {"family": "Funck Jensen", "given": "Dan", "initials": "D"}, {"family": "Brandstr\u00f6m Durling", "given": "Mikael", "initials": "M"}, {"family": "Karlsson", "given": "Magnus", "initials": "M", "orcid": "0000-0001-6098-138X", "researcher": {"href": "https://publications.scilifelab.se/researcher/34e4b8bad4e34912b011f2ead759b422.json"}}], "type": "journal article", "published": "2021-02-00", "journal": {"title": "Evol Appl", "issn": "1752-4571", "volume": "14", "issue": "2", "pages": "476-497", "issn-l": "1752-4571"}, "abstract": "Various strains of the mycoparasitic fungal species Clonostachys rosea are used commercially as biological control agents for the control of fungal plant diseases in agricultural crop production. Further improvements of the use and efficacy of C. rosea in biocontrol require a mechanistic understanding of the factors that determines the outcome of the interaction between C. rosea and plant pathogenic fungi. Here, we determined the genome sequences of 11 Clonostachys strains, representing five species in Clonostachys subgenus Bionectria, and performed a comparative genomic analysis with the aim to identify gene families evolving under selection for gene gains or losses. Several gene families predicted to encode proteins involved in biosynthesis of secondary metabolites, including polyketide synthases, nonribosomal peptide syntethases and cytochrome P450s, evolved under selection for gene gains (p \u2264 .05) in the Bionectria subgenus lineage. This was accompanied with gene copy number increases (p \u2264 .05) in ATP-binding cassette (ABC) transporters and major facilitator superfamily (MFS) transporters predicted to contribute to drug efflux. Most Clonostachys species were also characterized by high numbers of auxiliary activity (AA) family 9 lytic polysaccharide monooxygenases, AA3 glucose-methanol-choline oxidoreductases and additional carbohydrate-active enzyme gene families with putative activity (or binding) towards xylan and rhamnose/pectin substrates. Particular features of the C. rosea genome included expansions (p \u2264 .05) of the ABC-B4 multidrug resistance transporters, the ABC-C5 multidrug resistance-related transporters and the 2.A.1.3 drug:H + antiporter-2 MFS drug resistance transporters. The ABC-G1 pleiotropic drug resistance transporter gene abcG6 in C. rosea was induced (p \u2264 .009) by exposure to the antifungal Fusarium mycotoxin zearalenone (1121-fold) and various fungicides. Deletion of abcG6 resulted in mutants with reduced (p < .001) growth rates on media containing the fungicides boscalid, fenhexamid and iprodione. Our results emphasize the role of biosynthesis of, and protection against, secondary metabolites in Clonostachys subgenus Bionectria.", "doi": "10.1111/eva.13134", "pmid": "33664789", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "EVA13134"}, {"db": "pmc", "key": "PMC7896725"}], "notes": [], "created": "2021-03-07T08:33:37.082Z", "modified": "2024-01-16T13:48:40.848Z"}, {"entity": "publication", "iuid": "d3cfe9d2e86f4dac978bf4cd338134a9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d3cfe9d2e86f4dac978bf4cd338134a9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d3cfe9d2e86f4dac978bf4cd338134a9"}}, "title": "Divergence and Remarkable Diversity of the Y Chromosome in Guppies.", "authors": [{"family": "Almeida", "given": "Pedro", "initials": "P"}, {"family": "Sandkam", "given": "Benjamin A", "initials": "BA", "orcid": "0000-0002-5043-9295", "researcher": {"href": "https://publications.scilifelab.se/researcher/f002e335e3d34b93b84cfc886defd6e3.json"}}, {"family": "Morris", "given": "Jake", "initials": "J"}, {"family": "Darolti", "given": "Iulia", "initials": "I"}, {"family": "Breden", "given": "Felix", "initials": "F"}, {"family": "Mank", "given": "Judith E", "initials": "JE"}], "type": "journal article", "published": "2021-01-23", "journal": {"title": "Mol. Biol. Evol.", "issn": "1537-1719", "issn-l": "0737-4038", "volume": "38", "issue": "2", "pages": "619-633"}, "abstract": "The guppy sex chromosomes show an extraordinary diversity in divergence across populations and closely related species. In order to understand the dynamics of the guppy Y chromosome, we used linked-read sequencing to assess Y chromosome evolution and diversity across upstream and downstream population pairs that vary in predator and food abundance in three replicate watersheds. Based on our population-specific genome assemblies, we first confirmed and extended earlier reports of two strata on the guppy sex chromosomes. Stratum I shows significant accumulation of male-specific sequence, consistent with Y divergence, and predates the colonization of Trinidad. In contrast, Stratum II shows divergence from the X, but no Y-specific sequence, and this divergence is greater in three replicate upstream populations compared with their downstream pair. Despite longstanding assumptions that sex chromosome recombination suppression is achieved through inversions, we find no evidence of inversions associated with either Stratum I or Stratum II. Instead, we observe a remarkable diversity in Y chromosome haplotypes within each population, even in the ancestral Stratum I. This diversity is likely due to gradual mechanisms of recombination suppression, which, unlike an inversion, allow for the maintenance of multiple haplotypes. In addition, we show that this Y diversity is dominated by low-frequency haplotypes segregating in the population, suggesting a link between haplotype diversity and female preference for rare Y-linked color variation. Our results reveal the complex interplay between recombination suppression and Y chromosome divergence at the earliest stages of sex chromosome divergence.", "doi": "10.1093/molbev/msaa257", "pmid": "33022040", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "5918473"}, {"db": "pmc", "key": "PMC7826173"}], "notes": [], "created": "2020-12-08T23:32:43.215Z", "modified": "2021-11-10T12:27:25.014Z"}, {"entity": "publication", "iuid": "6af1151047da4113a5c5d19409927585", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6af1151047da4113a5c5d19409927585.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6af1151047da4113a5c5d19409927585"}}, "title": "Genome-wide association study and pathway analysis identify NTRK2 as a novel candidate gene for litter size in sheep.", "authors": [{"family": "Esmaeili-Fard", "given": "Seyed Mehdi", "initials": "SM", "orcid": "0000-0001-7509-5030", "researcher": {"href": "https://publications.scilifelab.se/researcher/364057dfaa3a466bb09db3c18235f88b.json"}}, {"family": "Gholizadeh", "given": "Mohsen", "initials": "M"}, {"family": "Hafezian", "given": "Seyed Hasan", "initials": "SH"}, {"family": "Abdollahi-Arpanahi", "given": "Rostam", "initials": "R"}], "type": "journal article", "published": "2021-01-22", "journal": {"title": "PLoS ONE", "issn": "1932-6203", "issn-l": "1932-6203", "volume": "16", "issue": "1", "pages": "e0244408"}, "abstract": "Litter size is one of the most important economic traits in sheep. Identification of gene variants that are associated with the prolificacy rate is an important step in breeding program success and profitability of the farm. So, to identify genetic mechanisms underlying the variation in litter size in Iranian Baluchi sheep, a two-step genome-wide association study (GWAS) was performed. GWAS was conducted using genotype data from 91 Baluchi sheep. Estimated breeding values (EBVs) for litter size calculated for 3848 ewes and then used as the response variable. Besides, a pathway analysis using GO and KEGG databases were applied as a complementary approach. A total of three single nucleotide polymorphisms (SNPs) associated with litter size were identified, one each on OAR2, OAR10, and OAR25. The SNP on OAR2 is located within a novel putative candidate gene, Neurotrophic receptor tyrosine kinase 2. This gene product works as a receptor which is essential for follicular assembly, early follicular growth, and oocyte survival. The SNP on OAR25 is located within RAB4A which is involved in blood vessel formation and proliferation through angiogenesis. The SNP on OAR10 was not associated with any gene in the 1Mb span. Moreover, gene-set analysis using the KEGG database identified several pathways, such as Ovarian steroidogenesis, Steroid hormone biosynthesis, Calcium signaling pathway, and Chemokine signaling. Also, pathway analysis using the GO database revealed several functional terms, such as cellular carbohydrate metabolic, biological adhesion, cell adhesion, cell junction, and cell-cell adherens junction, among others. This is the first study that reports the NTRK2 gene affecting litter size in sheep and our study of this gene functions showed that this gene could be a good candidate for further analysis.", "doi": "10.1371/journal.pone.0244408", "pmid": "33481819", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pii", "key": "PONE-D-20-25223"}, {"db": "pmc", "key": "PMC7822323"}, {"db": "figshare", "key": "10.6084/m9.figshare.12515189.v1"}], "notes": [], "created": "2021-03-03T14:45:54.059Z", "modified": "2021-12-07T13:37:54.855Z"}, {"entity": "publication", "iuid": "07220ba9675142568fe544ad74d55546", "links": {"self": {"href": "https://publications.scilifelab.se/publication/07220ba9675142568fe544ad74d55546.json"}, "display": {"href": "https://publications.scilifelab.se/publication/07220ba9675142568fe544ad74d55546"}}, "title": "The overlap of genetic susceptibility to schizophrenia and cardiometabolic disease can be used to identify metabolically different groups of individuals.", "authors": [{"family": "Strawbridge", "given": "Rona J", "initials": "RJ"}, {"family": "Johnston", "given": "Keira J A", "initials": "KJA"}, {"family": "Bailey", "given": "Mark E S", "initials": "MES"}, {"family": "Baldassarre", "given": "Damiano", "initials": "D"}, {"family": "Cullen", "given": "Breda", "initials": "B"}, {"family": "Eriksson", "given": "Per", "initials": "P"}, {"family": "deFaire", "given": "Ulf", "initials": "U"}, {"family": "Ferguson", "given": "Amy", "initials": "A"}, {"family": "Gigante", "given": "Bruna", "initials": "B"}, {"family": "Giral", "given": "Philippe", "initials": "P"}, {"family": "Graham", "given": "Nicholas", "initials": "N"}, {"family": "Hamsten", "given": "Anders", "initials": "A"}, {"family": "Humphries", "given": "Steve E", "initials": "SE"}, {"family": "Kurl", "given": "Sudhir", "initials": "S"}, {"family": "Lyall", "given": "Donald M", "initials": "DM"}, {"family": "Lyall", "given": "Laura M", "initials": "LM"}, {"family": "Pell", "given": "Jill P", "initials": "JP"}, {"family": "Pirro", "given": "Matteo", "initials": "M"}, {"family": "Savonen", "given": "Kai", "initials": "K"}, {"family": "Smit", "given": "Andries J", "initials": "AJ"}, {"family": "Tremoli", "given": "Elena", "initials": "E"}, {"family": "Tomainen", "given": "Tomi-Pekka", "initials": "T"}, {"family": "Veglia", "given": "Fabrizio", "initials": "F"}, {"family": "Ward", "given": "Joey", "initials": "J"}, {"family": "Sennblad", "given": "Bengt", "initials": "B"}, {"family": "Smith", "given": "Daniel J", "initials": "DJ"}], "type": "journal article", "published": "2021-01-12", "journal": {"title": "Sci Rep", "issn": "2045-2322", "issn-l": "2045-2322", "volume": "11", "issue": "1", "pages": "632"}, "abstract": "Understanding why individuals with severe mental illness (Schizophrenia, Bipolar Disorder and Major Depressive Disorder) have increased risk of cardiometabolic disease (including obesity, type 2 diabetes and cardiovascular disease), and identifying those at highest risk of cardiometabolic disease are important priority areas for researchers. For individuals with European ancestry we explored whether genetic variation could identify sub-groups with different metabolic profiles. Loci associated with schizophrenia, bipolar disorder and major depressive disorder from previous genome-wide association studies and loci that were also implicated in cardiometabolic processes and diseases were selected. In the IMPROVE study (a high cardiovascular risk sample) and UK Biobank (general population sample) multidimensional scaling was applied to genetic variants implicated in both psychiatric and cardiometabolic disorders. Visual inspection of the resulting plots used to identify distinct clusters. Differences between these clusters were assessed using chi-squared and Kruskall-Wallis tests. In IMPROVE, genetic loci associated with both schizophrenia and cardiometabolic disease (but not bipolar disorder or major depressive disorder) identified three groups of individuals with distinct metabolic profiles. This grouping was replicated within UK Biobank, with somewhat less distinction between metabolic profiles. This work focused on individuals of European ancestry and is unlikely to apply to more genetically diverse populations. Overall, this study provides proof of concept that common biology underlying mental and physical illness may help to stratify subsets of individuals with different cardiometabolic profiles.", "doi": "10.1038/s41598-020-79964-x", "pmid": "33436761", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-020-79964-x"}, {"db": "pmc", "key": "PMC7804422"}], "notes": [], "created": "2021-01-14T11:58:56.919Z", "modified": "2021-12-07T13:38:31.951Z"}, {"entity": "publication", "iuid": "238f626b7a75464994d9f84456327dc7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/238f626b7a75464994d9f84456327dc7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/238f626b7a75464994d9f84456327dc7"}}, "title": "Temporal changes in DNA methylation and RNA expression in a small song bird: within- and between-tissue comparisons.", "authors": [{"family": "Lindner", "given": "Melanie", "initials": "M", "orcid": "0000-0003-2931-265X", "researcher": {"href": "https://publications.scilifelab.se/researcher/cf37b79d5336408fb72f72c29b363a1b.json"}}, {"family": "Verhagen", "given": "Irene", "initials": "I"}, {"family": "Viitaniemi", "given": "Heidi M", "initials": "HM"}, {"family": "Laine", "given": "Veronika N", "initials": "VN"}, {"family": "Visser", "given": "Marcel E", "initials": "ME"}, {"family": "Husby", "given": "Arild", "initials": "A"}, {"family": "van Oers", "given": "Kees", "initials": "K"}], "type": "journal article", "published": "2021-01-07", "journal": {"title": "BMC Genomics", "issn": "1471-2164", "issn-l": "1471-2164", "volume": "22", "issue": "1", "pages": "36"}, "abstract": "DNA methylation is likely a key mechanism regulating changes in gene transcription in traits that show temporal fluctuations in response to environmental conditions. To understand the transcriptional role of DNA methylation we need simultaneous within-individual assessment of methylation changes and gene expression changes over time. Within-individual repeated sampling of tissues, which are essential for trait expression is, however, unfeasible (e.g. specific brain regions, liver and ovary for reproductive timing). Here, we explore to what extend between-individual changes in DNA methylation in a tissue accessible for repeated sampling (red blood cells (RBCs)) reflect such patterns in a tissue unavailable for repeated sampling (liver) and how these DNA methylation patterns are associated with gene expression in such inaccessible tissues (hypothalamus, ovary and liver). For this, 18 great tit (Parus major) females were sacrificed at three time points (n = 6 per time point) throughout the pre-laying and egg-laying period and their blood, hypothalamus, ovary and liver were sampled.\n\nWe simultaneously assessed DNA methylation changes (via reduced representation bisulfite sequencing) and changes in gene expression (via RNA-seq and qPCR) over time. In general, we found a positive correlation between changes in CpG site methylation in RBCs and liver across timepoints. For CpG sites in close proximity to the transcription start site, an increase in RBC methylation over time was associated with a decrease in the expression of the associated gene in the ovary. In contrast, no such association with gene expression was found for CpG site methylation within the gene body or the 10 kb up- and downstream regions adjacent to the gene body.\n\nTemporal changes in DNA methylation are largely tissue-general, indicating that changes in RBC methylation can reflect changes in DNA methylation in other, often less accessible, tissues such as the liver in our case. However, associations between temporal changes in DNA methylation with changes in gene expression are mostly tissue- and genomic location-dependent. The observation that temporal changes in DNA methylation within RBCs can relate to changes in gene expression in less accessible tissues is important for a better understanding of how environmental conditions shape traits that temporally change in expression in wild populations.", "doi": "10.1186/s12864-020-07329-9", "pmid": "33413102", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1186/s12864-020-07329-9"}, {"db": "pmc", "key": "PMC7792223"}], "notes": [], "created": "2021-02-22T10:20:10.020Z", "modified": "2024-01-16T13:48:40.957Z"}, {"entity": "publication", "iuid": "48f74c2afc0b4af8befb22016e4d7b0c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/48f74c2afc0b4af8befb22016e4d7b0c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/48f74c2afc0b4af8befb22016e4d7b0c"}}, "title": "Sex-dimorphic genetic effects and novel loci for fasting glucose and insulin variability.", "authors": [{"family": "Lagou", "given": "Vasiliki", "initials": "V"}, {"family": "M\u00e4gi", "given": "Reedik", "initials": "R"}, {"family": "Hottenga", "given": "Jouke- Jan", "initials": "JJ", "orcid": "0000-0002-5668-2368", "researcher": {"href": "https://publications.scilifelab.se/researcher/75553b594b1f4255833de730f7f7d170.json"}}, {"family": "Grallert", "given": "Harald", "initials": "H"}, {"family": "Perry", "given": "John R B", "initials": "JRB"}, {"family": "Bouatia-Naji", "given": "Nabila", "initials": "N", "orcid": "0000-0001-5424-2134", "researcher": {"href": "https://publications.scilifelab.se/researcher/a4f7af2cb2b7464abddf05692a292fc3.json"}}, {"family": "Marullo", "given": "Letizia", "initials": "L"}, {"family": "Rybin", "given": "Denis", "initials": "D"}, {"family": "Jansen", "given": "Rick", "initials": "R", "orcid": "0000-0002-3333-6737", "researcher": {"href": "https://publications.scilifelab.se/researcher/bcd392c9b9784ebe8c8730e05463377a.json"}}, {"family": "Min", "given": "Josine L", "initials": "JL", "orcid": "0000-0003-4456-9824", "researcher": {"href": "https://publications.scilifelab.se/researcher/5896cbc0cb8d427a954b194839adda52.json"}}, {"family": "Dimas", "given": "Antigone S", "initials": "AS"}, {"family": "Ulrich", "given": "Anna", "initials": "A"}, {"family": "Zudina", "given": "Liudmila", "initials": "L"}, {"family": "G\u00e5din", "given": "Jesper R", "initials": "JR"}, {"family": "Jiang", "given": "Longda", "initials": "L"}, {"family": "Faggian", "given": "Alessia", "initials": "A", "orcid": "0000-0002-3799-9722", "researcher": {"href": "https://publications.scilifelab.se/researcher/e4f320f96474406c82fef88f1f78dd23.json"}}, {"family": "Bonnefond", "given": "Am\u00e9lie", "initials": "A", "orcid": "0000-0001-9976-3005", "researcher": {"href": "https://publications.scilifelab.se/researcher/ea1984308c1544ba969d4df73971de69.json"}}, {"family": "Fadista", "given": "Joao", "initials": "J"}, {"family": "Stathopoulou", "given": "Maria G", "initials": "MG"}, {"family": "Isaacs", "given": "Aaron", "initials": "A", "orcid": "0000-0001-5037-4834", "researcher": {"href": "https://publications.scilifelab.se/researcher/38ebe49e62404f48bcb979d9671883e7.json"}}, {"family": "Willems", "given": "Sara M", "initials": "SM", "orcid": "0000-0002-6803-3007", "researcher": {"href": "https://publications.scilifelab.se/researcher/307c8a9b3ab54ab586c7b000c110e76b.json"}}, {"family": "Navarro", "given": "Pau", "initials": "P", "orcid": "0000-0001-5576-8584", "researcher": {"href": "https://publications.scilifelab.se/researcher/9420946aedec4a7b8925cc05c0a9abeb.json"}}, {"family": "Tanaka", "given": "Toshiko", "initials": "T"}, {"family": "Jackson", "given": "Anne U", "initials": "AU", "orcid": "0000-0002-9672-2547", "researcher": {"href": "https://publications.scilifelab.se/researcher/b8230afabb0b4dcda8dc58ead349aea0.json"}}, {"family": "Montasser", "given": "May E", "initials": "ME"}, {"family": "O'Connell", "given": "Jeff R", "initials": "JR"}, {"family": "Bielak", "given": "Lawrence F", "initials": "LF", "orcid": "0000-0002-3443-8030", "researcher": {"href": "https://publications.scilifelab.se/researcher/d1934e3543f14cbe83b95d1c1c3e24c7.json"}}, {"family": "Webster", "given": "Rebecca J", "initials": "RJ"}, {"family": "Saxena", "given": "Richa", "initials": "R", "orcid": "0000-0003-2233-1065", "researcher": {"href": "https://publications.scilifelab.se/researcher/a974c0165c8c4e79b5773f98dcd2ce0e.json"}}, {"family": "Stafford", "given": "Jeanette M", "initials": "JM"}, {"family": "Pourcain", "given": "Beate St", "initials": "BS"}, {"family": "Timpson", "given": "Nicholas J", "initials": "NJ"}, {"family": "Salo", "given": "Perttu", "initials": "P"}, {"family": "Shin", "given": "So-Youn", "initials": "SY"}, {"family": "Amin", "given": "Najaf", "initials": "N"}, {"family": "Smith", "given": "Albert V", "initials": "AV", "orcid": "0000-0003-1942-5845", "researcher": {"href": "https://publications.scilifelab.se/researcher/7b28739aa7d746718d670363d7c18a40.json"}}, {"family": "Li", "given": "Guo", "initials": "G"}, {"family": "Verweij", "given": "Niek", "initials": "N", "orcid": "0000-0002-4303-7685", "researcher": {"href": "https://publications.scilifelab.se/researcher/7306319d42a640a483b937de588a17a4.json"}}, {"family": "Goel", "given": "Anuj", "initials": "A", "orcid": "0000-0003-2307-4021", "researcher": {"href": "https://publications.scilifelab.se/researcher/0f16d9d2e2164938a12b027326c21316.json"}}, {"family": "Ford", "given": "Ian", "initials": "I"}, {"family": "Johnson", "given": "Paul C D", "initials": "PCD", "orcid": "0000-0001-6663-7520", "researcher": {"href": "https://publications.scilifelab.se/researcher/5d7b476aaf134a44862c87b7a6e6ee27.json"}}, {"family": "Johnson", "given": "Toby", "initials": "T"}, {"family": "Kapur", "given": "Karen", "initials": "K"}, {"family": "Thorleifsson", "given": "Gudmar", "initials": "G"}, {"family": "Strawbridge", "given": "Rona J", "initials": "RJ", "orcid": "0000-0001-8506-3585", "researcher": {"href": "https://publications.scilifelab.se/researcher/8ac5060a3b37466dae002d4ad8f4d0ac.json"}}, {"family": "Rasmussen-Torvik", "given": "Laura J", "initials": "LJ"}, {"family": "Esko", "given": "T\u00f5nu", "initials": "T"}, {"family": "Mihailov", "given": "Evelin", "initials": "E"}, {"family": "Fall", "given": "Tove", "initials": "T", "orcid": "0000-0003-2071-5866", "researcher": {"href": "https://publications.scilifelab.se/researcher/4ed3f066719f43b291743a8bdaf3d2a0.json"}}, {"family": "Fraser", "given": "Ross M", "initials": "RM", "orcid": "0000-0003-0488-2592", "researcher": {"href": "https://publications.scilifelab.se/researcher/cf6c3a799fdb4fc18d45ae47cfaa1daa.json"}}, {"family": "Mahajan", "given": "Anubha", "initials": "A"}, {"family": "Kanoni", "given": "Stavroula", "initials": "S", "orcid": "0000-0002-1691-9615", "researcher": {"href": "https://publications.scilifelab.se/researcher/95f9c5fce1fe44719ef772eda9a4f5e4.json"}}, {"family": "Giedraitis", "given": "Vilmantas", "initials": "V", "orcid": "0000-0003-3423-2021", "researcher": {"href": "https://publications.scilifelab.se/researcher/7c95879213664e00b66aeee2e8ece975.json"}}, {"family": "Kleber", "given": "Marcus E", "initials": "ME", "orcid": "0000-0003-0663-7275", "researcher": {"href": "https://publications.scilifelab.se/researcher/a51175112cfb4721b8c9fbfdc71c4307.json"}}, {"family": "Silbernagel", "given": "G\u00fcnther", "initials": "G"}, {"family": "Meyer", "given": "Julia", "initials": "J"}, {"family": "M\u00fcller-Nurasyid", "given": "Martina", "initials": "M", "orcid": "0000-0003-3793-5910", "researcher": {"href": "https://publications.scilifelab.se/researcher/4d21299bb41343f88142255e64a9da57.json"}}, {"family": "Ganna", "given": "Andrea", "initials": "A"}, {"family": "Sarin", "given": "Antti-Pekka", "initials": "AP"}, {"family": "Yengo", "given": "Loic", "initials": "L"}, {"family": "Shungin", "given": "Dmitry", "initials": "D"}, {"family": "Luan", "given": "Jian'an", "initials": "J", "orcid": "0000-0003-3137-6337", "researcher": {"href": "https://publications.scilifelab.se/researcher/7f0ea409f1a2462dbb1b266db8fcc33a.json"}}, {"family": "Horikoshi", "given": "Momoko", "initials": "M"}, {"family": "An", "given": "Ping", "initials": "P"}, {"family": "Sanna", "given": "Serena", "initials": "S", "orcid": "0000-0002-3768-1749", "researcher": {"href": "https://publications.scilifelab.se/researcher/7ecc352ae9264e3e9aaf58d2b1455ed0.json"}}, {"family": "Boettcher", "given": "Yvonne", "initials": "Y"}, {"family": "Rayner", "given": "N William", "initials": "NW"}, {"family": "Nolte", "given": "Ilja M", "initials": "IM", "orcid": "0000-0001-5047-4077", "researcher": {"href": 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"Rainer", "initials": "R"}, {"family": "Bandinelli", "given": "Stefania", "initials": "S"}, {"family": "Thorand", "given": "Barbara", "initials": "B", "orcid": "0000-0002-8416-6440", "researcher": {"href": "https://publications.scilifelab.se/researcher/728e3c1b330242baad2b08714ddc290e.json"}}, {"family": "Liu", "given": "Yongmei", "initials": "Y"}, {"family": "Miljkovic", "given": "Iva", "initials": "I"}, {"family": "Lind", "given": "Lars", "initials": "L"}, {"family": "Doney", "given": "Alex", "initials": "A"}, {"family": "Perola", "given": "Markus", "initials": "M"}, {"family": "Hingorani", "given": "Aroon", "initials": "A", "orcid": "0000-0001-8365-0081", "researcher": {"href": "https://publications.scilifelab.se/researcher/4fb817248c594f0288ff949c5195ad7f.json"}}, {"family": "Kivimaki", "given": "Mika", "initials": "M", "orcid": "0000-0002-4699-5627", "researcher": {"href": "https://publications.scilifelab.se/researcher/6f81f2fb70b14197829de8cd819ceaa6.json"}}, {"family": "Kumari", "given": "Meena", "initials": "M"}, {"family": "Bennett", "given": "Amanda J", "initials": "AJ"}, {"family": "Groves", "given": "Christopher J", "initials": "CJ"}, {"family": "Herder", "given": "Christian", "initials": "C"}, {"family": "Koistinen", "given": "Heikki A", "initials": "HA", "orcid": "0000-0001-7870-070X", "researcher": {"href": "https://publications.scilifelab.se/researcher/c57dc904034d47a8b43d6cae1b1bd6f4.json"}}, {"family": "Kinnunen", "given": "Leena", "initials": "L"}, {"family": "Faire", "given": "Ulf de", "initials": "U"}, {"family": "Bakker", "given": "Stephan J L", "initials": "SJL", "orcid": "0000-0003-3356-6791", "researcher": {"href": "https://publications.scilifelab.se/researcher/80180035048c45bf90b2e5f4460d1fe7.json"}}, {"family": "Uusitupa", "given": "Matti", "initials": "M"}, {"family": "Palmer", "given": "Colin N A", "initials": "CNA", "orcid": "0000-0002-6415-6560", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a0f019dcb7a453a84480953a5514dd5.json"}}, {"family": "Jukema", "given": "J Wouter", "initials": "JW", "orcid": "0000-0002-3246-8359", "researcher": {"href": "https://publications.scilifelab.se/researcher/0479b794031d4df7bed96340b3470c19.json"}}, {"family": "Sattar", "given": "Naveed", "initials": "N", "orcid": "0000-0002-1604-2593", "researcher": {"href": "https://publications.scilifelab.se/researcher/80fbc7cdcfc444acb066449f80f87181.json"}}, {"family": "Pouta", "given": "Anneli", "initials": "A"}, {"family": "Snieder", "given": "Harold", "initials": "H", "orcid": "0000-0003-1949-2298", "researcher": {"href": "https://publications.scilifelab.se/researcher/e9276827839a4f3cb50dcaa2ad4708a5.json"}}, {"family": "Boerwinkle", "given": "Eric", "initials": "E"}, {"family": "Pankow", "given": "James S", "initials": "JS"}, {"family": "Magnusson", "given": "Patrik K", "initials": "PK", "orcid": "0000-0002-7315-7899", "researcher": {"href": 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"initials": "JB", "orcid": "0000-0002-2439-2657", "researcher": {"href": "https://publications.scilifelab.se/researcher/32bc078bf52f4880be4876f073358d8d.json"}}, {"family": "Hovingh", "given": "G Kees", "initials": "GK"}, {"family": "Lindstr\u00f6m", "given": "Jaana", "initials": "J"}, {"family": "Wilson", "given": "James F", "initials": "JF", "orcid": "0000-0001-5751-9178", "researcher": {"href": "https://publications.scilifelab.se/researcher/b39e6e0f7210494cb4f80be0f7413b6f.json"}}, {"family": "Wright", "given": "Alan F", "initials": "AF"}, {"family": "Dedoussis", "given": "George V", "initials": "GV"}, {"family": "Bornstein", "given": "Stefan R", "initials": "SR"}, {"family": "Schwarz", "given": "Peter E H", "initials": "PEH", "orcid": "0000-0001-6317-7880", "researcher": {"href": "https://publications.scilifelab.se/researcher/6181d1a3da134b198d0bfd2fcd714561.json"}}, {"family": "T\u00f6njes", "given": "Anke", "initials": "A"}, {"family": "Winkelmann", "given": "Bernhard R", "initials": "BR"}, {"family": "Boehm", "given": "Bernhard O", "initials": "BO", "orcid": "0000-0002-2706-7710", "researcher": {"href": "https://publications.scilifelab.se/researcher/6dc879a5f8c1472fa0e1dc312a415e07.json"}}, {"family": "M\u00e4rz", "given": "Winfried", "initials": "W"}, {"family": "Metspalu", "given": "Andres", "initials": "A", "orcid": "0000-0002-3718-796X", "researcher": {"href": "https://publications.scilifelab.se/researcher/fd553a77a5a54258b4a4701f0e70a3f8.json"}}, {"family": "Price", "given": "Jackie F", "initials": "JF"}, {"family": "Deloukas", "given": "Panos", "initials": "P", "orcid": "0000-0001-9251-070X", "researcher": {"href": "https://publications.scilifelab.se/researcher/eb59dbd2f2204d41b801c41188611a9e.json"}}, {"family": "K\u00f6rner", "given": "Antje", "initials": "A", "orcid": "0000-0001-6001-0356", "researcher": {"href": "https://publications.scilifelab.se/researcher/1a5c730b0994413b95501b84717f8999.json"}}, {"family": "Lakka", "given": "Timo A", "initials": "TA"}, {"family": "Keinanen-Kiukaanniemi", "given": "Sirkka M", "initials": "SM"}, {"family": "Saaristo", "given": "Timo E", "initials": "TE"}, {"family": "Bergman", "given": "Richard N", "initials": "RN"}, {"family": "Tuomilehto", "given": "Jaakko", "initials": "J"}, {"family": "Wareham", "given": "Nicholas J", "initials": "NJ", "orcid": "0000-0003-1422-2993", "researcher": {"href": "https://publications.scilifelab.se/researcher/176d8605b9ac4ecbbd5c197335769814.json"}}, {"family": "Langenberg", "given": "Claudia", "initials": "C", "orcid": "0000-0002-5017-7344", "researcher": {"href": "https://publications.scilifelab.se/researcher/ca19370bb4d6437aa9df3905db9d3dd2.json"}}, {"family": "M\u00e4nnist\u00f6", "given": "Satu", "initials": "S", "orcid": "0000-0002-8668-3046", "researcher": {"href": "https://publications.scilifelab.se/researcher/63bf4bbef4b24e738d64cef445a9ff81.json"}}, {"family": "Franks", "given": "Paul W", "initials": "PW", "orcid": "0000-0002-0520-7604", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ebbf40c0f7e49dd8c75a2b6cbf27276.json"}}, {"family": "Hayward", "given": "Caroline", "initials": "C", "orcid": "0000-0002-9405-9550", "researcher": {"href": "https://publications.scilifelab.se/researcher/cd49e9ad5a024c7ca2f1aa97d9e58eba.json"}}, {"family": "Vitart", "given": "Veronique", "initials": "V", "orcid": "0000-0002-4991-3797", "researcher": {"href": "https://publications.scilifelab.se/researcher/0ca9835a494849af861673bf7989b523.json"}}, {"family": "Kaprio", "given": "Jaakko", "initials": "J", "orcid": "0000-0002-3716-2455", "researcher": {"href": "https://publications.scilifelab.se/researcher/814d362333844b72a70cba9ebcf61e6f.json"}}, {"family": "Visvikis-Siest", "given": "Sophie", "initials": "S", "orcid": "0000-0001-8104-8425", "researcher": {"href": "https://publications.scilifelab.se/researcher/c289bef4e6a44aa3a26755f7ed69e9e3.json"}}, {"family": "Balkau", "given": "Beverley", "initials": "B"}, {"family": "Altshuler", "given": "David", "initials": "D", "orcid": "0000-0002-7250-4107", "researcher": {"href": "https://publications.scilifelab.se/researcher/79e8e052a1f7417eadb0c85da8d2e0ba.json"}}, {"family": "Rudan", "given": "Igor", "initials": "I", "orcid": "0000-0001-6993-6884", "researcher": {"href": "https://publications.scilifelab.se/researcher/d50e1ca836e841f8a7a748ae93b59d75.json"}}, {"family": "Stumvoll", "given": "Michael", "initials": "M"}, {"family": "Campbell", "given": "Harry", "initials": "H"}, {"family": "van Duijn", "given": "Cornelia M", "initials": "CM", "orcid": "0000-0002-2374-9204", "researcher": {"href": "https://publications.scilifelab.se/researcher/354ccf94e95f40da96e61c89a0a60adb.json"}}, {"family": "Gieger", "given": "Christian", "initials": "C"}, {"family": "Illig", "given": "Thomas", "initials": "T"}, {"family": "Ferrucci", "given": "Luigi", "initials": "L"}, {"family": "Pedersen", "given": "Nancy L", "initials": "NL"}, {"family": "Pramstaller", "given": "Peter P", "initials": "PP", "orcid": "0000-0002-9831-8302", "researcher": {"href": "https://publications.scilifelab.se/researcher/02acd0fde415409d89da96014b493c84.json"}}, {"family": "Boehnke", "given": "Michael", "initials": "M", "orcid": "0000-0002-6442-7754", "researcher": {"href": "https://publications.scilifelab.se/researcher/b8cb72bdcea4492199a1b9d8ac406ac7.json"}}, {"family": "Frayling", "given": "Timothy M", "initials": "TM", "orcid": "0000-0001-8362-2603", "researcher": {"href": "https://publications.scilifelab.se/researcher/9722f7f6f1d546ebb8deaddfc21cdb10.json"}}, {"family": "Shuldiner", "given": "Alan R", "initials": "AR"}, {"family": "Peyser", "given": "Patricia A", "initials": "PA", "orcid": "0000-0002-9717-8459", "researcher": {"href": "https://publications.scilifelab.se/researcher/3ceeb9094357401e8a8702cb3dc53493.json"}}, {"family": "Kardia", "given": "Sharon L R", "initials": "SLR"}, {"family": "Palmer", "given": "Lyle J", "initials": "LJ"}, {"family": "Penninx", "given": "Brenda W", "initials": "BW"}, {"family": "Meneton", "given": "Pierre", "initials": "P"}, {"family": "Harris", "given": "Tamara B", "initials": "TB"}, {"family": "Navis", "given": "Gerjan", "initials": "G"}, {"family": "Harst", "given": "Pim van der", "initials": "PV", "orcid": "0000-0002-2713-686X", "researcher": {"href": "https://publications.scilifelab.se/researcher/a710eb0e12344e8fb5083599c95a1b2e.json"}}, {"family": "Smith", "given": "George Davey", "initials": "GD", "orcid": "0000-0002-1407-8314", "researcher": {"href": "https://publications.scilifelab.se/researcher/0790d5850377432087ad3900af0044e0.json"}}, {"family": "Forouhi", "given": "Nita G", "initials": "NG", "orcid": "0000-0002-5041-248X", "researcher": {"href": "https://publications.scilifelab.se/researcher/fb6627349ae8472fb738cbe8ae01c838.json"}}, {"family": "Loos", "given": "Ruth J F", "initials": "RJF", "orcid": "0000-0002-8532-5087", "researcher": {"href": "https://publications.scilifelab.se/researcher/e5b6c24c302d42828806076ded81afe1.json"}}, {"family": "Salomaa", "given": "Veikko", "initials": "V", "orcid": "0000-0001-7563-5324", "researcher": {"href": "https://publications.scilifelab.se/researcher/f2396c578c254e39b66538c3033c9ce9.json"}}, {"family": "Soranzo", "given": "Nicole", "initials": "N", "orcid": "0000-0003-1095-3852", "researcher": {"href": "https://publications.scilifelab.se/researcher/da75fa9ee333474fad5aadcb99a63d8f.json"}}, {"family": "Boomsma", "given": "Dorret I", "initials": "DI", "orcid": "0000-0002-7099-7972", "researcher": {"href": "https://publications.scilifelab.se/researcher/4b66ab2525fd4a468e7a4ad14c955cb4.json"}}, {"family": "Groop", "given": "Leif", "initials": "L", "orcid": "0000-0002-0187-3263", "researcher": {"href": "https://publications.scilifelab.se/researcher/8e1c35ae04cd4e9e9525fbc844d15e14.json"}}, {"family": "Tuomi", "given": "Tiinamaija", "initials": "T", "orcid": "0000-0002-8306-6202", "researcher": {"href": "https://publications.scilifelab.se/researcher/19f5ce9936ca454c85f0af966acac5c0.json"}}, {"family": "Hofman", "given": "Albert", "initials": "A"}, {"family": "Munroe", "given": "Patricia B", "initials": "PB", "orcid": "0000-0002-4176-2947", "researcher": {"href": "https://publications.scilifelab.se/researcher/657544a7f921459f926aae5cd0e2065c.json"}}, {"family": "Gudnason", "given": "Vilmundur", "initials": "V", "orcid": "0000-0001-5696-0084", "researcher": {"href": "https://publications.scilifelab.se/researcher/d18327939c1541acba054b2340ac174f.json"}}, {"family": "Siscovick", "given": "David S", "initials": "DS"}, {"family": "Watkins", "given": "Hugh", "initials": "H"}, {"family": "Lecoeur", "given": "Cecile", "initials": "C", "orcid": "0000-0003-0075-6417", "researcher": {"href": "https://publications.scilifelab.se/researcher/f6abf12d60c24032a1c2b315904b0721.json"}}, {"family": "Vollenweider", "given": "Peter", "initials": "P"}, {"family": "Franco-Cereceda", "given": "Anders", "initials": "A"}, {"family": "Eriksson", "given": "Per", "initials": "P"}, {"family": "Jarvelin", "given": "Marjo-Riitta", "initials": "MR", "orcid": "0000-0002-2149-0630", "researcher": {"href": "https://publications.scilifelab.se/researcher/a7d00b649d284101b0501e2024fb651a.json"}}, {"family": "Stefansson", "given": "Kari", "initials": "K", "orcid": "0000-0003-1676-864X", "researcher": {"href": "https://publications.scilifelab.se/researcher/679465193fba4887a68e2aec34ccfd8e.json"}}, {"family": "Hamsten", "given": "Anders", "initials": "A"}, {"family": "Nicholson", "given": "George", "initials": "G"}, {"family": "Karpe", "given": "Fredrik", "initials": "F"}, {"family": "Dermitzakis", "given": "Emmanouil T", "initials": "ET", "orcid": "0000-0002-9302-6490", "researcher": {"href": "https://publications.scilifelab.se/researcher/3560d19929e94af1bb858a54e29a10cc.json"}}, {"family": "Lindgren", "given": "Cecilia M", "initials": "CM", "orcid": "0000-0002-4903-9374", "researcher": {"href": "https://publications.scilifelab.se/researcher/822d2f2a99814a7498f19976ed6381ef.json"}}, {"family": "McCarthy", "given": "Mark I", "initials": "MI"}, {"family": "Froguel", "given": "Philippe", "initials": "P", "orcid": "0000-0003-2972-0784", "researcher": {"href": "https://publications.scilifelab.se/researcher/34edc6a0f1b343bb8a2abd439c2ee77f.json"}}, {"family": "Kaakinen", "given": "Marika A", "initials": "MA", "orcid": "0000-0002-9228-0462", "researcher": {"href": "https://publications.scilifelab.se/researcher/0e9f40717fdd4ce29b148bc569134451.json"}}, {"family": "Lyssenko", "given": "Valeriya", "initials": "V"}, {"family": "Watanabe", "given": "Richard M", "initials": "RM", "orcid": "0000-0003-1015-0531", "researcher": {"href": "https://publications.scilifelab.se/researcher/a4336f8845ac40dfb77ef0ea1a97bbd6.json"}}, {"family": "Ingelsson", "given": "Erik", "initials": "E", "orcid": "0000-0003-2256-6972", "researcher": {"href": "https://publications.scilifelab.se/researcher/689bc741ea6547d18de7080c84d0193e.json"}}, {"family": "Florez", "given": "Jose C", "initials": "JC"}, {"family": "Dupuis", "given": "Jos\u00e9e", "initials": "J", "orcid": "0000-0003-2871-3603", "researcher": {"href": "https://publications.scilifelab.se/researcher/c9edfafda7364890866115f5343a9583.json"}}, {"family": "Barroso", "given": "In\u00eas", "initials": "I", "orcid": "0000-0001-5800-4520", "researcher": {"href": "https://publications.scilifelab.se/researcher/c2dc6be9aa194bdc9a161e551d5e6747.json"}}, {"family": "Morris", "given": "Andrew P", "initials": "AP"}, {"family": "Prokopenko", "given": "Inga", "initials": "I"}, {"family": "Meta-Analyses of Glucose and Insulin-related traits Consortium (MAGIC)", "given": "", "initials": ""}], "type": "journal article", "published": "2021-01-05", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "12", "issue": "1", "pages": "24", "issn-l": "2041-1723"}, "abstract": "Differences between sexes contribute to variation in the levels of fasting glucose and insulin. Epidemiological studies established a higher prevalence of impaired fasting glucose in men and impaired glucose tolerance in women, however, the genetic component underlying this phenomenon is not established. We assess sex-dimorphic (73,089/50,404 women and 67,506/47,806 men) and sex-combined (151,188/105,056 individuals) fasting glucose/fasting insulin genetic effects via genome-wide association study meta-analyses in individuals of European descent without diabetes. Here we report sex dimorphism in allelic effects on fasting insulin at IRS1 and ZNF12 loci, the latter showing higher RNA expression in whole blood in women compared to men. We also observe sex-homogeneous effects on fasting glucose at seven novel loci. Fasting insulin in women shows stronger genetic correlations than in men with waist-to-hip ratio and anorexia nervosa. Furthermore, waist-to-hip ratio is causally related to insulin resistance in women, but not in men. These results position dissection of metabolic and glycemic health sex dimorphism as a steppingstone for understanding differences in genetic effects between women and men in related phenotypes.", "doi": "10.1038/s41467-020-19366-9", "pmid": "33402679", "labels": {"NGI Stockholm (Genomics Applications)": "Service", "National Genomics Infrastructure": null, "NGI Stockholm (Genomics Production)": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-020-19366-9"}, {"db": "pmc", "key": "PMC7785747"}], "notes": [], "created": "2021-01-08T16:30:26.062Z", "modified": "2021-11-10T12:27:48.827Z"}, {"entity": "publication", "iuid": "745edbeac38442aab206d775976a0101", "links": {"self": {"href": "https://publications.scilifelab.se/publication/745edbeac38442aab206d775976a0101.json"}, "display": {"href": "https://publications.scilifelab.se/publication/745edbeac38442aab206d775976a0101"}}, "title": "Post-treatment of dewatered digested sewage sludge by thermophilic high-solid digestion for pasteurization with positive energy output.", "authors": [{"family": "Nordell", "given": "E", "initials": "E"}, {"family": "Moestedt", "given": "J", "initials": "J"}, {"family": "\u00d6sterman", "given": "J", "initials": "J"}, {"family": "Shakeri Yekta", "given": "S", "initials": "S"}, {"family": "Bj\u00f6rn", "given": "A", "initials": "A"}, {"family": "Sun", "given": "L", "initials": "L"}, {"family": "Schn\u00fcrer", "given": "A", "initials": "A"}], "type": "journal article", "published": "2021-01-01", "journal": {"title": "Waste Management", "issn": "1879-2456", "volume": "119", "issue": null, "pages": "11-21", "issn-l": null}, "abstract": "This study investigated the possibility to use thermophilic anaerobic high solid digestion of dewatered digested sewage sludge (DDS) at a wastewater treatment plant (WWTP) as a measure to increase total methane yield, achieve pasteurization and reduce risk for methane emissions during storage of the digestate. A pilot-scale plug-flow reactor was used to mimic thermophilic post-treatment of DDS from a WWTP in Link\u00f6ping, Sweden. Process operation was evaluated with respect to biogas process performance, using both chemical and microbiological parameters. Initially, the process showed disturbance, with low methane yields and high volatile fatty acid (VFA) accumulation. However, after initiation of digestate recirculation performance improved and the specific methane production reached 46 mL CH4/g VS. Plug flow conditions were assessed with lithium chloride and the hydraulic retention time (HRT) was determined to be 19-29 days, sufficient to reach successful pasteurization. Degradation rate of raw protein was high and resulted in ammonia-nitrogen levels of up to 2.0 g/L and a 30% lower protein content in the digestate as compared to DDS. Microbial analysis suggested a shift in the methane producing pathway, with dominance of syntrophic acetate oxidation and the candidate methanogen family WSA2 by the end of the experiment. Energy balance calculations based on annual DDS production of 10000 ton/year showed that introduction of high-solid digestion as a post-treatment and pasteurization method would result in a positive energy output of 340 MWh/year. Post-digestion of DDS also decreased residual methane potential (RMP) by>96% compared with fresh DDS.", "doi": "10.1016/j.wasman.2020.09.028", "pmid": "33032154", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "S0956-053X(20)30539-0"}], "notes": [], "created": "2020-12-08T23:47:20.252Z", "modified": "2024-01-16T13:48:40.973Z"}, {"entity": "publication", "iuid": "0c0a09fa1f2f4f30be673fd70f9a329e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0c0a09fa1f2f4f30be673fd70f9a329e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0c0a09fa1f2f4f30be673fd70f9a329e"}}, "title": "Variable degree of mosaicism for tetrasomy 18p in phenotypically discordant monozygotic twins-Diagnostic implications.", "authors": [{"family": "Rydzanicz", "given": "Ma\u0142gorzata", "initials": "M", "orcid": "0000-0002-6969-0535", "researcher": {"href": "https://publications.scilifelab.se/researcher/a7b97ebd34ea401fb9643a0023e5c21d.json"}}, {"family": "Olszewski", "given": "Pawel", "initials": "P", "orcid": "0000-0002-2788-5254", "researcher": {"href": "https://publications.scilifelab.se/researcher/214b8864edb24164a1c9af68396603b9.json"}}, {"family": "Kedra", "given": "Darek", "initials": "D"}, {"family": "Davies", "given": "Hanna", "initials": "H"}, {"family": "Filipowicz", "given": "Natalia", "initials": "N"}, {"family": "Bruhn-Olszewska", "given": "Bozena", "initials": "B", "orcid": "0000-0003-2141-0247", "researcher": {"href": "https://publications.scilifelab.se/researcher/0fa96509bbe94834858aee3c16d41b97.json"}}, {"family": "Cavalli", "given": "Marco", "initials": "M"}, {"family": "Szcza\u0142uba", "given": "Krzysztof", "initials": "K", "orcid": "0000-0001-8803-646X", "researcher": {"href": "https://publications.scilifelab.se/researcher/4081a7a9da154a4a9e90a77dc5f04e77.json"}}, {"family": "M\u0142ynek", "given": "Marlena", "initials": "M"}, {"family": "Machnicki", "given": "Marcin M", "initials": "MM"}, {"family": "Stawi\u0144ski", "given": "Piotr", "initials": "P"}, {"family": "Kostrzewa", "given": "Gra\u017cyna", "initials": "G"}, {"family": "Krajewski", "given": "Pawe\u0142", "initials": "P"}, {"family": "\u015aladowski", "given": "Dariusz", "initials": "D"}, {"family": "Chrzanowska", "given": "Krystyna", "initials": "K"}, {"family": "Dumanski", "given": "Jan P", "initials": "JP", "orcid": "0000-0002-1489-1452", "researcher": {"href": "https://publications.scilifelab.se/researcher/15b14282209342cfa9c82cdbf02999f6.json"}}, {"family": "P\u0142oski", "given": "Rafa\u0142", "initials": "R", "orcid": "0000-0001-6286-5526", "researcher": {"href": "https://publications.scilifelab.se/researcher/04da42bc8a91436f91fcbf3b9f3d3d0e.json"}}], "type": "case reports", "published": "2021-01-00", "journal": {"title": "Mol Genet Genomic Med", "issn": "2324-9269", "volume": "9", "issue": "1", "pages": "e1526", "issn-l": "2324-9269"}, "abstract": "Phenotypically discordant monozygotic twins (PDMZTs) offer a unique opportunity to study post-zygotic genetic variation and provide insights into the linkage between genotype and phenotype. We report a comprehensive analysis of a pair of PDMZTs.\n\nDysmorphic features and delayed neuro-motor development were observed in the proband, whereas her twin sister was phenotypically normal. Four tissues (blood, skin, hair follicles, and buccal mucosa) from both twins were studied using four complementary methods, including whole-exome sequencing, karyotyping, array CGH, and SNP array.\n\nIn the proband, tetrasomy 18p affecting all studied tissues except for blood was identified. Karyotyping of fibroblasts revealed isochromosome 18p [i(18p)] in all metaphases. The corresponding analysis of the phenotypically normal sister surprisingly revealed low-level mosaicism (5.4%) for i(18p) in fibroblasts.\n\nWe emphasize that when mosaicism is suspected, multiple tissues should be studied and we highlight the usefulness of non-invasive sampling of hair follicles and buccal mucosa as a convenient source of non-mesoderm-derived DNA, which complements the analysis of mesoderm using blood. Moreover, low-level mosaic tetrasomy 18p is well tolerated and such low-level mosaicism, readily detected by karyotyping, can be missed by other methods. Finally, mosaicism for low-level tetrasomy 18p might be more common in the general population than it is currently recognized, due to detection limitations.", "doi": "10.1002/mgg3.1526", "pmid": "33319479", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": null, "National Genomics Infrastructure": null, "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC7963419"}], "notes": [], "created": "2020-12-28T17:52:36.852Z", "modified": "2024-01-16T13:48:40.986Z"}, {"entity": "publication", "iuid": "f5bd5ff4af6e4311aaa2b84a04fff62b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f5bd5ff4af6e4311aaa2b84a04fff62b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f5bd5ff4af6e4311aaa2b84a04fff62b"}}, "title": "Urbanization is associated with modifications in DNA methylation in a small passerine bird.", "authors": [{"family": "Watson", "given": "Hannah", "initials": "H", "orcid": "0000-0003-4656-0647", "researcher": {"href": "https://publications.scilifelab.se/researcher/897ef477ef2e4fa290cb67b245bdf3f5.json"}}, {"family": "Powell", "given": "Daniel", "initials": "D", "orcid": "0000-0001-6323-7791", "researcher": {"href": "https://publications.scilifelab.se/researcher/e8bd7fa790f9432d9d61cc1ab8d9b2d8.json"}}, {"family": "Salm\u00f3n", "given": "Pablo", "initials": "P", "orcid": "0000-0001-9718-6611", "researcher": {"href": "https://publications.scilifelab.se/researcher/b60bfa8b60174680a1546f283c2ccbc1.json"}}, {"family": "Jacobs", "given": "Arne", "initials": "A", "orcid": "0000-0001-7635-5447", "researcher": {"href": "https://publications.scilifelab.se/researcher/7c375694c76e48279bdc6e7dcc2808a6.json"}}, {"family": "Isaksson", "given": "Caroline", "initials": "C", "orcid": "0000-0002-6889-1386", "researcher": {"href": "https://publications.scilifelab.se/researcher/30ddbca044f64cb1b1feef58baf539ba.json"}}], "type": "journal article", "published": "2021-01-00", "journal": {"title": "Evol Appl", "issn": "1752-4571", "volume": "14", "issue": "1", "pages": "85-98", "issn-l": "1752-4571"}, "abstract": "Urbanization represents a fierce driver of phenotypic change, yet the molecular mechanisms underlying observed phenotypic patterns are poorly understood. Epigenetic changes are expected to facilitate more rapid adaption to changing or novel environments, such as our towns and cities, compared with slow changes in gene sequence. A comparison of liver and blood tissue from great tits Parus major originating from an urban and a forest site demonstrated that urbanization is associated with variation in genome-wide patterns of DNA methylation. Combining reduced representation bisulphite sequencing with transcriptome data, we revealed habitat differences in DNA methylation patterns that suggest a regulated and coordinated response to the urban environment. In the liver, genomic sites that were differentially methylated between urban- and forest-dwelling birds were over-represented in regulatory regions of the genome and more likely to occur in expressed genes. DNA methylation levels were also inversely correlated with gene expression at transcription start sites. Furthermore, differentially methylated CpG sites, in liver, were over-represented in pathways involved in (i) steroid biosynthesis, (ii) superoxide metabolism, (iii) secondary alcohol metabolism, (iv) chylomicron remodelling, (v) cholesterol transport, (vi) reactive oxygen species (ROS) metabolic process and (vii) epithelial cell proliferation. This corresponds with earlier studies identifying diet and exposure to ROS as two of the main drivers of divergence between organisms in urban and nonurban environments. Conversely, in blood, sites that were differentially methylated between urban- and forest-dwelling birds were under-represented in regulatory regions, more likely to occur in nonexpressed genes and not over-represented in specific biological pathways. It remains to be determined whether diverging patterns of DNA methylation represent adaptive evolutionary responses and whether the conclusions can be more widely attributed to urbanization.", "doi": "10.1111/eva.13160", "pmid": "33519958", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "EVA13160"}, {"db": "pmc", "key": "PMC7819559"}], "notes": [], "created": "2021-02-02T12:30:56.264Z", "modified": "2024-01-16T13:48:40.994Z"}, {"entity": "publication", "iuid": "5974a91775494998a7b205a65b2144cb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5974a91775494998a7b205a65b2144cb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5974a91775494998a7b205a65b2144cb"}}, "title": "Shared genetic risk between eating disorder- and substance-use-related phenotypes: Evidence from genome-wide association studies.", "authors": [{"family": "Munn-Chernoff", "given": "Melissa A", "initials": "MA", "orcid": "0000-0001-9368-9457", "researcher": {"href": "https://publications.scilifelab.se/researcher/e8b163171cb942509337b77f7cd14a61.json"}}, {"family": "Johnson", "given": "Emma C", "initials": "EC"}, {"family": "Chou", "given": "Yi-Ling", "initials": "YL"}, {"family": "Coleman", "given": "Jonathan R I", "initials": "JRI"}, {"family": "Thornton", "given": "Laura M", "initials": "LM"}, {"family": "Walters", "given": "Raymond K", "initials": "RK"}, {"family": "Yilmaz", "given": "Zeynep", "initials": "Z"}, {"family": "Baker", "given": "Jessica H", "initials": "JH"}, {"family": "H\u00fcbel", "given": "Christopher", "initials": "C"}, {"family": "Gordon", "given": "Scott", "initials": "S"}, {"family": "Medland", "given": "Sarah E", "initials": "SE"}, {"family": "Watson", "given": "Hunna J", "initials": "HJ"}, {"family": "Gaspar", "given": "H\u00e9l\u00e9na A", "initials": "HA"}, {"family": "Bryois", "given": "Julien", "initials": "J"}, {"family": "Hinney", "given": "Anke", "initials": "A"}, {"family": "Lepp\u00e4", "given": "Virpi M", "initials": "VM"}, {"family": "Mattheisen", "given": "Manuel", "initials": "M"}, {"family": "Ripke", "given": "Stephan", "initials": "S"}, {"family": "Yao", "given": "Shuyang", "initials": "S"}, {"family": "Giusti-Rodr\u00edguez", "given": "Paola", "initials": "P"}, {"family": "Hanscombe", "given": "Ken B", "initials": "KB"}, {"family": "Adan", "given": "Roger A H", "initials": "RAH"}, {"family": "Alfredsson", "given": "Lars", "initials": "L"}, {"family": "Ando", "given": "Tetsuya", "initials": "T"}, {"family": "Andreassen", "given": "Ole A", "initials": "OA"}, {"family": "Berrettini", "given": "Wade H", "initials": "WH"}, {"family": "Boehm", "given": "Ilka", "initials": "I"}, {"family": "Boni", "given": "Claudette", "initials": "C"}, {"family": "Boraska Perica", "given": "Vesna", "initials": "V"}, {"family": "Buehren", 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"Jessica E", "initials": "JE"}, {"family": "Sanchez-Roige", "given": "Sandra", "initials": "S"}, {"family": "Schwandt", "given": "Melanie", "initials": "M"}, {"family": "Sherva", "given": "Richard", "initials": "R"}, {"family": "Streit", "given": "Fabian", "initials": "F"}, {"family": "Strohmaier", "given": "Jana", "initials": "J"}, {"family": "Thomas", "given": "Nathaniel", "initials": "N"}, {"family": "Wang", "given": "Jen-Chyong", "initials": "JC"}, {"family": "Webb", "given": "Bradley T", "initials": "BT"}, {"family": "Wedow", "given": "Robbee", "initials": "R"}, {"family": "Wetherill", "given": "Leah", "initials": "L"}, {"family": "Wills", "given": "Amanda G", "initials": "AG"}, {"family": "Zhou", "given": "Hang", "initials": "H"}, {"family": "Boardman", "given": "Jason D", "initials": "JD"}, {"family": "Chen", "given": "Danfeng", "initials": "D"}, {"family": "Choi", "given": "Doo-Sup", "initials": "DS"}, {"family": "Copeland", "given": "William E", "initials": "WE"}, {"family": "Culverhouse", "given": "Robert C", "initials": "RC"}, {"family": "Dahmen", "given": "Norbert", "initials": "N"}, {"family": "Degenhardt", "given": "Louisa", "initials": "L"}, {"family": "Domingue", "given": "Benjamin W", "initials": "BW"}, {"family": "Frye", "given": "Mark A", "initials": "MA"}, {"family": "G\u00e4ebel", "given": "Wolfgang", "initials": "W"}, {"family": "Hayward", "given": "Caroline", "initials": "C"}, {"family": "Ising", "given": "Marcus", "initials": "M"}, {"family": "Keyes", "given": "Margaret", "initials": "M"}, {"family": "Kiefer", "given": "Falk", "initials": "F"}, {"family": "Koller", "given": "Gabriele", "initials": "G"}, {"family": "Kramer", "given": "John", "initials": "J"}, {"family": "Kuperman", "given": "Samuel", "initials": "S"}, {"family": "Lucae", "given": "Susanne", "initials": "S"}, {"family": "Lynskey", "given": "Michael T", "initials": "MT"}, {"family": "Maier", "given": "Wolfgang", "initials": "W"}, {"family": "Mann", "given": "Karl", "initials": "K"}, {"family": "M\u00e4nnist\u00f6", "given": "Satu", "initials": "S"}, {"family": "M\u00fcller-Myhsok", "given": "Bertram", "initials": "B"}, {"family": "Murray", "given": "Alison D", "initials": "AD"}, {"family": "Nurnberger", "given": "John I", "initials": "JI"}, {"family": "Preuss", "given": "Ulrich", "initials": "U"}, {"family": "R\u00e4ikk\u00f6nen", "given": "Katri", "initials": "K"}, {"family": "Reynolds", "given": "Maureen D", "initials": "MD"}, {"family": "Ridinger", "given": "Monika", "initials": "M"}, {"family": "Scherbaum", "given": "Norbert", "initials": "N"}, {"family": "Schuckit", "given": "Marc A", "initials": "MA"}, {"family": "Soyka", "given": "Michael", "initials": "M"}, {"family": "Treutlein", "given": "Jens", "initials": "J"}, {"family": "Witt", "given": "Stephanie H", "initials": "SH"}, {"family": "Wodarz", "given": "Norbert", "initials": "N"}, {"family": "Zill", "given": "Peter", "initials": "P"}, {"family": "Adkins", "given": "Daniel E", "initials": "DE"}, {"family": "Boomsma", "given": "Dorret I", "initials": "DI"}, {"family": "Bierut", "given": "Laura J", "initials": "LJ"}, {"family": "Brown", "given": "Sandra A", "initials": "SA"}, {"family": "Bucholz", "given": "Kathleen K", "initials": "KK"}, {"family": "Costello", "given": "E Jane", "initials": "EJ"}, {"family": "de Wit", "given": "Harriet", "initials": "H"}, {"family": "Diazgranados", "given": "Nancy", "initials": "N"}, {"family": "Eriksson", "given": "Johan G", "initials": "JG"}, {"family": "Farrer", "given": "Lindsay A", "initials": "LA"}, {"family": "Foroud", "given": "Tatiana M", "initials": "TM"}, {"family": "Gillespie", "given": "Nathan A", "initials": "NA"}, {"family": "Goate", "given": "Alison M", "initials": "AM"}, {"family": "Goldman", "given": "David", "initials": "D"}, {"family": "Grucza", "given": "Richard A", "initials": "RA"}, {"family": "Hancock", "given": "Dana B", "initials": "DB"}, {"family": "Harris", "given": "Kathleen Mullan", "initials": "KM"}, {"family": "Hesselbrock", "given": "Victor", "initials": "V"}, {"family": "Hewitt", "given": "John K", "initials": "JK"}, {"family": "Hopfer", "given": "Christian J", "initials": "CJ"}, {"family": "Iacono", "given": "William G", "initials": "WG"}, {"family": "Johnson", "given": "Eric O", "initials": "EO"}, {"family": "Karpyak", "given": "Victor M", "initials": "VM"}, {"family": "Kendler", "given": "Kenneth S", "initials": "KS"}, {"family": "Kranzler", "given": "Henry R", "initials": "HR"}, {"family": "Krauter", "given": "Kenneth", "initials": "K"}, {"family": "Lind", "given": "Penelope A", "initials": "PA"}, {"family": "McGue", "given": "Matt", "initials": "M"}, {"family": "MacKillop", "given": "James", "initials": "J"}, {"family": "Madden", "given": "Pamela A F", "initials": "PAF"}, {"family": "Maes", "given": "Hermine H", "initials": "HH"}, {"family": "Magnusson", "given": "Patrik K E", "initials": "PKE"}, {"family": "Nelson", "given": "Elliot C", "initials": "EC"}, {"family": "N\u00f6then", "given": "Markus M", "initials": "MM"}, {"family": "Palmer", "given": "Abraham A", "initials": "AA"}, {"family": "Penninx", "given": "Brenda W J H", "initials": "BWJH"}, {"family": "Porjesz", "given": "Bernice", "initials": "B"}, {"family": "Rice", "given": "John P", "initials": "JP"}, {"family": "Rietschel", "given": "Marcella", "initials": "M"}, {"family": "Riley", "given": "Brien P", "initials": "BP"}, {"family": "Rose", "given": "Richard J", "initials": "RJ"}, {"family": "Shen", "given": "Pei-Hong", "initials": "PH"}, {"family": "Silberg", "given": "Judy", "initials": "J"}, {"family": "Stallings", "given": "Michael C", "initials": "MC"}, {"family": "Tarter", "given": "Ralph E", "initials": "RE"}, {"family": "Vanyukov", "given": "Michael M", "initials": "MM"}, {"family": "Vrieze", "given": "Scott", "initials": "S"}, {"family": "Wall", "given": "Tamara L", "initials": "TL"}, {"family": "Whitfield", "given": "John B", "initials": "JB"}, {"family": "Zhao", "given": "Hongyu", "initials": "H"}, {"family": "Neale", "given": "Benjamin M", "initials": "BM"}, {"family": "Wade", "given": "Tracey D", "initials": "TD"}, {"family": "Heath", "given": "Andrew C", "initials": "AC"}, {"family": "Montgomery", "given": "Grant W", "initials": "GW"}, {"family": "Martin", "given": "Nicholas G", "initials": "NG"}, {"family": "Sullivan", "given": "Patrick F", "initials": "PF"}, {"family": "Kaprio", "given": "Jaakko", "initials": "J"}, {"family": "Breen", "given": "Gerome", "initials": "G"}, {"family": "Gelernter", "given": "Joel", "initials": "J"}, {"family": "Edenberg", "given": "Howard J", "initials": "HJ"}, {"family": "Bulik", "given": "Cynthia M", "initials": "CM"}, {"family": "Agrawal", "given": "Arpana", "initials": "A"}], "type": "journal article", "published": "2021-01-00", "journal": {"title": "Addict Biol", "issn": "1369-1600", "volume": "26", "issue": "1", "pages": "e12880", "issn-l": "1355-6215"}, "abstract": "Eating disorders and substance use disorders frequently co-occur. Twin studies reveal shared genetic variance between liabilities to eating disorders and substance use, with the strongest associations between symptoms of bulimia nervosa and problem alcohol use (genetic correlation [rg ], twin-based = 0.23-0.53). We estimated the genetic correlation between eating disorder and substance use and disorder phenotypes using data from genome-wide association studies (GWAS). Four eating disorder phenotypes (anorexia nervosa [AN], AN with binge eating, AN without binge eating, and a bulimia nervosa factor score), and eight substance-use-related phenotypes (drinks per week, alcohol use disorder [AUD], smoking initiation, current smoking, cigarettes per day, nicotine dependence, cannabis initiation, and cannabis use disorder) from eight studies were included. Significant genetic correlations were adjusted for variants associated with major depressive disorder and schizophrenia. Total study sample sizes per phenotype ranged from ~2400 to ~537 000 individuals. We used linkage disequilibrium score regression to calculate single nucleotide polymorphism-based genetic correlations between eating disorder- and substance-use-related phenotypes. Significant positive genetic associations emerged between AUD and AN (rg = 0.18; false discovery rate q = 0.0006), cannabis initiation and AN (rg = 0.23; q < 0.0001), and cannabis initiation and AN with binge eating (rg = 0.27; q = 0.0016). Conversely, significant negative genetic correlations were observed between three nondiagnostic smoking phenotypes (smoking initiation, current smoking, and cigarettes per day) and AN without binge eating (rgs = -0.19 to -0.23; qs < 0.04). The genetic correlation between AUD and AN was no longer significant after co-varying for major depressive disorder loci. The patterns of association between eating disorder- and substance-use-related phenotypes highlights the potentially complex and substance-specific relationships among these behaviors.", "doi": "10.1111/adb.12880", "pmid": "32064741", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC7429266"}, {"db": "mid", "key": "NIHMS1584390"}], "notes": [], "created": "2020-02-27T09:20:59.551Z", "modified": "2021-11-10T12:53:58.307Z"}, {"entity": "publication", "iuid": "6c96a8f8b09a4910a4aca433f982ec52", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6c96a8f8b09a4910a4aca433f982ec52.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6c96a8f8b09a4910a4aca433f982ec52"}}, "title": "Molecular pathways in patients with systemic lupus erythematosus revealed by gene-centred DNA sequencing.", "authors": [{"family": "Sandling", "given": "Johanna K", "initials": "JK", "orcid": "0000-0003-1382-2321", "researcher": {"href": "https://publications.scilifelab.se/researcher/9c7bae5a05ac47eeac96547ca7336767.json"}}, {"family": "Pucholt", "given": "Pascal", "initials": "P", "orcid": "0000-0003-3342-1373", "researcher": {"href": "https://publications.scilifelab.se/researcher/61a214ff2d494b568cb6da944e858acf.json"}}, {"family": "Hultin Rosenberg", "given": "Lina", "initials": "L"}, {"family": "Farias", "given": "Fabiana H G", "initials": "FHG"}, {"family": "Kozyrev", "given": "Sergey V", "initials": "SV"}, {"family": "Eloranta", "given": "Maija-Leena", "initials": "ML"}, {"family": "Alexsson", "given": "Andrei", "initials": "A"}, {"family": "Bianchi", "given": "Matteo", "initials": "M"}, {"family": "Padyukov", "given": "Leonid", "initials": "L"}, {"family": "Bengtsson", "given": "Christine", "initials": "C"}, {"family": "Jonsson", "given": "Roland", "initials": "R"}, {"family": "Omdal", "given": "Roald", "initials": "R"}, {"family": "Lie", "given": "Benedicte A", "initials": "BA"}, {"family": "Massarenti", "given": "Laura", "initials": "L"}, {"family": "Steffensen", "given": "Rudi", "initials": "R"}, {"family": "Jakobsen", "given": "Marianne A", "initials": "MA"}, {"family": "Lillevang", "given": "S\u00f8ren T", "initials": "ST"}, {"family": "ImmunoArray Development Consortium and DISSECT consortium", "given": "", "initials": ""}, {"family": "Lerang", "given": "Karoline", "initials": "K"}, {"family": "Molberg", "given": "\u00d8yvind", "initials": "\u00d8"}, {"family": "Voss", "given": "Anne", "initials": "A"}, {"family": "Troldborg", "given": "Anne", "initials": "A"}, {"family": "Jacobsen", "given": "S\u00f8ren", "initials": "S"}, {"family": "Syv\u00e4nen", "given": "Ann-Christine", "initials": "AC"}, {"family": "J\u00f6nsen", "given": "Andreas", "initials": "A"}, {"family": "Gunnarsson", "given": "Iva", "initials": "I"}, {"family": "Svenungsson", "given": "Elisabet", "initials": "E", "orcid": "0000-0003-3396-3244", "researcher": {"href": "https://publications.scilifelab.se/researcher/0ab5989c3c604a96bf42b1b6f90434a0.json"}}, {"family": "Rantap\u00e4\u00e4-Dahlqvist", "given": "Solbritt", "initials": "S"}, {"family": "Bengtsson", "given": "Anders A", "initials": "AA"}, {"family": "Sj\u00f6wall", "given": "Christopher", "initials": "C", "orcid": "0000-0003-0900-2048", "researcher": {"href": "https://publications.scilifelab.se/researcher/fe4dd47b8ca1436e8a26fdea33f5e7f6.json"}}, {"family": "Leonard", "given": "Dag", "initials": "D"}, {"family": "Lindblad-Toh", "given": "Kerstin", "initials": "K", "orcid": "0000-0001-8338-0253", "researcher": {"href": "https://publications.scilifelab.se/researcher/e0063145f7d6476f80ab42f94833f4cf.json"}}, {"family": "R\u00f6nnblom", "given": "Lars", "initials": "L", "orcid": "0000-0001-9403-6503", "researcher": {"href": "https://publications.scilifelab.se/researcher/053ed3b657124a1bab3a78dc685556e6.json"}}], "type": "journal article", "published": "2021-01-00", "journal": {"title": "Ann. Rheum. Dis.", "issn": "1468-2060", "issn-l": "0003-4967", "volume": "80", "issue": "1", "pages": "109-117"}, "abstract": "Systemic lupus erythematosus (SLE) is an autoimmune disease with extensive heterogeneity in disease presentation between patients, which is likely due to an underlying molecular diversity. Here, we aimed at elucidating the genetic aetiology of SLE from the immunity pathway level to the single variant level, and stratify patients with SLE into distinguishable molecular subgroups, which could inform treatment choices in SLE.\n\nWe undertook a pathway-centred approach, using sequencing of immunological pathway genes. Altogether 1832 candidate genes were analysed in 958 Swedish patients with SLE and 1026 healthy individuals. Aggregate and single variant association testing was performed, and we generated pathway polygenic risk scores (PRS).\n\nWe identified two main independent pathways involved in SLE susceptibility: T lymphocyte differentiation and innate immunity, characterised by HLA and interferon, respectively. Pathway PRS defined pathways in individual patients, who on average were positive for seven pathways. We found that SLE organ damage was more pronounced in patients positive for the T or B cell receptor signalling pathways. Further, pathway PRS-based clustering allowed stratification of patients into four groups with different risk score profiles. Studying sets of genes with priors for involvement in SLE, we observed an aggregate common variant contribution to SLE at genes previously reported for monogenic SLE as well as at interferonopathy genes.\n\nOur results show that pathway risk scores have the potential to stratify patients with SLE beyond clinical manifestations into molecular subsets, which may have implications for clinical follow-up and therapy selection.", "doi": "10.1136/annrheumdis-2020-218636", "pmid": "33037003", "labels": {"National Genomics Infrastructure": "Collaborative", "NGI Uppsala (SNP&SEQ Technology Platform)": "Collaborative", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC7788061"}, {"db": "pii", "key": "annrheumdis-2020-218636"}], "notes": [], "created": "2020-12-08T23:53:14.678Z", "modified": "2024-01-16T13:48:41.009Z"}, {"entity": "publication", "iuid": "ef732b8cd0214be1887c4a57bb492c04", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ef732b8cd0214be1887c4a57bb492c04.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ef732b8cd0214be1887c4a57bb492c04"}}, "title": "Epigenome-wide cross-tissue correlation of human bone and blood DNA methylation - can blood be used as a surrogate for bone?", "authors": [{"family": "Ebrahimi", "given": "Parvaneh", "initials": "P"}, {"family": "Luthman", "given": "Holger", "initials": "H"}, {"family": "McGuigan", "given": "Fiona E", "initials": "FE", "orcid": "0000-0002-8033-9981", "researcher": {"href": "https://publications.scilifelab.se/researcher/1cf48c3c6f71416799fca5100de388f5.json"}}, {"family": "Akesson", "given": "Kristina E", "initials": "KE"}], "type": "journal article", "published": "2021-01-00", "journal": {"title": "Epigenetics", "issn": "1559-2308", "volume": "16", "issue": "1", "pages": "92-105", "issn-l": "1559-2294"}, "abstract": "Difficulty in obtaining bone tissue is an obstacle to studying epigenetics to understand gene-environment interactions, and their role in disease pathogenesis. Blood is an obvious alternative and in this proof of principle study, our aim was to systematically investigate whether blood is a viable surrogate for bone. We measured epigenome-wide DNA methylation at 850 K CpG sites in matched trabecular bone and peripheral blood collected from the same patients at the same time-point (n = 12 women; 66-85y), to investigate the between-tissue correspondence. What constituted a CpG site with corresponding methylation in both tissues was stringently defined. Only sites highly correlated (r2 > 0.74; FDR q-value <0.05) and at least 80% similarity in methylation level (\u0394\u03b2 <0.2) between paired samples were retained. In total, 28,549 CpG sites were similarly methylated in bone and blood. Between 33% and 49% of loci associated with bone phenotypes through GWAS were represented among these sites, and major pathways relevant to bone regulation were enriched. The results from this study indicate that blood can mirror the bone methylome and capture sites related to bone regulation. This study shows that in principal, peripheral blood is a feasible surrogate for bone tissue in DNA methylation investigations. As the first step, this will provide a platform for future studies in bone epigenetics, and possibly for larger-scale epidemiological studies.", "doi": "10.1080/15592294.2020.1788325", "pmid": "32692944", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support and Infrastructure": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC7889104"}, {"db": "figshare", "key": "10.6084/m9.figshare.12851657.v1"}], "notes": [], "created": "2020-08-04T14:50:03.380Z", "modified": "2021-11-10T12:49:08.153Z"}, {"entity": "publication", "iuid": "68b97a92c535461cb6c041f6d14df2d1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/68b97a92c535461cb6c041f6d14df2d1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/68b97a92c535461cb6c041f6d14df2d1"}}, "title": "Defining eligible patients for allele-selective chemotherapies targeting NAT2 in colorectal cancer.", "authors": [{"family": "Rendo", "given": "Veronica", "initials": "V"}, {"family": "Kundu", "given": "Snehangshu", "initials": "S"}, {"family": "Rameika", "given": "Natallia", "initials": "N"}, {"family": "Ljungstr\u00f6m", "given": "Viktor", "initials": "V"}, {"family": "Svensson", "given": "Richard", "initials": "R"}, {"family": "Palin", "given": "Kimmo", "initials": "K"}, {"family": "Aaltonen", "given": "Lauri", "initials": "L"}, {"family": "Stoimenov", "given": "Ivaylo", "initials": "I"}, {"family": "Sj\u00f6blom", "given": "Tobias", "initials": "T"}], "type": "journal article", "published": "2020-12-31", "journal": {"title": "Sci Rep", "issn": "2045-2322", "issn-l": "2045-2322", "volume": "10", "issue": "1", "pages": "22436"}, "abstract": "Therapies targeting somatic bystander genetic events represent a new avenue for cancer treatment. We recently identified a subset of colorectal cancer (CRC) patients who are heterozygous for a wild-type and a low activity allele (NAT2*6) but lack the wild-type allele in their tumors due to loss of heterozygosity (LOH) at 8p22. These tumors were sensitive to treatment with a cytotoxic substrate of NAT2 (6-(4-aminophenyl)-N-(3,4,5-trimethoxyphenyl)pyrazin-2-amine, APA), and pointed to NAT2 loss being a therapeutically exploitable vulnerability of CRC tumors. To better estimate the total number of treatable CRC patients, we here determined whether tumor cells retaining also other NAT2 low activity variants after LOH respond to APA treatment. The prevalent low activity alleles NAT2*5 and NAT2*14, but not NAT2*7, were found to be low metabolizers with high sensitivity to APA. By analysis of two different CRC patient cohorts, we detected heterozygosity for NAT2 alleles targetable by APA, along with allelic imbalances pointing to LOH, in ~ 24% of tumors. Finally, to haplotype the NAT2 locus in tumor and patient-matched normal samples in a clinical setting, we develop and demonstrate a long-read sequencing based assay. In total, > 79.000 CRC patients per year fulfil genetic criteria for high sensitivity to a NAT2 LOH therapy and their eligibility can be assessed by clinical sequencing.", "doi": "10.1038/s41598-020-80288-z", "pmid": "33384440", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-020-80288-z"}, {"db": "pmc", "key": "PMC7775439"}], "notes": [], "created": "2021-01-08T12:11:29.314Z", "modified": "2024-01-16T13:48:41.098Z"}, {"entity": "publication", "iuid": "f046cb0689f843a8833a93b6acea2080", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f046cb0689f843a8833a93b6acea2080.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f046cb0689f843a8833a93b6acea2080"}}, "title": "You Had Me at \u201cMAGIC\u201d!: Four Barley MAGIC Populations Reveal Novel Resistance QTL for Powdery Mildew", "authors": [{"family": "Novakazi", "given": "Flutur\u00eb", "initials": "F", "orcid": "0000-0001-7151-6811", "researcher": {"href": "https://publications.scilifelab.se/researcher/5812b915262d44e4972483c8314675c3.json"}}, {"family": "Krusell", "given": "Lene", "initials": "L"}, {"family": "Jensen", "given": "Jens", "initials": "J"}, {"family": "Orabi", "given": "Jihad", "initials": "J", "orcid": "0000-0001-9641-6657", "researcher": {"href": "https://publications.scilifelab.se/researcher/ec5965b7edd0413791c990a978f17045.json"}}, {"family": "Jahoor", "given": "Ahmed", "initials": "A"}, {"family": "Bengtsson", "given": "Ther\u00e9se", "initials": "T", "orcid": "0000-0003-4784-1723", "researcher": {"href": "https://publications.scilifelab.se/researcher/0ec4d4a00bcf4fd59113eb264283b92a.json"}}, {"family": null, "given": "", "initials": ""}], "type": "journal-article", "published": "2020-12-18", "journal": {"title": "Genes", "issn": "2073-4425", "issn-l": "2073-4425", "volume": "11", "issue": "12", "pages": "1512"}, "abstract": "Blumeria graminis f. sp. hordei (Bgh), the causal agent of barley powdery mildew (PM), is one of the most important barley leaf diseases and is prevalent in most barley growing regions. Infection decreases grain quality and yields on average by 30%. Multi-parent advanced generation inter-cross (MAGIC) populations combine the advantages of bi-parental and association panels and offer the opportunity to incorporate exotic alleles into adapted material. Here, four barley MAGIC populations consisting of six to eight founders were tested for PM resistance in field trials in Denmark. Principle component and STRUCTURE analysis showed the populations were unstructured and genome-wide linkage disequilibrium (LD) decay varied between 14 and 38 Mbp. Genome-wide association studies (GWAS) identified 11 regions associated with PM resistance located on chromosomes 1H, 2H, 3H, 4H, 5H and 7H, of which three regions are putatively novel resistance quantitative trait locus/loci (QTL). For all regions high-confidence candidate genes were identified that are predicted to be involved in pathogen defense. Haplotype analysis of the significant SNPs revealed new allele combinations not present in the founders and associated with high resistance levels.", "doi": "10.3390/genes11121512", "pmid": "33352820", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC7766815"}, {"db": "pii", "key": "genes11121512"}], "notes": [], "created": "2020-12-28T17:52:37.985Z", "modified": "2023-06-19T11:38:46.230Z"}, {"entity": "publication", "iuid": "e8bf0479495541e6894495b69ec290b8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e8bf0479495541e6894495b69ec290b8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e8bf0479495541e6894495b69ec290b8"}}, "title": "Hodgkin Lymphoma Monozygotic Triplets Reveal Divergences in DNA Methylation Signatures.", "authors": [{"family": "Xia", "given": "Chuanyou", "initials": "C"}, {"family": "Olsen", "given": "Thale Kristin", "initials": "TK"}, {"family": "Zirakzadeh", "given": "A Ali", "initials": "AA"}, {"family": "Almamoun", "given": "Radwa", "initials": "R"}, {"family": "Sj\u00f6holm", "given": "Louise K", "initials": "LK"}, {"family": "Dahlstr\u00f6m", "given": "Jenny", "initials": "J"}, {"family": "Sj\u00f6berg", "given": "Jan", "initials": "J"}, {"family": "Claesson", "given": "Hans-Erik", "initials": "H"}, {"family": "Johnsen", "given": "John Inge", "initials": "JI"}, {"family": "Winqvist", "given": "Ola", "initials": "O"}, {"family": "Xu", "given": "Dawei", "initials": "D"}, {"family": "Ekstr\u00f6m", "given": "Tomas J", "initials": "TJ"}, {"family": "Bj\u00f6rkholm", "given": "Magnus", "initials": "M"}, {"family": "Str\u00e5\u00e5t", "given": "Klas", "initials": "K"}], "type": "journal article", "published": "2020-12-09", "journal": {"title": "Front Oncol", "issn": "2234-943X", "issn-l": "2234-943X", "volume": "10", "issue": null, "pages": "598872"}, "abstract": "We studied DNA methylation profiles in four different cell populations from a unique constellation of monozygotic triplets in whom two had developed Hodgkin Lymphoma (HL). We detected shared differences in DNA methylation signatures when comparing the two HL-affected triplets with the non-affected triplet. The differences were observed in na\u00efve B-cells and marginal zone-like B-cells. DNA methylation differences were also detected when comparing each of the HL-affected triplets against each other. Even though we cannot determine whether treatment and/or disease triggered the observed differences, we believe our data are important on behalf of forthcoming studies, and that it might provide important clues for a better understanding of HL pathogenesis.", "doi": "10.3389/fonc.2020.598872", "pmid": "33363029", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC7756121"}], "notes": [], "created": "2021-01-07T17:01:53.849Z", "modified": "2024-01-16T13:48:41.153Z"}, {"entity": "publication", "iuid": "a5d51dc3032f481e9020d1483b809ab8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a5d51dc3032f481e9020d1483b809ab8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a5d51dc3032f481e9020d1483b809ab8"}}, "title": "BMP signaling is a therapeutic target in ovarian cancer.", "authors": [{"family": "Fukuda", "given": "Tomohiko", "initials": "T"}, {"family": "Fukuda", "given": "Risa", "initials": "R"}, {"family": "Tanabe", "given": "Ryo", "initials": "R"}, {"family": "Koinuma", "given": "Daizo", "initials": "D"}, {"family": "Koyama", "given": "Hiroo", "initials": "H"}, {"family": "Hashizume", "given": "Yoshinobu", "initials": "Y"}, {"family": "Moustakas", "given": "Aristidis", "initials": "A", "orcid": "0000-0001-9131-3827", "researcher": {"href": "https://publications.scilifelab.se/researcher/6c1626d991f3485e81232db174537e6d.json"}}, {"family": "Miyazono", "given": "Kohei", "initials": "K"}, {"family": "Heldin", "given": "Carl-Henrik", "initials": "CH", "orcid": "0000-0002-9508-896X", "researcher": {"href": "https://publications.scilifelab.se/researcher/f705f7c509904a1db721ace2267ca48f.json"}}], "type": "journal article", "published": "2020-12-05", "journal": {"title": "Cell Death Discov", "issn": "2058-7716", "issn-l": "2058-7716", "volume": "6", "issue": "1", "pages": "139"}, "abstract": "BMP signaling has been found to have tumor-promoting as well as tumor-suppressing effects in different types of tumors. In this study, we investigated the effects of BMP signaling and of BMP inhibitors on ovarian cancer (OC) cells in vitro and in vivo. High expression of BMP receptor 2 (BMPR2) correlated with poor overall survival of OC patients in the TCGA dataset. Both BMP2 and BMPR2 enhanced OC cell proliferation, whereas BMP receptor kinase inhibitors inhibited OC cell growth in cell culture as well as in a mouse model. BMP2 also augmented sphere formation, migration, and invasion of OC cells, and induced EMT. High BMP2 expression was observed after chemotherapy of OC patients in the GSE109934 dataset. In accordance, carboplatin, used for the treatment of OC patients, increased BMP2 secretion from OC cells, and induced EMT partially via activation of BMP signaling. Our data suggest that BMP signaling has tumor-promoting effects in OC, and that BMP inhibitors might be useful therapeutic agents for OC patients. Considering that carboplatin treatment augmented BMP2 secretion, the possibility to use a combination of BMP inhibitors and carboplatin in the treatment of OC patients, would be worth exploring.", "doi": "10.1038/s41420-020-00377-w", "pmid": "33298901", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41420-020-00377-w"}, {"db": "pmc", "key": "PMC7719168"}], "notes": [], "created": "2021-01-11T06:31:10.635Z", "modified": "2021-11-10T12:44:15.555Z"}, {"entity": "publication", "iuid": "b35ea53385974fc2b330d4aa37a35fbc", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b35ea53385974fc2b330d4aa37a35fbc.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b35ea53385974fc2b330d4aa37a35fbc"}}, "title": "A shotgun metagenomic investigation of the microbiota of udder cleft dermatitis in comparison to healthy skin in dairy cows.", "authors": [{"family": "Ekman", "given": "Lisa", "initials": "L", "orcid": "0000-0002-6556-1111", "researcher": {"href": "https://publications.scilifelab.se/researcher/caf7be02284c489a937dd91b1ff7e743.json"}}, {"family": "Bagge", "given": "Elisabeth", "initials": "E"}, {"family": "Nyman", "given": "Ann", "initials": "A", "orcid": "0000-0002-6643-0404", "researcher": {"href": "https://publications.scilifelab.se/researcher/1affe77f7a6a432a8ed538cb0acc1001.json"}}, {"family": "Persson Waller", "given": "Karin", "initials": "K"}, {"family": "Pringle", "given": "M\u00e4rit", "initials": "M"}, {"family": "Segerman", "given": "Bo", "initials": "B"}], "type": "journal article", "published": "2020-12-02", "journal": {"title": "PLoS ONE", "issn": "1932-6203", "volume": "15", "issue": "12", "pages": "e0242880", "issn-l": "1932-6203"}, "abstract": "Udder cleft dermatitis (UCD) is a skin condition affecting the fore udder attachment of dairy cows. UCD may be defined as mild (eczematous skin changes) or severe (open wounds, large skin changes). Our aims were to compare the microbiota of mild and severe UCD lesions with the microbiota of healthy skin from the fore udder attachment of control cows, and to investigate whether mastitis-causing pathogens are present in UCD lesions. Samples were obtained from cows in six dairy herds. In total, 36 UCD samples categorized as mild (n = 17) or severe (n = 19) and 13 control samples were sequenced using a shotgun metagenomic approach and the reads were taxonomically classified based on their k-mer content. The Wilcoxon rank sum test was used to compare the abundance of different taxa between different sample types, as well as to compare the bacterial diversity between samples. A high proportion of bacteria was seen in all samples. Control samples had a higher proportion of archaeal reads, whereas most samples had low proportions of fungi, protozoa and viruses. The bacterial microbiota differed between controls and mild and severe UCD samples in both composition and diversity. Subgroups of UCD samples were visible, characterized by increased proportion of one or a few bacterial genera or species, e.g. Corynebacterium, Staphylococcus, Brevibacterium luteolum, Trueperella pyogenes and Fusobacterium necrophorum. Bifidobacterium spp. were more common in controls compared to UCD samples. The bacterial diversity was higher in controls compared to UCD samples. Bacteria commonly associated with mastitis were uncommon. In conclusion, a dysbiosis of the microbiota of mild and severe UCD samples was seen, characterized by decreased diversity and an increased proportion of certain bacteria. There was no evidence of a specific pathogen causing UCD or that UCD lesions are important reservoirs for mastitis-causing bacteria.", "doi": "10.1371/journal.pone.0242880", "pmid": "33264351", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "PONE-D-20-18567"}, {"db": "pmc", "key": "PMC7710049"}], "notes": [], "created": "2020-12-08T23:31:10.074Z", "modified": "2024-01-16T13:48:41.169Z"}, {"entity": "publication", "iuid": "144f11f34c2647769832d1490ea233c6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/144f11f34c2647769832d1490ea233c6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/144f11f34c2647769832d1490ea233c6"}}, "title": "Tissue-specific patterns of regulatory changes underlying gene expression differences among Ficedula flycatchers and their naturally occurring F1 hybrids.", "authors": [{"family": "Mugal", "given": "Carina F", "initials": "CF", "orcid": "0000-0003-4220-4928", "researcher": {"href": "https://publications.scilifelab.se/researcher/8b82f77594994c37b37c72b653e20c28.json"}}, {"family": "Wang", "given": "Mi", "initials": "M"}, {"family": "Backstr\u00f6m", "given": "Niclas", "initials": "N"}, {"family": "Wheatcroft", "given": "David", "initials": "D"}, {"family": "\u00c5lund", "given": "Murielle", "initials": "M"}, {"family": "S\u00e9mon", "given": "Marie", "initials": "M"}, {"family": "McFarlane", "given": "S Eryn", "initials": "SE"}, {"family": "Dutoit", "given": "Ludovic", "initials": "L"}, {"family": "Qvarnstr\u00f6m", "given": "Anna", "initials": "A"}, {"family": "Ellegren", "given": "Hans", "initials": "H", "orcid": "0000-0002-5035-1736", "researcher": {"href": "https://publications.scilifelab.se/researcher/819e68cc7125446baec6165aabd2d19c.json"}}], "type": "journal article", "published": "2020-12-00", "journal": {"title": "Genome Res.", "issn": "1549-5469", "volume": "30", "issue": "12", "pages": "1727-1739", "issn-l": "1088-9051"}, "abstract": "Changes in interacting cis- and trans-regulatory elements are important candidates for Dobzhansky-Muller hybrid incompatibilities and may contribute to hybrid dysfunction by giving rise to misexpression in hybrids. To gain insight into the molecular mechanisms and determinants of gene expression evolution in natural populations, we analyzed the transcriptome from multiple tissues of two recently diverged Ficedula flycatcher species and their naturally occurring F1 hybrids. Differential gene expression analysis revealed that the extent of differentiation between species and the set of differentially expressed genes varied across tissues. Common to all tissues, a higher proportion of Z-linked genes than autosomal genes showed differential expression, providing evidence for a fast-Z effect. We further found clear signatures of hybrid misexpression in brain, heart, kidney, and liver. However, while testis showed the highest divergence of gene expression among tissues, it showed no clear signature of misexpression in F1 hybrids, even though these hybrids were found to be sterile. It is therefore unlikely that incompatibilities between cis-trans regulatory changes explain the observed sterility. Instead, we found evidence that cis-regulatory changes play a significant role in the evolution of gene expression in testis, which illustrates the tissue-specific nature of cis-regulatory evolution bypassing constraints associated with pleiotropic effects of genes.", "doi": "10.1101/gr.254508.119", "pmid": "33144405", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "gr.254508.119"}, {"db": "pmc", "key": "PMC7706733"}], "notes": [], "created": "2020-12-08T23:45:03.587Z", "modified": "2024-01-16T13:48:41.199Z"}, {"entity": "publication", "iuid": "b60e781bbbf44adb903c7051344daab6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b60e781bbbf44adb903c7051344daab6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b60e781bbbf44adb903c7051344daab6"}}, "title": "Morphological characters and SNP markers suggest hybridization and introgression in sympatric populations of the pleurocarpous mosses Homalothecium lutescens and H. sericeum", "authors": [{"family": "Sawangproh", "given": "Weerachon", "initials": "W"}, {"family": "Lang", "given": "Annick S", "initials": "AS"}, {"family": "Heden\u00e4s", "given": "Lars", "initials": "L"}, {"family": "Cronberg", "given": "Nils", "initials": "N", "orcid": "0000-0002-3369-8420", "researcher": {"href": "https://publications.scilifelab.se/researcher/bb83910f16b84861934f459105f0bc93.json"}}], "type": "journal-article", "published": "2020-12-00", "journal": {"title": "Org Divers Evol", "issn": "1439-6092", "issn-l": null, "volume": "20", "issue": "4", "pages": "619-637"}, "abstract": null, "doi": "10.1007/s13127-020-00456-x", "pmid": null, "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [], "notes": [], "created": "2020-12-10T09:53:40.082Z", "modified": "2021-12-07T13:47:06.801Z"}, {"entity": "publication", "iuid": "0a90b284f37043df85ba89a51ee5cc2a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0a90b284f37043df85ba89a51ee5cc2a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0a90b284f37043df85ba89a51ee5cc2a"}}, "title": "Genome-wide association study of angioedema induced by angiotensin-converting enzyme inhibitor and angiotensin receptor blocker treatment.", "authors": [{"family": "Rasmussen", "given": "Eva Rye", "initials": "ER"}, {"family": "Hallberg", "given": "P\u00e4r", "initials": "P"}, {"family": "Baranova", "given": "Ekaterina V", "initials": "EV"}, {"family": "Eriksson", "given": "Niclas", "initials": "N"}, {"family": "Karawajczyk", "given": "Malgorzata", "initials": "M"}, {"family": "Johansson", "given": "Caroline", "initials": "C"}, {"family": "Cavalli", "given": "Marco", "initials": "M"}, {"family": "Maroteau", "given": "Cyrielle", "initials": "C"}, {"family": "Veluchamy", "given": "Abirami", "initials": "A"}, {"family": "Islander", "given": "Gunilla", "initials": "G"}, {"family": "Hugosson", "given": "Svante", "initials": "S"}, {"family": "Terreehorst", "given": "Ingrid", "initials": "I"}, {"family": "Asselbergs", "given": "Folkert W", "initials": "FW", "orcid": "0000-0002-1692-8669", "researcher": {"href": "https://publications.scilifelab.se/researcher/7037429ef1304bdaabd837d242b1e6f5.json"}}, {"family": "Norling", "given": "Pia", "initials": "P"}, {"family": "Johansson", "given": "Hans-Erik", "initials": "HE"}, {"family": "Kohnke", "given": "Hugo", "initials": "H"}, {"family": "Syv\u00e4nen", "given": "Ann-Christine", "initials": "AC", "orcid": "0000-0002-9681-9146", "researcher": {"href": "https://publications.scilifelab.se/researcher/f7012e35025543379380cb90efd71243.json"}}, {"family": "Siddiqui", "given": "Moneeza K", "initials": "MK"}, {"family": "Lang", "given": "Chim C", "initials": "CC"}, {"family": "Magnusson", "given": "Patrik K E", "initials": "PKE", "orcid": "0000-0002-7315-7899", "researcher": {"href": "https://publications.scilifelab.se/researcher/b277b6387de142bbab91fad82d9eff09.json"}}, {"family": "Yue", "given": "Qun-Ying", "initials": "QY"}, {"family": "Wadelius", "given": "Claes", "initials": "C"}, {"family": "von Buchwald", "given": "Christian", "initials": "C"}, {"family": "Bygum", "given": "Anette", "initials": "A"}, {"family": "Alfirevic", "given": "Ana", "initials": "A"}, {"family": "Maitland-van der Zee", "given": "Anke H", "initials": "AH"}, {"family": "Palmer", "given": "Colin N A", "initials": "CNA", "orcid": "0000-0002-6415-6560", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a0f019dcb7a453a84480953a5514dd5.json"}}, {"family": "Wadelius", "given": "Mia", "initials": "M", "orcid": "0000-0002-6368-2622", "researcher": {"href": "https://publications.scilifelab.se/researcher/ec07b9869a1f4b77b734c5dc567dc630.json"}}], "type": "journal article", "published": "2020-12-00", "journal": {"title": "Pharmacogenomics J.", "issn": "1473-1150", "volume": "20", "issue": "6", "pages": "770-783", "issn-l": "1470-269X"}, "abstract": "Angioedema in the mouth or upper airways is a feared adverse reaction to angiotensin-converting enzyme inhibitor (ACEi) and angiotensin receptor blocker (ARB) treatment, which is used for hypertension, heart failure and diabetes complications. This candidate gene and genome-wide association study aimed to identify genetic variants predisposing to angioedema induced by these drugs. The discovery cohort consisted of 173 cases and 4890 controls recruited in Sweden. In the candidate gene analysis, ETV6, BDKRB2, MME, and PRKCQ were nominally associated with angioedema (p < 0.05), but did not pass Bonferroni correction for multiple testing (p < 2.89 \u00d7 10-5). In the genome-wide analysis, intronic variants in the calcium-activated potassium channel subunit alpha-1 (KCNMA1) gene on chromosome 10 were significantly associated with angioedema (p < 5 \u00d7 10-8). Whilst the top KCNMA1 hit was not significant in the replication cohort (413 cases and 599 ACEi-exposed controls from the US and Northern Europe), a meta-analysis of the replication and discovery cohorts (in total 586 cases and 1944 ACEi-exposed controls) revealed that each variant allele increased the odds of experiencing angioedema 1.62 times (95% confidence interval 1.05-2.50, p = 0.030). Associated KCNMA1 variants are not known to be functional, but are in linkage disequilibrium with variants in transcription factor binding sites active in relevant tissues. In summary, our data suggest that common variation in KCNMA1 is associated with risk of angioedema induced by ACEi or ARB treatment. Future whole exome or genome sequencing studies will show whether rare variants in KCNMA1 or other genes contribute to the risk of ACEi- and ARB-induced angioedema.", "doi": "10.1038/s41397-020-0165-2", "pmid": "32080354", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41397-020-0165-2"}, {"db": "pmc", "key": "PMC7674154"}], "notes": [], "created": "2020-02-27T09:21:01.759Z", "modified": "2024-01-16T13:48:41.233Z"}, {"entity": "publication", "iuid": "92d63630ecd7441b85eecaa4c4b48a08", "links": {"self": {"href": "https://publications.scilifelab.se/publication/92d63630ecd7441b85eecaa4c4b48a08.json"}, "display": {"href": "https://publications.scilifelab.se/publication/92d63630ecd7441b85eecaa4c4b48a08"}}, "title": "Genetic Studies of Leptin Concentrations Implicate Leptin in the Regulation of Early Adiposity.", "authors": [{"family": "Yaghootkar", "given": "Hanieh", "initials": "H", "orcid": "0000-0001-9672-9477", "researcher": {"href": "https://publications.scilifelab.se/researcher/2202b216df584f7cb4a4cf3f38ba2cec.json"}}, {"family": "Zhang", "given": "Yiying", "initials": "Y"}, {"family": "Spracklen", "given": "Cassandra N", "initials": "CN"}, {"family": "Karaderi", "given": "Tugce", "initials": "T"}, {"family": "Huang", "given": "Lam Opal", "initials": "LO"}, {"family": "Bradfield", "given": "Jonathan", "initials": "J"}, {"family": "Schurmann", "given": "Claudia", "initials": "C"}, {"family": "Fine", "given": "Rebecca S", "initials": "RS"}, {"family": "Preuss", "given": "Michael H", "initials": "MH"}, {"family": "Kutalik", "given": "Zoltan", "initials": "Z"}, {"family": "Wittemans", "given": "Laura B L", "initials": "LBL"}, {"family": "Lu", "given": "Yingchang", "initials": "Y"}, {"family": "Metz", "given": "Sophia", "initials": "S"}, {"family": "Willems", "given": "Sara M", "initials": "SM"}, {"family": "Li-Gao", "given": "Ruifang", "initials": "R"}, {"family": "Grarup", "given": "Niels", "initials": "N"}, {"family": "Wang", "given": "Shuai", "initials": "S"}, {"family": "Molnos", "given": "Sophie", "initials": "S"}, {"family": "Sandoval-Z\u00e1rate", "given": "Am\u00e9rica A", "initials": "AA"}, {"family": "Nalls", "given": "Mike A", "initials": "MA"}, {"family": "Lange", "given": "Leslie A", "initials": "LA"}, {"family": "Haesser", "given": "Jeffrey", "initials": "J"}, {"family": "Guo", "given": "Xiuqing", "initials": "X"}, {"family": "Lyytik\u00e4inen", "given": "Leo-Pekka", "initials": "LP"}, {"family": "Feitosa", "given": "Mary F", "initials": "MF"}, {"family": "Sitlani", "given": "Colleen M", "initials": "CM"}, {"family": "Venturini", "given": "Cristina", "initials": "C"}, {"family": "Mahajan", "given": "Anubha", "initials": "A"}, {"family": "Kacprowski", "given": "Tim", "initials": "T"}, {"family": "Wang", "given": "Carol A", "initials": "CA"}, {"family": "Chasman", "given": "Daniel I", "initials": "DI"}, {"family": "Amin", "given": "Najaf", "initials": "N"}, {"family": "Broer", "given": "Linda", "initials": "L"}, {"family": "Robertson", "given": "Neil", "initials": "N"}, {"family": "Young", "given": "Kristin L", "initials": "KL"}, {"family": "Allison", "given": "Matthew", "initials": "M"}, {"family": "Auer", "given": "Paul L", "initials": "PL"}, {"family": "Bl\u00fcher", "given": "Matthias", "initials": "M"}, {"family": "Borja", "given": "Judith B", "initials": "JB"}, {"family": "Bork-Jensen", "given": "Jette", "initials": "J"}, {"family": "Carrasquilla", "given": "Germ\u00e1n D", "initials": "GD"}, {"family": "Christofidou", "given": "Paraskevi", "initials": "P"}, {"family": "Demirkan", "given": "Ayse", "initials": "A"}, {"family": "Doege", "given": "Claudia A", "initials": "CA"}, {"family": "Garcia", "given": "Melissa E", "initials": "ME"}, {"family": "Graff", "given": "Mariaelisa", "initials": "M"}, {"family": "Guo", "given": "Kaiying", "initials": "K"}, {"family": "Hakonarson", "given": "Hakon", "initials": "H"}, {"family": "Hong", "given": "Jaeyoung", "initials": "J"}, {"family": "Ida Chen", "given": "Yii-Der", "initials": "YD"}, {"family": "Jackson", "given": "Rebecca", "initials": "R"}, {"family": "Jakupovi\u0107", "given": "Hermina", "initials": "H"}, {"family": "Jousilahti", "given": "Pekka", "initials": "P"}, {"family": "Justice", "given": "Anne E", "initials": "AE"}, {"family": "K\u00e4h\u00f6nen", "given": "Mika", "initials": "M"}, {"family": "Kizer", "given": "Jorge R", "initials": "JR"}, {"family": "Kriebel", "given": "Jennifer", "initials": "J"}, {"family": "LeDuc", "given": "Charles A", "initials": "CA"}, {"family": "Li", "given": "Jin", "initials": "J"}, {"family": "Lind", "given": "Lars", "initials": "L"}, {"family": "Luan", "given": "Jian'an", "initials": "J"}, {"family": "Mackey", "given": "David A", "initials": "DA"}, {"family": "Mangino", "given": "Massimo", "initials": "M"}, {"family": "M\u00e4nnist\u00f6", "given": "Satu", "initials": "S"}, {"family": "Martin Carli", "given": "Jayne F", "initials": "JF"}, {"family": "Medina-Gomez", "given": "Carolina", "initials": "C"}, {"family": "Mook-Kanamori", "given": "Dennis O", "initials": "DO"}, {"family": "Morris", "given": "Andrew P", "initials": "AP"}, {"family": "de Mutsert", "given": "Ren\u00e9e", "initials": "R"}, {"family": "Nauck", "given": "Matthias", "initials": "M"}, {"family": "Prokic", "given": "Ivana", "initials": "I"}, {"family": "Pennell", "given": "Craig E", "initials": "CE"}, {"family": "Pradhan", "given": "Arund D", "initials": "AD"}, {"family": "Psaty", "given": "Bruce M", "initials": "BM"}, {"family": "Raitakari", "given": "Olli T", "initials": "OT"}, {"family": "Scott", "given": "Robert A", "initials": "RA"}, {"family": "Skaaby", "given": "Tea", "initials": "T"}, {"family": "Strauch", "given": "Konstantin", "initials": "K"}, {"family": "Taylor", "given": "Kent D", "initials": "KD"}, {"family": "Teumer", "given": "Alexander", "initials": "A"}, {"family": "Uitterlinden", "given": "Andre G", "initials": "AG"}, {"family": "Wu", "given": "Ying", "initials": "Y"}, {"family": "Yao", "given": "Jie", "initials": "J"}, {"family": "Walker", "given": "Mark", "initials": "M"}, {"family": "North", "given": "Kari E", "initials": "KE"}, {"family": "Kovacs", "given": "Peter", "initials": "P"}, {"family": "Ikram", "given": "M Arfan", "initials": "MA"}, {"family": "van Duijn", "given": "Cornelia M", "initials": "CM"}, {"family": "Ridker", "given": "Paul M", "initials": "PM"}, {"family": "Lye", "given": "Stephen", "initials": "S"}, {"family": "Homuth", "given": "Georg", "initials": "G"}, {"family": "Ingelsson", "given": "Erik", "initials": "E"}, {"family": "Spector", "given": "Tim D", "initials": "TD"}, {"family": "McKnight", "given": "Barbara", "initials": "B"}, {"family": "Province", "given": "Michael A", "initials": "MA"}, {"family": "Lehtim\u00e4ki", "given": "Terho", "initials": "T"}, {"family": "Adair", "given": "Linda S", "initials": "LS"}, {"family": "Rotter", "given": "Jerome I", "initials": "JI"}, {"family": "Reiner", "given": "Alexander P", "initials": "AP"}, {"family": "Wilson", "given": "James G", "initials": "JG"}, {"family": "Harris", "given": "Tamara B", "initials": "TB"}, {"family": "Ripatti", "given": "Samuli", "initials": "S"}, {"family": "Grallert", "given": "Harald", "initials": "H"}, {"family": "Meigs", "given": "James B", "initials": "JB"}, {"family": "Salomaa", "given": "Veikko", "initials": "V"}, {"family": "Hansen", "given": "Torben", "initials": "T"}, {"family": "Willems van Dijk", "given": "Ko", "initials": "K"}, {"family": "Wareham", "given": "Nicholas J", "initials": "NJ"}, {"family": "Grant", "given": "Struan F A", "initials": "SFA"}, {"family": "Langenberg", "given": "Claudia", "initials": "C"}, {"family": "Frayling", "given": "Timothy M", "initials": "TM"}, {"family": "Lindgren", "given": "Cecilia M", "initials": "CM"}, {"family": "Mohlke", "given": "Karen L", "initials": "KL"}, {"family": "Leibel", "given": "Rudolph L", "initials": "RL"}, {"family": "Loos", "given": "Ruth J F", "initials": "RJF"}, {"family": "Kilpel\u00e4inen", "given": "Tuomas O", "initials": "TO", "orcid": "0000-0002-8349-3028", "researcher": {"href": "https://publications.scilifelab.se/researcher/d805d86c7bf64a7491bef35e45a14485.json"}}], "type": "journal article", "published": "2020-12-00", "journal": {"title": "Diabetes", "issn": "1939-327X", "volume": "69", "issue": "12", "pages": "2806-2818", "issn-l": "0012-1797"}, "abstract": "Leptin influences food intake by informing the brain about the status of body fat stores. Rare LEP mutations associated with congenital leptin deficiency cause severe early-onset obesity that can be mitigated by administering leptin. However, the role of genetic regulation of leptin in polygenic obesity remains poorly understood. We performed an exome-based analysis in up to 57,232 individuals of diverse ancestries to identify genetic variants that influence adiposity-adjusted leptin concentrations. We identify five novel variants, including four missense variants, in LEP, ZNF800, KLHL31, and ACTL9, and one intergenic variant near KLF14. The missense variant Val94Met (rs17151919) in LEP was common in individuals of African ancestry only, and its association with lower leptin concentrations was specific to this ancestry (P = 2 \u00d7 10-16, n = 3,901). Using in vitro analyses, we show that the Met94 allele decreases leptin secretion. We also show that the Met94 allele is associated with higher BMI in young African-ancestry children but not in adults, suggesting that leptin regulates early adiposity.", "doi": "10.2337/db20-0070", "pmid": "32917775", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pii", "key": "db20-0070"}, {"db": "pmc", "key": "PMC7679778"}, {"db": "figshare", "key": "10.2337/figshare.12933737"}], "notes": [], "created": "2020-10-20T06:59:22.330Z", "modified": "2021-11-10T12:44:35.165Z"}, {"entity": "publication", "iuid": "06bdda0e02974b29a11b5fc22fa91b3b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/06bdda0e02974b29a11b5fc22fa91b3b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/06bdda0e02974b29a11b5fc22fa91b3b"}}, "title": "Genetic Predisposition to Coronary Artery Disease in Type 2 Diabetes Mellitus.", "authors": [{"family": "van Zuydam", "given": "Natalie R", "initials": "NR", "orcid": "0000-0002-9809-1398", "researcher": {"href": "https://publications.scilifelab.se/researcher/defa68cc40734fcdaffd7ba0aaad72b8.json"}}, {"family": "Ladenvall", "given": "Claes", "initials": "C", "orcid": "0000-0002-7501-6598", "researcher": {"href": "https://publications.scilifelab.se/researcher/4c5c362dc308476195eb55d2e588ba60.json"}}, {"family": "Voight", "given": "Benjamin F", "initials": "BF", "orcid": "0000-0002-6205-9994", "researcher": {"href": "https://publications.scilifelab.se/researcher/d3d9e9de96ee4983ba97efc14eb3d79b.json"}}, {"family": "Strawbridge", "given": "Rona J", "initials": "RJ", "orcid": "0000-0001-8506-3585", "researcher": {"href": "https://publications.scilifelab.se/researcher/8ac5060a3b37466dae002d4ad8f4d0ac.json"}}, {"family": "Fernandez-Tajes", "given": "Juan", "initials": "J", "orcid": "0000-0003-1515-2421", "researcher": {"href": "https://publications.scilifelab.se/researcher/dad51251fc8d42f793e4c991c4102667.json"}}, {"family": "Rayner", "given": "N William", "initials": "NW", "orcid": "0000-0003-0510-4792", "researcher": {"href": "https://publications.scilifelab.se/researcher/0e3c7e5bd20348629ba3fe232fc2bcd2.json"}}, {"family": "Robertson", "given": "Neil R", "initials": "NR"}, {"family": "Mahajan", "given": "Anubha", "initials": "A"}, {"family": "Vlachopoulou", "given": "Efthymia", "initials": "E"}, {"family": "Goel", "given": "Anuj", "initials": "A", "orcid": "0000-0003-2307-4021", "researcher": {"href": "https://publications.scilifelab.se/researcher/0f16d9d2e2164938a12b027326c21316.json"}}, {"family": "Kleber", "given": "Marcus E", "initials": "ME"}, {"family": "Nelson", "given": "Christopher P", "initials": "CP"}, {"family": "Kwee", "given": "Lydia Coulter", "initials": "LC", "orcid": "0000-0002-6997-8571", "researcher": {"href": "https://publications.scilifelab.se/researcher/aa16042af5d84f11927203fc564e8fcb.json"}}, {"family": "Esko", "given": "T\u00f5nu", "initials": "T", "orcid": "0000-0003-1982-6569", "researcher": {"href": "https://publications.scilifelab.se/researcher/d72619c1e29d44e8b8454902d2af8d9e.json"}}, {"family": "Mihailov", "given": "Evelin", "initials": "E"}, {"family": "M\u00e4gi", "given": "Reedik", "initials": "R", "orcid": "0000-0002-2964-6011", "researcher": {"href": "https://publications.scilifelab.se/researcher/61f337c26b414b8fa30bf0fdb77368a1.json"}}, {"family": "Milani", "given": "Lili", "initials": "L", "orcid": "0000-0002-5323-3102", "researcher": {"href": "https://publications.scilifelab.se/researcher/dec8d00c4b9d43458c5c895b164695d5.json"}}, {"family": "Fischer", "given": "Krista", "initials": "K", "orcid": "0000-0002-3521-0599", "researcher": {"href": "https://publications.scilifelab.se/researcher/bcd45c97a9c2450c9c88adbd83d36b24.json"}}, {"family": "Kanoni", "given": "Stavroula", "initials": "S", "orcid": "0000-0002-1691-9615", "researcher": {"href": "https://publications.scilifelab.se/researcher/95f9c5fce1fe44719ef772eda9a4f5e4.json"}}, {"family": "Kumar", "given": "Jitender", "initials": "J"}, {"family": "Song", "given": "Ci", "initials": "C"}, {"family": "Hartiala", "given": "Jaana A", "initials": "JA", "orcid": "0000-0003-4883-9318", "researcher": {"href": "https://publications.scilifelab.se/researcher/f39400df71774cf8ae408eccbe34d981.json"}}, {"family": "Pedersen", "given": "Nancy L", "initials": "NL", "orcid": "0000-0001-8057-3543", "researcher": {"href": "https://publications.scilifelab.se/researcher/cbee4e5f6d10460cac50f00ee92d5bdf.json"}}, {"family": "Perola", "given": "Markus", "initials": "M", "orcid": "0000-0003-4842-1667", "researcher": {"href": "https://publications.scilifelab.se/researcher/ef3cdf94ecb543f1a449a7704f8be7b2.json"}}, {"family": "Gieger", "given": "Christian", "initials": "C"}, {"family": "Peters", "given": "Annette", "initials": "A", "orcid": "0000-0001-6645-0985", "researcher": {"href": "https://publications.scilifelab.se/researcher/05465e52a0f6412e81752d2249af30de.json"}}, {"family": "Qu", "given": "Liming", "initials": "L"}, {"family": "Willems", "given": "Sara M", "initials": "SM", "orcid": "0000-0002-6803-3007", "researcher": {"href": "https://publications.scilifelab.se/researcher/307c8a9b3ab54ab586c7b000c110e76b.json"}}, {"family": "Doney", "given": "Alex S F", "initials": "ASF"}, {"family": "Morris", "given": "Andrew D", "initials": "AD"}, {"family": "Zheng", "given": "Yan", "initials": "Y", "orcid": "0000-0003-1129-3147", "researcher": {"href": "https://publications.scilifelab.se/researcher/c0baf9bc398345709fcfe2f635c6d443.json"}}, {"family": "Sesti", "given": "Giorgio", "initials": "G", "orcid": "0000-0002-1618-7688", "researcher": {"href": "https://publications.scilifelab.se/researcher/3c564dce3a584837a595ad7c9630092d.json"}}, {"family": "Hu", "given": "Frank B", "initials": "FB", "orcid": "0000-0002-8233-6274", "researcher": {"href": 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"https://publications.scilifelab.se/researcher/de249cb6c3774f04985a39ca9828b97e.json"}}, {"family": "Ingelsson", "given": "Erik", "initials": "E"}, {"family": "Deloukas", "given": "Panos", "initials": "P", "orcid": "0000-0001-9251-070X", "researcher": {"href": "https://publications.scilifelab.se/researcher/eb59dbd2f2204d41b801c41188611a9e.json"}}, {"family": "Kathiresan", "given": "Sek", "initials": "S", "orcid": "0000-0002-3711-7101", "researcher": {"href": "https://publications.scilifelab.se/researcher/58fd968293e94da49c506c743a74222e.json"}}, {"family": "Metspalu", "given": "Andres", "initials": "A", "orcid": "0000-0002-3718-796X", "researcher": {"href": "https://publications.scilifelab.se/researcher/fd553a77a5a54258b4a4701f0e70a3f8.json"}}, {"family": "Shah", "given": "Svati H", "initials": "SH"}, {"family": "Sinisalo", "given": "Juha", "initials": "J", "orcid": "0000-0002-0169-5137", "researcher": {"href": "https://publications.scilifelab.se/researcher/6fde24cdfda24aed83d888da0d9b6811.json"}}, {"family": "Salomaa", "given": "Veikko", "initials": "V", "orcid": "0000-0001-7563-5324", "researcher": {"href": "https://publications.scilifelab.se/researcher/f2396c578c254e39b66538c3033c9ce9.json"}}, {"family": "Hamsten", "given": "Anders", "initials": "A"}, {"family": "Samani", "given": "Nilesh J", "initials": "NJ", "orcid": "0000-0002-3286-8133", "researcher": {"href": "https://publications.scilifelab.se/researcher/2227aaf274e8424f8408318f336f3bf1.json"}}, {"family": "M\u00e4rz", "given": "Winfried", "initials": "W"}, {"family": "Hazen", "given": "Stanley L", "initials": "SL", "orcid": "0000-0001-7124-6639", "researcher": {"href": "https://publications.scilifelab.se/researcher/abce9cd916c94667a73bc348ede57a01.json"}}, {"family": "Watkins", "given": "Hugh", "initials": "H", "orcid": "0000-0002-5287-9016", "researcher": {"href": "https://publications.scilifelab.se/researcher/7ea10989397546f9a027f88bd491bb8b.json"}}, {"family": "Saleheen", "given": "Danish", "initials": "D"}, {"family": "Morris", "given": "Andrew P", "initials": "AP"}, {"family": "Colhoun", "given": "Helen M", "initials": "HM", "orcid": "0000-0002-8345-3288", "researcher": {"href": "https://publications.scilifelab.se/researcher/e79cb60e3d734232b7cfad20c4f1c13e.json"}}, {"family": "Groop", "given": "Leif", "initials": "L"}, {"family": "McCarthy", "given": "Mark I", "initials": "MI", "orcid": "0000-0002-4393-0510", "researcher": {"href": "https://publications.scilifelab.se/researcher/5e44f4b1ca3a49cb8f83450ef9482e91.json"}}, {"family": "Palmer", "given": "Colin N A", "initials": "CNA", "orcid": "0000-0002-6415-6560", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a0f019dcb7a453a84480953a5514dd5.json"}}, {"family": "SUMMIT Steering Committee; CARDIOGRAMplusC4D Steering Committee*", "given": "", "initials": ""}], "type": "journal article", "published": "2020-12-00", "journal": {"title": "Circ Genom Precis Med", "issn": "2574-8300", "issn-l": "2574-8300", "volume": "13", "issue": "6", "pages": "e002769"}, "abstract": "Coronary artery disease (CAD) is accelerated in subjects with type 2 diabetes mellitus (T2D).\r\n\r\nTo test whether this reflects differential genetic influences on CAD risk in subjects with T2D, we performed a systematic assessment of genetic overlap between CAD and T2D in 66 643 subjects (27 708 with CAD and 24 259 with T2D). Variants showing apparent association with CAD in stratified analyses or evidence of interaction were evaluated in a further 117 787 subjects (16 694 with CAD and 11 537 with T2D).\r\n\r\nNone of the previously characterized CAD loci was found to have specific effects on CAD in T2D individuals, and a genome-wide interaction analysis found no new variants for CAD that could be considered T2D specific. When we considered the overall genetic correlations between CAD and its risk factors, we found no substantial differences in these relationships by T2D background.\r\n\r\nThis study found no evidence that the genetic architecture of CAD differs in those with T2D compared with those without T2D.", "doi": "10.1161/CIRCGEN.119.002769", "pmid": "33321069", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC7748049"}], "notes": [], "created": "2021-01-07T17:01:51.462Z", "modified": "2021-12-07T13:47:48.005Z"}, {"entity": "publication", "iuid": "d52fe9ba559d4dbcb12811ce80a182df", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d52fe9ba559d4dbcb12811ce80a182df.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d52fe9ba559d4dbcb12811ce80a182df"}}, "title": "Exome Sequencing Reveals Common and Rare Variants in F5 Associated With ACE Inhibitor and Angiotensin Receptor Blocker-Induced Angioedema.", "authors": [{"family": "Maroteau", "given": "Cyrielle", "initials": "C", "orcid": "0000-0001-7816-5508", "researcher": {"href": "https://publications.scilifelab.se/researcher/ebfc9425cb394843ac30847955e53ebe.json"}}, {"family": "Siddiqui", "given": "Moneeza Kalhan", "initials": "MK"}, {"family": "Veluchamy", "given": "Abirami", "initials": "A"}, {"family": "Carr", "given": "Fiona", "initials": "F"}, {"family": "White", "given": "Myra", "initials": "M"}, {"family": "Cassidy", "given": "Andrew J", "initials": "AJ"}, {"family": "Baranova", "given": "Ekaterina V", "initials": "EV"}, {"family": "Rasmussen", "given": "Eva R", "initials": "ER"}, {"family": "Eriksson", "given": "Niclas", "initials": "N", "orcid": "0000-0002-2152-4343", "researcher": {"href": "https://publications.scilifelab.se/researcher/64611a83caba46d597f45371b77de26b.json"}}, {"family": "Bloch", "given": "Katarzyna M", "initials": "KM"}, {"family": "Brown", "given": "Nancy J", "initials": "NJ"}, {"family": "Bygum", "given": "Anette", "initials": "A"}, {"family": "Hallberg", "given": "Par", "initials": "P", "orcid": "0000-0003-3465-3280", "researcher": {"href": "https://publications.scilifelab.se/researcher/968cb3fe072d4ed09739e8be6668d168.json"}}, {"family": "Karawajczyk", "given": "Malgorzata", "initials": "M"}, {"family": "Magnusson", "given": "Patrik K E", "initials": "PKE"}, {"family": "Yue", "given": "Qun-Ying", "initials": "QY"}, {"family": "Syv\u00e4nen", "given": "Ann-Christine", "initials": "AC"}, {"family": "von Buchwald", "given": "Christian", "initials": "C"}, {"family": "Alfirevic", "given": "Ana", "initials": "A"}, {"family": "Maitland-van der Zee", "given": "Anke H", "initials": "AH"}, {"family": "Wadelius", "given": "Mia", "initials": "M", "orcid": "0000-0002-6368-2622", "researcher": {"href": "https://publications.scilifelab.se/researcher/ec07b9869a1f4b77b734c5dc567dc630.json"}}, {"family": "Palmer", "given": "Colin N A", "initials": "CNA"}, {"family": "PREDICTION-ADR", "given": "", "initials": ""}], "type": "journal article", "published": "2020-12-00", "journal": {"title": "Clin. Pharmacol. Ther.", "issn": "1532-6535", "volume": "108", "issue": "6", "pages": "1195-1202", "issn-l": "0009-9236"}, "abstract": "Angioedema occurring in the head and neck region is a rare and sometimes life-threatening adverse reaction to angiotensin-converting enzyme inhibitors (ACEIs) and angiotensin receptor blockers (ARBs). Few studies have investigated the association of common variants with this extreme reaction, but none have explored the combined influence of rare variants yet. Adjudicated cases of ACEI-induced angioedema (ACEI-AE) or ARB-induced angioedema (ARB-AE) and controls were recruited at five different centers. Sequencing of 1,066 samples (408 ACEI-AE, ARB-AE, and 658 controls) was performed using exome-enriched sequence data. A common variant of the F5 gene that causes an increase in blood clotting (rs6025, p.Arg506Gln, also called factor V Leiden), was significantly associated with both ACEI-AE and ARB-AE (odds ratio: 2.85, 95% confidence interval (CI), 1.89-4.25). A burden test analysis of five rare missense variants in F5 was also found to be associated with ACEI-AE or ARB-AE, P = 2.09 \u00d7 10-3 . A combined gene risk score of these variants, and the common variants rs6025 and rs6020, showed that individuals carrying at least one variant had 2.21 (95% CI, 1.49-3.27, P = 6.30 \u00d7 10-9 ) times the odds of having ACEI-AE or ARB-AE. The increased risk due to the common Leiden allele was confirmed in a genome-wide association study from the United States. A high risk of angioedema was also observed for the rs6020 variant that is the main coagulation defect-causing variant in black African and Asian populations. We found that deleterious missense variants in F5 are associated with an increased risk of ACEI-AE or ARB-AE.", "doi": "10.1002/cpt.1927", "pmid": "32496628", "labels": {"National Genomics Infrastructure": "Collaborative", "NGI Uppsala (SNP&SEQ Technology Platform)": "Collaborative"}, "xrefs": [], "notes": [], "created": "2020-11-16T09:14:47.719Z", "modified": "2021-11-10T12:44:38.679Z"}, {"entity": "publication", "iuid": "ee2e40bee1cc4d14944c57aac8d0f1c9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ee2e40bee1cc4d14944c57aac8d0f1c9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ee2e40bee1cc4d14944c57aac8d0f1c9"}}, "title": "Discovery of rare variants associated with blood pressure regulation through meta-analysis of 1.3 million individuals.", "authors": [{"family": "Surendran", "given": "Praveen", "initials": "P"}, {"family": "Feofanova", "given": "Elena V", "initials": "EV", "orcid": "0000-0003-1428-7199", "researcher": {"href": "https://publications.scilifelab.se/researcher/1045cc4a1b224b40bc61748fb55836c9.json"}}, {"family": "Lahrouchi", "given": "Najim", "initials": "N"}, {"family": "Ntalla", "given": "Ioanna", "initials": "I"}, {"family": "Karthikeyan", "given": "Savita", "initials": "S"}, {"family": "Cook", "given": "James", "initials": "J"}, {"family": "Chen", "given": "Lingyan", "initials": "L"}, {"family": "Mifsud", "given": "Borbala", "initials": "B"}, {"family": "Yao", "given": "Chen", "initials": "C"}, {"family": "Kraja", "given": "Aldi T", "initials": "AT"}, {"family": "Cartwright", "given": "James H", "initials": "JH"}, {"family": "Hellwege", "given": "Jacklyn N", "initials": "JN"}, {"family": "Giri", "given": "Ayush", "initials": "A"}, {"family": "Tragante", "given": "Vinicius", "initials": "V"}, {"family": "Thorleifsson", "given": "Gudmar", "initials": "G"}, {"family": "Liu", "given": "Dajiang J", "initials": "DJ"}, {"family": "Prins", "given": "Bram P", "initials": "BP"}, {"family": "Stewart", "given": "Isobel D", "initials": "ID"}, {"family": "Cabrera", "given": "Claudia P", "initials": "CP"}, {"family": "Eales", "given": "James M", "initials": "JM"}, {"family": "Akbarov", "given": "Artur", "initials": "A"}, {"family": "Auer", "given": "Paul L", "initials": "PL"}, {"family": "Bielak", "given": "Lawrence F", "initials": "LF"}, {"family": "Bis", "given": "Joshua C", "initials": "JC"}, {"family": "Braithwaite", "given": "Vickie S", "initials": "VS"}, {"family": "Brody", "given": "Jennifer A", "initials": "JA"}, {"family": "Daw", "given": "E Warwick", "initials": "EW"}, {"family": "Warren", "given": "Helen R", "initials": "HR"}, {"family": "Drenos", "given": "Fotios", "initials": "F"}, {"family": "Nielsen", "given": "Sune Fallgaard", "initials": "SF"}, {"family": "Faul", "given": "Jessica D", "initials": "JD"}, {"family": "Fauman", "given": "Eric B", "initials": "EB"}, {"family": "Fava", "given": "Cristiano", "initials": "C"}, {"family": "Ferreira", "given": 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{"family": "Lindstr\u00f6m", "given": "Jaana", "initials": "J"}, {"family": "Lotta", "given": "Luca A", "initials": "LA"}, {"family": "Lu", "given": "Yingchang", "initials": "Y"}, {"family": "Luan", "given": "Jian'an", "initials": "J"}, {"family": "Mahajan", "given": "Anubha", "initials": "A"}, {"family": "Malerba", "given": "Giovanni", "initials": "G"}, {"family": "Masca", "given": "Nicholas G D", "initials": "NGD"}, {"family": "Mei", "given": "Hao", "initials": "H"}, {"family": "Menni", "given": "Cristina", "initials": "C"}, {"family": "Mook-Kanamori", "given": "Dennis O", "initials": "DO"}, {"family": "Mosen-Ansorena", "given": "David", "initials": "D"}, {"family": "M\u00fcller-Nurasyid", "given": "Martina", "initials": "M"}, {"family": "Par\u00e9", "given": "Guillaume", "initials": "G"}, {"family": "Paul", "given": "Dirk S", "initials": "DS"}, {"family": "Perola", "given": "Markus", "initials": "M"}, {"family": "Poveda", "given": "Alaitz", "initials": "A"}, {"family": "Rauramaa", 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"given": "Stefan", "initials": "S"}, {"family": "Willems", "given": "Sara M", "initials": "SM"}, {"family": "Yao", "given": "Jie", "initials": "J"}, {"family": "Young", "given": "Robin", "initials": "R"}, {"family": "Yu", "given": "Bing", "initials": "B"}, {"family": "Zhang", "given": "Weihua", "initials": "W"}, {"family": "Zhao", "given": "Jing-Hua", "initials": "J"}, {"family": "Zhao", "given": "Wei", "initials": "W"}, {"family": "Evangelou", "given": "Evangelos", "initials": "E"}, {"family": "Aeschbacher", "given": "Stefanie", "initials": "S"}, {"family": "Asllanaj", "given": "Eralda", "initials": "E"}, {"family": "Blankenberg", "given": "Stefan", "initials": "S"}, {"family": "Bonnycastle", "given": "Lori L", "initials": "LL"}, {"family": "Bork-Jensen", "given": "Jette", "initials": "J"}, {"family": "Brandslund", "given": "Ivan", "initials": "I"}, {"family": "Braund", "given": "Peter S", "initials": "PS"}, {"family": "Burgess", "given": "Stephen", "initials": "S"}, {"family": "Cho", "given": "Kelly", "initials": "K"}, {"family": "Christensen", "given": "Cramer", "initials": "C"}, {"family": "Connell", "given": "John", "initials": "J"}, {"family": "Mutsert", "given": "Ren\u00e9e de", "initials": "Rd"}, {"family": "Dominiczak", "given": "Anna F", "initials": "AF"}, {"family": "D\u00f6rr", "given": "Marcus", "initials": "M"}, {"family": "Eiriksdottir", "given": "Gudny", "initials": "G"}, {"family": "Farmaki", "given": "Aliki-Eleni", "initials": "A"}, {"family": "Gaziano", "given": "J Michael", "initials": "JM"}, {"family": "Grarup", "given": "Niels", "initials": "N"}, {"family": "Grove", "given": "Megan L", "initials": "ML"}, {"family": "Hallmans", "given": "G\u00f6ran", "initials": "G"}, {"family": "Hansen", "given": "Torben", "initials": "T"}, {"family": "Have", "given": "Christian T", "initials": "CT"}, {"family": "Heiss", "given": "Gerardo", "initials": "G"}, {"family": "J\u00f8rgensen", "given": "Marit E", "initials": "ME"}, {"family": "Jousilahti", "given": "Pekka", "initials": "P"}, {"family": "Kajantie", "given": "Eero", "initials": "E"}, {"family": "Kamat", "given": "Mihir", "initials": "M"}, {"family": "K\u00e4r\u00e4j\u00e4m\u00e4ki", "given": "AnneMari", "initials": "A"}, {"family": "Karpe", "given": "Fredrik", "initials": "F"}, {"family": "Koistinen", "given": "Heikki A", "initials": "HA"}, {"family": "Kovesdy", "given": "Csaba P", "initials": "CP"}, {"family": "Kuulasmaa", "given": "Kari", "initials": "K"}, {"family": "Laatikainen", "given": "Tiina", "initials": "T"}, {"family": "Lannfelt", "given": "Lars", "initials": "L"}, {"family": "Lee", "given": "I-Te", "initials": "I"}, {"family": "Lee", "given": "Wen-Jane", "initials": "W"}, {"family": "LifeLines Cohort Study", "given": "", "initials": ""}, {"family": "Linneberg", "given": "Allan", "initials": "A"}, {"family": "Martin", "given": "Lisa W", "initials": "LW"}, {"family": "Moitry", "given": "Marie", "initials": "M"}, {"family": "Nadkarni", "given": "Girish", "initials": "G"}, {"family": "Neville", "given": "Matt J", "initials": "MJ"}, {"family": "Palmer", "given": "Colin N A", "initials": "CNA"}, {"family": "Papanicolaou", "given": "George J", "initials": "GJ"}, {"family": "Pedersen", "given": "Oluf", "initials": "O"}, {"family": "Peters", "given": "James", "initials": "J"}, {"family": "Poulter", "given": "Neil", "initials": "N"}, {"family": "Rasheed", "given": "Asif", "initials": "A"}, {"family": "Rasmussen", "given": "Katrine L", "initials": "KL"}, {"family": "Rayner", "given": "N William", "initials": "NW"}, {"family": "M\u00e4gi", "given": "Reedik", "initials": "R"}, {"family": "Renstr\u00f6m", "given": "Frida", "initials": "F"}, {"family": "Rettig", "given": "Rainer", "initials": "R"}, {"family": "Rossouw", "given": "Jacques", "initials": "J"}, {"family": "Schreiner", "given": "Pamela J", "initials": "PJ"}, {"family": "Sever", "given": "Peter S", "initials": "PS"}, {"family": "Sigurdsson", "given": "Emil L", "initials": "EL"}, {"family": "Skaaby", 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{"family": "Loos", "given": "Ruth J F", "initials": "RJF"}, {"family": "Majumder", "given": "Abdulla Al Shafi", "initials": "AAS"}, {"family": "Laakso", "given": "Markku", "initials": "M"}, {"family": "McCarthy", "given": "Mark I", "initials": "MI"}, {"family": "Melander", "given": "Olle", "initials": "O"}, {"family": "Mohlke", "given": "Karen L", "initials": "KL"}, {"family": "Murray", "given": "Alison D", "initials": "AD"}, {"family": "Nordestgaard", "given": "B\u00f8rge Gr\u00f8nne", "initials": "BG"}, {"family": "Orho-Melander", "given": "Marju", "initials": "M"}, {"family": "Packard", "given": "Chris J", "initials": "CJ"}, {"family": "Padmanabhan", "given": "Sandosh", "initials": "S"}, {"family": "Palmas", "given": "Walter", "initials": "W"}, {"family": "Polasek", "given": "Ozren", "initials": "O"}, {"family": "Porteous", "given": "David J", "initials": "DJ"}, {"family": "Prentice", "given": "Andrew M", "initials": "AM"}, {"family": "Province", "given": "Michael A", "initials": "MA"}, {"family": "Relton", "given": "Caroline L", "initials": "CL"}, {"family": "Rice", "given": "Kenneth", "initials": "K"}, {"family": "Ridker", "given": "Paul M", "initials": "PM"}, {"family": "Rolandsson", "given": "Olov", "initials": "O"}, {"family": "Rosendaal", "given": "Frits R", "initials": "FR"}, {"family": "Rotter", "given": "Jerome I", "initials": "JI"}, {"family": "Rudan", "given": "Igor", "initials": "I"}, {"family": "Salomaa", "given": "Veikko", "initials": "V"}, {"family": "Samani", "given": "Nilesh J", "initials": "NJ"}, {"family": "Sattar", "given": "Naveed", "initials": "N"}, {"family": "Sheu", "given": "Wayne H-H", "initials": "WH"}, {"family": "Smith", "given": "Blair H", "initials": "BH"}, {"family": "Soranzo", "given": "Nicole", "initials": "N"}, {"family": "Spector", "given": "Timothy D", "initials": "TD"}, {"family": "Starr", "given": "John M", "initials": "JM"}, {"family": "Sebert", "given": "Sylvain", "initials": "S"}, {"family": "Taylor", "given": "Kent D", "initials": "KD"}, {"family": "Lakka", "given": "Timo A", "initials": "TA"}, {"family": "Timpson", "given": "Nicholas J", "initials": "NJ"}, {"family": "Tobin", "given": "Martin D", "initials": "MD"}, {"family": "Understanding Society Scientific Group", "given": "", "initials": ""}, {"family": "van der Harst", "given": "Pim", "initials": "P"}, {"family": "van der Meer", "given": "Peter", "initials": "P"}, {"family": "Ramachandran", "given": "Vasan S", "initials": "VS"}, {"family": "Verweij", "given": "Niek", "initials": "N"}, {"family": "Virtamo", "given": "Jarmo", "initials": "J"}, {"family": "V\u00f6lker", "given": "Uwe", "initials": "U"}, {"family": "Weir", "given": "David R", "initials": "DR"}, {"family": "Zeggini", "given": "Eleftheria", "initials": "E"}, {"family": "Charchar", "given": "Fadi J", "initials": "FJ"}, {"family": "Million Veteran Program", "given": "", "initials": ""}, {"family": "Wareham", "given": "Nicholas J", "initials": "NJ"}, {"family": "Langenberg", "given": "Claudia", "initials": "C"}, {"family": "Tomaszewski", "given": "Maciej", "initials": "M"}, {"family": "Butterworth", "given": "Adam S", "initials": "AS"}, {"family": "Caulfield", "given": "Mark J", "initials": "MJ"}, {"family": "Danesh", "given": "John", "initials": "J"}, {"family": "Edwards", "given": "Todd L", "initials": "TL"}, {"family": "Holm", "given": "Hilma", "initials": "H"}, {"family": "Hung", "given": "Adriana M", "initials": "AM"}, {"family": "Lindgren", "given": "Cecilia M", "initials": "CM"}, {"family": "Liu", "given": "Chunyu", "initials": "C"}, {"family": "Manning", "given": "Alisa K", "initials": "AK"}, {"family": "Morris", "given": "Andrew P", "initials": "AP"}, {"family": "Morrison", "given": "Alanna C", "initials": "AC"}, {"family": "O'Donnell", "given": "Christopher J", "initials": "CJ"}, {"family": "Psaty", "given": "Bruce M", "initials": "BM"}, {"family": "Saleheen", "given": "Danish", "initials": "D"}, {"family": "Stefansson", "given": "Kari", "initials": "K"}, {"family": "Boerwinkle", "given": "Eric", "initials": "E"}, {"family": "Chasman", "given": "Daniel I", "initials": "DI", "orcid": "0000-0003-3357-0862", "researcher": {"href": "https://publications.scilifelab.se/researcher/1c06690291064fe58836958edbcaafbc.json"}}, {"family": "Levy", "given": "Daniel", "initials": "D"}, {"family": "Newton-Cheh", "given": "Christopher", "initials": "C"}, {"family": "Munroe", "given": "Patricia B", "initials": "PB", "orcid": "0000-0002-4176-2947", "researcher": {"href": "https://publications.scilifelab.se/researcher/657544a7f921459f926aae5cd0e2065c.json"}}, {"family": "Howson", "given": "Joanna M M", "initials": "JMM", "orcid": "0000-0001-7618-0050", "researcher": {"href": "https://publications.scilifelab.se/researcher/d427fc29d217410fa1d84c0f9e2bf015.json"}}], "type": "journal article", "published": "2020-12-00", "journal": {"title": "Nat. Genet.", "issn": "1546-1718", "issn-l": "1061-4036", "volume": "52", "issue": "12", "pages": "1314-1332"}, "abstract": "Genetic studies of blood pressure (BP) to date have mainly analyzed common variants (minor allele frequency > 0.05). In a meta-analysis of up to ~1.3 million participants, we discovered 106 new BP-associated genomic regions and 87 rare (minor allele frequency \u2264 0.01) variant BP associations (P < 5 \u00d7 10-8), of which 32 were in new BP-associated loci and 55 were independent BP-associated single-nucleotide variants within known BP-associated regions. Average effects of rare variants (44% coding) were ~8 times larger than common variant effects and indicate potential candidate causal genes at new and known loci (for example, GATA5 and PLCB3). BP-associated variants (including rare and common) were enriched in regions of active chromatin in fetal tissues, potentially linking fetal development with BP regulation in later life. Multivariable Mendelian randomization suggested possible inverse effects of elevated systolic and diastolic BP on large artery stroke. Our study demonstrates the utility of rare-variant analyses for identifying candidate genes and the results highlight potential therapeutic targets.", "doi": "10.1038/s41588-020-00713-x", "pmid": "33230300", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41588-020-00713-x"}, {"db": "pmc", "key": "PMC7610439"}, {"db": "mid", "key": "EMS118016"}], "notes": [], "created": "2021-01-07T17:01:50.081Z", "modified": "2021-12-07T13:35:55.172Z"}, {"entity": "publication", "iuid": "8fbdb10cceb14b808433587b60f51045", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8fbdb10cceb14b808433587b60f51045.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8fbdb10cceb14b808433587b60f51045"}}, "title": "A genome-wide association study revealed five SNPs affecting 8-month weight in sheep.", "authors": [{"family": "Pasandideh", "given": "M", "initials": "M", "orcid": "0000-0001-5340-7072", "researcher": {"href": "https://publications.scilifelab.se/researcher/431b9c421917406c8d4f3769bfde17ed.json"}}, {"family": "Gholizadeh", "given": "M", "initials": "M"}, {"family": "Rahimi-Mianji", "given": "G", "initials": "G"}], "type": "journal article", "published": "2020-12-00", "journal": {"title": "Anim Genet", "issn": "1365-2052", "volume": "51", "issue": "6", "pages": "973-976", "issn-l": "0268-9146"}, "abstract": "Lamb weight at 8 months of age is an important trait in the sheep industry in terms of the onset of puberty around this age; however, knowledge of its effective genetic factors is limited. Therefore, a GWAS using the 50K SNP-Chip was performed on 96 Baluchi sheep to identify the genomic regions associated with 8-month weight. The results of the present study revealed five SNPs on chromosomes 4, 14 and 16 at 5% chromosome-wide significance level, jointly accounting for 0.95% of total genetic variance. Four genes - MTPN, HYDIN, LRGUK and ZFP90 - were found in 50 kb intervals around the significant SNPs, of which MTPN is involved in regulation of skeletal muscle growth. Our results may provide a new vision to identify the genomic regions affecting growth traits in sheep.", "doi": "10.1111/age.12996", "pmid": "32910467", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [], "notes": [], "created": "2020-10-20T06:59:17.372Z", "modified": "2021-11-10T12:44:54.023Z"}, {"entity": "publication", "iuid": "5f2e4baa8bb24a13a4e27bafb78c7f35", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5f2e4baa8bb24a13a4e27bafb78c7f35.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5f2e4baa8bb24a13a4e27bafb78c7f35"}}, "title": "Association between Aquatic Micropollutant Dissipation and River Sediment Bacterial Communities.", "authors": [{"family": "Coll", "given": "Claudia", "initials": "C", "orcid": "0000-0003-1100-1263", "researcher": {"href": "https://publications.scilifelab.se/researcher/d5bdee5b986a4dfda04324367a6a8c4f.json"}}, {"family": "Bier", "given": "Raven", "initials": "R"}, {"family": "Li", "given": "Zhe", "initials": "Z", "orcid": "0000-0002-2379-0768", "researcher": {"href": "https://publications.scilifelab.se/researcher/45eed765d4944b9ebe33a7f4536ce36f.json"}}, {"family": "Langenheder", "given": "Silke", "initials": "S"}, {"family": "Gorokhova", "given": "Elena", "initials": "E"}, {"family": "Sobek", "given": "Anna", "initials": "A", "orcid": "0000-0002-1549-7449", "researcher": {"href": "https://publications.scilifelab.se/researcher/4d5f089d428b4c1b9b0805dcbf4c6fbc.json"}}], "type": "journal article", "published": "2020-11-17", "journal": {"title": "Environ. Sci. Technol.", "issn": "1520-5851", "volume": "54", "issue": "22", "pages": "14380-14392", "issn-l": "0013-936X"}, "abstract": "Assessment of micropollutant biodegradation is essential to determine the persistence of potentially hazardous chemicals in aquatic ecosystems. We studied the dissipation half-lives of 10 micropollutants in sediment-water incubations (based on the OECD 308 standard) with sediment from two European rivers sampled upstream and downstream of wastewater treatment plant (WWTP) discharge. Dissipation half-lives (DT50s) were highly variable between the tested compounds, ranging from 1.5 to 772 days. Sediment from one river sampled downstream from the WWTP showed the fastest dissipation of all micropollutants after sediment RNA normalization. By characterizing sediment bacteria using 16S rRNA sequences, bacterial community composition of a sediment was associated with its capacity for dissipating micropollutants. Bacterial amplicon sequence variants of the genera Ralstonia, Pseudomonas, Hyphomicrobium, and Novosphingobium, which are known degraders of contaminants, were significantly more abundant in the sediment incubations where fast dissipation was observed. Our study illuminates the limitations of the OECD 308 standard to account for variation of dissipation rates of micropollutants due to differences in bacterial community composition. This limitation is problematic particularly for those compounds with DT50s close to regulatory persistence criteria. Thus, it is essential to consider bacterial community composition as a source of variability in regulatory biodegradation and persistence assessments.", "doi": "10.1021/acs.est.0c04393", "pmid": "33104348", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC7676288"}], "notes": [], "created": "2020-12-08T23:52:07.112Z", "modified": "2021-11-10T12:45:14.866Z"}, {"entity": "publication", "iuid": "4eaba3d139bf427eb332f2f93f77bf0a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4eaba3d139bf427eb332f2f93f77bf0a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4eaba3d139bf427eb332f2f93f77bf0a"}}, "title": "Evaluation of the efficiency of genomic versus pedigree predictions for growth and wood quality traits in Scots pine.", "authors": [{"family": "Calleja-Rodriguez", "given": "Ainhoa", "initials": "A"}, {"family": "Pan", "given": "Jin", "initials": "J"}, {"family": "Funda", "given": "Tomas", "initials": "T"}, {"family": "Chen", "given": "Zhiqiang", "initials": "Z"}, {"family": "Baison", "given": "John", "initials": "J"}, {"family": "Isik", "given": "Fikret", "initials": "F"}, {"family": "Abrahamsson", "given": "Sara", "initials": "S"}, {"family": "Wu", "given": "Harry X", "initials": "HX"}], "type": "journal article", "published": "2020-11-16", "journal": {"title": "BMC Genomics", "issn": "1471-2164", "volume": "21", "issue": "1", "pages": "796", "issn-l": "1471-2164"}, "abstract": "Genomic selection (GS) or genomic prediction is a promising approach for tree breeding to obtain higher genetic gains by shortening time of progeny testing in breeding programs. As proof-of-concept for Scots pine (Pinus sylvestris L.), a genomic prediction study was conducted with 694 individuals representing 183 full-sib families that were genotyped with genotyping-by-sequencing (GBS) and phenotyped for growth and wood quality traits. 8719 SNPs were used to compare different genomic with pedigree prediction models. Additionally, four prediction efficiency methods were used to evaluate the impact of genomic breeding value estimations by assigning diverse ratios of training and validation sets, as well as several subsets of SNP markers.\n\nGenomic Best Linear Unbiased Prediction (GBLUP) and Bayesian Ridge Regression (BRR) combined with expectation maximization (EM) imputation algorithm showed slightly higher prediction efficiencies than Pedigree Best Linear Unbiased Prediction (PBLUP) and Bayesian LASSO, with some exceptions. A subset of approximately 6000 SNP markers, was enough to provide similar prediction efficiencies as the full set of 8719 markers. Additionally, prediction efficiencies of genomic models were enough to achieve a higher selection response, that varied between 50-143% higher than the traditional pedigree-based selection.\n\nAlthough prediction efficiencies were similar for genomic and pedigree models, the relative selection response was doubled for genomic models by assuming that earlier selections can be done at the seedling stage, reducing the progeny testing time, thus shortening the breeding cycle length roughly by 50%.", "doi": "10.1186/s12864-020-07188-4", "pmid": "33198692", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1186/s12864-020-07188-4"}, {"db": "pmc", "key": "PMC7667760"}], "notes": [], "created": "2020-12-08T23:32:05.662Z", "modified": "2024-01-16T13:48:41.324Z"}, {"entity": "publication", "iuid": "ba07627b1e2248a8a43555deaf34e3ba", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ba07627b1e2248a8a43555deaf34e3ba.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ba07627b1e2248a8a43555deaf34e3ba"}}, "title": "Association of aberrant ASNS imprinting with asparaginase sensitivity and chromosomal abnormality in childhood BCP-ALL.", "authors": [{"family": "Watanabe", "given": "Atsushi", "initials": "A", "orcid": "0000-0002-4181-8111", "researcher": {"href": "https://publications.scilifelab.se/researcher/665105919804451f904064e4a5d9b09f.json"}}, {"family": "Miyake", "given": "Kunio", "initials": "K", "orcid": "0000-0001-9196-2229", "researcher": {"href": "https://publications.scilifelab.se/researcher/a0c7fbd039fb4cb3bfac5060038111fb.json"}}, {"family": "Nordlund", "given": "Jessica", "initials": "J", "orcid": "0000-0001-8699-9959", "researcher": {"href": "https://publications.scilifelab.se/researcher/ddf48c9262134821bcc6ce1180049753.json"}}, {"family": "Syv\u00e4nen", "given": "Ann-Christine", "initials": "AC", "orcid": "0000-0002-9681-9146", "researcher": {"href": "https://publications.scilifelab.se/researcher/f7012e35025543379380cb90efd71243.json"}}, {"family": "van der Weyden", "given": "Louise", "initials": "L", "orcid": "0000-0002-0645-1879", "researcher": {"href": "https://publications.scilifelab.se/researcher/ad8d71311de74b26bf7b706854478854.json"}}, {"family": "Honda", "given": "Hiroaki", "initials": "H"}, {"family": "Yamasaki", "given": "Norimasa", "initials": "N"}, {"family": "Nagamachi", "given": "Akiko", "initials": "A"}, {"family": "Inaba", "given": "Toshiya", "initials": "T", "orcid": "0000-0002-3455-6010", "researcher": {"href": "https://publications.scilifelab.se/researcher/9592ee7afe1d4969be71f057bfc9fb66.json"}}, {"family": "Ikawa", "given": "Tomokatsu", "initials": "T", "orcid": "0000-0001-9615-8889", "researcher": {"href": "https://publications.scilifelab.se/researcher/4c7ce37a92cb48fdbb2563ea23c64972.json"}}, {"family": "Urayama", "given": "Kevin Y", "initials": "KY"}, {"family": "Kiyokawa", "given": "Nobutaka", "initials": "N"}, {"family": "Ohara", "given": "Akira", "initials": "A"}, {"family": "Kimura", "given": "Shunsuke", "initials": "S", "orcid": "0000-0002-2158-467X", "researcher": {"href": "https://publications.scilifelab.se/researcher/04a614b852f740db90c696c0274dc814.json"}}, {"family": "Kubota", "given": "Yasuo", "initials": "Y", "orcid": "0000-0002-7909-5422", "researcher": {"href": "https://publications.scilifelab.se/researcher/1d8c368135b047868a9cedf7142fbd8f.json"}}, {"family": "Takita", "given": "Junko", "initials": "J", "orcid": "0000-0002-2452-6520", "researcher": {"href": "https://publications.scilifelab.se/researcher/379d0df3460e400486fd6e4657bd8bf9.json"}}, {"family": "Goto", "given": "Hiroaki", "initials": "H"}, {"family": "Sakaguchi", "given": "Kimiyoshi", "initials": "K", "orcid": "0000-0002-3665-401X", "researcher": {"href": "https://publications.scilifelab.se/researcher/325662e23fc442c49edfe8bfb79f3aa5.json"}}, {"family": "Minegishi", "given": "Masayoshi", "initials": "M"}, {"family": "Iwamoto", "given": "Shotaro", "initials": "S"}, {"family": "Shinohara", "given": "Tamao", "initials": "T", "orcid": "0000-0003-0714-1239", "researcher": {"href": "https://publications.scilifelab.se/researcher/11d525e15d2940ad8eec61f3d9a88afe.json"}}, {"family": "Kagami", "given": "Keiko", "initials": "K"}, {"family": "Abe", "given": "Masako", "initials": "M"}, {"family": "Akahane", "given": "Koshi", "initials": "K", "orcid": "0000-0001-8591-1281", "researcher": {"href": "https://publications.scilifelab.se/researcher/d89f4af20f634416906fdc8d1554c91e.json"}}, {"family": "Goi", "given": "Kumiko", "initials": "K"}, {"family": "Sugita", "given": "Kanji", "initials": "K"}, {"family": "Inukai", "given": "Takeshi", "initials": "T"}], "type": "journal article", "published": "2020-11-12", "journal": {"title": "Blood", "issn": "1528-0020", "volume": "136", "issue": "20", "pages": "2319-2333", "issn-l": "0006-4971"}, "abstract": "Karyotype is an important prognostic factor in childhood B-cell precursor acute lymphoblastic leukemia (BCP-ALL), but the underlying pharmacogenomics remain unknown. Asparaginase is an integral component in current chemotherapy for childhood BCP-ALL. Asparaginase therapy depletes serum asparagine. Normal hematopoietic cells can produce asparagine by asparagine synthetase (ASNS) activity, but ALL cells are unable to synthesize adequate amounts of asparagine. The ASNS gene has a typical CpG island in its promoter. Thus, methylation of the ASNS CpG island could be one of the epigenetic mechanisms for ASNS gene silencing in BCP-ALL. To gain deep insights into the pharmacogenomics of asparaginase therapy, we investigated the association of ASNS methylation status with asparaginase sensitivity. The ASNS CpG island is largely unmethylated in normal hematopoietic cells, but it is allele-specifically methylated in BCP-ALL cells. The ASNS gene is located at 7q21, an evolutionally conserved imprinted gene cluster. ASNS methylation in childhood BCP-ALL is associated with an aberrant methylation of the imprinted gene cluster at 7q21. Aberrant methylation of mouse Asns and a syntenic imprinted gene cluster is also confirmed in leukemic spleen samples from ETV6-RUNX1 knockin mice. In 3 childhood BCP-ALL cohorts, ASNS is highly methylated in BCP-ALL patients with favorable karyotypes but is mostly unmethylated in BCP-ALL patients with poor prognostic karyotypes. Higher ASNS methylation is associated with higher L-asparaginase sensitivity in BCP-ALL through lower ASNS gene and protein expression levels. These observations demonstrate that silencing of the ASNS gene as a result of aberrant imprinting is a pharmacogenetic mechanism for the leukemia-specific activity of asparaginase therapy in BCP-ALL.", "doi": "10.1182/blood.2019004090", "pmid": "32573712", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "S0006-4971(20)79932-5"}, {"db": "pmc", "key": "PMC7702480"}], "notes": [], "created": "2020-11-05T12:22:54.859Z", "modified": "2024-01-16T13:48:41.370Z"}, {"entity": "publication", "iuid": "a8fd622b15c7467f997c96de28f1a14e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a8fd622b15c7467f997c96de28f1a14e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a8fd622b15c7467f997c96de28f1a14e"}}, "title": "Targeted sequencing reveals the somatic mutation landscape in a Swedish breast cancer cohort.", "authors": [{"family": "Mathioudaki", "given": "Argyri", "initials": "A"}, {"family": "Ljungstr\u00f6m", "given": "Viktor", "initials": "V"}, {"family": "Melin", "given": "Malin", "initials": "M", "orcid": "0000-0002-6589-2375", "researcher": {"href": "https://publications.scilifelab.se/researcher/190c3991975c43ec952a81df72292c9a.json"}}, {"family": "Arendt", "given": "Maja Louise", "initials": "ML"}, {"family": "Nordin", "given": "Jessika", "initials": "J", "orcid": "0000-0002-8414-2190", "researcher": {"href": "https://publications.scilifelab.se/researcher/2603df7f3ff84e6980605b9e8eef4c2f.json"}}, {"family": "Karlsson", "given": "\u00c5sa", "initials": "\u00c5"}, {"family": "Mur\u00e9n", "given": "Eva", "initials": "E"}, {"family": "Saksena", "given": "Pushpa", "initials": "P"}, {"family": "Meadows", "given": "Jennifer R S", "initials": "JRS"}, {"family": "Marinescu", "given": "Voichita D", "initials": "VD"}, {"family": "Sj\u00f6blom", "given": "Tobias", "initials": "T", "orcid": "0000-0001-6668-4140", "researcher": {"href": "https://publications.scilifelab.se/researcher/909f00a5bf6e465f9ff560b12bcd863a.json"}}, {"family": "Lindblad-Toh", "given": "Kerstin", "initials": "K", "orcid": "0000-0001-8338-0253", "researcher": {"href": "https://publications.scilifelab.se/researcher/e0063145f7d6476f80ab42f94833f4cf.json"}}], "type": "journal article", "published": "2020-11-09", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "10", "issue": "1", "pages": "19304", "issn-l": "2045-2322"}, "abstract": "Breast cancer (BC) is a genetically heterogeneous disease with high prevalence in Northern Europe. However, there has been no detailed investigation into the Scandinavian somatic landscape. Here, in a homogeneous Swedish cohort, we describe the somatic events underlying BC, leveraging a targeted next-generation sequencing approach. We designed a 20.5 Mb array targeting coding and regulatory regions of genes with a known role in BC (n = 765). The selected genes were either from human BC studies (n = 294) or from within canine mammary tumor associated regions (n = 471). A set of predominantly estrogen receptor positive tumors (ER + 85%) and their normal tissue counterparts (n = 61) were sequenced to ~ 140 \u00d7 and 85 \u00d7 mean target coverage, respectively. MuTect2 and VarScan2 were employed to detect single nucleotide variants (SNVs) and copy number aberrations (CNAs), while MutSigCV (SNVs) and GISTIC (CNAs) algorithms estimated the significance of recurrent somatic events. The significantly mutated genes (q \u2264 0.01) were PIK3CA (28% of patients), TP53 (21%) and CDH1 (11%). However, histone modifying genes contained the largest number of variants (KMT2C and ARID1A, together 28%). Mutations in KMT2C were mutually exclusive with PI3KCA mutations (p \u2264 0. 001) and half of these affect the formation of a functional PHD domain. The tumor suppressor CDK10 was deleted in 80% of the cohort while the oncogene MDM4 was amplified. Mutational signature analyses pointed towards APOBEC deaminase activity (COSMIC signature 2) and DNA mismatch repair (COSMIC signature 6). We noticed two significantly distinct patterns related to patient age; TP53 being more mutated in the younger group (29% vs 9% of patients) and CDH23 mutations were absent from the older group. The increased somatic mutation prevalence in the histone modifying genes KMT2C and ARID1A distinguishes the Swedish cohort from previous studies. KMT2C regulates enhancer activation and assists tumor proliferation in a hormone-rich environment, possibly pointing to a role in ER + BC, especially in older cases. Finally, age of onset appears to affect the mutational landscape suggesting that a larger age-diverse population incorporating more molecular subtypes should be studied to elucidate the underlying mechanisms.", "doi": "10.1038/s41598-020-74580-1", "pmid": "33168853", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-020-74580-1"}, {"db": "pmc", "key": "PMC7653953"}], "notes": [], "created": "2020-12-08T23:29:22.318Z", "modified": "2024-01-16T13:48:41.384Z"}, {"entity": "publication", "iuid": "8278837d4b3745bab6470962fe1dc162", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8278837d4b3745bab6470962fe1dc162.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8278837d4b3745bab6470962fe1dc162"}}, "title": "Identification of candidate genetic variants and altered protein expression in neural stem and mature neural cells support altered microtubule function to be an essential component in bipolar disorder.", "authors": [{"family": "Truv\u00e9", "given": "Katarina", "initials": "K", "orcid": "0000-0002-2449-8283", "researcher": {"href": "https://publications.scilifelab.se/researcher/0c36d2ff5111435aa23416cdfc359b2d.json"}}, {"family": "Parris", "given": "Toshima Z", "initials": "TZ", "orcid": "0000-0003-0834-5540", "researcher": {"href": "https://publications.scilifelab.se/researcher/0d528a2bce6c40829c1a6fed69c9f9ef.json"}}, {"family": "Vizlin-Hodzic", "given": "Dzeneta", "initials": "D", "orcid": "0000-0002-9696-7982", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a86a4c8b32a4af8a90240d44504b32b.json"}}, {"family": "Salmela", "given": "Susanne", "initials": "S"}, {"family": "Berger", "given": "Evelin", "initials": "E"}, {"family": "\u00c5gren", "given": "Hans", "initials": "H", "orcid": "0000-0003-0847-6700", "researcher": {"href": "https://publications.scilifelab.se/researcher/51b06f6b0b8d48fcabe31e6eaf1a08ce.json"}}, {"family": "Funa", "given": "Keiko", "initials": "K"}], "type": "journal article", "published": "2020-11-09", "journal": {"title": "Transl Psychiatry", "issn": "2158-3188", "issn-l": "2158-3188", "volume": "10", "issue": "1", "pages": "390"}, "abstract": "Identification of causative genetic variants leading to the development of bipolar disorder (BD) could result in genetic tests that would facilitate diagnosis. A better understanding of affected genes and pathways is also necessary for targeting of genes that may improve treatment strategies. To date several susceptibility genes have been reported from genome-wide association studies (GWAS), but little is known about specific variants that affect disease development. Here, we performed quantitative proteomics and whole-genome sequencing (WGS). Quantitative proteomics revealed NLRP2 as the most significantly up-regulated protein in neural stem cells and mature neural cells obtained from BD-patient cell samples. These results are in concordance with our previously published transcriptome analysis. Furthermore, the levels of FEZ2 and CADM2 proteins were also significantly differentially expressed in BD compared to control derived cells. The levels of FEZ2 were significantly downregulated in neural stem cells (NSC) while CADM2 was significantly up-regulated in mature neuronal cell culture. Promising novel candidate mutations were identified in the ANK3, NEK3, NEK7, TUBB, ANKRD1, and BRD2 genes. A literature search of candidate variants and deregulated proteins revealed that there are several connections to microtubule function for the molecules putatively involved. Microtubule function in neurons is critical for axon structure and axonal transport. A functional dynamic microtubule is also needed for an advocate response to cellular and environmental stress. If microtubule dynamics is compromised by mutations, it could be followed by deregulated expression forming a possible explanation for the inherited vulnerability to stressful life events that have been proposed to trigger mood episodes in BD patients.", "doi": "10.1038/s41398-020-01056-1", "pmid": "33168801", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41398-020-01056-1"}, {"db": "pmc", "key": "PMC7652854"}], "notes": [], "created": "2020-12-07T16:38:26.771Z", "modified": "2024-01-16T13:48:41.392Z"}, {"entity": "publication", "iuid": "e572bce7ac984e7ea1ff903fed9a1293", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e572bce7ac984e7ea1ff903fed9a1293.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e572bce7ac984e7ea1ff903fed9a1293"}}, "title": "Draft Genome Assembly of the Freshwater Apex Predator Wels Catfish (Silurus glanis) Using Linked-Read Sequencing.", "authors": [{"family": "Ozerov", "given": "Mikhail Yu", "initials": "MY", "orcid": "0000-0002-1817-7707", "researcher": {"href": "https://publications.scilifelab.se/researcher/952f3c17dea44942be07ff8d52cf59c0.json"}}, {"family": "Flaj\u0161hans", "given": "Martin", "initials": "M", "orcid": "0000-0002-0357-5788", "researcher": {"href": "https://publications.scilifelab.se/researcher/d53be81465624a1cb6d3f47d3b1b9b40.json"}}, {"family": "Noreikiene", "given": "Kristina", "initials": "K", "orcid": "0000-0001-7529-4902", "researcher": {"href": "https://publications.scilifelab.se/researcher/2ac9138a3a55468e99283202735f7489.json"}}, {"family": "Vasem\u00e4gi", "given": "Anti", "initials": "A", "orcid": "0000-0002-2184-5534", "researcher": {"href": "https://publications.scilifelab.se/researcher/ad9186f5720d493980b92869fb504cb8.json"}}, {"family": "Gross", "given": "Riho", "initials": "R", "orcid": "0000-0003-0311-3003", "researcher": {"href": "https://publications.scilifelab.se/researcher/6d4530137e284124a79fd721f567703f.json"}}], "type": "journal article", "published": "2020-11-05", "journal": {"title": "G3 (Bethesda)", "issn": "2160-1836", "volume": "10", "issue": "11", "pages": "3897-3906", "issn-l": "2160-1836"}, "abstract": "The wels catfish (Silurus glanis) is one of the largest freshwater fish species in the world. This top predator plays a key role in ecosystem stability, and represents an iconic trophy-fish for recreational fishermen. S. glanis is also a highly valued species for its high-quality boneless flesh, and has been cultivated for over 100 years in Eastern and Central Europe. The interest in rearing S. glanis continues to grow; the aquaculture production of this species has almost doubled during the last decade. However, despite its high ecological, cultural and economic importance, the available genomic resources for S. glanis are very limited. To fulfill this gap we report a de novo assembly and annotation of the whole genome sequence of a female S. glanis The linked-read based technology with 10X Genomics Chromium chemistry and Supernova assembler produced a highly continuous draft genome of S. glanis: \u223c0.8Gb assembly (scaffold N 50 = 3.2 Mb; longest individual scaffold = 13.9 Mb; BUSCO completeness = 84.2%), which included 313.3 Mb of putative repeated sequences. In total, 21,316 protein-coding genes were predicted, of which 96% were annotated functionally from either sequence homology or protein signature searches. The highly continuous genome assembly will be an invaluable resource for aquaculture genomics, genetics, conservation, and breeding research of S. glanis.", "doi": "10.1534/g3.120.401711", "pmid": "32917720", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "g3.120.401711"}, {"db": "pmc", "key": "PMC7642921"}], "notes": [], "created": "2020-11-16T09:14:08.125Z", "modified": "2024-01-16T13:48:41.407Z"}, {"entity": "publication", "iuid": "0356d54a7a4c443ca3b5ba481e0ea20b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0356d54a7a4c443ca3b5ba481e0ea20b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0356d54a7a4c443ca3b5ba481e0ea20b"}}, "title": "Putative Epigenetic Biomarkers of Stress in Red Blood Cells of Chickens Reared Across Different Biomes.", "authors": [{"family": "P\u00e9rtille", "given": "F\u00e1bio", "initials": "F"}, {"family": "Ibelli", "given": "Adriana Mercia Guaratini", "initials": "AMG"}, {"family": "Sharif", "given": "Maj El", "initials": "ME"}, {"family": "Poleti", "given": "Mirele Daiana", "initials": "MD"}, {"family": "Fr\u00f6hlich", "given": "Anna Sophie", "initials": "AS"}, {"family": "Rezaei", "given": "Shiva", "initials": "S"}, {"family": "Ledur", "given": "M\u00f4nica Corr\u00eaa", "initials": "MC"}, {"family": "Jensen", "given": "Per", "initials": "P"}, {"family": "Guerrero-Bosagna", "given": "Carlos", "initials": "C"}, {"family": "Coutinho", "given": "Luiz Lehmann", "initials": "LL"}], "type": "journal article", "published": "2020-11-02", "journal": {"title": "Front Genet", "issn": "1664-8021", "issn-l": "1664-8021", "volume": "11", "issue": null, "pages": "508809"}, "abstract": "Production animals are constantly subjected to early adverse environmental conditions that influence the adult phenotype and produce epigenetic effects. CpG dinucleotide methylation in red blood cells (RBC) could be a useful epigenetic biomarker to identify animals subjected to chronic stress in the production environment. Here we compared a reduced fraction of the RBC methylome of chickens exposed to social isolation to non-exposed. These experiments were performed in two different locations: Brazil and Sweden. The aim was to identify stress-associated DNA methylation profiles in RBC across these populations, in spite of the variable conditions to which birds are exposed in each facility and their different lineages. Birds were increasingly exposed to a social isolation treatment, combined with food and water deprivation, at random periods of the day from weeks 1-4 after hatching. We then collected the RBC DNA from individuals and compared a reduced fraction of their methylome between the experimental groups using two bioinformatic approaches to identify differentially methylated regions (DMRs): one using fixed-size windows and another that preselected differential peaks with MACS2. Three levels of significance were used (P \u2264 0.05, P \u2264 0.005, and P \u2264 0.0005) to identify DMRs between experimental groups, which were then used for different analyses. With both of the approaches more DMRs reached the defined significance thresholds in BR individuals compared to SW. However, more DMRs had higher fold change values in SW compared to BR individuals. Interestingly, ChrZ was enriched above expectancy for the presence of DMRs. Additionally, when analyzing the locations of these DMRs in relation to the transcription starting site (TSS), we found three peaks with high DMR presence: 10 kb upstream, the TSS itself, and 20-40 kb downstream. Interestingly, these peaks had DMRs with a high presence (>50%) of specific transcription factor binding sites. Three overlapping DMRs were found between the BR and SW population using the most relaxed p-value (P \u2264 0.05). With the most stringent p-value (P \u2264 0.0005), we found 7 and 4 DMRs between treatments in the BR and SW populations, respectively. This study is the first approximation to identify epigenetic biomarkers of long-term exposure to stress in different lineages of production animals.", "doi": "10.3389/fgene.2020.508809", "pmid": "33240310", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC7667380"}], "notes": [], "created": "2020-12-07T16:38:30.735Z", "modified": "2021-11-10T12:45:39.955Z"}, {"entity": "publication", "iuid": "a0dda33b98ee48789e7ac7a800a80bb5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a0dda33b98ee48789e7ac7a800a80bb5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a0dda33b98ee48789e7ac7a800a80bb5"}}, "title": "Pericyte dysfunction due to Shb gene deficiency increases B16F10 melanoma lung metastasis.", "authors": [{"family": "He", "given": "Qi", "initials": "Q"}, {"family": "Li", "given": "Xiujuan", "initials": "X"}, {"family": "He", "given": "Liqun", "initials": "L"}, {"family": "Li", "given": "Yousheng", "initials": "Y"}, {"family": "Betsholtz", "given": "Christer", "initials": "C"}, {"family": "Welsh", "given": "Michael", "initials": "M", "orcid": "0000-0002-5467-9755", "researcher": {"href": "https://publications.scilifelab.se/researcher/c01673aeb9be429c80da30d5407b2725.json"}}], "type": "journal article", "published": "2020-11-01", "journal": {"title": "Int. J. Cancer", "issn": "1097-0215", "volume": "147", "issue": "9", "pages": "2634-2644", "issn-l": "0020-7136"}, "abstract": "Intravasation, vascular dissemination and metastasis of malignant tumor cells require their passage through the vascular wall which is commonly composed of pericytes and endothelial cells. We currently decided to investigate the relative contribution of these cell types to B16F10 melanoma metastasis in mice using an experimental model of host Shb gene (Src homology 2 domain-containing protein B) inactivation. Conditional inactivation of Shb in endothelial cells using Cdh5-CreERt2 resulted in decreased tumor growth, reduced vascular leakage, increased hypoxia and no effect on pericyte coverage and lung metastasis. RNAseq of tumor endothelial cells from these mice revealed changes in cellular components such as adherens junctions and focal adhesions by gene ontology analysis that were in line with the observed effects on leakage and junction morphology. Conditional inactivation of Shb in pericytes using Pdgfrb-CreERt2 resulted in decreased pericyte coverage of small tumor vessels with lumen, increased leakage, aberrant platelet-derived growth factor receptor B (PDGFRB) signaling and a higher frequency of lung metastasis without concomitant effects on tumor growth or oxygenation. Flow cytometry failed to reveal immune cell alterations that could explain the metastatic phenotype in this genetic model of Shb deficiency. It is concluded that proper pericyte function plays a significant role in suppressing B16F10 lung metastasis.", "doi": "10.1002/ijc.33110", "pmid": "32441314", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2020-12-08T23:56:20.495Z", "modified": "2024-01-16T13:48:41.445Z"}, {"entity": "publication", "iuid": "2fcbe860666e49c1a3a45f5de295f491", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2fcbe860666e49c1a3a45f5de295f491.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2fcbe860666e49c1a3a45f5de295f491"}}, "title": "Angiotensin-converting enzyme 2 (ACE2) levels in relation to risk factors for COVID-19 in two large cohorts of patients with atrial fibrillation.", "authors": [{"family": "Wallentin", "given": "Lars", "initials": "L", "orcid": "0000-0003-0378-6531", "researcher": {"href": "https://publications.scilifelab.se/researcher/388a76db2e4d423882d1cf2bf6b7d985.json"}}, {"family": "Lindb\u00e4ck", "given": "Johan", "initials": "J", "orcid": "0000-0002-6473-8798", "researcher": {"href": "https://publications.scilifelab.se/researcher/3cea1044231d40b5a3bf186485d97cd4.json"}}, {"family": "Eriksson", "given": "Niclas", "initials": "N", "orcid": "0000-0002-2152-4343", "researcher": {"href": "https://publications.scilifelab.se/researcher/64611a83caba46d597f45371b77de26b.json"}}, {"family": "Hijazi", "given": "Ziad", "initials": "Z"}, {"family": "Eikelboom", "given": "John W", "initials": "JW"}, {"family": "Ezekowitz", "given": "Michael D", "initials": "MD", "orcid": "0000-0003-3623-2252", "researcher": {"href": "https://publications.scilifelab.se/researcher/43f3a6f18de74bb6a632b1b16d1b778c.json"}}, {"family": "Granger", "given": "Christopher B", "initials": "CB"}, {"family": "Lopes", "given": "Renato D", "initials": "RD"}, {"family": "Yusuf", "given": "Salim", "initials": "S"}, {"family": "Oldgren", "given": "Jonas", "initials": "J", "orcid": "0000-0002-9969-3921", "researcher": {"href": "https://publications.scilifelab.se/researcher/14e1774fd1674edeaaa64a3f86d051d7.json"}}, {"family": "Siegbahn", "given": "Agneta", "initials": "A"}], "type": "journal article", "published": "2020-11-01", "journal": {"title": "Eur. Heart J.", "issn": "1522-9645", "volume": "41", "issue": "41", "pages": "4037-4046", "issn-l": "0195-668X"}, "abstract": "The global COVID-19 pandemic is caused by the SARS-CoV-2 virus entering human cells using angiotensin-converting enzyme 2 (ACE2) as a cell surface receptor. ACE2 is shed to the circulation, and a higher plasma level of soluble ACE2 (sACE2) might reflect a higher cellular expression of ACE2. The present study explored the associations between sACE2 and clinical factors, cardiovascular biomarkers, and genetic variability.\n\nPlasma and DNA samples were obtained from two international cohorts of elderly patients with atrial fibrillation (n = 3999 and n = 1088). The sACE2 protein level was measured by the Olink Proteomics\u00ae Multiplex CVD II96 \u00d7 96 panel. Levels of the biomarkers high-sensitive cardiac troponin T (hs-cTnT), N-terminal probrain natriuretic peptide (NT-proBNP), growth differentiation factor 15 (GDF-15), C-reactive protein, interleukin-6, D-dimer, and cystatin-C were determined by immunoassays. Genome-wide association studies were performed by Illumina chips. Higher levels of sACE2 were statistically significantly associated with male sex, cardiovascular disease, diabetes, and older age. The sACE2 level was most strongly associated with the levels of GDF-15, NT-proBNP, and hs-cTnT. When adjusting for these biomarkers, only male sex remained associated with sACE2. We found no statistically significant genetic regulation of the sACE2 level.\n\nMale sex and clinical or biomarker indicators of biological ageing, cardiovascular disease, and diabetes are associated with higher sACE2 levels. The levels of GDF-15 and NT-proBNP, which are associated both with the sACE2 level and a higher risk for mortality and cardiovascular disease, might contribute to better identification of risk for severe COVID-19 infection.", "doi": "10.1093/eurheartj/ehaa697", "pmid": "32984892", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Affinity Proteomics Uppsala": "Service"}, "xrefs": [{"db": "pii", "key": "5912214"}, {"db": "pmc", "key": "PMC7543499"}, {"db": "ClinicalTrials.gov", "key": "NCT00262600"}, {"db": "ClinicalTrials.gov", "key": "NCT00412984"}], "notes": [], "created": "2020-10-20T06:59:27.289Z", "modified": "2021-12-10T09:29:55.907Z"}, {"entity": "publication", "iuid": "f4c47f02826749cbafe16bedd0a59d3b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f4c47f02826749cbafe16bedd0a59d3b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f4c47f02826749cbafe16bedd0a59d3b"}}, "title": "The proliferative history shapes the DNA methylome of B-cell tumors and predicts clinical outcome.", "authors": [{"family": "Duran-Ferrer", "given": "Mart\u00ed", "initials": "M", "orcid": "0000-0003-1666-5819", "researcher": {"href": "https://publications.scilifelab.se/researcher/00de5a3a802143d184c21e397fc9b3e3.json"}}, {"family": "Clot", "given": "Guillem", "initials": "G"}, {"family": "Nadeu", "given": "Ferran", "initials": "F", "orcid": "0000-0003-2910-9440", "researcher": {"href": "https://publications.scilifelab.se/researcher/d4654f6b3cd74ddfb4d859edff5fbc95.json"}}, {"family": "Beekman", "given": "Ren\u00e9e", "initials": "R"}, {"family": "Baumann", "given": "Tycho", "initials": "T"}, {"family": "Nordlund", "given": "Jessica", "initials": "J"}, {"family": "Marincevic-Zuniga", "given": "Yanara", "initials": "Y"}, {"family": "L\u00f6nnerholm", "given": "Gudmar", "initials": "G"}, {"family": "Rivas-Delgado", "given": "Alfredo", "initials": "A", "orcid": "0000-0003-0385-3415", "researcher": {"href": "https://publications.scilifelab.se/researcher/7fad7e4db089481582fbc48fe312b7c2.json"}}, {"family": "Mart\u00edn", "given": "Silvia", "initials": "S"}, {"family": "Ordo\u00f1ez", "given": "Raquel", "initials": "R"}, {"family": "Castellano", "given": "Giancarlo", "initials": "G"}, {"family": "Kulis", "given": "Marta", "initials": "M"}, {"family": "Queir\u00f3s", "given": "Ana C", "initials": "AC"}, {"family": "Lee", "given": "Seung-Tae", "initials": "S"}, {"family": "Wiemels", "given": "Joseph", "initials": "J"}, {"family": "Royo", "given": "Romina", "initials": "R"}, {"family": "Puiggr\u00f3s", "given": "Montserrat", "initials": "M", "orcid": "0000-0001-5034-7924", "researcher": {"href": "https://publications.scilifelab.se/researcher/c92c686a51b44dae85d15e867dc8a9b3.json"}}, {"family": "Lu", "given": "Junyan", "initials": "J"}, {"family": "Gin\u00e9", "given": "Eva", "initials": "E"}, {"family": "Be\u00e0", "given": "S\u00edlvia", "initials": "S"}, {"family": "Jares", "given": "Pedro", "initials": "P", "orcid": "0000-0002-8401-579X", "researcher": {"href": "https://publications.scilifelab.se/researcher/763b4efd77664b8aa47a70bb9a577b0f.json"}}, {"family": "Agirre", "given": "Xabier", "initials": "X", "orcid": "0000-0002-6558-9560", "researcher": {"href": "https://publications.scilifelab.se/researcher/4226533ab5484c698a0aa6471dabf848.json"}}, {"family": "Prosper", "given": "Felipe", "initials": "F"}, {"family": "L\u00f3pez-Ot\u00edn", "given": "Carlos", "initials": "C", "orcid": "0000-0001-6964-1904", "researcher": {"href": "https://publications.scilifelab.se/researcher/accdad365e904fd9a8b3c64dcaabbaf5.json"}}, {"family": "Puente", "given": "Xos\u00e9 S", "initials": "XS", "orcid": "0000-0001-9525-1483", "researcher": {"href": "https://publications.scilifelab.se/researcher/3c757bd329184ea2a2aa9183802fefb1.json"}}, {"family": "Oakes", "given": "Christopher C", "initials": "CC"}, {"family": "Zenz", "given": "Thorsten", "initials": "T", "orcid": "0000-0001-7890-9845", "researcher": {"href": "https://publications.scilifelab.se/researcher/8f6b107b1ec94de7bbc260f92f2dcc9f.json"}}, {"family": "Delgado", "given": "Julio", "initials": "J"}, {"family": "L\u00f3pez-Guillermo", "given": "Armando", "initials": "A"}, {"family": "Campo", "given": "El\u00edas", "initials": "E", "orcid": "0000-0001-9850-9793", "researcher": {"href": "https://publications.scilifelab.se/researcher/5642afaa4ed648dfabe66194e42bc01b.json"}}, {"family": "Mart\u00edn-Subero", "given": "Jos\u00e9 Ignacio", "initials": "JI", "orcid": "0000-0001-8809-5195", "researcher": {"href": "https://publications.scilifelab.se/researcher/06ccbd6b7051490fb2764ce9da7a418e.json"}}], "type": "journal article", "published": "2020-11-00", "journal": {"title": "Nat Cancer", "issn": "2662-1347", "issn-l": null, "volume": "1", "issue": "11", "pages": "1066-1081"}, "abstract": "We report a systematic analysis of the DNA methylation variability in 1,595 samples of normal cell subpopulations and 14 tumor subtypes spanning the entire human B-cell lineage. Differential methylation among tumor entities relates to differences in cellular origin and to de novo epigenetic alterations, which allowed us to build an accurate machine learning-based diagnostic algorithm. We identify extensive patient-specific methylation variability in silenced chromatin associated with the proliferative history of normal and neoplastic B cells. Mitotic activity generally leaves both hyper- and hypomethylation imprints, but some B-cell neoplasms preferentially gain or lose DNA methylation. Subsequently, we construct a DNA methylation-based mitotic clock called epiCMIT, whose lapse magnitude represents a strong independent prognostic variable in B-cell tumors and is associated with particular driver genetic alterations. Our findings reveal DNA methylation as a holistic tracer of B-cell tumor developmental history, with implications in the differential diagnosis and prediction of clinical outcome.", "doi": "10.1038/s43018-020-00131-2", "pmid": "34079956", "labels": {"NGI SNP genotyping": "Collaborative", "National Genomics Infrastructure": "Collaborative", "NGI Uppsala (SNP&SEQ Technology Platform)": "Collaborative"}, "xrefs": [{"db": "mid", "key": "NIHMS1700108"}, {"db": "pmc", "key": "PMC8168619"}, {"db": "pii", "key": "10.1038/s43018-020-00131-2"}], "notes": [], "created": "2023-01-03T14:47:04.559Z", "modified": "2023-01-03T14:53:28.577Z"}, {"entity": "publication", "iuid": "b8dd2d1744ce4b89a006f7ffdedaaf6d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b8dd2d1744ce4b89a006f7ffdedaaf6d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b8dd2d1744ce4b89a006f7ffdedaaf6d"}}, "title": "Sahelian pastoralism from the perspective of variants associated with lactase persistence.", "authors": [{"family": "Priehodov\u00e1", "given": "Edita", "initials": "E"}, {"family": "Austerlitz", "given": "Fr\u00e9d\u00e9ric", "initials": "F"}, {"family": "\u010c\u00ed\u017ekov\u00e1", "given": "Martina", "initials": "M"}, {"family": "Nov\u00e1\u010dkov\u00e1", "given": "Jana", "initials": "J"}, {"family": "Ricaut", "given": "Fran\u00e7ois-Xavier", "initials": "FX"}, {"family": "Hofmanov\u00e1", "given": "Zuzana", "initials": "Z"}, {"family": "Schlebusch", "given": "Carina M", "initials": "CM"}, {"family": "\u010cern\u00fd", "given": "Viktor", "initials": "V", "orcid": "0000-0003-1197-6634", "researcher": {"href": "https://publications.scilifelab.se/researcher/4eb871a8b08b461b9d308db875f4f8b9.json"}}], "type": "journal article", "published": "2020-11-00", "journal": {"title": "Am. J. Phys. Anthropol.", "issn": "1096-8644", "volume": "173", "issue": "3", "pages": "423-436", "issn-l": "0002-9483"}, "abstract": "Archeological evidence shows that first nomadic pastoralists came to the African Sahel from northeastern Sahara, where milking is reported by ~7.5 ka. A second wave of pastoralists arrived with the expansion of Arabic tribes in 7th-14th century CE. All Sahelian pastoralists depend on milk production but genetic diversity underlying their lactase persistence (LP) is poorly understood.\n\nWe investigated SNP variants associated with LP in 1,241 individuals from 29 mostly pastoralist populations in the Sahel. Then, we analyzed six SNPs in the neighboring fragment (419 kb) in the Fulani and Tuareg with the -13910*T mutation, reconstructed haplotypes, and calculated expansion age and growth rate of this variant.\n\nOur results reveal a geographic localization of two different LP variants in the Sahel: -13910*T west of Lake Chad (Fulani and Tuareg pastoralists) and -13915*G east of there (mostly Arabic-speaking pastoralists). We show that -13910*T has a more diversified haplotype background among the Fulani than among the Tuareg and that the age estimate for expansion of this variant among the Fulani (~8.5 ka) corresponds to introduction of cattle to the area.\n\nThis is the first study showing that the \"Eurasian\" LP allele -13910*T is widespread both in northern Europe and in the Sahel; however, it is limited to pastoralists in the Sahel. Since the Fulani haplotype with -13910*T is shared with contemporary Eurasians, its origin could be in a region encompassing the Near East and northeastern Africa in a population ancestral to both Saharan pastoralists and European farmers.", "doi": "10.1002/ajpa.24116", "pmid": "32812238", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2020-10-20T06:59:12.759Z", "modified": "2024-01-16T13:48:41.456Z"}, {"entity": "publication", "iuid": "1fcb59bfe89a4aa2bc5101cd706fe80f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1fcb59bfe89a4aa2bc5101cd706fe80f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1fcb59bfe89a4aa2bc5101cd706fe80f"}}, "title": "Optimized metabarcoding with Pacific biosciences enables semi-quantitative analysis of fungal communities.", "authors": [{"family": "Casta\u00f1o", "given": "Carles", "initials": "C", "orcid": "0000-0002-2403-7006", "researcher": {"href": "https://publications.scilifelab.se/researcher/b7bfa857714f425886c4484c15eb59a5.json"}}, {"family": "Berlin", "given": "Anna", "initials": "A", "orcid": "0000-0002-9518-5719", "researcher": {"href": "https://publications.scilifelab.se/researcher/023743c670cc408bb4ed767cb8ee558a.json"}}, {"family": "Brandstr\u00f6m Durling", "given": "Mikael", "initials": "M", "orcid": "0000-0001-6485-197X", "researcher": {"href": "https://publications.scilifelab.se/researcher/7be72d0dcc48489495509b23c7ad3d38.json"}}, {"family": "Ihrmark", "given": "Katharina", "initials": "K"}, {"family": "Lindahl", "given": "Bj\u00f6rn D", "initials": "BD", "orcid": "0000-0002-3384-4547", "researcher": {"href": "https://publications.scilifelab.se/researcher/b7a40688d33545a19c3c666940bda255.json"}}, {"family": "Stenlid", "given": "Jan", "initials": "J", "orcid": "0000-0002-5344-2094", "researcher": {"href": "https://publications.scilifelab.se/researcher/eac6fc31e38c4552a986310015fcb1b4.json"}}, {"family": "Clemmensen", "given": "Karina E", "initials": "KE", "orcid": "0000-0002-9627-6428", "researcher": {"href": "https://publications.scilifelab.se/researcher/73a4e19bdfc1431c9dd1c3f1cd58c766.json"}}, {"family": "Olson", "given": "\u00c5ke", "initials": "\u00c5", "orcid": "0000-0001-8998-6096", "researcher": {"href": "https://publications.scilifelab.se/researcher/83a79139c2b94d9f97cf038e1cab8c03.json"}}], "type": "journal article", "published": "2020-11-00", "journal": {"title": "New Phytol.", "issn": "1469-8137", "issn-l": "0028-646X", "volume": "228", "issue": "3", "pages": null}, "abstract": "Recent studies have questioned the use of high-throughput sequencing of the nuclear ribosomal internal transcribed spacer (ITS) region to derive a semi-quantitative representation of fungal community composition. However, comprehensive studies that quantify biases occurring during PCR and sequencing of ITS amplicons are still lacking. We used artificially assembled communities consisting of 10 ITS-like fragments of varying lengths and guanine-cytosine (GC) contents to evaluate and quantify biases during PCR and sequencing with Illumina MiSeq, PacBio RS II and PacBio Sequel I technologies. Fragment length variation was the main source of bias in observed community composition relative to the template, with longer fragments generally being under-represented for all sequencing platforms. This bias was three times higher for Illumina MiSeq than for PacBio RS II and Sequel I. All 10 fragments in the artificial community were recovered when sequenced with PacBio technologies, whereas the three longest fragments (> 447 bases) were lost when sequenced with Illumina MiSeq. Fragment length bias also increased linearly with increasing number of PCR cycles but could be mitigated by optimization of the PCR setup. No significant biases related to GC content were observed. Despite lower sequencing output, PacBio sequencing was better able to reflect the community composition of the template than Illumina MiSeq sequencing.", "doi": "10.1111/nph.16731", "pmid": "32531109", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [], "notes": [], "created": "2020-08-19T09:21:07.482Z", "modified": "2021-11-10T12:45:47.178Z"}, {"entity": "publication", "iuid": "11f33634ab3146e69138a533798e7438", "links": {"self": {"href": "https://publications.scilifelab.se/publication/11f33634ab3146e69138a533798e7438.json"}, "display": {"href": "https://publications.scilifelab.se/publication/11f33634ab3146e69138a533798e7438"}}, "title": "Identification and rescue of a tRNA wobble inosine deficiency causing intellectual disability disorder.", "authors": [{"family": "Ramos", "given": "Jillian", "initials": "J", "orcid": "0000-0001-8139-5793", "researcher": {"href": "https://publications.scilifelab.se/researcher/d56276e8c1ca41c7afe82887f174caf4.json"}}, {"family": "Proven", "given": "Melissa", "initials": "M"}, {"family": "Halvardson", "given": "Jonatan", "initials": "J"}, {"family": "Hagelskamp", "given": "Felix", "initials": "F"}, {"family": "Kuchinskaya", "given": "Ekaterina", "initials": "E"}, {"family": "Phelan", "given": "Benjamin", "initials": "B"}, {"family": "Bell", "given": "Ryan", "initials": "R"}, {"family": "Kellner", "given": "Stefanie M", "initials": "SM"}, {"family": "Feuk", "given": "Lars", "initials": "L", "orcid": "0000-0003-2355-2919", "researcher": {"href": "https://publications.scilifelab.se/researcher/3eb2f826b3554d4b9971bf0766b275c4.json"}}, {"family": "Thuresson", "given": "Ann-Charlotte", "initials": "AC"}, {"family": "Fu", "given": "Dragony", "initials": "D", "orcid": "0000-0002-8725-8658", "researcher": {"href": "https://publications.scilifelab.se/researcher/77103dd473a54326a9af7151af9d2ef7.json"}}], "type": "journal article", "published": "2020-11-00", "journal": {"title": "RNA", "issn": "1469-9001", "issn-l": "1355-8382", "volume": "26", "issue": "11", "pages": "1654-1666"}, "abstract": "The deamination of adenosine to inosine at the wobble position of tRNA is an essential post-transcriptional RNA modification required for wobble decoding in bacteria and eukaryotes. In humans, the wobble inosine modification is catalyzed by the heterodimeric ADAT2/3 complex. Here, we describe novel pathogenic ADAT3 variants impairing adenosine deaminase activity through a distinct mechanism that can be corrected through expression of the heterodimeric ADAT2 subunit. The variants were identified in a family in which all three siblings exhibit intellectual disability linked to biallelic variants in the ADAT3 locus. The biallelic ADAT3 variants result in a missense variant converting alanine to valine at a conserved residue or the introduction of a premature stop codon in the deaminase domain. Fibroblast cells derived from two ID-affected individuals exhibit a reduction in tRNA wobble inosine levels and severely diminished adenosine tRNA deaminase activity. Notably, the ADAT3 variants exhibit impaired interaction with the ADAT2 subunit and alterations in ADAT2-dependent nuclear localization. Based upon these findings, we find that tRNA adenosine deaminase activity and wobble inosine modification can be rescued in patient cells by overexpression of the ADAT2 catalytic subunit. These results uncover a key role for the inactive ADAT3 deaminase domain in proper assembly with ADAT2 and demonstrate that ADAT2/3 nuclear import is required for maintaining proper levels of the wobble inosine modification in tRNA.", "doi": "10.1261/rna.076380.120", "pmid": "32763916", "labels": {"NGI Uppsala (Uppsala Genome Center)": "Service", "National Genomics Infrastructure": "Service", "Clinical Genomics Uppsala": "Collaborative", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service", "Clinical Genomics": "Collaborative"}, "xrefs": [{"db": "pii", "key": "rna.076380.120"}, {"db": "pmc", "key": "PMC7566568"}], "notes": [], "created": "2020-09-15T07:06:13.955Z", "modified": "2024-01-16T13:48:41.471Z"}, {"entity": "publication", "iuid": "3648126ca4f64fc7a30a03f8065b00fd", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3648126ca4f64fc7a30a03f8065b00fd.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3648126ca4f64fc7a30a03f8065b00fd"}}, "title": "A family-based genome-wide association study of recurrent aphthous stomatitis.", "authors": [{"family": "Bankvall", "given": "Maria", "initials": "M", "orcid": "0000-0003-3949-6739", "researcher": {"href": "https://publications.scilifelab.se/researcher/aa1610a7b02e4460a6da70cd0ee8ae80.json"}}, {"family": "\u00d6stman", "given": "Sofia", "initials": "S"}, {"family": "Jontell", "given": "Mats", "initials": "M"}, {"family": "Torinsson Naluai", "given": "\u00c5sa", "initials": "\u00c5"}], "type": "journal article", "published": "2020-11-00", "journal": {"title": "Oral Dis", "issn": "1601-0825", "volume": "26", "issue": "8", "pages": "1696-1705", "issn-l": "1354-523X"}, "abstract": "The aetiology of recurrent aphthous stomatitis (RAS) remains unknown. Individuals may share features of genetic susceptibility, and there may also be a hereditary component. The aim was to identify patterns of association and segregation for genetic variants and to identify the genes and signalling pathways that determine the risk of developing RAS, through a family-based genome-wide association study (GWAS).\n\nDNA was extracted from buccal swabs of 91 individuals in 16 families and analysed in an Illumina core exome single nucleotide polymorphism (SNP) array. A family-based association test (dFAM) was used to derive SNP association values across all chromosomes.\n\nNone of the final 288,452 SNPs reached the genome-wide significant threshold of 5 \u00d7 10-8 . The most significant pathways were the Ras and PI3K-Akt signalling pathways, pathways in cancer, circadian entrainment and the Rap 1 signalling pathway.\n\nThis confirms that RAS is not monogenic but results as a consequence of interactions between multiple host genes and possibly also environmental factors. The present approach provides novel insights into the mechanisms underlying RAS and raises the possibility of identifying individuals at risk of acquiring this condition.", "doi": "10.1111/odi.13490", "pmid": "32558109", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [], "notes": [], "created": "2020-06-23T11:11:11.532Z", "modified": "2021-11-10T12:45:55.331Z"}, {"entity": "publication", "iuid": "a4c3fac414964931b8a6301041dbf23d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a4c3fac414964931b8a6301041dbf23d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a4c3fac414964931b8a6301041dbf23d"}}, "title": "A comparative genomics multitool for scientific discovery and conservation.", "authors": [{"family": "Zoonomia Consortium", "given": "", "initials": ""}], "type": "journal article", "published": "2020-11-00", "journal": {"title": "Nature", "issn": "1476-4687", "volume": "587", "issue": "7833", "pages": "240-245", "issn-l": "0028-0836"}, "abstract": "The Zoonomia Project is investigating the genomics of shared and specialized traits in eutherian mammals. Here we provide genome assemblies for 131 species, of which all but 9 are previously uncharacterized, and describe a whole-genome alignment of 240 species of considerable phylogenetic diversity, comprising representatives from more than 80% of mammalian families. We find that regions of reduced genetic diversity are more abundant in species at a high risk of extinction, discern signals of evolutionary selection at high resolution and provide insights from individual reference genomes. By prioritizing phylogenetic diversity and making data available quickly and without restriction, the Zoonomia Project aims to support biological discovery, medical research and the conservation of biodiversity.", "doi": "10.1038/s41586-020-2876-6", "pmid": "33177664", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41586-020-2876-6"}, {"db": "pmc", "key": "PMC7759459"}], "notes": [], "created": "2021-06-01T20:49:28.688Z", "modified": "2021-11-10T12:45:56.515Z"}, {"entity": "publication", "iuid": "fdff2262424e46cc949c4ce71f7b8f59", "links": {"self": {"href": "https://publications.scilifelab.se/publication/fdff2262424e46cc949c4ce71f7b8f59.json"}, "display": {"href": "https://publications.scilifelab.se/publication/fdff2262424e46cc949c4ce71f7b8f59"}}, "title": "Intra-Individual Behavioural Variability: A Trait under Genetic Control.", "authors": [{"family": "Henriksen", "given": "Rie", "initials": "R"}, {"family": "H\u00f6glund", "given": "Andrey", "initials": "A", "orcid": "0000-0002-1130-374X", "researcher": {"href": "https://publications.scilifelab.se/researcher/70a484451caf40f2a1a196b36bb9c423.json"}}, {"family": "Fogelholm", "given": "Jesper", "initials": "J", "orcid": "0000-0002-0868-8722", "researcher": {"href": "https://publications.scilifelab.se/researcher/5dc8c561c04f437991504aca4c86593d.json"}}, {"family": "Abbey-Lee", "given": "Robin", "initials": "R"}, {"family": "Johnsson", "given": "Martin", "initials": "M"}, {"family": "Dingemanse", "given": "Niels J", "initials": "NJ", "orcid": "0000-0003-3320-0861", "researcher": {"href": "https://publications.scilifelab.se/researcher/364e2f2173244470bc7f9c1feff13bc9.json"}}, {"family": "Wright", "given": "Dominic", "initials": "D", "orcid": "0000-0003-2329-2635", "researcher": {"href": "https://publications.scilifelab.se/researcher/6447b896ea3b453ab10136b5f44ae241.json"}}], "type": "journal article", "published": "2020-10-29", "journal": {"title": "Int J Mol Sci", "issn": "1422-0067", "issn-l": null, "volume": "21", "issue": "21", "pages": "8069"}, "abstract": "When individuals are measured more than once in the same context they do not behave in exactly the same way each time. The degree of predictability differs between individuals, with some individuals showing low levels of variation around their behavioural mean while others show high levels of variation. This intra-individual variability in behaviour has received much less attention than between-individual variability in behaviour, and very little is known about the underlying mechanisms that affect this potentially large but understudied component of behavioural variation. In this study, we combine standardized behavioural tests in a chicken intercross to estimate intra-individual behavioural variability with a large-scale genomics analysis to identify genes affecting intra-individual behavioural variability in an avian population. We used a variety of different anxiety-related behavioural phenotypes for this purpose. Our study shows that intra-individual variability in behaviour has a direct genetic basis that is largely unique compared to the genetic architecture for the standard behavioural measures they are based on (at least in the detected quantitative trait locus). We identify six suggestive candidate genes that may underpin differences in intra-individual behavioural variability, with several of these candidates having previously been linked to behaviour and mental health. These findings demonstrate that intra-individual variability in behaviour appears to be a heritable trait in and of itself on which evolution can act.", "doi": "10.3390/ijms21218069", "pmid": "33138119", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "ijms21218069"}, {"db": "pmc", "key": "PMC7663371"}], "notes": [], "created": "2021-01-12T13:47:04.128Z", "modified": "2024-01-16T13:48:41.496Z"}, {"entity": "publication", "iuid": "9e62b2cc7c8f49ee82a29100eaf8594f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9e62b2cc7c8f49ee82a29100eaf8594f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9e62b2cc7c8f49ee82a29100eaf8594f"}}, "title": "DNA methylation in canine brains is related to domestication and dog-breed formation.", "authors": [{"family": "Sundman", "given": "Ann-Sofie", "initials": "AS"}, {"family": "P\u00e9rtille", "given": "F\u00e1bio", "initials": "F", "orcid": "0000-0002-7214-9184", "researcher": {"href": "https://publications.scilifelab.se/researcher/2279c5ebf16f419bab7c3af87bac81d3.json"}}, {"family": "Lehmann Coutinho", "given": "Luiz", "initials": "L"}, {"family": "Jazin", "given": "Elena", "initials": "E"}, {"family": "Guerrero-Bosagna", "given": "Carlos", "initials": "C"}, {"family": "Jensen", "given": "Per", "initials": "P", "orcid": "0000-0001-5491-0649", "researcher": {"href": "https://publications.scilifelab.se/researcher/b83892cd7d6a46898629107a11205254.json"}}], "type": "journal article", "published": "2020-10-29", "journal": {"title": "PLoS ONE", "issn": "1932-6203", "volume": "15", "issue": "10", "pages": "e0240787", "issn-l": "1932-6203"}, "abstract": "Epigenetic factors such as DNA methylation act as mediators in the interaction between genome and environment. Variation in the epigenome can both affect phenotype and be inherited, and epigenetics has been suggested to be an important factor in the evolutionary process. During domestication, dogs have evolved an unprecedented between-breed variation in morphology and behavior in an evolutionary short period. In the present study, we explore DNA methylation differences in brain, the most relevant tissue with respect to behavior, between wolf and dog breeds. We optimized a combined method of genotype-by-sequencing (GBS) and methylated DNA immunoprecipitation (MeDIP) for its application in canines. Genomic DNA from the frontal cortex of 38 dogs of 8 breeds and three wolves was used. GBS and GBS-MeDIP libraries were prepared and sequenced on Illuma HiSeq2500 platform. The reduced sample represented 1.18 \u00b1 0.4% of the total dog genome (2,4 billion BP), while the GBS-MeDIP covered 11,250,788 \u00b1 4,042,106 unique base pairs. We find substantial DNA methylation differences between wolf and dog and between the dog breeds. The methylation profiles of the different groups imply that epigenetic factors may have been important in the speciation from dog to wolf, but also in the divergence of different dog breeds. Specifically, we highlight methylation differences in genes related to behavior and morphology. We hypothesize that these differences are involved in the phenotypic variation found among dogs, whereas future studies will have to find the specific mechanisms. Our results not only add an intriguing new dimension to dog breeding but are also useful to further understanding of epigenetic involvement.", "doi": "10.1371/journal.pone.0240787", "pmid": "33119634", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "PONE-D-20-11468"}, {"db": "pmc", "key": "PMC7595415"}], "notes": [], "created": "2020-11-04T06:05:40.841Z", "modified": "2021-11-10T12:46:05.356Z"}, {"entity": "publication", "iuid": "889f5ed4ead54d3c9a1615ea937c77fb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/889f5ed4ead54d3c9a1615ea937c77fb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/889f5ed4ead54d3c9a1615ea937c77fb"}}, "title": "Microbiomes in a manganese oxide producing ecosystem in the Ytterby mine, Sweden: impact on metal mobility.", "authors": [{"family": "Sj\u00f6berg", "given": "Susanne", "initials": "S"}, {"family": "Stairs", "given": "Courtney W", "initials": "CW"}, {"family": "Allard", "given": "Bert", "initials": "B"}, {"family": "Homa", "given": "Felix", "initials": "F"}, {"family": "Martin", "given": "Tom", "initials": "T"}, {"family": "Sj\u00f6berg", "given": "Viktor", "initials": "V"}, {"family": "Ettema", "given": "Thijs J G", "initials": "TJG"}, {"family": "Dupraz", "given": "Christophe", "initials": "C"}], "type": "journal article", "published": "2020-10-28", "journal": {"title": "FEMS Microbiol. Ecol.", "issn": "1574-6941", "issn-l": "0168-6496", "volume": "96", "issue": "11", "pages": null}, "abstract": "Microbe-mediated precipitation of Mn-oxides enriched in rare earth elements (REE) and other trace elements was discovered in tunnels leading to the main shaft of the Ytterby mine, Sweden. Defining the spatial distribution of microorganisms and elements in this ecosystem provide a better understanding of specific niches and parameters driving the emergence of these communities and associated mineral precipitates. Along with elemental analyses, high-throughput sequencing of the following four subsystems were conducted: (i) water seeping from a rock fracture into the tunnel, (ii) Mn-oxides and associated biofilm; referred to as the Ytterby Black Substance (YBS) biofilm (iii) biofilm forming bubbles on the Mn-oxides; referred to as the bubble biofilm and (iv) fracture water that has passed through the biofilms. Each subsystem hosts a specific collection of microorganisms. Differentially abundant bacteria in the YBS biofilm were identified within the Rhizobiales (e.g. Pedomicrobium), PLTA13 Gammaproteobacteria, Pirellulaceae, Hyphomonadaceae, Blastocatellia and Nitrospira. These taxa, likely driving the Mn-oxide production, were not detected in the fracture water. This biofilm binds Mn, REE and other trace elements in an efficient, dynamic process, as indicated by substantial depletion of these metals from the fracture water as it passes through the Mn deposit zone. Microbe-mediated oxidation of Mn(II) and formation of Mn(III/IV)-oxides can thus have considerable local environmental impact by removing metals from aquatic environments.", "doi": "10.1093/femsec/fiaa169", "pmid": "32815988", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "5894917"}, {"db": "pmc", "key": "PMC7593233"}], "notes": [], "created": "2020-12-08T23:17:35.910Z", "modified": "2021-11-10T12:46:08.740Z"}, {"entity": "publication", "iuid": "3d6084989c4c436bb04585ec88b5f5f5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3d6084989c4c436bb04585ec88b5f5f5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3d6084989c4c436bb04585ec88b5f5f5"}}, "title": "Polycomb Repressive Complex 2-mediated histone modification H3K27me3 is associated with embryogenic potential in Norway spruce.", "authors": [{"family": "Nakamura", "given": "Miyuki", "initials": "M", "orcid": "0000-0002-8153-7293", "researcher": {"href": "https://publications.scilifelab.se/researcher/fa9f227109b54fa9a1457a1f7af197af.json"}}, {"family": "Batista", "given": "Rita A", "initials": "RA"}, {"family": "K\u00f6hler", "given": "Claudia", "initials": "C", "orcid": "0000-0002-2619-4857", "researcher": {"href": "https://publications.scilifelab.se/researcher/accd3f9307614c8ab67154dd5e50cdac.json"}}, {"family": "Hennig", "given": "Lars", "initials": "L", "orcid": "0000-0002-6645-1862", "researcher": {"href": "https://publications.scilifelab.se/researcher/9b350e5d9ba74c27bf1709ff0457e605.json"}}], "type": "journal article", "published": "2020-10-22", "journal": {"title": "J. Exp. Bot.", "issn": "1460-2431", "volume": "71", "issue": "20", "pages": "6366-6378", "issn-l": "0022-0957"}, "abstract": "Epigenetic reprogramming during germ cell formation is essential to gain pluripotency and thus embryogenic potential. The histone modification H3K27me3, which is catalysed by the Polycomb repressive complex 2 (PRC2), regulates important developmental processes in both plants and animals, and defects in PRC2 components cause pleiotropic developmental abnormalities. Nevertheless, the role of H3K27me3 in determining embryogenic potential in gymnosperms is still elusive. To address this, we generated H3K27me3 profiles of Norway spruce (Picea abies) embryonic callus and non-embryogenic callus using CUT&RUN, which is a powerful method for chromatin profiling. Here, we show that H3K27me3 mainly accumulated in genic regions in the Norway spruce genome, similarly to what is observed in other plant species. Interestingly, H3K27me3 levels in embryonic callus were much lower than those in the other examined tissues, but markedly increased upon embryo induction. These results show that H3K27me3 levels are associated with the embryogenic potential of a given tissue, and that the early phase of somatic embryogenesis is accompanied by changes in H3K27me3 levels. Thus, our study provides novel insights into the role of this epigenetic mark in spruce embryogenesis and reinforces the importance of PRC2 as a key regulator of cell fate determination across different plant species.", "doi": "10.1093/jxb/eraa365", "pmid": "32894759", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "5902563"}, {"db": "pmc", "key": "PMC7586741"}], "notes": [], "created": "2020-11-16T09:34:27.793Z", "modified": "2021-11-10T12:46:16.725Z"}, {"entity": "publication", "iuid": "98c56bf4a6f549c0895f3cef98a9f04d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/98c56bf4a6f549c0895f3cef98a9f04d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/98c56bf4a6f549c0895f3cef98a9f04d"}}, "title": "Genetic Variants Associated with Non-Alcoholic Fatty Liver Disease Do Not Associate with Measures of Sub-Clinical Atherosclerosis: Results from the IMPROVE Study.", "authors": [{"family": "Castaldo", "given": "Luigi", "initials": "L", "orcid": "0000-0001-6883-9396", "researcher": {"href": "https://publications.scilifelab.se/researcher/2e444841bc62402e82952cc4d24be1b9.json"}}, {"family": "Laguzzi", "given": "Federica", "initials": "F"}, {"family": "Strawbridge", "given": "Rona J", "initials": "RJ", "orcid": "0000-0001-8506-3585", "researcher": {"href": "https://publications.scilifelab.se/researcher/8ac5060a3b37466dae002d4ad8f4d0ac.json"}}, {"family": "Baldassarre", "given": "Damiano", "initials": "D"}, {"family": "Veglia", "given": "Fabrizio", "initials": "F", "orcid": "0000-0002-9378-8874", "researcher": {"href": "https://publications.scilifelab.se/researcher/46cd876aad8b495d982cf2a3ac7bb6aa.json"}}, {"family": "Vigo", "given": "Lorenzo", "initials": "L"}, {"family": "Tremoli", "given": "Elena", "initials": "E"}, {"family": "de Faire", "given": "Ulf", "initials": "U"}, {"family": "Eriksson", "given": "Per", "initials": "P"}, {"family": "Smit", "given": "Andries J", "initials": "AJ"}, {"family": "Aubrecht", "given": "Jiri", "initials": "J"}, {"family": "Leander", "given": "Karin", "initials": "K"}, {"family": "Pirro", "given": "Matteo", "initials": "M"}, {"family": "Giral", "given": "Philippe", "initials": "P"}, {"family": "Ritieni", "given": "Alberto", "initials": "A", "orcid": "0000-0003-0314-8839", "researcher": {"href": "https://publications.scilifelab.se/researcher/920e6797a9ac4ea088cd481b11e85a7f.json"}}, {"family": "Di Minno", "given": "Giovanni", "initials": "G"}, {"family": "M\u00e4larstig", "given": "Anders", "initials": "A", "orcid": "0000-0003-2608-1358", "researcher": {"href": "https://publications.scilifelab.se/researcher/e70c845d32264b448e0b4631b826be6d.json"}}, {"family": "Gigante", "given": "Bruna", "initials": "B"}], "type": "journal article", "published": "2020-10-22", "journal": {"title": "Genes", "issn": "2073-4425", "volume": "11", "issue": "11", "pages": "1243", "issn-l": "2073-4425"}, "abstract": "Non-alcoholic fatty liver disease (NAFLD) and atherosclerosis-related cardiovascular diseases (CVD) share common metabolic pathways. We explored the association between three NAFLD-associated single nucleotide polymorphisms (SNPs) rs738409, rs10401969, and rs1260326 with sub-clinical atherosclerosis estimated by the carotid intima-media thickness (c-IMT) and the inter-adventitia common carotid artery diameter (ICCAD) in patients free from clinically overt NAFLD and CVD. The study population is the IMPROVE, a multicenter European study (n = 3711). C-IMT measures and ICCAD were recorded using a standardized protocol. Linear regression with an additive genetic model was used to test for association of the three SNPs with c-IMT and ICCAD. In secondary analyses, the association of the three SNPs with c-IMT and ICCAD was tested after stratification by alanine aminotransferase levels (ALT). No associations were found between rs738409, rs1260326, rs10401969, and c-IMT or ICCAD. Rs738409-G and rs10401969-C were associated with ALT levels (p < 0.001). In patients with ALT levels above 28 U/L (highest quartile), we observed an association between rs10401969-C and c-IMT measures of c-IMTmax and c-IMTmean-max (p = 0.018 and 0.021, respectively). In conclusion, NAFLD-associated SNPs do not associate with sub-clinical atherosclerosis measures. However, our results suggest a possible mediating function of impaired liver function on atherosclerosis development.", "doi": "10.3390/genes11111243", "pmid": "33105679", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "genes11111243"}, {"db": "pmc", "key": "PMC7690395"}], "notes": [], "created": "2020-11-05T14:07:51.289Z", "modified": "2021-11-10T12:46:17.904Z"}, {"entity": "publication", "iuid": "26891b7047fe4d50971760420593e083", "links": {"self": {"href": "https://publications.scilifelab.se/publication/26891b7047fe4d50971760420593e083.json"}, "display": {"href": "https://publications.scilifelab.se/publication/26891b7047fe4d50971760420593e083"}}, "title": "Khoe-San Genomes Reveal Unique Variation and Confirm the Deepest Population Divergence in Homo sapiens.", "authors": [{"family": "Schlebusch", "given": "Carina M", "initials": "CM", "orcid": "0000-0002-8160-9621", "researcher": {"href": "https://publications.scilifelab.se/researcher/682f10853c1145649b8c76680605dd9b.json"}}, {"family": "Sj\u00f6din", "given": "Per", "initials": "P"}, {"family": "Breton", "given": "Gwenna", "initials": "G", "orcid": "0000-0002-4100-9963", "researcher": {"href": "https://publications.scilifelab.se/researcher/757353d5314b4c20ac2ef4833dd207d9.json"}}, {"family": "G\u00fcnther", "given": "Torsten", "initials": "T"}, {"family": "Naidoo", "given": "Thijessen", "initials": "T"}, {"family": "Hollfelder", "given": "Nina", "initials": "N"}, {"family": "Sj\u00f6strand", "given": "Agnes E", "initials": "AE"}, {"family": "Xu", "given": "Jingzi", "initials": "J"}, {"family": "Gattepaille", "given": "Lucie M", "initials": "LM"}, {"family": "Vicente", "given": "M\u00e1rio", "initials": "M"}, {"family": "Scofield", "given": "Douglas G", "initials": "DG", "orcid": "0000-0001-5235-6461", "researcher": {"href": "https://publications.scilifelab.se/researcher/62a8063a48a446a7947d55f9900894a6.json"}}, {"family": "Malmstr\u00f6m", "given": "Helena", "initials": "H"}, {"family": "de Jongh", "given": "Michael", "initials": "M"}, {"family": "Lombard", "given": "Marlize", "initials": "M", "orcid": "0000-0002-0675-0414", "researcher": {"href": "https://publications.scilifelab.se/researcher/e04e97bbc9914f358864988174b9b58d.json"}}, {"family": "Soodyall", "given": "Himla", "initials": "H"}, {"family": "Jakobsson", "given": "Mattias", "initials": "M", "orcid": "0000-0001-7840-7853", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a4abe0fcb20492d9ec849c9fbf58a71.json"}}], "type": "journal article", "published": "2020-10-01", "journal": {"title": "Mol. Biol. Evol.", "issn": "1537-1719", "issn-l": "0737-4038", "volume": "37", "issue": "10", "pages": "2944-2954"}, "abstract": "The southern African indigenous Khoe-San populations harbor the most divergent lineages of all living peoples. Exploring their genomes is key to understanding deep human history. We sequenced 25 full genomes from five Khoe-San populations, revealing many novel variants, that 25% of variants are unique to the Khoe-San, and that the Khoe-San group harbors the greatest level of diversity across the globe. In line with previous studies, we found several gene regions with extreme values in genome-wide scans for selection, potentially caused by natural selection in the lineage leading to Homo sapiens and more recent in time. These gene regions included immunity-, sperm-, brain-, diet-, and muscle-related genes. When accounting for recent admixture, all Khoe-San groups display genetic diversity approaching the levels in other African groups and a reduction in effective population size starting around 100,000 years ago. Hence, all human groups show a reduction in effective population size commencing around the time of the Out-of-Africa migrations, which coincides with changes in the paleoclimate records, changes that potentially impacted all humans at the time.", "doi": "10.1093/molbev/msaa140", "pmid": "32697301", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "5874945"}, {"db": "pmc", "key": "PMC7530619"}], "notes": [], "created": "2020-12-08T23:26:14.491Z", "modified": "2024-01-16T13:48:41.609Z"}, {"entity": "publication", "iuid": "154532dd2cc14c359aedcbc68f77a29c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/154532dd2cc14c359aedcbc68f77a29c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/154532dd2cc14c359aedcbc68f77a29c"}}, "title": "Brain Transcriptomics of Wild and Domestic Rabbits Suggests That Changes in Dopamine Signaling and Ciliary Function Contributed to Evolution of Tameness.", "authors": [{"family": "Sato", "given": "Daiki X", "initials": "DX", "orcid": "0000-0002-9527-8253", "researcher": {"href": "https://publications.scilifelab.se/researcher/7ad2eafb0bce4d2ba7c4f9cf7ed05eac.json"}}, {"family": "Rafati", "given": "Nima", "initials": "N", "orcid": "0000-0002-3687-9745", "researcher": {"href": "https://publications.scilifelab.se/researcher/8b5c32bab72f430a80485c0312ca0e21.json"}}, {"family": "Ring", "given": "Henrik", "initials": "H"}, {"family": "Younis", "given": "Shady", "initials": "S"}, {"family": "Feng", "given": "Chungang", "initials": "C"}, {"family": "Blanco-Aguiar", "given": "Jos\u00e9 A", "initials": "JA"}, {"family": "Rubin", "given": "Carl-Johan", "initials": "CJ"}, {"family": "Villafuerte", "given": "Rafael", "initials": "R"}, {"family": "Hallb\u00f6\u00f6k", "given": "Finn", "initials": "F", "orcid": "0000-0001-7552-187X", "researcher": {"href": "https://publications.scilifelab.se/researcher/6fd6bad55b67431c82e2e54e5b007917.json"}}, {"family": "Carneiro", "given": "Miguel", "initials": "M"}, {"family": "Andersson", "given": "Leif", "initials": "L", "orcid": "0000-0002-4085-6968", "researcher": {"href": "https://publications.scilifelab.se/researcher/bd3343c12f994b1fabcae23027d3a76d.json"}}], "type": "comparative study", "published": "2020-10-01", "journal": {"title": "Genome Biol Evol", "issn": "1759-6653", "volume": "12", "issue": "10", "pages": "1918-1928", "issn-l": "1759-6653"}, "abstract": "Domestication has resulted in immense phenotypic changes in animals despite their relatively short evolutionary history. The European rabbit is one of the most recently domesticated animals, but exhibits distinct morphological, physiological, and behavioral differences from their wild conspecifics. A previous study revealed that sequence variants with striking allele frequency differences between wild and domestic rabbits were enriched in conserved noncoding regions, in the vicinity of genes involved in nervous system development. This suggests that a large proportion of the genetic changes targeted by selection during domestication might affect gene regulation. Here, we generated RNA-sequencing data for four brain regions (amygdala, hypothalamus, hippocampus, and parietal/temporal cortex) sampled at birth and revealed hundreds of differentially expressed genes (DEGs) between wild and domestic rabbits. DEGs in amygdala were significantly enriched for genes associated with dopaminergic function and all 12 DEGs in this category showed higher expression in domestic rabbits. DEGs in hippocampus were enriched for genes associated with ciliary function, all 21 genes in this category showed lower expression in domestic rabbits. These results indicate an important role of dopamine signaling and ciliary function in the evolution of tameness during rabbit domestication. Our study shows that gene expression in specific pathways has been profoundly altered during domestication, but that the majority of genes showing differential expression in this study have not been the direct targets of selection.", "doi": "10.1093/gbe/evaa158", "pmid": "32835359", "labels": {"NGI Uppsala (Uppsala Genome Center)": "Service", "National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "5896528"}, {"db": "pmc", "key": "PMC7594241"}], "notes": [], "created": "2020-09-15T07:00:59.512Z", "modified": "2024-01-16T13:48:41.617Z"}, {"entity": "publication", "iuid": "cbca211bcfb64e4f9988962d8cef7fdb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/cbca211bcfb64e4f9988962d8cef7fdb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/cbca211bcfb64e4f9988962d8cef7fdb"}}, "title": "Genomic and drug target evaluation of 90 cardiovascular proteins in 30,931 individuals.", "authors": [{"family": "Folkersen", "given": "Lasse", "initials": "L", "orcid": "0000-0003-0708-9530", "researcher": {"href": "https://publications.scilifelab.se/researcher/7202a83ff6484d5c9d77f448f93c6520.json"}}, {"family": "Gustafsson", "given": "Stefan", "initials": "S"}, {"family": "Wang", "given": "Qin", "initials": "Q"}, {"family": "Hansen", "given": "Daniel Hvidberg", "initials": "DH", "orcid": "0000-0003-3285-605X", "researcher": {"href": "https://publications.scilifelab.se/researcher/c74393b778ad4c989c6f6f2290eb5f94.json"}}, {"family": "Hedman", "given": "\u00c5sa K", "initials": "\u00c5K"}, {"family": "Schork", "given": "Andrew", "initials": "A"}, {"family": "Page", "given": "Karen", "initials": "K"}, {"family": "Zhernakova", "given": "Daria V", "initials": "DV"}, {"family": "Wu", "given": "Yang", "initials": "Y", "orcid": "0000-0002-0128-7280", "researcher": {"href": "https://publications.scilifelab.se/researcher/5c005cb8ac0a40c38b07b26fc3184354.json"}}, {"family": "Peters", "given": "James", "initials": "J"}, {"family": "Eriksson", "given": "Niclas", "initials": "N", "orcid": "0000-0002-2152-4343", "researcher": {"href": "https://publications.scilifelab.se/researcher/64611a83caba46d597f45371b77de26b.json"}}, {"family": "Bergen", "given": "Sarah E", "initials": "SE"}, {"family": "Boutin", "given": "Thibaud S", "initials": "TS"}, {"family": "Bretherick", "given": "Andrew D", "initials": "AD", "orcid": "0000-0001-9258-3140", "researcher": {"href": "https://publications.scilifelab.se/researcher/177c5c98460c44a79ff1f07c5df05b55.json"}}, {"family": "Enroth", "given": "Stefan", "initials": "S", "orcid": "0000-0002-5056-9137", "researcher": {"href": "https://publications.scilifelab.se/researcher/16bb97ef16ee49f3ae0c7ea0495fd971.json"}}, {"family": "Kalnapenkis", "given": "Anette", "initials": "A"}, {"family": "G\u00e5din", "given": "Jesper R", "initials": "JR"}, {"family": "Suur", "given": "Bianca E", "initials": "BE"}, {"family": "Chen", "given": "Yan", "initials": "Y"}, {"family": "Matic", "given": "Ljubica", "initials": "L"}, {"family": "Gale", "given": "Jeremy D", "initials": "JD"}, {"family": "Lee", "given": "Julie", "initials": "J", "orcid": "0000-0001-6090-6718", "researcher": {"href": "https://publications.scilifelab.se/researcher/724fc189ac8d4764a924f07fe7806058.json"}}, {"family": "Zhang", "given": "Weidong", "initials": "W"}, {"family": "Quazi", "given": "Amira", "initials": "A"}, {"family": "Ala-Korpela", "given": "Mika", "initials": "M", "orcid": "0000-0001-5905-1206", "researcher": {"href": "https://publications.scilifelab.se/researcher/9a1d51911c554533b4f458993efd95e7.json"}}, {"family": "Choi", "given": "Seung Hoan", "initials": "SH"}, {"family": "Claringbould", "given": "Annique", "initials": "A", "orcid": "0000-0002-9201-6557", "researcher": {"href": "https://publications.scilifelab.se/researcher/f273594a78dd47b88de6322bfae64900.json"}}, {"family": "Danesh", "given": "John", "initials": "J"}, {"family": "Davey Smith", "given": "George", "initials": "G", "orcid": "0000-0002-1407-8314", "researcher": {"href": "https://publications.scilifelab.se/researcher/0790d5850377432087ad3900af0044e0.json"}}, {"family": "de Masi", "given": "Federico", "initials": "F"}, {"family": "Elmst\u00e5hl", "given": "S\u00f6lve", "initials": "S"}, {"family": "Engstr\u00f6m", "given": "Gunnar", "initials": "G"}, {"family": "Fauman", "given": "Eric", "initials": "E", "orcid": "0000-0002-9739-0249", "researcher": {"href": "https://publications.scilifelab.se/researcher/33640d6d585f4715ad0754af256954fd.json"}}, {"family": "Fernandez", "given": "Celine", "initials": "C", "orcid": "0000-0003-1290-4982", "researcher": {"href": "https://publications.scilifelab.se/researcher/0403fdacd924464a913261e53f6e6083.json"}}, {"family": "Franke", "given": "Lude", "initials": "L", "orcid": "0000-0002-5159-8802", "researcher": {"href": "https://publications.scilifelab.se/researcher/ee63161f78274a53b615c05555b81a10.json"}}, {"family": "Franks", "given": "Paul W", "initials": "PW", "orcid": "0000-0002-0520-7604", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ebbf40c0f7e49dd8c75a2b6cbf27276.json"}}, {"family": "Giedraitis", "given": "Vilmantas", "initials": "V", "orcid": "0000-0003-3423-2021", "researcher": {"href": "https://publications.scilifelab.se/researcher/7c95879213664e00b66aeee2e8ece975.json"}}, {"family": "Haley", "given": "Chris", "initials": "C", "orcid": "0000-0002-9811-0210", "researcher": {"href": "https://publications.scilifelab.se/researcher/c4fee769cfe84186abbc285881e0529c.json"}}, {"family": "Hamsten", "given": "Anders", "initials": "A"}, {"family": "Ingason", "given": "Andres", "initials": "A"}, {"family": "Johansson", "given": "\u00c5sa", "initials": "\u00c5", "orcid": "0000-0002-2915-4498", "researcher": {"href": "https://publications.scilifelab.se/researcher/76265c54961046e99bdb0439f9ae1d34.json"}}, {"family": "Joshi", "given": "Peter K", "initials": "PK"}, {"family": "Lind", "given": "Lars", "initials": "L"}, {"family": "Lindgren", "given": "Cecilia M", "initials": "CM"}, {"family": "Lubitz", "given": "Steven", "initials": "S", "orcid": "0000-0002-9599-4866", "researcher": {"href": "https://publications.scilifelab.se/researcher/25bb007311104c92983dbcce80f72260.json"}}, {"family": "Palmer", "given": "Tom", "initials": "T", "orcid": "0000-0003-4655-4511", "researcher": {"href": "https://publications.scilifelab.se/researcher/7f71dc0736834c72a59b9b14f1ae471a.json"}}, {"family": "Macdonald-Dunlop", "given": "Erin", "initials": "E", "orcid": "0000-0001-6569-6086", "researcher": {"href": "https://publications.scilifelab.se/researcher/af015c7cf68b470cbca81fe7fa1b58c4.json"}}, {"family": "Magnusson", "given": "Martin", "initials": "M", "orcid": "0000-0003-1710-5936", "researcher": {"href": "https://publications.scilifelab.se/researcher/6126a96481bb4c398a6e8ab6fa596b28.json"}}, {"family": "Melander", "given": "Olle", "initials": "O"}, {"family": "Michaelsson", "given": "Karl", "initials": "K", "orcid": "0000-0003-2815-1217", "researcher": {"href": "https://publications.scilifelab.se/researcher/eff63868e95240f695d47e871e31947f.json"}}, {"family": "Morris", "given": "Andrew P", "initials": "AP"}, {"family": "M\u00e4gi", "given": "Reedik", "initials": "R"}, {"family": "Nagle", "given": "Michael W", "initials": "MW", "orcid": "0000-0002-4677-7582", "researcher": {"href": "https://publications.scilifelab.se/researcher/5da07a509b1740648199997ee5ea73a3.json"}}, {"family": "Nilsson", "given": "Peter M", "initials": "PM", "orcid": "0000-0002-5652-8459", "researcher": {"href": "https://publications.scilifelab.se/researcher/f23c2a10ac2a4d73a8f62b94855635f1.json"}}, {"family": "Nilsson", "given": "Jan", "initials": "J", "orcid": "0000-0002-9752-7479", "researcher": {"href": "https://publications.scilifelab.se/researcher/8777140448bc47f0a7984db3c15c0e23.json"}}, {"family": "Orho-Melander", "given": "Marju", "initials": "M"}, {"family": "Polasek", "given": "Ozren", "initials": "O"}, {"family": "Prins", "given": "Bram", "initials": "B", "orcid": "0000-0001-5774-034X", "researcher": {"href": "https://publications.scilifelab.se/researcher/fd911c5f0da149afb2b4184892ed4b71.json"}}, {"family": "P\u00e5lsson", "given": "Erik", "initials": "E"}, {"family": "Qi", "given": "Ting", "initials": "T"}, {"family": "Sj\u00f6gren", "given": "Marketa", "initials": "M"}, {"family": "Sundstr\u00f6m", "given": "Johan", "initials": "J", "orcid": "0000-0003-2247-8454", "researcher": {"href": "https://publications.scilifelab.se/researcher/91a40d3c138d43f2b0d38f66be4b71c7.json"}}, {"family": "Surendran", "given": "Praveen", "initials": "P"}, {"family": "V\u00f5sa", "given": "Urmo", "initials": "U"}, {"family": "Werge", "given": "Thomas", "initials": "T", "orcid": "0000-0003-1829-0766", "researcher": {"href": "https://publications.scilifelab.se/researcher/89e727c9b54c4e23b9104fbc10b7b4e3.json"}}, {"family": "Wernersson", "given": "Rasmus", "initials": "R"}, {"family": "Westra", "given": "Harm-Jan", "initials": "H"}, {"family": "Yang", "given": "Jian", "initials": "J"}, {"family": "Zhernakova", "given": "Alexandra", "initials": "A"}, {"family": "\u00c4rnl\u00f6v", "given": "Johan", "initials": "J"}, {"family": "Fu", "given": "Jingyuan", "initials": "J", "orcid": "0000-0001-5578-1236", "researcher": {"href": "https://publications.scilifelab.se/researcher/e55de478e461486087cec6a8d073666f.json"}}, {"family": "Smith", "given": "J Gustav", "initials": "JG"}, {"family": "Esko", "given": "T\u00f5nu", "initials": "T", "orcid": "0000-0003-1982-6569", "researcher": {"href": "https://publications.scilifelab.se/researcher/d72619c1e29d44e8b8454902d2af8d9e.json"}}, {"family": "Hayward", "given": "Caroline", "initials": "C", "orcid": "0000-0002-9405-9550", "researcher": {"href": "https://publications.scilifelab.se/researcher/cd49e9ad5a024c7ca2f1aa97d9e58eba.json"}}, {"family": "Gyllensten", "given": "Ulf", "initials": "U"}, {"family": "Landen", "given": "Mikael", "initials": "M", "orcid": "0000-0002-4496-6451", "researcher": {"href": "https://publications.scilifelab.se/researcher/792e2b8b8da94572a4d2815703d29749.json"}}, {"family": "Siegbahn", "given": "Agneta", "initials": "A"}, {"family": "Wilson", "given": "James F", "initials": "JF"}, {"family": "Wallentin", "given": "Lars", "initials": "L"}, {"family": "Butterworth", "given": "Adam S", "initials": "AS", "orcid": "0000-0002-6915-9015", "researcher": {"href": "https://publications.scilifelab.se/researcher/7b8c140c80d942c4b1b684876e4d6180.json"}}, {"family": "Holmes", "given": "Michael V", "initials": "MV", "orcid": "0000-0001-6617-0879", "researcher": {"href": "https://publications.scilifelab.se/researcher/2fc91d91672d47fa9759a2af3e3f1f3a.json"}}, {"family": "Ingelsson", "given": "Erik", "initials": "E", "orcid": "0000-0003-2256-6972", "researcher": {"href": "https://publications.scilifelab.se/researcher/689bc741ea6547d18de7080c84d0193e.json"}}, {"family": "M\u00e4larstig", "given": "Anders", "initials": "A", "orcid": "0000-0003-2608-1358", "researcher": {"href": "https://publications.scilifelab.se/researcher/e70c845d32264b448e0b4631b826be6d.json"}}], "type": "journal article", "published": "2020-10-00", "journal": {"title": "Nat Metab", "issn": "2522-5812", "issn-l": "2522-5812", "volume": "2", "issue": "10", "pages": "1135-1148"}, "abstract": "Circulating proteins are vital in human health and disease and are frequently used as biomarkers for clinical decision-making or as targets for pharmacological intervention. Here, we map and replicate protein quantitative trait loci (pQTL) for 90 cardiovascular proteins in over 30,000 individuals, resulting in 451 pQTLs for 85 proteins. For each protein, we further perform pathway mapping to obtain trans-pQTL gene and regulatory designations. We substantiate these regulatory findings with orthogonal evidence for trans-pQTLs using mouse knockdown experiments (ABCA1 and TRIB1) and clinical trial results (chemokine receptors CCR2 and CCR5), with consistent regulation. Finally, we evaluate known drug targets, and suggest new target candidates or repositioning opportunities using Mendelian randomization. This identifies 11 proteins with causal evidence of involvement in human disease that have not previously been targeted, including EGF, IL-16, PAPPA, SPON1, F3, ADM, CASP-8, CHI3L1, CXCL16, GDF15 and MMP-12. Taken together, these findings demonstrate the utility of large-scale mapping of the genetics of the proteome and provide a resource for future precision studies of circulating proteins in human health.", "doi": "10.1038/s42255-020-00287-2", "pmid": "33067605", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Affinity Proteomics Uppsala": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s42255-020-00287-2"}, {"db": "pmc", "key": "PMC7611474"}, {"db": "mid", "key": "EMS131454"}], "notes": [], "created": "2020-10-20T06:59:28.770Z", "modified": "2024-11-27T16:17:54.447Z"}, {"entity": "publication", "iuid": "7a14c5167e074030981441eb5dcefaad", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7a14c5167e074030981441eb5dcefaad.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7a14c5167e074030981441eb5dcefaad"}}, "title": "Function of multiple sclerosis-protective HLA class I alleles revealed by genome-wide protein-quantitative trait loci mapping of interferon signalling.", "authors": [{"family": "Lundtoft", "given": "Christian", "initials": "C", "orcid": "0000-0001-5872-4253", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a05532d3aad4e2dbe00a4724e8dddd8.json"}}, {"family": "Pucholt", "given": "Pascal", "initials": "P", "orcid": "0000-0003-3342-1373", "researcher": {"href": "https://publications.scilifelab.se/researcher/61a214ff2d494b568cb6da944e858acf.json"}}, {"family": "Imgenberg-Kreuz", "given": "Juliana", "initials": "J", "orcid": "0000-0002-7230-8990", "researcher": {"href": "https://publications.scilifelab.se/researcher/5d4c2f630d484ee780c2c12aaabdb939.json"}}, {"family": "Carlsson-Alml\u00f6f", "given": "Jonas", "initials": "J", "orcid": "0000-0002-1211-9821", "researcher": {"href": "https://publications.scilifelab.se/researcher/046904cd12eb4764bd2dcadc876f65d7.json"}}, {"family": "Eloranta", "given": "Maija-Leena", "initials": "ML", "orcid": "0000-0002-8454-1351", "researcher": {"href": "https://publications.scilifelab.se/researcher/d162e060954d420e825884f254886dcd.json"}}, {"family": "Syv\u00e4nen", "given": "Ann-Christine", "initials": "AC", "orcid": "0000-0002-9681-9146", "researcher": {"href": "https://publications.scilifelab.se/researcher/f7012e35025543379380cb90efd71243.json"}}, {"family": "Nordmark", "given": "Gunnel", "initials": "G", "orcid": "0000-0002-3829-7431", "researcher": {"href": "https://publications.scilifelab.se/researcher/188fda53498740dbb007441cc94bb1ad.json"}}, {"family": "Sandling", "given": "Johanna K", "initials": "JK", "orcid": "0000-0003-1382-2321", "researcher": {"href": "https://publications.scilifelab.se/researcher/9c7bae5a05ac47eeac96547ca7336767.json"}}, {"family": "Kockum", "given": "Ingrid", "initials": "I", "orcid": "0000-0002-0867-4726", "researcher": {"href": "https://publications.scilifelab.se/researcher/03ebcc6a01ef4d0db4e4673aff8de5d8.json"}}, {"family": "Olsson", "given": "Tomas", "initials": "T", "orcid": "0000-0002-2938-1877", "researcher": {"href": "https://publications.scilifelab.se/researcher/fd9a20a941214f97a22f010df37cd8e1.json"}}, {"family": "R\u00f6nnblom", "given": "Lars", "initials": "L", "orcid": "0000-0001-9403-6503", "researcher": {"href": "https://publications.scilifelab.se/researcher/053ed3b657124a1bab3a78dc685556e6.json"}}, {"family": "Hagberg", "given": "Niklas", "initials": "N", "orcid": "0000-0003-2064-2716", "researcher": {"href": "https://publications.scilifelab.se/researcher/0d0998bb419c424083b0978ebdbe8629.json"}}], "type": "journal article", "published": "2020-10-00", "journal": {"title": "PLoS Genet.", "issn": "1553-7404", "volume": "16", "issue": "10", "pages": "e1009199", "issn-l": "1553-7390"}, "abstract": "Interferons (IFNs) are cytokines that are central to the host defence against viruses and other microorganisms. If not properly regulated, IFNs may contribute to the pathogenesis of inflammatory autoimmune, or infectious diseases. To identify genetic polymorphisms regulating the IFN system we performed an unbiased genome-wide protein-quantitative trait loci (pQTL) mapping of cell-type specific type I and type II IFN receptor levels and their responses in immune cells from 303 healthy individuals. Seven genome-wide significant (p < 5.0E-8) pQTLs were identified. Two independent SNPs that tagged the multiple sclerosis (MS)-protective HLA class I alleles A*02/A*68 and B*44, respectively, were associated with increased levels of IFNAR2 in B and T cells, with the most prominent effect in IgD-CD27+ memory B cells. The increased IFNAR2 levels in B cells were replicated in cells from an independent set of healthy individuals and in MS patients. Despite increased IFNAR2 levels, B and T cells carrying the MS-protective alleles displayed a reduced response to type I IFN stimulation. Expression and methylation-QTL analysis demonstrated increased mRNA expression of the pseudogene HLA-J in B cells carrying the MS-protective class I alleles, possibly driven via methylation-dependent transcriptional regulation. Together these data suggest that the MS-protective effects of HLA class I alleles are unrelated to their antigen-presenting function, and propose a previously unappreciated function of type I IFN signalling in B and T cells in MS immune-pathogenesis.", "doi": "10.1371/journal.pgen.1009199", "pmid": "33104735", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "PGENETICS-D-20-01001"}, {"db": "pmc", "key": "PMC7644105"}], "notes": [], "created": "2020-11-05T14:07:48.822Z", "modified": "2024-01-16T13:48:41.667Z"}, {"entity": "publication", "iuid": "6c604e82b0474bec8f83ce513a50bfc1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6c604e82b0474bec8f83ce513a50bfc1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6c604e82b0474bec8f83ce513a50bfc1"}}, "title": "Toll-like receptors revisited; a possible role for TLR1 in lupus nephritis.", "authors": [{"family": "Yavuz", "given": "Sule", "initials": "S", "orcid": "0000-0001-5053-6426", "researcher": {"href": "https://publications.scilifelab.se/researcher/21855da83e524b939d9e7aec390e49fc.json"}}, {"family": "Bianchi", "given": "Matteo", "initials": "M"}, {"family": "Kozyrev", "given": "Sergey", "initials": "S"}, {"family": "Bolin", "given": "Karin", "initials": "K"}, {"family": "Leonard", "given": "Dag", "initials": "D"}, {"family": "Pucholt", "given": "Pascal", "initials": "P"}, {"family": "Sandling", "given": "Johanna K", "initials": "JK", "orcid": "0000-0003-1382-2321", "researcher": {"href": "https://publications.scilifelab.se/researcher/9c7bae5a05ac47eeac96547ca7336767.json"}}, {"family": "Bengtsson", "given": "Anders", "initials": "A"}, {"family": "J\u00f6nsen", "given": "Andreas", "initials": "A"}, {"family": "Rantap\u00e4\u00e4-Dahlqvist", "given": "Solbritt", "initials": "S"}, {"family": "Sj\u00f6wall", "given": "Christopher", "initials": "C", "orcid": "0000-0003-0900-2048", "researcher": {"href": "https://publications.scilifelab.se/researcher/fe4dd47b8ca1436e8a26fdea33f5e7f6.json"}}, {"family": "Svenungsson", "given": "Elisabet", "initials": "E", "orcid": "0000-0003-3396-3244", "researcher": {"href": "https://publications.scilifelab.se/researcher/0ab5989c3c604a96bf42b1b6f90434a0.json"}}, {"family": "Gunnarsson", "given": "Iva", "initials": "I"}, {"family": "Lindblad-Toh", "given": "Kerstin", "initials": "K", "orcid": "0000-0001-8338-0253", "researcher": {"href": "https://publications.scilifelab.se/researcher/e0063145f7d6476f80ab42f94833f4cf.json"}}, {"family": "R\u00f6nnblom", "given": "Lars", "initials": "L"}], "type": "letter", "published": "2020-09-29", "journal": {"title": "Ann. Rheum. Dis.", "issn": "1468-2060", "volume": "80", "issue": "3", "pages": "404-406", "issn-l": "0003-4967"}, "abstract": null, "doi": "10.1136/annrheumdis-2020-218373", "pmid": "32994161", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "annrheumdis-2020-218373"}, {"db": "pmc", "key": "PMC7892377"}], "notes": [], "created": "2020-12-08T23:29:04.091Z", "modified": "2021-11-10T12:46:58.369Z"}, {"entity": "publication", "iuid": "69582af9423d4a7eb71db69bd379e100", "links": {"self": {"href": "https://publications.scilifelab.se/publication/69582af9423d4a7eb71db69bd379e100.json"}, "display": {"href": "https://publications.scilifelab.se/publication/69582af9423d4a7eb71db69bd379e100"}}, "title": "Streamlined and Abundant Bacterioplankton Thrive in Functional Cohorts.", "authors": [{"family": "Mondav", "given": "Rhiannon", "initials": "R", "orcid": "0000-0002-5574-5531", "researcher": {"href": "https://publications.scilifelab.se/researcher/0c421592deaa4c1a80abe628c621c901.json"}}, {"family": "Bertilsson", "given": "Stefan", "initials": "S", "orcid": "0000-0002-4265-1835", "researcher": {"href": "https://publications.scilifelab.se/researcher/2c17765c2a9f4383b5383138d11ae93f.json"}}, {"family": "Buck", "given": "Moritz", "initials": "M"}, {"family": "Langenheder", "given": "Silke", "initials": "S", "orcid": "0000-0002-5245-9935", "researcher": {"href": "https://publications.scilifelab.se/researcher/efa9e8f2174a4c7cb903b0f9b895a183.json"}}, {"family": "Lindstr\u00f6m", "given": "Eva S", "initials": "ES", "orcid": "0000-0001-8920-3071", "researcher": {"href": "https://publications.scilifelab.se/researcher/9290d334ce5a4488b8afd2af511e02ad.json"}}, {"family": "Garcia", "given": "Sarahi L", "initials": "SL", "orcid": "0000-0002-8622-0308", "researcher": {"href": "https://publications.scilifelab.se/researcher/8aabc8c17d5b4ad7872c7380301d4562.json"}}], "type": "journal article", "published": "2020-09-29", "journal": {"title": "mSystems", "issn": "2379-5077", "volume": "5", "issue": "5", "pages": null, "issn-l": "2379-5077"}, "abstract": "While fastidious microbes can be abundant and ubiquitous in their natural communities, many fail to grow axenically in laboratories due to auxotrophies or other dependencies. To overcome auxotrophies, these microbes rely on their surrounding cohort. A cohort may consist of kin (ecotypes) or more distantly related organisms (community) with the cooperation being reciprocal or nonreciprocal and expensive (Black Queen hypothesis) or costless (by-product). These metabolic partnerships (whether at single species population or community level) enable dominance by and coexistence of these lineages in nature. Here we examine the relevance of these cooperation models to explain the abundance and ubiquity of the dominant fastidious bacterioplankton of a dimictic mesotrophic freshwater lake. Using both culture-dependent (dilution mixed cultures) and culture-independent (small subunit [SSU] rRNA gene time series and environmental metagenomics) methods, we independently identified the primary cohorts of actinobacterial genera \"Candidatus Planktophila\" (acI-A) and \"Candidatus Nanopelagicus\" (acI-B) and the proteobacterial genus \"Candidatus Fonsibacter\" (LD12). While \"Ca Planktophila\" and \"Ca. Fonsibacter\" had no correlation in their natural habitat, they have the potential to be complementary in laboratory settings. We also investigated the bifunctional catalase-peroxidase enzyme KatG (a common good which \"Ca Planktophila\" is dependent upon) and its most likely providers in the lake. Further, we found that while ecotype and community cooperation combined may explain \"Ca Planktophila\" population abundance, the success of \"Ca. Nanopelagicus\" and \"Ca. Fonsibacter\" is better explained as a community by-product. Ecotype differentiation of \"Ca. Fonsibacter\" as a means of escaping predation was supported but not for overcoming auxotrophies.IMPORTANCE This study examines evolutionary and ecological relationships of three of the most ubiquitous and abundant freshwater bacterial genera: \"Ca Planktophila\" (acI-A), \"Ca. Nanopelagicus\" (acI-B), and \"Ca. Fonsibacter\" (LD12). Due to high abundance, these genera might have a significant influence on nutrient cycling in freshwaters worldwide, and this study adds a layer of understanding to how seemingly competing clades of bacteria can coexist by having different cooperation strategies. Our synthesis ties together network and ecological theory with empirical evidence and lays out a framework for how the functioning of populations within complex microbial communities can be studied.", "doi": "10.1128/mSystems.00316-20", "pmid": "32994284", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "5/5/e00316-20"}, {"db": "pmc", "key": "PMC7527133"}], "notes": [], "created": "2020-12-08T23:35:11.349Z", "modified": "2024-01-16T13:48:41.686Z"}, {"entity": "publication", "iuid": "3cdb55a424e240c89126260f60182ab5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3cdb55a424e240c89126260f60182ab5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3cdb55a424e240c89126260f60182ab5"}}, "title": "Diversity and Abundance of Microbial Communities in UASB Reactors during Methane Production from Hydrolyzed Wheat Straw and Lucerne.", "authors": [{"family": "Liu", "given": "Tong", "initials": "T", "orcid": "0000-0002-6456-4767", "researcher": {"href": "https://publications.scilifelab.se/researcher/1deea3cff23c4ae98c971c82f013ef45.json"}}, {"family": "Schn\u00fcrer", "given": "Anna", "initials": "A", "orcid": "0000-0003-0038-553X", "researcher": {"href": "https://publications.scilifelab.se/researcher/0f81992bc8ed48318f8197fc8caabb4f.json"}}, {"family": "Bj\u00f6rkmalm", "given": "Johanna", "initials": "J"}, {"family": "Willquist", "given": "Karin", "initials": "K"}, {"family": "Kreuger", "given": "Emma", "initials": "E", "orcid": "0000-0002-7797-8854", "researcher": {"href": "https://publications.scilifelab.se/researcher/d7467affb7384af2b78e9a74efbd9c86.json"}}], "type": "journal article", "published": "2020-09-11", "journal": {"title": "Microorganisms", "issn": "2076-2607", "volume": "8", "issue": "9", "pages": "1394", "issn-l": "2076-2607"}, "abstract": "The use of straw for biofuel production is encouraged by the European Union. A previous study showed the feasibility of producing biomethane in upflow anaerobic sludge blanket (UASB) reactors using hydrolyzed, steam-pretreated wheat straw, before and after dark fermentation with Caldicellulosiruptor saccharolyticus, and lucerne. This study provides information on overall microbial community development in those UASB processes and changes related to acidification. The bacterial and archaeal community in granular samples was analyzed using high-throughput amplicon sequencing. Anaerobic digestion model no. 1 (ADM1) was used to predict the abundance of microbial functional groups. The sequencing results showed decreased richness and diversity in the microbial community, and decreased relative abundance of bacteria in relation to archaea, after process acidification. Canonical correspondence analysis showed significant negative correlations between the concentration of organic acids and three phyla, and positive correlations with seven phyla. Organic loading rate and total COD fed also showed significant correlations with microbial community structure, which changed over time. ADM1 predicted a decrease in acetate degraders after a decrease to pH \u2264 6.5. Acidification had a sustained effect on the microbial community and process performance.", "doi": "10.3390/microorganisms8091394", "pmid": "32932830", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "microorganisms8091394"}, {"db": "pmc", "key": "PMC7565072"}], "notes": [], "created": "2020-12-08T23:46:54.290Z", "modified": "2024-01-16T13:48:41.725Z"}, {"entity": "publication", "iuid": "946798060ff74dd29d4437469e57b3d1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/946798060ff74dd29d4437469e57b3d1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/946798060ff74dd29d4437469e57b3d1"}}, "title": "A whole-genome sequenced control population in northern Sweden reveals subregional genetic differences.", "authors": [{"family": "Svensson", "given": "Daniel", "initials": "D", "orcid": "0000-0002-4476-9255", "researcher": {"href": "https://publications.scilifelab.se/researcher/75bc51f60237478abec1fb2969abc873.json"}}, {"family": "Rentoft", "given": "Matilda", "initials": "M"}, {"family": "Dahlin", "given": "Anna M", "initials": "AM"}, {"family": "Lundholm", "given": "Emma", "initials": "E"}, {"family": "Olason", "given": "Pall I", "initials": "PI"}, {"family": "Sj\u00f6din", "given": "Andreas", "initials": "A", "orcid": "0000-0001-5350-4219", "researcher": {"href": "https://publications.scilifelab.se/researcher/6398d7c06a414ea6bcaf2579a8587452.json"}}, {"family": "Nylander", "given": "Carin", "initials": "C"}, {"family": "Melin", "given": "Beatrice S", "initials": "BS"}, {"family": "Trygg", "given": "Johan", "initials": "J", "orcid": "0000-0003-3799-6094", "researcher": {"href": "https://publications.scilifelab.se/researcher/7df02186ac1a4a60952737b1690363b7.json"}}, {"family": "Johansson", "given": "Erik", "initials": "E", "orcid": "0000-0002-8526-6224", "researcher": {"href": "https://publications.scilifelab.se/researcher/3503f87335764d4185fade92739855e9.json"}}], "type": "journal article", "published": "2020-09-11", "journal": {"title": "PLoS ONE", "issn": "1932-6203", "volume": "15", "issue": "9", "pages": "e0237721", "issn-l": "1932-6203"}, "abstract": "The number of national reference populations that are whole-genome sequenced are rapidly increasing. Partly driving this development is the fact that genetic disease studies benefit from knowing the genetic variation typical for the geographical area of interest. A whole-genome sequenced Swedish national reference population (n = 1000) has been recently published but with few samples from northern Sweden. In the present study we have whole-genome sequenced a control population (n = 300) (ACpop) from V\u00e4sterbotten County, a sparsely populated region in northern Sweden previously shown to be genetically different from southern Sweden. The aggregated variant frequencies within ACpop are publicly available (DOI 10.17044/NBIS/G000005) to function as a basic resource in clinical genetics and for genetic studies. Our analysis of ACpop, representing approximately 0.11% of the population in V\u00e4sterbotten, indicates the presence of a genetic substructure within the county. Furthermore, a demographic analysis showed that the population from which samples were drawn was to a large extent geographically stationary, a finding that was corroborated in the genetic analysis down to the level of municipalities. Including ACpop in the reference population when imputing unknown variants in a V\u00e4sterbotten cohort resulted in a strong increase in the number of high-confidence imputed variants (up to 81% for variants with minor allele frequency < 5%). ACpop was initially designed for cancer disease studies, but the genetic structure within the cohort will be of general interest for all genetic disease studies in northern Sweden.", "doi": "10.1371/journal.pone.0237721", "pmid": "32915809", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "PONE-D-20-06062"}, {"db": "pmc", "key": "PMC7485808"}], "notes": [], "created": "2020-12-08T23:48:26.250Z", "modified": "2024-01-16T13:48:41.742Z"}, {"entity": "publication", "iuid": "f944b02e41bf428d8dfb2d7c6a8a8221", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f944b02e41bf428d8dfb2d7c6a8a8221.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f944b02e41bf428d8dfb2d7c6a8a8221"}}, "title": "River biofilms adapted to anthropogenic disturbances are more resistant to WWTP inputs.", "authors": [{"family": "Freixa", "given": "Anna", "initials": "A", "orcid": "0000-0003-1149-6526", "researcher": {"href": "https://publications.scilifelab.se/researcher/69bacfaa677d4e53afdcac4c46070093.json"}}, {"family": "Perujo", "given": "N\u00faria", "initials": "N"}, {"family": "Langenheder", "given": "Silke", "initials": "S"}, {"family": "Roman\u00ed", "given": "Anna M", "initials": "AM"}], "type": "journal article", "published": "2020-09-01", "journal": {"title": "FEMS Microbiol. Ecol.", "issn": "1574-6941", "issn-l": "0168-6496", "volume": "96", "issue": "9", "pages": null}, "abstract": "The sensitivity and spatial recovery of river sediment biofilms along 1 km after the input of two wastewater treatment plants (WWTPs) located in two river reaches with different degrees of anthropogenic influence were investigated. First, at the upper reach, we observed an inhibition of some microbial functions (microbial respiration and extracellular enzyme activities) and strong shifts in bacterial community composition (16S rRNA gene), whereas an increase in microbial biomass and activity and less pronounced effect on microbial diversity and community composition were seen at the lower reach. Second, at the lower reach we observed a quick spatial recovery (around 200 m downstream of the effluent) as most of the functions and community composition were similar to those from reference sites. On the other hand, bacterial community composition and water quality at the upper reach was still altered 1 km from the WWTP effluent. Our results indicate that biofilms in the upstream sites were more sensitive to the effect of WWTPs due to a lower degree of tolerance after a disturbance than communities located in more anthropogenically impacted sites.", "doi": "10.1093/femsec/fiaa152", "pmid": "32766791", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "5884858"}], "notes": [], "created": "2020-12-08T23:18:43.974Z", "modified": "2024-01-16T13:48:41.772Z"}, {"entity": "publication", "iuid": "adf88ccfb5234e1a956955924cb042b7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/adf88ccfb5234e1a956955924cb042b7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/adf88ccfb5234e1a956955924cb042b7"}}, "title": "Genetic comorbidity between major depression and cardio-metabolic traits, stratified by age at onset of major depression.", "authors": [{"family": "Hagenaars", "given": "Saskia P", "initials": "SP", "orcid": "0000-0001-9697-8596", "researcher": {"href": "https://publications.scilifelab.se/researcher/2648f5c01c0d497c96f18f3836117aac.json"}}, {"family": "Coleman", "given": "Jonathan R I", "initials": "JRI", "orcid": "0000-0002-6759-0944", "researcher": {"href": "https://publications.scilifelab.se/researcher/91f9f96c887447918926b36de9cfc820.json"}}, {"family": "Choi", "given": "Shing Wan", "initials": "SW"}, {"family": "Gaspar", "given": "H\u00e9l\u00e9na", "initials": "H"}, {"family": "Adams", "given": "Mark J", "initials": "MJ"}, {"family": "Howard", "given": "David M", "initials": "DM"}, {"family": "Hodgson", "given": "Karen", "initials": "K"}, {"family": "Traylor", "given": "Matthew", "initials": "M"}, {"family": "Air", "given": "Tracy M", "initials": "TM"}, {"family": "Andlauer", "given": "Till F M", "initials": "TFM", "orcid": "0000-0002-2917-5889", "researcher": {"href": "https://publications.scilifelab.se/researcher/66b66e6c499e459ba61db4cbae3e22a9.json"}}, {"family": "Arolt", "given": "Volker", "initials": "V"}, {"family": "Baune", "given": "Bernhard T", "initials": "BT"}, {"family": "Binder", "given": "Elisabeth B", "initials": "EB"}, {"family": "Blackwood", "given": "Douglas H R", "initials": "DHR"}, {"family": "Boomsma", "given": "Dorret I", "initials": "DI"}, {"family": "Campbell", "given": "Archie", "initials": "A"}, {"family": "Cearns", "given": "Micah", "initials": "M"}, {"family": "Czamara", "given": "Darina", "initials": "D", "orcid": "0000-0001-7381-904X", "researcher": {"href": "https://publications.scilifelab.se/researcher/0e9a8a7d605d4f63a311fc8a211422a6.json"}}, {"family": "Dannlowski", "given": "Udo", "initials": "U"}, {"family": "Domschke", "given": "Katharina", "initials": "K"}, {"family": "de Geus", "given": "Eco J C", "initials": "EJC"}, {"family": "Hamilton", "given": "Steven P", "initials": "SP"}, {"family": "Hayward", "given": "Caroline", "initials": "C"}, {"family": "Hickie", "given": "Ian B", "initials": "IB"}, {"family": "Hottenga", "given": "Jouke Jan", "initials": "JJ"}, {"family": "Ising", "given": "Marcus", "initials": "M"}, {"family": "Jones", "given": "Ian", "initials": "I"}, {"family": "Jones", "given": "Lisa", "initials": "L"}, {"family": "Kutalik", "given": "Zoltan", "initials": "Z"}, {"family": "Lucae", "given": "Susanne", "initials": "S"}, {"family": "Martin", "given": "Nicholas G", "initials": "NG", "orcid": "0000-0003-4069-8020", "researcher": {"href": "https://publications.scilifelab.se/researcher/1b445e5935f74fd6a71b2e92a9dac176.json"}}, {"family": "Milaneschi", "given": "Yuri", "initials": "Y"}, {"family": "Mueller-Myhsok", "given": "Bertram", "initials": "B"}, {"family": "Owen", "given": "Michael J", "initials": "MJ"}, {"family": "Padmanabhan", "given": "Sandosh", "initials": "S"}, {"family": "Penninx", "given": "Brenda W J H", "initials": "BWJH"}, {"family": "Pistis", "given": "Giorgio", "initials": "G"}, {"family": "Porteous", "given": "David J", "initials": "DJ"}, {"family": "Preisig", "given": "Martin", "initials": "M"}, {"family": "Ripke", "given": "Stephan", "initials": "S"}, {"family": "Shyn", "given": "Stanley I", "initials": "SI"}, {"family": "Sullivan", "given": "Patrick F", "initials": "PF"}, {"family": "Whitfield", "given": "John B", "initials": "JB"}, {"family": "Wray", "given": "Naomi R", "initials": "NR", "orcid": "0000-0001-7421-3357", "researcher": {"href": "https://publications.scilifelab.se/researcher/15a175036d9f44f9b4090d7d431f78d7.json"}}, {"family": "McIntosh", "given": "Andrew M", "initials": "AM"}, {"family": "Deary", "given": "Ian J", "initials": "IJ"}, {"family": "Breen", "given": "Gerome", "initials": "G"}, {"family": "Lewis", "given": "Cathryn M", "initials": "CM"}], "type": "journal article", "published": "2020-09-00", "journal": {"title": "Am. J. Med. Genet. B Neuropsychiatr. Genet.", "issn": "1552-485X", "volume": "183", "issue": "6", "pages": "309-330", "issn-l": "1552-4841"}, "abstract": "It is imperative to understand the specific and shared etiologies of major depression and cardio-metabolic disease, as both traits are frequently comorbid and each represents a major burden to society. This study examined whether there is a genetic association between major depression and cardio-metabolic traits and if this association is stratified by age at onset for major depression. Polygenic risk scores analysis and linkage disequilibrium score regression was performed to examine whether differences in shared genetic etiology exist between depression case control status (N cases = 40,940, N controls = 67,532), earlier (N = 15,844), and later onset depression (N = 15,800) with body mass index, coronary artery disease, stroke, and type 2 diabetes in 11 data sets from the Psychiatric Genomics Consortium, Generation Scotland, and UK Biobank. All cardio-metabolic polygenic risk scores were associated with depression status. Significant genetic correlations were found between depression and body mass index, coronary artery disease, and type 2 diabetes. Higher polygenic risk for body mass index, coronary artery disease, and type 2 diabetes was associated with both early and later onset depression, while higher polygenic risk for stroke was associated with later onset depression only. Significant genetic correlations were found between body mass index and later onset depression, and between coronary artery disease and both early and late onset depression. The phenotypic associations between major depression and cardio-metabolic traits may partly reflect their overlapping genetic etiology irrespective of the age depression first presents.", "doi": "10.1002/ajmg.b.32807", "pmid": "32681593", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC7991693"}, {"db": "mid", "key": "NIHMS1669188"}], "notes": [], "created": "2020-08-04T14:50:09.256Z", "modified": "2021-11-10T12:49:11.517Z"}, {"entity": "publication", "iuid": "c5bf06f322094e4e9cd44ec502fe6de1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c5bf06f322094e4e9cd44ec502fe6de1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c5bf06f322094e4e9cd44ec502fe6de1"}}, "title": "High Cysteine Membrane Proteins (HCMPs) Are Up-Regulated During Giardia-Host Cell Interactions.", "authors": [{"family": "Peirasmaki", "given": "Dimitra", "initials": "D"}, {"family": "Ma'ayeh", "given": "Showgy Y", "initials": "SY"}, {"family": "Xu", "given": "Feifei", "initials": "F"}, {"family": "Ferella", "given": "Marcela", "initials": "M"}, {"family": "Campos", "given": "Sara", "initials": "S"}, {"family": "Liu", "given": "Jingyi", "initials": "J"}, {"family": "Sv\u00e4rd", "given": "Staffan G", "initials": "SG"}], "type": "journal article", "published": "2020-08-18", "journal": {"title": "Front Genet", "issn": "1664-8021", "volume": "11", "issue": null, "pages": "913", "issn-l": "1664-8021"}, "abstract": "Giardia intestinalis colonizes the upper small intestine of humans and animals, causing the diarrheal disease giardiasis. This unicellular eukaryotic parasite is not invasive but it attaches to the surface of small intestinal epithelial cells (IECs), disrupting the epithelial barrier. Here, we used an in vitro model of the parasite's interaction with host IECs (differentiated Caco-2 cells) and RNA sequencing (RNAseq) to identify differentially expressed genes (DEGs) in Giardia, which might relate to the establishment of infection and disease induction. Giardia trophozoites interacted with differentiated Caco-2 cells for 1.5, 3, and 4.5 h and at each time point, 61, 89, and 148 parasite genes were up-regulated more than twofold, whereas 209, 265, and 313 parasite genes were down-regulated more than twofold. The most abundant DEGs encode hypothetical proteins and members of the High Cysteine Membrane Protein (HCMP) family. Among the up-regulated genes we also observed proteins associated with proteolysis, cellular redox balance, as well as lipid and nucleic acid metabolic pathways. In contrast, genes encoding kinases, regulators of the cell cycle and arginine metabolism and cytoskeletal proteins were down-regulated. Immunofluorescence imaging of selected, up-regulated HCMPs, using C-terminal HA-tagging, showed localization to the plasma membrane and peripheral vesicles (PVs). The expression of the HCMPs was affected by histone acetylation and free iron-levels. In fact, the latter was shown to regulate the expression of many putative giardial virulence factors in subsequent RNAseq experiments. We suggest that the plasma membrane localized and differentially expressed HCMPs play important roles during Giardia-host cell interactions.", "doi": "10.3389/fgene.2020.00913", "pmid": "33014015", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC7461913"}], "notes": [], "created": "2020-10-06T11:59:57.373Z", "modified": "2021-11-10T12:48:13.692Z"}, {"entity": "publication", "iuid": "e761b3a5d96f4efbba18f980378013bf", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e761b3a5d96f4efbba18f980378013bf.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e761b3a5d96f4efbba18f980378013bf"}}, "title": "Association of Established Blood Pressure Loci With 10-Year Change in Blood Pressure and Their Ability to Predict Incident Hypertension.", "authors": [{"family": "Poveda", "given": "Alaitz", "initials": "A", "orcid": "0000-0001-6349-3955", "researcher": {"href": "https://publications.scilifelab.se/researcher/791a243b5c494d1688d757a7096895ea.json"}}, {"family": "Atabaki-Pasdar", "given": "Naeimeh", "initials": "N"}, {"family": "Ahmad", "given": "Shafqat", "initials": "S"}, {"family": "Hallmans", "given": "G\u00f6ran", "initials": "G"}, {"family": "Renstr\u00f6m", "given": "Frida", "initials": "F"}, {"family": "Franks", "given": "Paul W", "initials": "PW"}], "type": "journal article", "published": "2020-08-18", "journal": {"title": "J Am Heart Assoc", "issn": "2047-9980", "volume": "9", "issue": "16", "pages": "e014513", "issn-l": "2047-9980"}, "abstract": "Background Genome-wide association studies have identified >1000 genetic variants cross-sectionally associated with blood pressure variation and prevalent hypertension. These discoveries might aid the early identification of subpopulations at risk of developing hypertension or provide targets for drug development, amongst other applications. The aim of the present study was to analyze the association of blood pressure-associated variants with long-term changes (10 years) in blood pressure and also to assess their ability to predict hypertension incidence compared with traditional risk variables in a Swedish population. Methods and Results We constructed 6 genetic risk scores (GRSs) by summing the dosage of the effect allele at each locus of genetic variants previously associated with blood pressure traits (systolic blood pressure GRS (GRSSBP): 554 variants; diastolic blood pressure GRS (GRSDBP): 481 variants; mean arterial pressure GRS (GRSMAP): 20 variants; pulse pressure GRS (GRSPP): 478 variants; hypertension GRS (GRSHTN): 22 variants; combined GRS (GRScomb): 1152 variants). Each GRS was longitudinally associated with its corresponding blood pressure trait, with estimated effects per GRS SD unit of 0.50 to 1.21 mm Hg for quantitative traits and odds ratios (ORs) of 1.10 to 1.35 for hypertension incidence traits. The GRScomb was also significantly associated with hypertension incidence defined according to European guidelines (OR, 1.22 per SD; 95% CI, 1.10\u20121.35) but not US guidelines (OR, 1.11 per SD; 95% CI, 0.99\u20121.25) while controlling for traditional risk factors. The addition of GRScomb to a model containing traditional risk factors only marginally improved discrimination (\u0394area under the ROC curve = 0.001-0.002). Conclusions GRSs based on discovered blood pressure-associated variants are associated with long-term changes in blood pressure traits and hypertension incidence, but the inclusion of genetic factors in a model composed of conventional hypertension risk factors did not yield a material increase in predictive ability.", "doi": "10.1161/JAHA.119.014513", "pmid": "32805198", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC7660819"}], "notes": [], "created": "2020-08-19T11:12:18.535Z", "modified": "2021-11-10T12:48:16.010Z"}, {"entity": "publication", "iuid": "d04f44cd62564eadad0ce47ce505ff71", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d04f44cd62564eadad0ce47ce505ff71.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d04f44cd62564eadad0ce47ce505ff71"}}, "title": "Association of Factor V Leiden With Subsequent Atherothrombotic Events: A GENIUS-CHD Study of Individual Participant Data.", "authors": [{"family": "Mahmoodi", "given": "Bakhtawar K", "initials": "BK"}, {"family": "Tragante", "given": "Vinicius", "initials": "V"}, {"family": "Kleber", "given": "Marcus E", "initials": "ME"}, {"family": "Holmes", "given": "Michael V", "initials": "MV"}, {"family": "Schmidt", "given": "Amand F", "initials": "AF"}, {"family": "McCubrey", "given": "Raymond O", "initials": "RO"}, {"family": "Howe", "given": "Laurence J", "initials": "LJ"}, {"family": "Direk", "given": "Kenan", "initials": "K"}, {"family": "Allayee", "given": "Hooman", "initials": "H"}, {"family": "Baranova", "given": "Ekaterina V", "initials": "EV"}, {"family": "Braund", "given": "Peter S", "initials": "PS"}, {"family": "Delgado", "given": "Graciela E", "initials": "GE"}, {"family": "Eriksson", "given": "Niclas", "initials": "N"}, {"family": "Gijsberts", "given": "Crystel M", "initials": "CM"}, {"family": "Gong", "given": "Yan", "initials": "Y"}, {"family": "Hartiala", "given": "Jaana", "initials": "J", "orcid": "0000-0003-4883-9318", "researcher": {"href": "https://publications.scilifelab.se/researcher/f39400df71774cf8ae408eccbe34d981.json"}}, {"family": "Heydarpour", "given": "Mahyar", "initials": "M"}, {"family": "Pasterkamp", "given": "Gerard", "initials": "G"}, {"family": "Kotti", "given": "Salma", "initials": "S"}, {"family": "Kuukasj\u00e4rvi", "given": "Pekka", "initials": "P"}, {"family": "Lenzini", "given": "Petra A", "initials": "PA"}, {"family": "Levin", "given": "Daniel", "initials": "D"}, {"family": "Lyytik\u00e4inen", "given": "Leo-Pekka", "initials": "LP"}, {"family": "Muehlschlegel", "given": "Jochen D", "initials": "JD", "orcid": "0000-0002-6209-7253", "researcher": {"href": "https://publications.scilifelab.se/researcher/3211e8bb09c64d748cb153c358831d82.json"}}, {"family": "Nelson", "given": "Christopher P", "initials": "CP"}, {"family": "Nikus", "given": "Kjell", "initials": "K", "orcid": "0000-0002-9345-9851", "researcher": {"href": "https://publications.scilifelab.se/researcher/99b4b0a2893c42efbc24bed6370451ba.json"}}, {"family": "Pilbrow", "given": "Anna P", "initials": "AP", "orcid": "0000-0003-1949-9449", "researcher": {"href": "https://publications.scilifelab.se/researcher/b86a1225a68e403e806a07b42e96c991.json"}}, {"family": "Wilson Tang", "given": "W H", "initials": "WH", "orcid": "0000-0002-8335-735X", "researcher": {"href": "https://publications.scilifelab.se/researcher/5aab6a5657004a79aeda81c22a077268.json"}}, {"family": "van der Laan", "given": "Sander W", "initials": "SW", "orcid": "0000-0001-6888-1404", "researcher": {"href": "https://publications.scilifelab.se/researcher/9bd54ab413974b9096ff3d924f8b8eb6.json"}}, {"family": "van Setten", "given": "Jessica", "initials": "J"}, {"family": "Vilmundarson", "given": "Ragnar O", "initials": "RO"}, {"family": "Deanfield", "given": "John", "initials": "J"}, {"family": "Deloukas", "given": "Panos", "initials": "P", "orcid": "0000-0001-9251-070X", "researcher": {"href": "https://publications.scilifelab.se/researcher/eb59dbd2f2204d41b801c41188611a9e.json"}}, {"family": "Dudbridge", "given": "Frank", "initials": "F"}, {"family": "James", "given": "Stefan", "initials": "S"}, {"family": "Mordi", "given": "Ify R", "initials": "IR", "orcid": "0000-0002-2686-729X", "researcher": {"href": "https://publications.scilifelab.se/researcher/1081c6ce996d4f7e944be05db1a3e7c0.json"}}, {"family": "Teren", "given": "Andrej", "initials": "A"}, {"family": "Bergmeijer", "given": "Thomas O", "initials": "TO"}, {"family": "Body", "given": "Simon C", "initials": "SC"}, {"family": "Bots", "given": "Michiel", "initials": "M"}, {"family": "Burkhardt", "given": "Ralph", "initials": "R"}, {"family": "Cooper-DeHoff", "given": "Rhonda M", "initials": "RM"}, {"family": "Cresci", "given": "Sharon", "initials": "S"}, {"family": "Danchin", "given": "Nicolas", "initials": "N", "orcid": "0000-0001-9263-5051", "researcher": {"href": "https://publications.scilifelab.se/researcher/4c86ecd847894f7cb79f1f625881d60b.json"}}, {"family": "Doughty", "given": "Robert N", "initials": "RN"}, {"family": "Grobbee", "given": "Diederick E", "initials": "DE"}, {"family": "Hagstr\u00f6m", "given": "Emil", "initials": "E"}, {"family": "Hazen", "given": "Stanley L", "initials": "SL", "orcid": "0000-0001-7124-6639", "researcher": {"href": "https://publications.scilifelab.se/researcher/abce9cd916c94667a73bc348ede57a01.json"}}, {"family": "Held", "given": "Claes", "initials": "C"}, {"family": "Hoefer", "given": "Imo E", "initials": "IE"}, {"family": "Hovingh", "given": "G Kees", "initials": "GK"}, {"family": "Johnson", "given": "Julie A", "initials": "JA"}, {"family": "Kaczor", "given": "Marcin P", "initials": "MP"}, {"family": "K\u00e4h\u00f6nen", "given": "Mika", "initials": "M"}, {"family": "Klungel", "given": "Olaf H", "initials": "OH"}, {"family": "Laurikka", "given": "Jari O", "initials": "JO"}, {"family": "Lehtim\u00e4ki", "given": "Terho", "initials": "T"}, {"family": "Maitland-van der Zee", "given": "Anke H", "initials": "AH"}, {"family": "McPherson", "given": "Ruth", "initials": "R", "orcid": "0000-0002-9087-6107", "researcher": {"href": "https://publications.scilifelab.se/researcher/a563e055adb14878a8af46f235944082.json"}}, {"family": "Palmer", "given": "Colin N", "initials": "CN", "orcid": "0000-0002-6415-6560", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a0f019dcb7a453a84480953a5514dd5.json"}}, {"family": "Kraaijeveld", "given": "Adriaan O", "initials": "AO"}, {"family": "Pepine", "given": "Carl J", "initials": "CJ", "orcid": "0000-0002-6011-681X", "researcher": {"href": "https://publications.scilifelab.se/researcher/a3b76ccaa8a749bd83a0bc35a2d97557.json"}}, {"family": "Sanak", "given": "Marek", "initials": "M"}, {"family": "Sattar", "given": "Naveed", "initials": "N", "orcid": "0000-0002-1604-2593", "researcher": {"href": "https://publications.scilifelab.se/researcher/80fbc7cdcfc444acb066449f80f87181.json"}}, {"family": "Scholz", "given": "Markus", "initials": "M"}, {"family": "Simon", "given": "Tabassome", "initials": "T"}, {"family": "Spertus", "given": "John A", "initials": "JA"}, {"family": "Stewart", "given": "Alexandre F R", "initials": "AFR", "orcid": "0000-0003-2673-9164", "researcher": {"href": "https://publications.scilifelab.se/researcher/f6cd21cc0681418d845ab97d09f953c1.json"}}, {"family": "Szczeklik", "given": "Wojciech", "initials": "W"}, {"family": "Thiery", "given": "Joachim", "initials": "J"}, {"family": "Visseren", "given": "Frank L J", "initials": "FLJ"}, {"family": "Waltenberger", "given": "Johannes", "initials": "J", "orcid": "0000-0002-2417-9880", "researcher": {"href": "https://publications.scilifelab.se/researcher/a541817a1b1c49d79273fe61df23886e.json"}}, {"family": "Richards", "given": "A Mark", "initials": "AM"}, {"family": "Lang", "given": "Chim C", "initials": "CC"}, {"family": "Cameron", "given": "Vicky A", "initials": "VA"}, {"family": "\u00c5kerblom", "given": "Axel", "initials": "A"}, {"family": "Pare", "given": "Guillaume", "initials": "G", "orcid": "0000-0002-6795-4760", "researcher": {"href": "https://publications.scilifelab.se/researcher/4e23d12d8f5340a79e86a293593c9598.json"}}, {"family": "M\u00e4rz", "given": "Winfried", "initials": "W"}, {"family": "Samani", "given": "Nilesh J", "initials": "NJ", "orcid": "0000-0002-3286-8133", "researcher": {"href": "https://publications.scilifelab.se/researcher/2227aaf274e8424f8408318f336f3bf1.json"}}, {"family": "Hingorani", "given": "Aroon D", "initials": "AD"}, {"family": "Ten Berg", "given": "Jurri\u00ebn M", "initials": "JM"}, {"family": "Wallentin", "given": "Lars", "initials": "L"}, {"family": "Asselbergs", "given": "Folkert W", "initials": "FW", "orcid": "0000-0002-1692-8669", "researcher": {"href": "https://publications.scilifelab.se/researcher/7037429ef1304bdaabd837d242b1e6f5.json"}}, {"family": "Patel", "given": "Riyaz S", "initials": "RS"}], "type": "journal article", "published": "2020-08-11", "journal": {"title": "Circulation", "issn": "1524-4539", "volume": "142", "issue": "6", "pages": "546-555", "issn-l": "0009-7322"}, "abstract": "Studies examining the role of factor V Leiden among patients at higher risk of atherothrombotic events, such as those with established coronary heart disease (CHD), are lacking. Given that coagulation is involved in the thrombus formation stage on atherosclerotic plaque rupture, we hypothesized that factor V Leiden may be a stronger risk factor for atherothrombotic events in patients with established CHD.\n\nWe performed an individual-level meta-analysis including 25 prospective studies (18 cohorts, 3 case-cohorts, 4 randomized trials) from the GENIUS-CHD (Genetics of Subsequent Coronary Heart Disease) consortium involving patients with established CHD at baseline. Participating studies genotyped factor V Leiden status and shared risk estimates for the outcomes of interest using a centrally developed statistical code with harmonized definitions across studies. Cox proportional hazards regression models were used to obtain age- and sex-adjusted estimates. The obtained estimates were pooled using fixed-effect meta-analysis. The primary outcome was composite of myocardial infarction and CHD death. Secondary outcomes included any stroke, ischemic stroke, coronary revascularization, cardiovascular mortality, and all-cause mortality.\n\nThe studies included 69 681 individuals of whom 3190 (4.6%) were either heterozygous or homozygous (n=47) carriers of factor V Leiden. Median follow-up per study ranged from 1.0 to 10.6 years. A total of 20 studies with 61 147 participants and 6849 events contributed to analyses of the primary outcome. Factor V Leiden was not associated with the combined outcome of myocardial infarction and CHD death (hazard ratio, 1.03 [95% CI, 0.92-1.16]; I=28%; 2P-heterogeneity=0.12). Subgroup analysis according to baseline characteristics or strata of traditional cardiovascular risk factors did not show relevant differences. Similarly, risk estimates for the secondary outcomes including stroke, coronary revascularization, cardiovascular mortality, and all-cause mortality were also close to identity.\n\nFactor V Leiden was not associated with increased risk of subsequent atherothrombotic events and mortality in high-risk participants with established and treated CHD. Routine assessment of factor V Leiden status is unlikely to improve atherothrombotic events risk stratification in this population.", "doi": "10.1161/CIRCULATIONAHA.119.045526", "pmid": "32654539", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC7493828"}, {"db": "mid", "key": "NIHMS1610813"}], "notes": [], "created": "2020-08-04T14:50:04.900Z", "modified": "2021-11-10T12:49:19.053Z"}, {"entity": "publication", "iuid": "e73200548370435db06387414d40b7e2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e73200548370435db06387414d40b7e2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e73200548370435db06387414d40b7e2"}}, "title": "The importance of the ZBED6-IGF2 axis for metabolic regulation in mouse myoblast cells.", "authors": [{"family": "Younis", "given": "Shady", "initials": "S"}, {"family": "Naboulsi", "given": "Rakan", "initials": "R"}, {"family": "Wang", "given": "Xuan", "initials": "X"}, {"family": "Cao", "given": "Xiaofang", "initials": "X"}, {"family": "Larsson", "given": "M\u00e5rten", "initials": "M"}, {"family": "Sargsyan", "given": "Ernest", "initials": "E"}, {"family": "Bergsten", "given": "Peter", "initials": "P"}, {"family": "Welsh", "given": "Nils", "initials": "N"}, {"family": "Andersson", "given": "Leif", "initials": "L"}], "type": "journal article", "published": "2020-08-00", "journal": {"title": "FASEB J.", "issn": "1530-6860", "issn-l": "0892-6638", "volume": "34", "issue": "8", "pages": "10250-10266"}, "abstract": "The transcription factor ZBED6 acts as a repressor of Igf2 and affects directly or indirectly the transcriptional regulation of thousands of genes. Here, we use gene editing in mouse C2C12 myoblasts and show that ZBED6 regulates Igf2 exclusively through its binding site 5'-GGCTCG-3' in intron 1 of Igf2. Deletion of this motif (Igf2\u0394GGCT ) or complete ablation of Zbed6 leads to ~20-fold upregulation of the IGF2 protein. Quantitative proteomics revealed an activation of Ras signaling pathway in both Zbed6-/- and Igf2\u0394GGCT myoblasts, and a significant enrichment of mitochondrial membrane proteins among proteins showing altered expression in Zbed6-/- myoblasts. Both Zbed6-/- and Igf2\u0394GGCT myoblasts showed a faster growth rate and developed myotube hypertrophy. These cells exhibited an increased O2 consumption rate, due to IGF2 upregulation. Transcriptome analysis revealed ~30% overlap between differentially expressed genes in Zbed6-/- and Igf2\u0394GGCT myotubes, with an enrichment of upregulated genes involved in muscle development. In contrast, ZBED6-overexpression in myoblasts led to cell apoptosis, cell cycle arrest, reduced mitochondrial activities, and ceased myoblast differentiation. The similarities in growth and differentiation phenotypes observed in Zbed6-/- and Igf2\u0394GGCT myoblasts demonstrates that ZBED6 affects mitochondrial activity and myogenesis largely through its regulation of IGF2 expression. This study adds new insights how the ZBED6-Igf2 axis affects muscle metabolism.", "doi": "10.1096/fj.201901321R", "pmid": "32557799", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2020-12-08T23:27:45.177Z", "modified": "2024-01-16T13:48:41.959Z"}, {"entity": "publication", "iuid": "56bd5b3292d745ebbee0c2a369c5a13c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/56bd5b3292d745ebbee0c2a369c5a13c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/56bd5b3292d745ebbee0c2a369c5a13c"}}, "title": "The Neolithic Pitted Ware culture foragers were culturally but not genetically influenced by the Battle Axe culture herders.", "authors": [{"family": "Coutinho", "given": "Alexandra", "initials": "A"}, {"family": "G\u00fcnther", "given": "Torsten", "initials": "T"}, {"family": "Munters", "given": "Arielle R", "initials": "AR"}, {"family": "Svensson", "given": "Emma M", "initials": "EM"}, {"family": "G\u00f6therstr\u00f6m", "given": "Anders", "initials": "A", "orcid": "0000-0001-6307-8188", "researcher": {"href": "https://publications.scilifelab.se/researcher/2a1a0a680ab8456cbf5a941e9718fd5a.json"}}, {"family": "Stor\u00e5", "given": "Jan", "initials": "J"}, {"family": "Malmstr\u00f6m", "given": "Helena", "initials": "H"}, {"family": "Jakobsson", "given": "Mattias", "initials": "M", "orcid": "0000-0001-7840-7853", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a4abe0fcb20492d9ec849c9fbf58a71.json"}}], "type": "historical article", "published": "2020-08-00", "journal": {"title": "Am. J. Phys. Anthropol.", "issn": "1096-8644", "volume": "172", "issue": "4", "pages": "638-649", "issn-l": "0002-9483"}, "abstract": "In order to understand contacts between cultural spheres in the third millennium BC, we investigated the impact of a new herder culture, the Battle Axe culture, arriving to Scandinavia on the people of the sub-Neolithic hunter-gatherer Pitted Ware culture. By investigating the genetic make-up of Pitted Ware culture people from two types of burials (typical Pitted Ware culture burials and Battle Axe culture-influenced burials), we could determine the impact of migration and the impact of cultural influences.\n\nWe sequenced and analyzed the genomes of 25 individuals from typical Pitted Ware culture burials and from Pitted Ware culture burials with Battle Axe culture influences in order to determine if the different burial types were associated with different gene-pools.\n\nThe genomic data show that all individuals belonged to one genetic population-a population associated with the Pitted Ware culture-irrespective of the burial style.\n\nWe conclude that the Pitted Ware culture communities were not impacted by gene-flow, that is, via migration or exchange of mates. These different cultural expressions in the Pitted Ware culture burials are instead a consequence of cultural exchange.", "doi": "10.1002/ajpa.24079", "pmid": "32497286", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2020-12-08T23:25:31.764Z", "modified": "2024-01-16T13:48:41.973Z"}, {"entity": "publication", "iuid": "f0b41ac9f87d4487a698a8e955193a8f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f0b41ac9f87d4487a698a8e955193a8f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f0b41ac9f87d4487a698a8e955193a8f"}}, "title": "SWEDEGENE-a Swedish nation-wide DNA sample collection for pharmacogenomic studies of serious adverse drug reactions.", "authors": [{"family": "Hallberg", "given": "P\u00e4r", "initials": "P"}, {"family": "Yue", "given": "Qun-Ying", "initials": "QY"}, {"family": "Eliasson", "given": "Erik", "initials": "E"}, {"family": "Melhus", "given": "H\u00e5kan", "initials": "H"}, {"family": "\u00c5s", "given": "Joel", "initials": "J"}, {"family": "Wadelius", "given": "Mia", "initials": "M", "orcid": "0000-0002-6368-2622", "researcher": {"href": "https://publications.scilifelab.se/researcher/ec07b9869a1f4b77b734c5dc567dc630.json"}}], "type": "journal article", "published": "2020-08-00", "journal": {"volume": "20", "issn": "1473-1150", "issue": "4", "title": "Pharmacogenomics J.", "pages": "579-585", "issn-l": "1470-269X"}, "abstract": "SWEDEGENE is a Swedish nation-wide sample collection established to facilitate studies of clinical and genetic risk factors for adverse drug reactions (ADRs). Most cases are recruited among patients reported to the ADR registry at the Swedish Medical Products Agency by health-care professionals. Clinical data are collected both from medical and laboratory records and through interviews using standardized questionnaires. Genome-wide scans and whole-genome sequencing are done, and association studies are conducted using mainly controls from the Swedish TwinGene biobank with data on diagnoses and prescribed drugs. SWEDEGENE was established in 2008 and currently contains DNA and information from about 2550 adults who have experienced specific ADRs, and from 580 drug exposed controls. Results from genome-wide association studies have now been published, and data from whole-genome sequencing are being analyzed. SWEDEGENE has the potential to offer a new means of developing individualized and safe drug therapy through patient pre-treatment screening.", "doi": "10.1038/s41397-020-0148-3", "pmid": "31949290", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41397-020-0148-3"}, {"db": "pmc", "key": "PMC7375949"}], "notes": [], "created": "2020-01-22T08:25:49.135Z", "modified": "2024-01-16T13:48:41.982Z"}, {"entity": "publication", "iuid": "efc537477cec47219f48e554a101fc12", "links": {"self": {"href": "https://publications.scilifelab.se/publication/efc537477cec47219f48e554a101fc12.json"}, "display": {"href": "https://publications.scilifelab.se/publication/efc537477cec47219f48e554a101fc12"}}, "title": "Recent introgression between Taiga Bean Goose and Tundra Bean Goose results in a largely homogeneous landscape of genetic differentiation.", "authors": [{"family": "Ottenburghs", "given": "Jente", "initials": "J", "orcid": "0000-0002-0335-9655", "researcher": {"href": "https://publications.scilifelab.se/researcher/ba165a24313c45a2bb601a47bf851eef.json"}}, {"family": "Honka", "given": "Johanna", "initials": "J"}, {"family": "M\u00fcskens", "given": "Gerard J D M", "initials": "GJDM"}, {"family": "Ellegren", "given": "Hans", "initials": "H", "orcid": "0000-0002-5035-1736", "researcher": {"href": "https://publications.scilifelab.se/researcher/819e68cc7125446baec6165aabd2d19c.json"}}], "type": "journal article", "published": "2020-08-00", "journal": {"title": "Heredity (Edinb)", "issn": "1365-2540", "volume": "125", "issue": "1-2", "pages": "73-84", "issn-l": "0018-067X"}, "abstract": "Several studies have uncovered a highly heterogeneous landscape of genetic differentiation across the genomes of closely related species. Specifically, genetic differentiation is often concentrated in particular genomic regions (\"islands of differentiation\") that might contain barrier loci contributing to reproductive isolation, whereas the rest of the genome is homogenized by introgression. Alternatively, linked selection can produce differentiation islands in allopatry without introgression. We explored the influence of introgression on the landscape of genetic differentiation in two hybridizing goose taxa: the Taiga Bean Goose (Anser fabalis) and the Tundra Bean Goose (A. serrirostris). We re-sequenced the whole genomes of 18 individuals (9 of each taxon) and, using a combination of population genomic summary statistics and demographic modeling, we reconstructed the evolutionary history of these birds. Next, we quantified the impact of introgression on the build-up and maintenance of genetic differentiation. We found evidence for a scenario of allopatric divergence (about 2.5 million years ago) followed by recent secondary contact (about 60,000 years ago). Subsequent introgression events led to high levels of gene flow, mainly from the Tundra Bean Goose into the Taiga Bean Goose. This scenario resulted in a largely undifferentiated genomic landscape (genome-wide FST = 0.033) with a few notable differentiation peaks that were scattered across chromosomes. The summary statistics indicated that some peaks might contain barrier loci while others arose in allopatry through linked selection. Finally, based on the low genetic differentiation, considerable morphological variation and incomplete reproductive isolation, we argue that the Taiga and the Tundra Bean Goose should be treated as subspecies.", "doi": "10.1038/s41437-020-0322-z", "pmid": "32451423", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41437-020-0322-z"}, {"db": "pmc", "key": "PMC7413267"}], "notes": [], "created": "2020-11-16T10:27:10.732Z", "modified": "2024-01-16T13:48:41.989Z"}, {"entity": "publication", "iuid": "3eb0ebe5e75646b48dd8e63889251ad4", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3eb0ebe5e75646b48dd8e63889251ad4.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3eb0ebe5e75646b48dd8e63889251ad4"}}, "title": "Joint impact of common risk factors on incident dementia: A cohort study of the Swedish Twin Registry.", "authors": [{"family": "Tomata", "given": "Y", "initials": "Y", "orcid": "0000-0003-4189-5245", "researcher": {"href": "https://publications.scilifelab.se/researcher/4f84f8bceff94af780a4a3bd8a4f09db.json"}}, {"family": "Li", "given": "X", "initials": "X", "orcid": "0000-0003-1922-7152", "researcher": {"href": "https://publications.scilifelab.se/researcher/862fd8b41938458f9105c5bb73c35294.json"}}, {"family": "Karlsson", "given": "I K", "initials": "IK"}, {"family": "Mosing", "given": "M A", "initials": "MA"}, {"family": "Pedersen", "given": "N L", "initials": "NL"}, {"family": "H\u00e4gg", "given": "S", "initials": "S"}], "type": "journal article", "published": "2020-08-00", "journal": {"volume": "288", "issn": "1365-2796", "issue": "2", "title": "J. Intern. Med.", "pages": "234-247", "issn-l": "0954-6820"}, "abstract": "As common risk factors of dementia, nine factors (low education, hearing loss, obesity, hypertension, smoking, depression, physical inactivity, diabetes and social isolation) were proposed. However, the joint impact of these factors on incident dementia is still uncertain; hence, we aimed to examine this impact.\n\nWe conducted a cohort study of 9017 cognitively intact individuals aged \u2265 65 years in the Swedish Twin Registry. The main exposure was the total number of reported risk factors (ranging from 0 to 9). Data on dementia diagnoses were based on clinical workup and national health registers. After estimating the adjusted hazard ratios of incident dementia, the population attributable fraction (PAF) was calculated. We then conducted additional analyses, including APOE \u03b54 status in a genotyped subsample (n = 2810) to check the relative impact of the main exposure and discordant twin pair (n = 1158) analysis to consider confounding by familial effects (shared genetic or familial environmental factors).\n\nThe number of dementia cases was 1950 (21.6%). A dose-response relationship between the number of risk factors and incident dementia was observed; hazard ratio (95% confidence interval) per one-unit increment in number of risk factors was 1.07 (1.03 to 1.11). The PAF for the combination of the nine risk factors was 10.4%. The PAF of all nine risk factors was smaller than that of APOE \u03b54 genotype (20.8%) in the subsample. Discordant pair analysis suggested that the observed association was not likely explained by familial effects.\n\nThe nine risk factors may have considerable impact as modifiable factors on incident dementia.", "doi": "10.1111/joim.13071", "pmid": "32363599", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2020-05-06T12:23:57.088Z", "modified": "2024-01-16T13:48:42.033Z"}, {"entity": "publication", "iuid": "2ec4096268f347c79eedea7bb77234a9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2ec4096268f347c79eedea7bb77234a9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2ec4096268f347c79eedea7bb77234a9"}}, "title": "Determinants of genetic variation across eco-evolutionary scales in pinnipeds.", "authors": [{"family": "Peart", "given": "Claire R", "initials": "CR", "orcid": "0000-0002-0433-0299", "researcher": {"href": "https://publications.scilifelab.se/researcher/39ca9ce827fb435195a0d5bee245ba6a.json"}}, {"family": "Tusso", "given": "Sergio", "initials": "S", "orcid": "0000-0002-0612-9230", "researcher": {"href": "https://publications.scilifelab.se/researcher/027fc05d9bd843afaa82aeecce0747e8.json"}}, {"family": "Pophaly", "given": "Saurabh D", "initials": "SD"}, {"family": "Botero-Castro", "given": "Fidel", "initials": "F", "orcid": "0000-0002-5062-8272", "researcher": {"href": "https://publications.scilifelab.se/researcher/7ef9abb38c5d4c259d64e6f59ee7440c.json"}}, {"family": "Wu", "given": "Chi-Chih", "initials": "CC"}, {"family": "Aurioles-Gamboa", "given": "David", "initials": "D"}, {"family": "Baird", "given": "Amy B", "initials": "AB"}, {"family": "Bickham", "given": "John W", "initials": "JW", "orcid": "0000-0001-9624-7806", "researcher": {"href": "https://publications.scilifelab.se/researcher/5b8ef9c3991c4da38ad3010bb30977be.json"}}, {"family": "Forcada", "given": "Jaume", "initials": "J", "orcid": "0000-0002-2115-0150", "researcher": {"href": "https://publications.scilifelab.se/researcher/c9fddd47f5b64f779913b9fd631edb2e.json"}}, {"family": "Galimberti", "given": "Filippo", "initials": "F", "orcid": "0000-0001-5537-6409", "researcher": {"href": "https://publications.scilifelab.se/researcher/9d82a8f8835145619fbac351091bfbec.json"}}, {"family": "Gemmell", "given": "Neil J", "initials": "NJ", "orcid": "0000-0003-0671-3637", "researcher": {"href": "https://publications.scilifelab.se/researcher/9ca2b0a676d84b878b3f9faa8748e148.json"}}, {"family": "Hoffman", "given": "Joseph I", "initials": "JI", "orcid": "0000-0001-5895-8949", "researcher": {"href": "https://publications.scilifelab.se/researcher/5455275134754093b050bee85b8f88c5.json"}}, {"family": "Kovacs", "given": "Kit M", "initials": "KM"}, {"family": "Kunnasranta", "given": "Mervi", "initials": "M"}, {"family": "Lydersen", "given": "Christian", "initials": "C"}, {"family": "Nyman", "given": "Tommi", "initials": "T"}, {"family": "de Oliveira", "given": "Larissa Rosa", "initials": "LR"}, {"family": "Orr", "given": "Anthony J", "initials": "AJ"}, {"family": "Sanvito", "given": "Simona", "initials": "S", "orcid": "0000-0003-1427-6414", "researcher": {"href": "https://publications.scilifelab.se/researcher/1f65216b298b4575adb46bfeea38d8d3.json"}}, {"family": "Valtonen", "given": "Mia", "initials": "M", "orcid": "0000-0003-2034-2019", "researcher": {"href": "https://publications.scilifelab.se/researcher/601fe0084ca1460486e607e509f46c3a.json"}}, {"family": "Shafer", "given": "Aaron B A", "initials": "ABA", "orcid": "0000-0001-7652-225X", "researcher": {"href": "https://publications.scilifelab.se/researcher/65325cc227b74704ab85e14385a1673e.json"}}, {"family": "Wolf", "given": "Jochen B W", "initials": "JBW", "orcid": "0000-0002-2958-5183", "researcher": {"href": "https://publications.scilifelab.se/researcher/6c4445d760a64905a9ea6d8664f6a32d.json"}}], "type": "journal article", "published": "2020-08-00", "journal": {"title": "Nat Ecol Evol", "issn": "2397-334X", "volume": "4", "issue": "8", "pages": "1095-1104", "issn-l": "2397-334X"}, "abstract": "The effective size of a population (Ne), which determines its level of neutral variability, is a key evolutionary parameter. Ne can substantially depart from census sizes of present-day breeding populations (NC) as a result of past demographic changes, variation in life-history traits and selection at linked sites. Using genome-wide data we estimated the long-term coalescent Ne for 17 pinniped species represented by 36 population samples (total n = 458 individuals). Ne estimates ranged from 8,936 to 91,178, were highly consistent within (sub)species and showed a strong positive correlation with NC ([Formula: see text] = 0.59; P = 0.0002). Ne/NC ratios were low (mean, 0.31; median, 0.13) and co-varied strongly with demographic history and, to a lesser degree, with species' ecological and life-history variables such as breeding habitat. Residual variation in Ne/NC, after controlling for past demographic fluctuations, contained information about recent population size changes during the Anthropocene. Specifically, species of conservation concern typically had positive residuals indicative of a smaller contemporary NC than would be expected from their long-term Ne. This study highlights the value of comparative population genomic analyses for gauging the evolutionary processes governing genetic variation in natural populations, and provides a framework for identifying populations deserving closer conservation attention.", "doi": "10.1038/s41559-020-1215-5", "pmid": "32514167", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41559-020-1215-5"}], "notes": [], "created": "2020-12-08T23:33:13.775Z", "modified": "2024-01-16T13:48:42.060Z"}, {"entity": "publication", "iuid": "22914a13727a400bbc7bf78b4c9dfd22", "links": {"self": {"href": "https://publications.scilifelab.se/publication/22914a13727a400bbc7bf78b4c9dfd22.json"}, "display": {"href": "https://publications.scilifelab.se/publication/22914a13727a400bbc7bf78b4c9dfd22"}}, "title": "Archaea in boreal Swedish lakes are diverse, dominated by Woesearchaeota and follow deterministic community assembly.", "authors": [{"family": "Juottonen", "given": "Heli", "initials": "H", "orcid": "0000-0003-3769-239X", "researcher": {"href": "https://publications.scilifelab.se/researcher/1af9df805f914a21be382248c50b9d03.json"}}, {"family": "Fontaine", "given": "Laurent", "initials": "L"}, {"family": "Wurzbacher", "given": "Christian", "initials": "C"}, {"family": "Drakare", "given": "Stina", "initials": "S"}, {"family": "Peura", "given": "Sari", "initials": "S", "orcid": "0000-0003-3892-8157", "researcher": {"href": "https://publications.scilifelab.se/researcher/c430ad5c3bd14387b768c588a9b12ce0.json"}}, {"family": "Eiler", "given": "Alexander", "initials": "A", "orcid": "0000-0001-9916-9567", "researcher": {"href": "https://publications.scilifelab.se/researcher/e7286785c9334dcba90273b69f81c018.json"}}], "type": "journal article", "published": "2020-08-00", "journal": {"title": "Environ. Microbiol.", "issn": "1462-2920", "volume": "22", "issue": "8", "pages": "3158-3171", "issn-l": "1462-2912"}, "abstract": "Despite their key role in biogeochemical processes, particularly the methane cycle, archaea are widely underrepresented in molecular surveys because of their lower abundance compared with bacteria and eukaryotes. Here, we use parallel high-resolution small subunit rRNA gene sequencing to explore archaeal diversity in 109 Swedish lakes and correlate archaeal community assembly mechanisms to large-scale latitudinal, climatic (nemoral to arctic) and nutrient (oligotrophic to eutrophic) gradients. Sequencing with universal primers showed the contribution of archaea was on average 0.8% but increased up to 1.5% of the three domains in forest lakes. Archaea-specific sequencing revealed that freshwater archaeal diversity could be partly explained by lake variables associated with nutrient status. Combined with deterministic co-occurrence patterns this finding suggests that ecological drift is overridden by environmental sorting, as well as other deterministic processes such as biogeographic and evolutionary history, leading to lake-specific archaeal biodiversity. Acetoclastic, hydrogenotrophic and methylotrophic methanogens as well as ammonia-oxidizing archaea were frequently detected across the lakes. Archaea-specific sequencing also revealed representatives of Woesearchaeota and other phyla of the DPANN superphylum. This study adds to our understanding of the ecological range of key archaea in freshwaters and links these taxa to hypotheses about processes governing biogeochemical cycles in lakes.", "doi": "10.1111/1462-2920.15058", "pmid": "32372550", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2020-12-08T23:57:02.276Z", "modified": "2024-01-16T13:48:42.081Z"}, {"entity": "publication", "iuid": "4a9b528a26aa47e38f232b961ded646c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4a9b528a26aa47e38f232b961ded646c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4a9b528a26aa47e38f232b961ded646c"}}, "title": "A decade of epigenetic change in aging twins: Genetic and environmental contributions to longitudinal DNA methylation.", "authors": [{"family": "Reynolds", "given": "Chandra A", "initials": "CA", "orcid": "0000-0001-6502-7173", "researcher": {"href": "https://publications.scilifelab.se/researcher/6b7cd2b82d81463c8dd3f13c4d75ab6f.json"}}, {"family": "Tan", "given": "Qihua", "initials": "Q"}, {"family": "Munoz", "given": "Elizabeth", "initials": "E"}, {"family": "Jylh\u00e4v\u00e4", "given": "Juulia", "initials": "J"}, {"family": "Hjelmborg", "given": "Jacob", "initials": "J"}, {"family": "Christiansen", "given": "Lene", "initials": "L"}, {"family": "H\u00e4gg", "given": "Sara", "initials": "S", "orcid": "0000-0002-2452-1500", "researcher": {"href": "https://publications.scilifelab.se/researcher/e1d010dfe5d84a33b6a6c7ec815ca3dc.json"}}, {"family": "Pedersen", "given": "Nancy L", "initials": "NL"}], "type": "journal article", "published": "2020-08-00", "journal": {"title": "Aging Cell", "issn": "1474-9726", "volume": "19", "issue": "8", "pages": "e13197", "issn-l": "1474-9718"}, "abstract": "Epigenetic changes may result from the interplay of environmental exposures and genetic influences and contribute to differences in age-related disease, disability, and mortality risk. However, the etiologies contributing to stability and change in DNA methylation have rarely been examined longitudinally.\n\nWe considered DNA methylation in whole blood leukocyte DNA across a 10-year span in two samples of same-sex aging twins: (a) Swedish Adoption Twin Study of Aging (SATSA; N = 53 pairs, 53% female; 62.9 and 72.5 years, SD = 7.2 years); (b) Longitudinal Study of Aging Danish Twins (LSADT; N = 43 pairs, 72% female, 76.2 and 86.1 years, SD=1.8 years). Joint biometrical analyses were conducted on 358,836 methylation probes in common. Bivariate twin models were fitted, adjusting for age, sex, and country.\n\nOverall, results suggest genetic contributions to DNA methylation across 358,836 sites tended to be small and lessen across 10 years (broad heritability M = 23.8% and 18.0%) but contributed to stability across time while person-specific factors explained emergent influences across the decade. Aging-specific sites identified from prior EWAS and methylation age clocks were more heritable than background sites. The 5037 sites that showed the greatest heritable/familial-environmental influences (p < 1E-07) were enriched for immune and inflammation pathways while 2020 low stability sites showed enrichment in stress-related pathways.\n\nAcross time, stability in methylation is primarily due to genetic contributions, while novel experiences and exposures contribute to methylation differences. Elevated genetic contributions at age-related methylation sites suggest that adaptions to aging and senescence may be differentially impacted by genetic background.", "doi": "10.1111/acel.13197", "pmid": "32710526", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC7431820"}], "notes": [], "created": "2020-08-04T14:50:02.748Z", "modified": "2024-01-16T13:48:42.094Z"}, {"entity": "publication", "iuid": "d191a7af04da4afea9d0e9e07fe20a75", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d191a7af04da4afea9d0e9e07fe20a75.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d191a7af04da4afea9d0e9e07fe20a75"}}, "title": "The genetic regulation of size variation in the transcriptome of the cerebrum in the chicken and its role in domestication and brain size evolution.", "authors": [{"family": "H\u00f6glund", "given": "Andrey", "initials": "A"}, {"family": "Strempfl", "given": "Katharina", "initials": "K"}, {"family": "Fogelholm", "given": "Jesper", "initials": "J"}, {"family": "Wright", "given": "Dominic", "initials": "D"}, {"family": "Henriksen", "given": "Rie", "initials": "R", "orcid": "0000-0002-7290-6376", "researcher": {"href": "https://publications.scilifelab.se/researcher/ca679685607b4187bffa818ee1168c81.json"}}], "type": "journal article", "published": "2020-07-29", "journal": {"title": "BMC Genomics", "issn": "1471-2164", "volume": "21", "issue": "1", "pages": "518", "issn-l": "1471-2164"}, "abstract": "Large difference in cerebrum size exist between avian species and populations of the same species and is believed to reflect differences in processing power, i.e. in the speed and efficiency of processing information in this brain region. During domestication chickens developed a larger cerebrum compared to their wild progenitor, the Red jungle fowl. The underlying mechanisms that control cerebrum size and the extent to which genetic regulation is similar across brain regions is not well understood. In this study, we combine measurement of cerebrum size with genome-wide genetical genomics analysis to identify the genetic architecture of the cerebrum, as well as compare the regulation of gene expression in this brain region with gene expression in other regions of the brain (the hypothalamus) and somatic tissue (liver).\n\nWe identify one candidate gene that putatively regulates cerebrum size (MTF2) as well as a large number of eQTL that regulate the transcriptome in cerebrum tissue, with the majority of these eQTL being trans-acting. The overall regulation of gene expression variation in the cerebrum was markedly different to the hypothalamus, with relatively few eQTL in common. In comparison, the cerebrum tissue shared more eQTL with a distant tissue (liver) than with a neighboring tissue (hypothalamus).\n\nThe candidate gene for cerebrum size (MTF2) has previously been linked to brain development making it a good candidate for further investigation as a regulator of inter-population variation in cerebrum size. The lack of shared eQTL between the two brain regions implies that genetic regulation of gene expression appears to be relatively independent between the two brain regions and suggest that coevolution between these two brain regions might be more functionally driven than developmental. These findings have relevance for current brain size evolution theories.", "doi": "10.1186/s12864-020-06908-0", "pmid": "32727510", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1186/s12864-020-06908-0"}, {"db": "pmc", "key": "PMC7392834"}], "notes": [], "created": "2020-08-04T14:50:06.953Z", "modified": "2024-01-16T13:48:42.102Z"}, {"entity": "publication", "iuid": "800346346d7a4a988909546711807aeb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/800346346d7a4a988909546711807aeb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/800346346d7a4a988909546711807aeb"}}, "title": "Combining transcriptomics and genetic linkage based information to identify candidate genes associated with Heterobasidion-resistance in Norway spruce.", "authors": [{"family": "Chaudhary", "given": "Rajiv", "initials": "R"}, {"family": "Lund\u00e9n", "given": "Karl", "initials": "K"}, {"family": "Dalman", "given": "Kerstin", "initials": "K"}, {"family": "Dubey", "given": "Mukesh", "initials": "M"}, {"family": "Nemesio-Gorriz", "given": "Miguel", "initials": "M"}, {"family": "Karlsson", "given": "Bo", "initials": "B"}, {"family": "Stenlid", "given": "Jan", "initials": "J"}, {"family": "Elfstrand", "given": "Malin", "initials": "M"}], "type": "journal article", "published": "2020-07-29", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "10", "issue": "1", "pages": "12711", "issn-l": "2045-2322"}, "abstract": "The Heterobasidion annosum s.l species complex comprises the most damaging forest pathogens to Norway spruce. We revisited previously identified Quantitative Trait Loci (QTLs) related to Heterobasidion-resistance in Norway spruce to identify candidate genes associated with these QTLs. We identified 329 candidate genes associated with the resistance QTLs using a gene-based composite map for Pinaceae. To evaluate the transcriptional responses of these candidate genes to H. parviporum, we inoculated Norway spruce plants and sequenced the transcriptome of the interaction at 3 and 7 days post inoculation. Out of 298 expressed candidate genes 124 were differentially expressed between inoculation and wounding control treatment. Interestingly, PaNAC04 and two of its paralogs in the subgroup III-3 of the NAC family transcription factors were found to be associated with one of the QTLs and was also highly induced in response to H. parviporum. These genes are possibly involved in the regulation of biosynthesis of flavonoid compounds. Furthermore, several of the differentially expressed candidate genes were associated with the phenylpropanoid pathway including a phenylalanine ammonia-lyase, a cinnamoyl-CoA reductase, a caffeoyl-CoA O-methyltransferase and a PgMYB11-like transcription factor gene. Combining transcriptome and genetic linkage analyses can help identifying candidate genes for functional studies and molecular breeding in non-model species.", "doi": "10.1038/s41598-020-69386-0", "pmid": "32728135", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-020-69386-0"}, {"db": "pmc", "key": "PMC7391732"}], "notes": [], "created": "2020-12-08T23:27:29.107Z", "modified": "2024-01-16T13:48:42.109Z"}, {"entity": "publication", "iuid": "87e07ded7de44a53ae4395ae27dfc8d4", "links": {"self": {"href": "https://publications.scilifelab.se/publication/87e07ded7de44a53ae4395ae27dfc8d4.json"}, "display": {"href": "https://publications.scilifelab.se/publication/87e07ded7de44a53ae4395ae27dfc8d4"}}, "title": "Translating GWAS-identified loci for cardiac rhythm and rate using an in vivo image- and CRISPR/Cas9-based approach", "authors": [{"family": "von der Heyde", "given": "Benedikt", "initials": "B", "orcid": "0000-0002-9889-4027", "researcher": {"href": "https://publications.scilifelab.se/researcher/803c0e0639174a50b59ae597802e824f.json"}}, {"family": "Emmanouilidou", "given": "Anastasia", "initials": "A"}, {"family": "Mazzaferro", "given": "Eugenia", "initials": "E"}, {"family": "Vicenzi", "given": "Silvia", "initials": "S"}, {"family": "H\u00f6ijer", "given": "Ida", "initials": "I"}, {"family": "Klingstr\u00f6m", "given": "Tiffany", "initials": "T"}, {"family": "Jumaa", "given": "Sitaf", "initials": "S"}, {"family": "Dethlefsen", "given": "Olga", "initials": "O"}, {"family": "Snieder", "given": "Harold", "initials": "H", "orcid": "0000-0003-1949-2298", "researcher": {"href": "https://publications.scilifelab.se/researcher/e9276827839a4f3cb50dcaa2ad4708a5.json"}}, {"family": "de Geus", "given": "Eco", "initials": "E", "orcid": "0000-0001-6022-2666", "researcher": {"href": "https://publications.scilifelab.se/researcher/9abb01a905f347df8214d469d6c5ac45.json"}}, {"family": "Ameur", "given": "Adam", "initials": "A", "orcid": "0000-0001-6085-6749", "researcher": {"href": "https://publications.scilifelab.se/researcher/e960811513664a78b2804a00ee70f7c3.json"}}, {"family": "Ingelsson", "given": "Erik", "initials": "E", "orcid": "0000-0003-2256-6972", "researcher": {"href": "https://publications.scilifelab.se/researcher/689bc741ea6547d18de7080c84d0193e.json"}}, {"family": "Allalou", "given": "Amin", "initials": "A"}, {"family": "Brooke", "given": "Hannah L", "initials": "HL"}, {"family": "den Hoed", "given": "Marcel", "initials": "M", "orcid": "0000-0001-8081-428X", "researcher": {"href": "https://publications.scilifelab.se/researcher/d712cc087d344b15ab9a7971640acebe.json"}}], "type": "journal-article", "published": "2020-07-16", "journal": {"title": "Sci Rep", "issn": "2045-2322", "issn-l": "2045-2322", "volume": "10", "issue": "1", "pages": "11831"}, "abstract": "A meta-analysis of genome-wide association studies (GWAS) identified eight loci that are associated with heart rate variability (HRV), but candidate genes in these loci remain uncharacterized. We developed an image- and CRISPR/Cas9-based pipeline to systematically characterize candidate genes for HRV in live zebrafish embryos. Nine zebrafish orthologues of six human candidate genes were targeted simultaneously in eggs from fish that transgenically express GFP on smooth muscle cells (Tg[acta2:GFP]), to visualize the beating heart. An automated analysis of repeated 30 s recordings of beating atria in 381 live, intact zebrafish embryos at 2 and 5 days post-fertilization highlighted genes that influence HRV (hcn4 and si:dkey-65j6.2 [KIAA1755]); heart rate (rgs6 and hcn4); and the risk of sinoatrial pauses and arrests (hcn4). Exposure to 10 or 25 \u00b5M ivabradine-an open channel blocker of HCNs-for 24 h resulted in a dose-dependent higher HRV and lower heart rate at 5 days post-fertilization. Hence, our screen confirmed the role of established genes for heart rate and rhythm (RGS6 and HCN4); showed that ivabradine reduces heart rate and increases HRV in zebrafish embryos, as it does in humans; and highlighted a novel gene that plays a role in HRV (KIAA1755).", "doi": "10.1038/s41598-020-68567-1", "pmid": "32678143", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (Uppsala Genome Center)": "Collaborative", "BioImage Informatics": "Collaborative", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Genome Engineering Zebrafish": "Service", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC7367351"}, {"db": "pii", "key": "10.1038/s41598-020-68567-1"}], "notes": [], "created": "2020-08-19T09:27:04.550Z", "modified": "2024-01-16T13:48:42.137Z"}, {"entity": "publication", "iuid": "eb85d8ec7f9746d88a03ac6981ab0223", "links": {"self": {"href": "https://publications.scilifelab.se/publication/eb85d8ec7f9746d88a03ac6981ab0223.json"}, "display": {"href": "https://publications.scilifelab.se/publication/eb85d8ec7f9746d88a03ac6981ab0223"}}, "title": "Transcriptional responses in Parascaris univalens after in vitro exposure to ivermectin, pyrantel citrate and thiabendazole.", "authors": [{"family": "Martin", "given": "Frida", "initials": "F", "orcid": "0000-0002-3149-3835", "researcher": {"href": "https://publications.scilifelab.se/researcher/eacd9c056fb1451994bf6ab3289bbeb1.json"}}, {"family": "Dube", "given": "Faruk", "initials": "F"}, {"family": "Karlsson Lindsj\u00f6", "given": "Oskar", "initials": "O"}, {"family": "Eydal", "given": "Matth\u00edas", "initials": "M"}, {"family": "H\u00f6glund", "given": "Johan", "initials": "J"}, {"family": "Bergstr\u00f6m", "given": "Tomas F", "initials": "TF"}, {"family": "Tyd\u00e9n", "given": "Eva", "initials": "E"}], "type": "journal article", "published": "2020-07-09", "journal": {"title": "Parasit Vectors", "issn": "1756-3305", "volume": "13", "issue": "1", "pages": "342", "issn-l": "1756-3305"}, "abstract": "Parascaris univalens is a pathogenic parasite of foals and yearlings worldwide. In recent years, Parascaris spp. worms have developed resistance to several of the commonly used anthelmintics, though currently the mechanisms behind this development are unknown. The aim of this study was to investigate the transcriptional responses in adult P. univalens worms after in vitro exposure to different concentrations of three anthelmintic drugs, focusing on drug targets and drug metabolising pathways.\n\nAdult worms were collected from the intestines of two foals at slaughter. The foals were naturally infected and had never been treated with anthelmintics. Worms were incubated in cell culture media containing different concentrations of either ivermectin (10-9 M, 10-11 M, 10-13 M), pyrantel citrate (10-6 M, 10-8 M, 10-10 M), thiabendazole (10-5 M, 10-7 M, 10-9 M) or without anthelmintics (control) at 37 \u00b0C for 24 h. After incubation, the viability of the worms was assessed and RNA extracted from the anterior region of 36 worms and sequenced on an Illumina NovaSeq 6000 system.\n\nAll worms were alive at the end of the incubation but showed varying degrees of viability depending on the drug and concentration used. Differential expression (Padj < 0.05 and log2 fold change \u2265 1 or \u2264 - 1) analysis showed similarities and differences in the transcriptional response after exposure to the different drug classes. Candidate genes upregulated or downregulated in drug exposed worms include members of the phase I metabolic pathway short-chain dehydrogenase/reductase superfamily (SDR), flavin containing monooxygenase superfamily (FMO) and cytochrome P450-family (CYP), as well as members of the membrane transporters major facilitator superfamily (MFS) and solute carrier superfamily (SLC). Generally, different targets of the anthelmintics used were found to be upregulated and downregulated in an unspecific pattern after drug exposure, apart from the GABA receptor subunit lgc-37, which was upregulated only in worms exposed to 10-9 M of ivermectin.\n\nTo our knowledge, this is the first time the expression of lgc-37 and members of the FMO, SDR, MFS and SLC superfamilies have been described in P. univalens and future work should be focused on characterising these candidate genes to further explore their potential involvement in drug metabolism and anthelmintic resistance.", "doi": "10.1186/s13071-020-04212-0", "pmid": "32646465", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1186/s13071-020-04212-0"}, {"db": "pmc", "key": "PMC7346371"}], "notes": [], "created": "2020-12-08T23:34:23.929Z", "modified": "2024-01-16T13:48:42.174Z"}, {"entity": "publication", "iuid": "9415049166944ab6990231e492323800", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9415049166944ab6990231e492323800.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9415049166944ab6990231e492323800"}}, "title": "Disturbance history can increase functional stability in the face of both repeated disturbances of the same type and novel disturbances.", "authors": [{"family": "Renes", "given": "Sophia Elise", "initials": "SE"}, {"family": "Sj\u00f6stedt", "given": "Johanna", "initials": "J"}, {"family": "Fetzer", "given": "Ingo", "initials": "I"}, {"family": "Langenheder", "given": "Silke", "initials": "S"}], "type": "journal article", "published": "2020-07-09", "journal": {"title": "Sci Rep", "issn": "2045-2322", "issn-l": "2045-2322", "volume": "10", "issue": "1", "pages": "11333"}, "abstract": "Climate change is expected to increase the incidences of extremes in environmental conditions. To investigate how repeated disturbances affect microbial ecosystem resistance, natural lake bacterioplankton communities were subjected to repeated temperature disturbances of two intensities (25 \u00b0C and 35 \u00b0C), and subsequently to an acidification event. We measured functional parameters (bacterial production, abundance, extracellular enzyme activities) and community composition parameters (richness, evenness, niche width) and found that, compared to undisturbed control communities, the 35 \u00b0C treatment was strongly affected in all parameters, while the 25 \u00b0C treatment did not significantly differ from the control. Interestingly, exposure to multiple temperature disturbances caused gradually increasing stability in the 35 \u00b0C treatment in some parameters, while others parameters showed the opposite, indicating that the choice of parameters can strongly affect the outcome of a study. The acidification event did not lead to stronger changes in community structure, but functional resistance of bacterial production towards acidification in the 35 \u00b0C treatments increased. This indicates that functional resistance in response to a novel disturbance can be increased by previous exposure to another disturbance, suggesting similarity in stress tolerance mechanisms for both disturbances. These results highlight the need for understanding function- and disturbance-specific responses, since general responses are likely to be unpredictable.", "doi": "10.1038/s41598-020-68104-0", "pmid": "32647292", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-020-68104-0"}, {"db": "pmc", "key": "PMC7347917"}], "notes": [], "created": "2020-12-08T23:18:02.286Z", "modified": "2024-01-16T13:48:42.181Z"}, {"entity": "publication", "iuid": "c7e200350fda45a291ec77006ecc5bbb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c7e200350fda45a291ec77006ecc5bbb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c7e200350fda45a291ec77006ecc5bbb"}}, "title": "Discovery and population genomics of structural variation in a songbird genus.", "authors": [{"family": "Weissensteiner", "given": "Matthias H", "initials": "MH", "orcid": "0000-0001-9302-798X", "researcher": {"href": "https://publications.scilifelab.se/researcher/5550a93e906d4e25985cd7641f8be554.json"}}, {"family": "Bunikis", "given": "Ignas", "initials": "I"}, {"family": "Catal\u00e1n", "given": "Ana", "initials": "A"}, {"family": "Francoijs", "given": "Kees-Jan", "initials": "KJ"}, {"family": "Knief", "given": "Ulrich", "initials": "U", "orcid": "0000-0001-6959-3033", "researcher": {"href": "https://publications.scilifelab.se/researcher/5d8858c7c7b44a008a172bc637957ce1.json"}}, {"family": "Heim", "given": "Wieland", "initials": "W", "orcid": "0000-0002-3262-2491", "researcher": {"href": "https://publications.scilifelab.se/researcher/a88dd35e7b8a46b49c9e2ccc6d712b45.json"}}, {"family": "Peona", "given": "Valentina", "initials": "V", "orcid": "0000-0001-5119-1837", "researcher": {"href": "https://publications.scilifelab.se/researcher/d4903a935025452f88e4f1c02483829b.json"}}, {"family": "Pophaly", "given": "Saurabh D", "initials": "SD"}, {"family": "Sedlazeck", "given": "Fritz J", "initials": "FJ"}, {"family": "Suh", "given": "Alexander", "initials": "A", "orcid": "0000-0002-8979-9992", "researcher": {"href": "https://publications.scilifelab.se/researcher/4e39e1313d894596a6c4ed949e43e019.json"}}, {"family": "Warmuth", "given": "Vera M", "initials": "VM"}, {"family": "Wolf", "given": "Jochen B W", "initials": "JBW"}], "type": "journal article", "published": "2020-07-07", "journal": {"title": "Nat Commun", "issn": "2041-1723", "issn-l": "2041-1723", "volume": "11", "issue": "1", "pages": "3403"}, "abstract": "Structural variation (SV) constitutes an important type of genetic mutations providing the raw material for evolution. Here, we uncover the genome-wide spectrum of intra- and interspecific SV segregating in natural populations of seven songbird species in the genus Corvus. Combining short-read (N = 127) and long-read re-sequencing (N = 31), as well as optical mapping (N = 16), we apply both assembly- and read mapping approaches to detect SV and characterize a total of 220,452 insertions, deletions and inversions. We exploit sampling across wide phylogenetic timescales to validate SV genotypes and assess the contribution of SV to evolutionary processes in an avian model of incipient speciation. We reveal an evolutionary young (~530,000 years) cis-acting 2.25-kb LTR retrotransposon insertion reducing expression of the NDP gene with consequences for premating isolation. Our results attest to the wealth and evolutionary significance of SV segregating in natural populations and highlight the need for reliable SV genotyping.", "doi": "10.1038/s41467-020-17195-4", "pmid": "32636372", "labels": {"National Genomics Infrastructure": "Collaborative", "NGI Uppsala (Uppsala Genome Center)": "Collaborative", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-020-17195-4"}, {"db": "pmc", "key": "PMC7341801"}, {"db": "Dryad", "key": "10.5061/dryad.ns1rn8ppj"}], "notes": [], "created": "2020-08-25T12:55:18.199Z", "modified": "2024-01-16T13:48:42.202Z"}, {"entity": "publication", "iuid": "a1d31987288449ba8a738404fa44921b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a1d31987288449ba8a738404fa44921b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a1d31987288449ba8a738404fa44921b"}}, "title": "meQTL and ncRNA functional analyses of 102 GWAS-SNPs associated with depression implicate HACE1 and SHANK2 genes.", "authors": [{"family": "Ciuculete", "given": "Diana M", "initials": "DM", "orcid": "0000-0001-6377-0270", "researcher": {"href": "https://publications.scilifelab.se/researcher/1facf036e83a4fd1934204cc1dc7ee4d.json"}}, {"family": "Voisin", "given": "Sarah", "initials": "S"}, {"family": "Kular", "given": "Lara", "initials": "L"}, {"family": "Jonsson", "given": "J\u00f6rgen", "initials": "J"}, {"family": "Rask-Andersen", "given": "Mathias", "initials": "M"}, {"family": "Mwinyi", "given": "Jessica", "initials": "J"}, {"family": "Schi\u00f6th", "given": "Helgi B", "initials": "HB"}], "type": "journal article", "published": "2020-07-02", "journal": {"title": "Clin Epigenetics", "issn": "1868-7083", "volume": "12", "issue": "1", "pages": "99", "issn-l": "1868-7075"}, "abstract": "Little is known about how genetics and epigenetics interplay in depression. Evidence suggests that genetic variants may change vulnerability to depression by modulating DNA methylation (DNAm) and non-coding RNA (ncRNA) levels. Therefore, the aim of the study was to investigate the effect of the genetic variation, previously identified in the largest genome-wide association study for depression, on proximal DNAm and ncRNA levels.\n\nWe performed DNAm quantitative trait locus (meQTL) analysis in two independent cohorts (total n = 435 healthy individuals), testing associations between 102 single-nucleotide polymorphisms (SNPs) and DNAm levels in whole blood. We identified and replicated 64 SNP-CpG pairs (padj. < 0.05) with meQTL effect. Lower DNAm at cg02098413 located in the HACE1 promoter conferred by the risk allele (C allele) at rs1933802 was associated with higher risk for depression (praw = 0.014, DNAm = 2.3%). In 1202 CD14+ cells sorted from blood, DNAm at cg02088412 positively correlated with HACE1 mRNA expression. Investigation in postmortem brain tissue of adults diagnosed with major depressive disorder (MDD) indicated 1% higher DNAm at cg02098413 in neurons and lower HACE1 mRNA expression in CA1 hippocampus of MDD patients compared with healthy controls (p = 0.008 and 0.012, respectively). Expression QTL analysis in blood of 74 adolescent revealed that hsa-miR-3664-5p was associated with rs7117514 (SHANK2) (padj. = 0.015, mRNA difference = 5.2%). Gene ontology analysis of the miRNA target genes highlighted implication in neuronal processes.\n\nCollectively, our findings from a multi-tissue (blood and brain) and multi-layered (genetic, epigenetic, transcriptomic) approach suggest that genetic factors may influence depression by modulating DNAm and miRNA levels. Alterations at HACE1 and SHANK2 loci imply potential mechanisms, such as oxidative stress in the brain, underlying depression. Our results deepened the knowledge of molecular mechanisms in depression and suggest new epigenetic targets that should be further evaluated.", "doi": "10.1186/s13148-020-00884-8", "pmid": "32616021", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1186/s13148-020-00884-8"}, {"db": "pmc", "key": "PMC7333393"}], "notes": [], "created": "2020-08-04T14:50:04.126Z", "modified": "2024-01-16T13:48:42.216Z"}, {"entity": "publication", "iuid": "55dcf41e17e8459fb3c49cd79e48f71c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/55dcf41e17e8459fb3c49cd79e48f71c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/55dcf41e17e8459fb3c49cd79e48f71c"}}, "title": "Y-Chromosome Variation in Southern African Khoe-San Populations Based on Whole-Genome Sequences.", "authors": [{"family": "Naidoo", "given": "Thijessen", "initials": "T"}, {"family": "Xu", "given": "Jingzi", "initials": "J"}, {"family": "Vicente", "given": "M\u00e1rio", "initials": "M"}, {"family": "Malmstr\u00f6m", "given": "Helena", "initials": "H"}, {"family": "Soodyall", "given": "Himla", "initials": "H"}, {"family": "Jakobsson", "given": "Mattias", "initials": "M", "orcid": "0000-0001-7840-7853", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a4abe0fcb20492d9ec849c9fbf58a71.json"}}, {"family": "Schlebusch", "given": "Carina M", "initials": "CM", "orcid": "0000-0002-8160-9621", "researcher": {"href": "https://publications.scilifelab.se/researcher/682f10853c1145649b8c76680605dd9b.json"}}], "type": "comparative study", "published": "2020-07-01", "journal": {"title": "Genome Biol Evol", "issn": "1759-6653", "issn-l": "1759-6653", "volume": "12", "issue": "7", "pages": "1031-1039"}, "abstract": "Although the human Y chromosome has effectively shown utility in uncovering facets of human evolution and population histories, the ascertainment bias present in early Y-chromosome variant data sets limited the accuracy of diversity and TMRCA estimates obtained from them. The advent of next-generation sequencing, however, has removed this bias and allowed for the discovery of thousands of new variants for use in improving the Y-chromosome phylogeny and computing estimates that are more accurate. Here, we describe the high-coverage sequencing of the whole Y chromosome in a data set of 19 male Khoe-San individuals in comparison with existing whole Y-chromosome sequence data. Due to the increased resolution, we potentially resolve the source of haplogroup B-P70 in the Khoe-San, and reconcile recently published haplogroup A-M51 data with the most recent version of the ISOGG Y-chromosome phylogeny. Our results also improve the positioning of tentatively placed new branches of the ISOGG Y-chromosome phylogeny. The distribution of major Y-chromosome haplogroups in the Khoe-San and other African groups coincide with the emerging picture of African demographic history; with E-M2 linked to the agriculturalist Bantu expansion, E-M35 linked to pastoralist eastern African migrations, B-M112 linked to earlier east-south gene flow, A-M14 linked to shared ancestry with central African rainforest hunter-gatherers, and A-M51 potentially unique to the Khoe-San.", "doi": "10.1093/gbe/evaa098", "pmid": "32697300", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "5874966"}, {"db": "pmc", "key": "PMC7375190"}], "notes": [], "created": "2020-12-08T23:25:49.670Z", "modified": "2024-01-16T13:48:42.238Z"}, {"entity": "publication", "iuid": "b71fefd3189648368056856a895f0346", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b71fefd3189648368056856a895f0346.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b71fefd3189648368056856a895f0346"}}, "title": "Genetic Associations Between Childhood Psychopathology and Adult Depression and Associated Traits in 42 998 Individuals: A Meta-analysis.", "authors": [{"family": "Akingbuwa", "given": "Wonuola A", "initials": "WA"}, {"family": "Hammerschlag", "given": "Anke R", "initials": "AR"}, {"family": "Jami", "given": "Eshim S", "initials": "ES"}, {"family": "Allegrini", "given": "Andrea G", "initials": "AG"}, {"family": "Karhunen", "given": "Ville", "initials": "V"}, {"family": "Sallis", "given": "Hannah", "initials": "H"}, {"family": "Ask", "given": "Helga", "initials": "H"}, {"family": "Askeland", "given": "Ragna B", "initials": "RB"}, {"family": "Baselmans", "given": "Bart", "initials": "B"}, {"family": "Diemer", "given": "Elizabeth", "initials": "E"}, {"family": "Hagenbeek", "given": "Fiona A", "initials": "FA"}, {"family": "Havdahl", "given": "Alexandra", "initials": "A"}, {"family": "Hottenga", "given": "Jouke-Jan", "initials": "JJ"}, {"family": "Mbarek", "given": "Hamdi", "initials": "H"}, {"family": "Rivadeneira", "given": "Fernando", "initials": "F"}, {"family": "Tesli", "given": "Martin", "initials": "M"}, {"family": "van Beijsterveldt", "given": "Catharina", "initials": "C"}, {"family": "Breen", "given": "Gerome", "initials": "G"}, {"family": "Lewis", "given": "Cathryn M", "initials": "CM"}, {"family": "Thapar", "given": "Anita", "initials": "A"}, {"family": "Boomsma", "given": "Dorret I", "initials": "DI"}, {"family": "Kuja-Halkola", "given": "Ralf", "initials": "R"}, {"family": "Reichborn-Kjennerud", "given": "Ted", "initials": "T"}, {"family": "Magnus", "given": "Per", "initials": "P"}, {"family": "Rimfeld", "given": "Kaili", "initials": "K"}, {"family": "Ystrom", "given": "Eivind", "initials": "E"}, {"family": "Jarvelin", "given": "Marjo-Riitta", "initials": "MR"}, {"family": "Lichtenstein", "given": "Paul", "initials": "P"}, {"family": "Lundstrom", "given": "Sebastian", "initials": "S"}, {"family": "Munaf\u00f2", "given": "Marcus R", "initials": "MR"}, {"family": "Plomin", "given": "Robert", "initials": "R"}, {"family": "Tiemeier", "given": "Henning", "initials": "H"}, {"family": "Nivard", "given": "Michel G", "initials": "MG"}, {"family": "Bartels", "given": "Meike", "initials": "M"}, {"family": "Middeldorp", "given": "Christel M", "initials": "CM"}, {"family": "Bipolar Disorder and Major Depressive Disorder Working Groups of the Psychiatric Genomics Consortium", "given": "", "initials": ""}], "type": "journal article", "published": "2020-07-01", "journal": {"title": "JAMA Psychiatry", "issn": "2168-6238", "volume": "77", "issue": "7", "pages": "715-728", "issn-l": "2168-622X"}, "abstract": "Adult mood disorders are often preceded by behavioral and emotional problems in childhood. It is yet unclear what explains the associations between childhood psychopathology and adult traits.\n\nTo investigate whether genetic risk for adult mood disorders and associated traits is associated with childhood disorders.\n\nThis meta-analysis examined data from 7 ongoing longitudinal birth and childhood cohorts from the UK, the Netherlands, Sweden, Norway, and Finland. Starting points of data collection ranged from July 1985 to April 2002. Participants were repeatedly assessed for childhood psychopathology from ages 6 to 17 years. Data analysis occurred from September 2017 to May 2019.\n\nIndividual polygenic scores (PGS) were constructed in children based on genome-wide association studies of adult major depression, bipolar disorder, subjective well-being, neuroticism, insomnia, educational attainment, and body mass index (BMI).\n\nRegression meta-analyses were used to test associations between PGS and attention-deficit/hyperactivity disorder (ADHD) symptoms and internalizing and social problems measured repeatedly across childhood and adolescence and whether these associations depended on childhood phenotype, age, and rater.\n\nThe sample included 42 998 participants aged 6 to 17 years. Male participants varied from 43.0% (1040 of 2417 participants) to 53.1% (2434 of 4583 participants) by age and across all cohorts. The PGS of adult major depression, neuroticism, BMI, and insomnia were positively associated with childhood psychopathology (\u03b2 estimate range, 0.023-0.042 [95% CI, 0.017-0.049]), while associations with PGS of subjective well-being and educational attainment were negative (\u03b2, -0.026 to -0.046 [95% CI, -0.020 to -0.057]). There was no moderation of age, type of childhood phenotype, or rater with the associations. The exceptions were stronger associations between educational attainment PGS and ADHD compared with internalizing problems (\u0394\u03b2, 0.0561 [\u039495% CI, 0.0318-0.0804]; \u0394SE, 0.0124) and social problems (\u0394\u03b2, 0.0528 [\u039495% CI, 0.0282-0.0775]; \u0394SE, 0.0126), and between BMI PGS and ADHD and social problems (\u0394\u03b2, -0.0001 [\u039495% CI, -0.0102 to 0.0100]; \u0394SE, 0.0052), compared with internalizing problems (\u0394\u03b2, -0.0310 [\u039495% CI, -0.0456 to -0.0164]; \u0394SE, 0.0074). Furthermore, the association between educational attainment PGS and ADHD increased with age (\u0394\u03b2, -0.0032 [\u0394 95% CI, -0.0048 to -0.0017]; \u0394SE, 0.0008).\n\nResults from this study suggest the existence of a set of genetic factors influencing a range of traits across the life span with stable associations present throughout childhood. Knowledge of underlying mechanisms may affect treatment and long-term outcomes of individuals with psychopathology.", "doi": "10.1001/jamapsychiatry.2020.0527", "pmid": "32293669", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "2763801"}, {"db": "pmc", "key": "PMC7160753"}], "notes": [], "created": "2020-05-06T12:23:53.890Z", "modified": "2021-11-10T12:52:04.518Z"}, {"entity": "publication", "iuid": "ce6d56617d5243ee9bf1a8d1257c006e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ce6d56617d5243ee9bf1a8d1257c006e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ce6d56617d5243ee9bf1a8d1257c006e"}}, "title": "Transcriptomes from German shepherd dogs reveal differences in immune activity between atopic dermatitis affected and control skin.", "authors": [{"family": "Tengvall", "given": "K", "initials": "K", "orcid": "0000-0003-0424-3571", "researcher": {"href": "https://publications.scilifelab.se/researcher/59b02aaaf03b4cd39150c3034888c81d.json"}}, {"family": "Bergvall", "given": "K", "initials": "K"}, {"family": "Olsson", "given": "M", "initials": "M", "orcid": "0000-0002-7228-2575", "researcher": {"href": "https://publications.scilifelab.se/researcher/a544f6e122da4b1ebf7a2ad70fd5bceb.json"}}, {"family": "Ardesj\u00f6-Lundgren", "given": "B", "initials": "B"}, {"family": "Farias", "given": "F H G", "initials": "FHG", "orcid": "0000-0002-5215-7304", "researcher": {"href": "https://publications.scilifelab.se/researcher/1b8a07dda61d4fc3a3f837cdb5dbcd5a.json"}}, {"family": "Kierczak", "given": "M", "initials": "M", "orcid": "0000-0003-2629-5655", "researcher": {"href": "https://publications.scilifelab.se/researcher/6c13f96fb81f4ae2bfff5e91ac45388e.json"}}, {"family": "Hedhammar", "given": "\u00c5", "initials": "\u00c5", "orcid": "0000-0001-7048-3851", "researcher": {"href": "https://publications.scilifelab.se/researcher/fa01be589a4b4939a01c06ad57bfc356.json"}}, {"family": "Lindblad-Toh", "given": "K", "initials": "K", "orcid": "0000-0001-8338-0253", "researcher": {"href": "https://publications.scilifelab.se/researcher/e0063145f7d6476f80ab42f94833f4cf.json"}}, {"family": "Andersson", "given": "G", "initials": "G", "orcid": "0000-0001-5131-3144", "researcher": {"href": "https://publications.scilifelab.se/researcher/39ce81c314db47c8ad63c3ed38dffcb3.json"}}], "type": "journal article", "published": "2020-07-00", "journal": {"title": "Immunogenetics", "issn": "1432-1211", "volume": "72", "issue": "5", "pages": "315-323", "issn-l": "0093-7711"}, "abstract": "Canine atopic dermatitis (CAD) is an inflammatory and pruritic allergic skin disease with both genetic and environmental risk factors described. We performed mRNA sequencing of non-lesional axillary skin biopsies from nine German shepherd dogs. Obtained RNA sequences were mapped to the dog genome (CanFam3.1) and a high-quality skin transcriptome was generated with 23,510 expressed gene transcripts. Differentially expressed genes (DEGs) were defined by comparing three controls to five treated CAD cases. Using a leave-one-out analysis, we identified seven DEGs: five known to encode proteins with functions related to an activated immune system (CD209, CLEC4G, LOC102156842 (lipopolysaccharide-binding protein-like), LOC480601 (regakine-1-like), LOC479668 (haptoglobin-like)), one (OBP) encoding an odorant-binding protein potentially connected to rhinitis, and the last (LOC607095) encoding a novel long non-coding RNA. Furthermore, high mRNA expression of inflammatory genes was found in axillary skin from an untreated mild CAD case compared with healthy skin. In conclusion, we define genes with different expression patterns in CAD case skin helping us understand post-treatment atopic skin. Further studies in larger sample sets are warranted to confirm and to transfer these results into clinical practice.", "doi": "10.1007/s00251-020-01169-3", "pmid": "32556497", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1007/s00251-020-01169-3"}, {"db": "pmc", "key": "PMC7320941"}], "notes": [], "created": "2020-07-03T05:20:56.396Z", "modified": "2024-01-16T13:48:42.253Z"}, {"entity": "publication", "iuid": "f005a36d6a6944bc939d90904088154d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f005a36d6a6944bc939d90904088154d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f005a36d6a6944bc939d90904088154d"}}, "title": "Pre- and postnatal Lactobacillus reuteri treatment alters DNA methylation of infant T helper cells.", "authors": [{"family": "Forsberg", "given": "Anna", "initials": "A"}, {"family": "Huoman", "given": "Johanna", "initials": "J", "orcid": "0000-0003-2509-2418", "researcher": {"href": "https://publications.scilifelab.se/researcher/471444d05e834a9b86a5a6d187da2c04.json"}}, {"family": "S\u00f6derholm", "given": "Simon", "initials": "S", "orcid": "0000-0001-5350-7102", "researcher": {"href": "https://publications.scilifelab.se/researcher/75f4744864904171b6a708e7a8d2b471.json"}}, {"family": "Bhai Mehta", "given": "Ratnesh", "initials": "R"}, {"family": "Nilsson", "given": "Lennart", "initials": "L", "orcid": "0000-0002-5680-6367", "researcher": {"href": "https://publications.scilifelab.se/researcher/19f74feeb54c4d588b879ea9e8843662.json"}}, {"family": "Abrahamsson", "given": "Thomas R", "initials": "TR"}, {"family": "Ernerudh", "given": "Jan", "initials": "J"}, {"family": "Gustafsson", "given": "Mika", "initials": "M"}, {"family": "Jenmalm", "given": "Maria C", "initials": "MC", "orcid": "0000-0002-2117-5366", "researcher": {"href": "https://publications.scilifelab.se/researcher/bf1f485192744e0c95ccecdb5471b577.json"}}], "type": "journal article", "published": "2020-07-00", "journal": {"title": "Pediatr Allergy Immunol", "issn": "1399-3038", "volume": "31", "issue": "5", "pages": "544-553", "issn-l": "0905-6157"}, "abstract": "Perinatal childhood exposures, including probiotic supplementation, may affect epigenetic modifications and impact on immune maturation and allergy development. The aim of this study was to assess the effects of pre- and postnatal Lactobacillus reuteri supplementation on DNA methylation in relation to immune maturation and allergy development.\n\nDNA methylation patterns were investigated for allergy-related T helper subsets using a locus-specific method and at a genome-wide scale using the Illumina 450K array. From a randomised, double-blind, placebo-controlled allergy prevention trial with pre- and postnatal probiotic supplementation, CD4+ T helper cells were obtained at birth (from cord blood), and 12 and 24 months of age (total (placebo/probiotics); locus-specific method: CB = 32 (17/15), 12 months = 24 (9/15), 24 months = 35 (15/20); Illumina: CB = 19 (10/9), 12 months = 10 (6/4), 24 months = 19(11/8)).\n\nComparing probiotics to placebo, the greatest genome-wide differential DNA methylation was observed at birth, where the majority of sites were hypomethylated, indicating transcriptional accessibility in the probiotic group. Bioinformatic analyses, including network analyses, revealed a module containing 91 genes, enriched for immune-related pathways such as chemotaxis, PI3K-Akt, MAPK and TGF-\u03b2 signalling. A majority of the module genes were associated with atopic manifestations (OR = 1.43, P = 2.4 \u00d7 10-6 ), and a classifier built on this model could predict allergy development (AUC = 0.78, P = 3.0 \u00d7 10e-3 ). Pathways such as IFN-\u03b3 signalling and T-cell activation were more hypermethylated at birth compared with later in life in both intervention groups over time, in line with DNA methylation patterns in the IFNG locus obtained by the locus-specific methodology.\n\nMaternal L. reuteri supplementation during pregnancy alters DNA methylation patterns in CD4+ T cells towards enhanced immune activation at birth, which may affect immune maturation and allergy development.", "doi": "10.1111/pai.13240", "pmid": "32150651", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2020-03-12T15:01:36.562Z", "modified": "2024-01-16T13:48:42.269Z"}, {"entity": "publication", "iuid": "5cb7cdbae68246d59af83a96584bf906", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5cb7cdbae68246d59af83a96584bf906.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5cb7cdbae68246d59af83a96584bf906"}}, "title": "Growth-Inhibitory Activity of Bone Morphogenetic Protein 4 in Human Glioblastoma Cell Lines Is Heterogeneous and Dependent on Reduced SOX2 Expression.", "authors": [{"family": "Dalmo", "given": "Erika", "initials": "E", "orcid": "0000-0003-0272-9893", "researcher": {"href": "https://publications.scilifelab.se/researcher/fc28d8e2dc16417eafd87d3bd1a1229f.json"}}, {"family": "Johansson", "given": "Patrik", "initials": "P"}, {"family": "Niklasson", "given": "Mia", "initials": "M"}, {"family": "Gustavsson", "given": "Ida", "initials": "I"}, {"family": "Nelander", "given": "Sven", "initials": "S"}, {"family": "Westermark", "given": "Bengt", "initials": "B", "orcid": "0000-0001-7153-5545", "researcher": {"href": "https://publications.scilifelab.se/researcher/dbaf3a1cdd7d48e5ba9e147bfb5055b6.json"}}], "type": "journal article", "published": "2020-07-00", "journal": {"title": "Mol Cancer Res", "issn": "1541-7786", "volume": "18", "issue": "7", "pages": "981-991", "issn-l": null}, "abstract": "Glioblastoma multiforme continues to have a dismal prognosis. Even though detailed information on the genetic aberrations in cell signaling and cell-cycle checkpoint control is available, no effective targeted treatment has been developed. Despite the advanced molecular defects, glioblastoma cells may have remnants of normal growth-inhibitory pathways, such as the bone morphogenetic protein (BMP) signaling pathway. We have evaluated the growth-inhibitory effect of BMP4 across a broad spectrum of patient samples, using a panel of 40 human glioblastoma initiating cell (GIC) cultures. A wide range of responsiveness was observed. BMP4 sensitivity was positively correlated with a proneural mRNA expression profile, high SOX2 activity, and BMP4-dependent upregulation of genes associated with inhibition of the MAPK pathway, as demonstrated by gene set enrichment analysis. BMP4 response in sensitive cells was mediated by the canonical BMP receptor pathway involving SMAD1/5/9 phosphorylation and SMAD4 expression. SOX2 was consistently downregulated in BMP4-treated cells. Forced expression of SOX2 attenuated the BMP4 sensitivity including a reduced upregulation of MAPK-inhibitory genes, implying a functional relationship between SOX2 downregulation and sensitivity. The results show an extensive heterogeneity in BMP4 responsiveness among GICs and identify a BMP4-sensitive subgroup, in which SOX2 is a mediator of the response. IMPLICATIONS: Development of agonists targeting the BMP signaling pathway in glioblastoma is an attractive avenue toward a better treatment. Our study may help find biomarkers that predict the outcome of such treatment and enable stratification of patients.", "doi": "10.1158/1541-7786.MCR-19-0638", "pmid": "32234828", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "1541-7786.MCR-19-0638"}], "notes": [], "created": "2020-12-08T23:44:27.982Z", "modified": "2024-01-16T13:48:42.299Z"}, {"entity": "publication", "iuid": "9d7fcd3fe5d84966ab5d1e2cf5d5137b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9d7fcd3fe5d84966ab5d1e2cf5d5137b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9d7fcd3fe5d84966ab5d1e2cf5d5137b"}}, "title": "Female-biased gene flow between two species of Darwin's finches.", "authors": [{"family": "Lamichhaney", "given": "Sangeet", "initials": "S", "orcid": "0000-0003-4826-0349", "researcher": {"href": "https://publications.scilifelab.se/researcher/602a2f371eae45e4b9d8f9748f285ef4.json"}}, {"family": "Han", "given": "Fan", "initials": "F"}, {"family": "Webster", "given": "Matthew T", "initials": "MT", "orcid": "0000-0003-1141-2863", "researcher": {"href": "https://publications.scilifelab.se/researcher/579df0da95b94e5087512b76d7f1c058.json"}}, {"family": "Grant", "given": "B Rosemary", "initials": "BR"}, {"family": "Grant", "given": "Peter R", "initials": "PR"}, {"family": "Andersson", "given": "Leif", "initials": "L", "orcid": "0000-0002-4085-6968", "researcher": {"href": "https://publications.scilifelab.se/researcher/bd3343c12f994b1fabcae23027d3a76d.json"}}], "type": "journal article", "published": "2020-07-00", "journal": {"title": "Nat Ecol Evol", "issn": "2397-334X", "volume": "4", "issue": "7", "pages": "979-986", "issn-l": "2397-334X"}, "abstract": "The mosaic nature of hybrid genomes is well recognized, but little is known of how they are shaped initially by patterns of breeding, selection, recombination and differential incompatibilities. On the small Gal\u00e1pagos island of Daphne Major, two species of Darwin's finches, Geospiza fortis and G. scandens, hybridize rarely and back-cross bidirectionally with little or no loss of fitness under conditions of plentiful food. We used whole-genome sequences to compare genomes from periods before and after successful interbreeding followed by back-crossing. We inferred extensive introgression from G. fortis to G. scandens on autosomes and mitochondria but not on the Z chromosome. The unique combination of long-term field observations and genomic data shows that the reduction of gene flow for Z-linked loci primarily reflects female-biased gene flow, arising from a hybrid-male disadvantage in competition for high-quality territories and mates, rather than from genetic incompatibilities at Z-linked loci.", "doi": "10.1038/s41559-020-1183-9", "pmid": "32367030", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41559-020-1183-9"}], "notes": [], "created": "2020-07-03T05:28:11.615Z", "modified": "2024-01-16T13:48:42.318Z"}, {"entity": "publication", "iuid": "c1da6115eb61449fbd3f03367a285fc9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c1da6115eb61449fbd3f03367a285fc9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c1da6115eb61449fbd3f03367a285fc9"}}, "title": "Genome assembly of the basket willow, Salix viminalis, reveals earliest stages of sex chromosome expansion.", "authors": [{"family": "Almeida", "given": "Pedro", "initials": "P", "orcid": "0000-0001-6790-8687", "researcher": {"href": "https://publications.scilifelab.se/researcher/bb2e2881fe7449659d89e9beb407e0a4.json"}}, {"family": "Proux-Wera", "given": "Estelle", "initials": "E"}, {"family": "Churcher", "given": "Allison", "initials": "A"}, {"family": "Soler", "given": "Lucile", "initials": "L"}, {"family": "Dainat", "given": "Jacques", "initials": "J"}, {"family": "Pucholt", "given": "Pascal", "initials": "P"}, {"family": "Nordlund", "given": "Jessica", "initials": "J", "orcid": "0000-0001-8699-9959", "researcher": {"href": "https://publications.scilifelab.se/researcher/ddf48c9262134821bcc6ce1180049753.json"}}, {"family": "Martin", "given": "Tom", "initials": "T"}, {"family": "R\u00f6nnberg-W\u00e4stljung", "given": "Ann-Christin", "initials": "AC"}, {"family": "Nystedt", "given": "Bj\u00f6rn", "initials": "B", "orcid": "0000-0001-7809-7664", "researcher": {"href": "https://publications.scilifelab.se/researcher/f0af5a168baa4b00a6fab8d3447ebfb4.json"}}, {"family": "Berlin", "given": "Sofia", "initials": "S"}, {"family": "Mank", "given": "Judith E", "initials": "JE"}], "type": "journal article", "published": "2020-06-30", "journal": {"title": "BMC Biol.", "issn": "1741-7007", "issn-l": "1741-7007", "volume": "18", "issue": "1", "pages": "78"}, "abstract": "Sex chromosomes have evolved independently multiple times in eukaryotes and are therefore considered a prime example of convergent genome evolution. Sex chromosomes are known to emerge after recombination is halted between a homologous pair of chromosomes, and this leads to a range of non-adaptive modifications causing gradual degeneration and gene loss on the sex-limited chromosome. However, the proximal causes of recombination suppression and the pace at which degeneration subsequently occurs remain unclear.\n\nHere, we use long- and short-read single-molecule sequencing approaches to assemble and annotate a draft genome of the basket willow, Salix viminalis, a species with a female heterogametic system at the earliest stages of sex chromosome emergence. Our single-molecule approach allowed us to phase the emerging Z and W haplotypes in a female, and we detected very low levels of Z/W single-nucleotide divergence in the non-recombining region. Linked-read sequencing of the same female and an additional male (ZZ) revealed the presence of two evolutionary strata supported by both divergence between the Z and W haplotypes and by haplotype phylogenetic trees. Gene order is still largely conserved between the Z and W homologs, although the W-linked region contains genes involved in cytokinin signaling regulation that are not syntenic with the Z homolog. Furthermore, we find no support across multiple lines of evidence for inversions, which have long been assumed to halt recombination between the sex chromosomes.\n\nOur data suggest that selection against recombination is a more gradual process at the earliest stages of sex chromosome formation than would be expected from an inversion and may result instead from the accumulation of transposable elements. Our results present a cohesive understanding of the earliest genomic consequences of recombination suppression as well as valuable insights into the initial stages of sex chromosome formation and regulation of sex differentiation.", "doi": "10.1186/s12915-020-00808-1", "pmid": "32605573", "labels": {"National Genomics Infrastructure": "Collaborative", "NGI Uppsala (SNP&SEQ Technology Platform)": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1186/s12915-020-00808-1"}, {"db": "pmc", "key": "PMC7329446"}], "notes": [], "created": "2020-07-03T05:25:52.141Z", "modified": "2021-11-10T12:50:00.669Z"}, {"entity": "publication", "iuid": "194d913bd2654246bcdf9732ca06b6e2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/194d913bd2654246bcdf9732ca06b6e2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/194d913bd2654246bcdf9732ca06b6e2"}}, "title": "An efficient single-cell transcriptomics workflow for microbial eukaryotes benchmarked on Giardia intestinalis cells.", "authors": [{"family": "Onsbring", "given": "Henning", "initials": "H"}, {"family": "Tice", "given": "Alexander K", "initials": "AK"}, {"family": "Barton", "given": "Brandon T", "initials": "BT"}, {"family": "Brown", "given": "Matthew W", "initials": "MW"}, {"family": "Ettema", "given": "Thijs J G", "initials": "TJG", "orcid": "0000-0002-6898-6377", "researcher": {"href": "https://publications.scilifelab.se/researcher/42fc4acc111f4c488b23fa41341705e2.json"}}], "type": "journal article", "published": "2020-06-29", "journal": {"title": "BMC Genomics", "issn": "1471-2164", "volume": "21", "issue": "1", "pages": "448", "issn-l": "1471-2164"}, "abstract": "Most diversity in the eukaryotic tree of life is represented by microbial eukaryotes, which is a polyphyletic group also referred to as protists. Among the protists, currently sequenced genomes and transcriptomes give a biased view of the actual diversity. This biased view is partly caused by the scientific community, which has prioritized certain microbes of biomedical and agricultural importance. Additionally, some protists remain difficult to maintain in cultures, which further influences what has been studied. It is now possible to bypass the time-consuming process of cultivation and directly analyze the gene content of single protist cells. Single-cell genomics was used in the first experiments where individual protists cells were genomically explored. Unfortunately, single-cell genomics for protists is often associated with low genome recovery and the assembly process can be complicated because of repetitive intergenic regions. Sequencing repetitive sequences can be avoided if single-cell transcriptomics is used, which only targets the part of the genome that is transcribed.\n\nIn this study we test different modifications of Smart-seq2, a single-cell RNA sequencing protocol originally developed for mammalian cells, to establish a robust and more cost-efficient workflow for protists. The diplomonad Giardia intestinalis was used in all experiments and the available genome for this species allowed us to benchmark our results. We could observe increased transcript recovery when freeze-thaw cycles were added as an extra step to the Smart-seq2 protocol. Further we reduced the reaction volume and purified the amplified cDNA with alternative beads to test different cost-reducing changes of Smart-seq2. Neither improved the procedure, and reducing the volumes by half led to significantly fewer genes detected. We also added a 5' biotin modification to our primers and reduced the concentration of oligo-dT, to potentially reduce generation of artifacts. Except adding freeze-thaw cycles and reducing the volume, no other modifications lead to a significant change in gene detection. Therefore, we suggest adding freeze-thaw cycles to Smart-seq2 when working with protists and further consider our other modification described to improve cost and time-efficiency.\n\nThe presented single-cell RNA sequencing workflow represents an efficient method to explore the diversity and cell biology of individual protist cells.", "doi": "10.1186/s12864-020-06858-7", "pmid": "32600266", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Microbial Single Cell Genomics": "Service"}, "xrefs": [{"db": "pii", "key": "10.1186/s12864-020-06858-7"}, {"db": "pmc", "key": "PMC7325058"}], "notes": [], "created": "2020-07-03T05:25:51.570Z", "modified": "2021-11-10T12:44:49.955Z"}, {"entity": "publication", "iuid": "3f9436baa42849ed95e219bbf949416e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3f9436baa42849ed95e219bbf949416e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3f9436baa42849ed95e219bbf949416e"}}, "title": "Whole genome sequencing of familial isolated oesophagus atresia uncover shared structural variants.", "authors": [{"family": "Klar", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4185-7409", "researcher": {"href": "https://publications.scilifelab.se/researcher/3310cb2ab70f43d78cc7cd7e36ac8f83.json"}}, {"family": "Engstrand-Lilja", "given": "Helene", "initials": "H"}, {"family": "Maqbool", "given": "Khurram", "initials": "K"}, {"family": "Mattisson", "given": "Jonas", "initials": "J"}, {"family": "Feuk", "given": "Lars", "initials": "L", "orcid": "0000-0003-2355-2919", "researcher": {"href": "https://publications.scilifelab.se/researcher/3eb2f826b3554d4b9971bf0766b275c4.json"}}, {"family": "Dahl", "given": "Niklas", "initials": "N"}], "type": "journal article", "published": "2020-06-26", "journal": {"title": "BMC Med Genomics", "issn": "1755-8794", "volume": "13", "issue": "1", "pages": "85", "issn-l": "1755-8794"}, "abstract": "Oesophageal atresia (OA) is a life-threatening developmental defect characterized by a lost continuity between the upper and lower oesophagus. The most common form is a distal connection between the trachea and the oesophagus, i.e. a tracheoesophageal fistula (TEF). The condition may be part of a syndrome or occurs as an isolated feature. The recurrence risk in affected families is increased compared to the population-based incidence suggesting contributing genetic factors.\n\nTo gain insight into gene variants and genes associated with isolated OA we conducted whole genome sequencing on samples from three families with recurrent cases affected by congenital and isolated TEF.\n\nWe identified a combination of single nucleotide variants (SNVs), splice site variants (SSV) and structural variants (SV) annotated to altogether 100 coding genes in the six affected individuals.\n\nThis study highlights rare SVs among candidate gene variants in our individuals with OA and provides a gene framework for further investigations of genetic factors behind this malformation.", "doi": "10.1186/s12920-020-00737-6", "pmid": "32586322", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1186/s12920-020-00737-6"}, {"db": "pmc", "key": "PMC7318369"}], "notes": [], "created": "2020-07-03T05:25:29.915Z", "modified": "2024-01-16T13:48:42.333Z"}, {"entity": "publication", "iuid": "f5a7e37bfcd94531a0f810b49efccd16", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f5a7e37bfcd94531a0f810b49efccd16.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f5a7e37bfcd94531a0f810b49efccd16"}}, "title": "Removal of H2Aub1 by ubiquitin-specific proteases 12 and 13 is required for stable Polycomb-mediated gene repression in Arabidopsis.", "authors": [{"family": "Kralemann", "given": "Lejon E M", "initials": "LEM"}, {"family": "Liu", "given": "Shujing", "initials": "S"}, {"family": "Trejo-Arellano", "given": "Minerva S", "initials": "MS"}, {"family": "Mu\u00f1oz-Viana", "given": "Rafael", "initials": "R"}, {"family": "K\u00f6hler", "given": "Claudia", "initials": "C", "orcid": "0000-0002-2619-4857", "researcher": {"href": "https://publications.scilifelab.se/researcher/accd3f9307614c8ab67154dd5e50cdac.json"}}, {"family": "Hennig", "given": "Lars", "initials": "L"}], "type": "journal article", "published": "2020-06-16", "journal": {"title": "Genome Biol.", "issn": "1474-760X", "volume": "21", "issue": "1", "pages": "144", "issn-l": "1474-7596"}, "abstract": "Stable gene repression is essential for normal growth and development. Polycomb repressive complexes 1 and 2 (PRC1&2) are involved in this process by establishing monoubiquitination of histone 2A (H2Aub1) and subsequent trimethylation of lysine 27 of histone 3 (H3K27me3). Previous work proposed that H2Aub1 removal by the ubiquitin-specific proteases 12 and 13 (UBP12 and UBP13) is part of the repressive PRC1&2 system, but its functional role remains elusive.\n\nWe show that UBP12 and UBP13 work together with PRC1, PRC2, and EMF1 to repress genes involved in stimulus response. We find that PRC1-mediated H2Aub1 is associated with gene responsiveness, and its repressive function requires PRC2 recruitment. We further show that the requirement of PRC1 for PRC2 recruitment depends on the initial expression status of genes. Lastly, we demonstrate that removal of H2Aub1 by UBP12/13 prevents loss of H3K27me3, consistent with our finding that the H3K27me3 demethylase REF6 is positively associated with H2Aub1.\n\nOur data allow us to propose a model in which deposition of H2Aub1 permits genes to switch between repression and activation by H3K27me3 deposition and removal. Removal of H2Aub1 by UBP12/13 is required to achieve stable PRC2-mediated repression.", "doi": "10.1186/s13059-020-02062-8", "pmid": "32546254", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1186/s13059-020-02062-8"}, {"db": "pmc", "key": "PMC7296913"}], "notes": [], "created": "2020-11-16T09:39:43.051Z", "modified": "2021-11-10T12:50:14.951Z"}, {"entity": "publication", "iuid": "8d78208f9c61424e8b5e04dceec58d6b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8d78208f9c61424e8b5e04dceec58d6b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8d78208f9c61424e8b5e04dceec58d6b"}}, "title": "Illuminating Genetic Mysteries of the Dead Sea Scrolls.", "authors": [{"family": "Anava", "given": "Sarit", "initials": "S"}, {"family": "Neuhof", "given": "Moran", "initials": "M"}, {"family": "Gingold", "given": "Hila", "initials": "H"}, {"family": "Sagy", "given": "Or", "initials": "O"}, {"family": "Munters", "given": "Arielle", "initials": "A"}, {"family": "Svensson", "given": "Emma M", "initials": "EM"}, {"family": "Afshinnekoo", "given": "Ebrahim", "initials": "E"}, {"family": "Danko", "given": "David", "initials": "D"}, {"family": "Foox", "given": "Jonathan", "initials": "J"}, {"family": "Shor", "given": "Pnina", "initials": "P"}, {"family": "Riestra", "given": "Beatriz", "initials": "B"}, {"family": "Huchon", "given": "Doroth\u00e9e", "initials": "D"}, {"family": "Mason", "given": "Christopher E", "initials": "CE"}, {"family": "Mizrahi", "given": "Noam", "initials": "N"}, {"family": "Jakobsson", "given": "Mattias", "initials": "M"}, {"family": "Rechavi", "given": "Oded", "initials": "O"}], "type": "historical article", "published": "2020-06-11", "journal": {"title": "Cell", "issn": "1097-4172", "volume": "181", "issue": "6", "pages": "1218-1231.e27", "issn-l": "0092-8674"}, "abstract": "The discovery of the 2,000-year-old Dead Sea Scrolls had an incomparable impact on the historical understanding of Judaism and Christianity. \"Piecing together\" scroll fragments is like solving jigsaw puzzles with an unknown number of missing parts. We used the fact that most scrolls are made from animal skins to \"fingerprint\" pieces based on DNA sequences. Genetic sorting of the scrolls illuminates their textual relationship and historical significance. Disambiguating the contested relationship between Jeremiah fragments supplies evidence that some scrolls were brought to the Qumran caves from elsewhere; significantly, they demonstrate that divergent versions of Jeremiah circulated in parallel throughout Israel (ancient Judea). Similarly, patterns discovered in non-biblical scrolls, particularly the Songs of the Sabbath Sacrifice, suggest that the Qumran scrolls represent the broader cultural milieu of the period. Finally, genetic analysis divorces debated fragments from the Qumran scrolls. Our study demonstrates that interdisciplinary approaches enrich the scholar's toolkit.", "doi": "10.1016/j.cell.2020.04.046", "pmid": "32492404", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "S0092-8674(20)30552-3"}], "notes": [], "created": "2020-06-03T09:42:05.526Z", "modified": "2024-01-16T13:48:42.381Z"}, {"entity": "publication", "iuid": "e913056a4e7f4aad822efbc06d4f28d5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e913056a4e7f4aad822efbc06d4f28d5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e913056a4e7f4aad822efbc06d4f28d5"}}, "title": "Whole-genome sequencing of glioblastoma reveals enrichment of non-coding constraint mutations in known and novel genes.", "authors": [{"family": "Sakthikumar", "given": "Sharadha", "initials": "S"}, {"family": "Roy", "given": "Ananya", "initials": "A"}, {"family": "Haseeb", "given": "Lulu", "initials": "L"}, {"family": "Pettersson", "given": "Mats E", "initials": "ME"}, {"family": "Sundstr\u00f6m", "given": "Elisabeth", "initials": "E"}, {"family": "Marinescu", "given": "Voichita D", "initials": "VD"}, {"family": "Lindblad-Toh", "given": "Kerstin", "initials": "K", "orcid": "0000-0001-8338-0253", "researcher": {"href": "https://publications.scilifelab.se/researcher/e0063145f7d6476f80ab42f94833f4cf.json"}}, {"family": "Forsberg-Nilsson", "given": "Karin", "initials": "K", "orcid": "0000-0003-0692-6245", "researcher": {"href": "https://publications.scilifelab.se/researcher/5da04859250141a0a7271a69c7da9176.json"}}], "type": "journal article", "published": "2020-06-09", "journal": {"title": "Genome Biol.", "issn": "1474-760X", "volume": "21", "issue": "1", "pages": "127", "issn-l": "1474-7596"}, "abstract": "Glioblastoma (GBM) has one of the worst 5-year survival rates of all cancers. While genomic studies of the disease have been performed, alterations in the non-coding regulatory regions of GBM have largely remained unexplored. We apply whole-genome sequencing (WGS) to identify non-coding mutations, with regulatory potential in GBM, under the hypothesis that regions of evolutionary constraint are likely to be functional, and somatic mutations are likely more damaging than in unconstrained regions.\n\nWe validate our GBM cohort, finding similar copy number aberrations and mutated genes based on coding mutations as previous studies. Performing analysis on non-coding constraint mutations and their position relative to nearby genes, we find a significant enrichment of non-coding constraint mutations in the neighborhood of 78 genes that have previously been implicated in GBM. Among them, SEMA3C and DYNC1I1 show the highest frequencies of alterations, with multiple mutations overlapping transcription factor binding sites. We find that a non-coding constraint mutation in the SEMA3C promoter reduces the DNA binding capacity of the region. We also identify 1776 other genes enriched for non-coding constraint mutations with likely regulatory potential, providing additional candidate GBM genes. The mutations in the top four genes, DLX5, DLX6, FOXA1, and ISL1, are distributed over promoters, UTRs, and multiple transcription factor binding sites.\n\nThese results suggest that non-coding constraint mutations could play an essential role in GBM, underscoring the need to connect non-coding genomic variation to biological function and disease pathology.", "doi": "10.1186/s13059-020-02035-x", "pmid": "32513296", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Long-term Support WABI": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1186/s13059-020-02035-x"}, {"db": "pmc", "key": "PMC7281935"}], "notes": [], "created": "2020-06-10T22:06:24.696Z", "modified": "2024-01-16T13:48:42.389Z"}, {"entity": "publication", "iuid": "2dadaa51e19d416ba463c2fc9ac561b3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2dadaa51e19d416ba463c2fc9ac561b3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2dadaa51e19d416ba463c2fc9ac561b3"}}, "title": "The regulation and pharmacological modulation of immune complex induced type III IFN production by plasmacytoid dendritic cells.", "authors": [{"family": "Hjorton", "given": "Karin", "initials": "K"}, {"family": "Hagberg", "given": "Niklas", "initials": "N"}, {"family": "Pucholt", "given": "Pascal", "initials": "P"}, {"family": "Eloranta", "given": "Maija-Leena", "initials": "ML"}, {"family": "R\u00f6nnblom", "given": "Lars", "initials": "L"}], "type": "journal article", "published": "2020-06-05", "journal": {"title": "Arthritis Res. Ther.", "issn": "1478-6362", "issn-l": "1478-6354", "volume": "22", "issue": "1", "pages": "130"}, "abstract": "Patients with systemic lupus erythematosus (SLE) have an ongoing interferon (IFN) production due to an activation of plasmacytoid dendritic cells (pDCs), which can be triggered to type I IFN synthesis by RNA containing immune complexes (RNA-IC). Considering emerging data suggesting a role of type III IFN in the SLE disease process, we asked if RNA-IC can induce type III IFN production in pDC and how this production can be regulated.\n\nPeripheral blood mononuclear cells (PBMCs) or immune cell subsets were isolated from healthy blood donors or SLE patients and stimulated with IC containing U1 snRNP and SLE-IgG (RNA-IC). Hydroxychloroquine (HCQ) and an interleukin receptor 1-associated kinase 4 inhibitor (IRAK4i) were added to cell cultures. Cytokine mRNA levels were determined with a microarray and protein levels with immunoassays. Single-cell RNA sequencing of pDCs using ddSEQ technology was performed.\n\nType III IFN mRNA and protein was induced in RNA-IC-stimulated pDC-NK and pDC-B cell co-cultures. A subset of activated pDCs (3%) expressed both type III and type I IFN mRNA. IFN-\u03bb2, IFN-\u03b12b, interleukin (IL)-3, IL-6, or granulocyte-macrophage colony-stimulating factor (GM-CSF) enhanced IFN-\u03bb1/3 production 2-5-fold. HCQ and an IRAK4i blocked the RNA-IC-triggered IFN-\u03bb1/3 production (p < 0.01). IFN-\u03b12b and GM-CSF increased the proportion of SLE patients producing IFN-\u03bb1/3 in response to RNA-IC from 11 to 33%.\n\nType III IFN production is triggered by RNA-IC in pDCs in a TLR-MyD88-dependent manner, enhanced by NK and B cells as well as several pro-inflammatory cytokines. These results support a contributing role for both type I and type III IFNs in SLE, which needs to be considered when targeting the IFN system in this disease.", "doi": "10.1186/s13075-020-02186-z", "pmid": "32503683", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1186/s13075-020-02186-z"}, {"db": "pmc", "key": "PMC7275601"}], "notes": [], "created": "2020-06-08T05:31:54.214Z", "modified": "2024-01-16T13:48:42.402Z"}, {"entity": "publication", "iuid": "65338b6f4c55448b9e4454def5c0cc0d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/65338b6f4c55448b9e4454def5c0cc0d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/65338b6f4c55448b9e4454def5c0cc0d"}}, "title": "LPS-treatment of bovine endometrial epithelial cells causes differential DNA methylation of genes associated with inflammation and endometrial function.", "authors": [{"family": "Jhamat", "given": "Naveed", "initials": "N"}, {"family": "Niazi", "given": "Adnan", "initials": "A", "orcid": "0000-0003-0311-5279", "researcher": {"href": "https://publications.scilifelab.se/researcher/c9e07c9891804a60980eb07956a7cd0d.json"}}, {"family": "Guo", "given": "Yongzhi", "initials": "Y"}, {"family": "Chanrot", "given": "Metasu", "initials": "M"}, {"family": "Ivanova", "given": "Elena", "initials": "E"}, {"family": "Kelsey", "given": "Gavin", "initials": "G"}, {"family": "Bongcam-Rudloff", "given": "Erik", "initials": "E"}, {"family": "Andersson", "given": "G\u00f6ran", "initials": "G"}, {"family": "Humblot", "given": "Patrice", "initials": "P"}], "type": "journal article", "published": "2020-06-03", "journal": {"title": "BMC Genomics", "issn": "1471-2164", "volume": "21", "issue": "1", "pages": "385", "issn-l": "1471-2164"}, "abstract": "Lipopolysaccharide (LPS) endotoxin stimulates pro-inflammatory pathways and is a key player in the pathological mechanisms involved in the development of endometritis. This study aimed to investigate LPS-induced DNA methylation changes in bovine endometrial epithelial cells (bEECs), which may affect endometrial function. Following in vitro culture, bEECs from three cows were either untreated (0) or exposed to 2 and 8 \u03bcg/mL LPS for 24 h.\n\nDNA samples extracted at 0 h and 24 h were sequenced using reduced representation bisulfite sequencing (RRBS). When comparing DNA methylation results at 24 h to time 0 h, a larger proportion of hypomethylated regions were identified in the LPS-treated groups, whereas the trend was opposite in controls. When comparing LPS groups to controls at 24 h, a total of 1291 differentially methylated regions (DMRs) were identified (55% hypomethylated and 45% hypermethylated). Integration of DNA methylation data obtained here with our previously published gene expression data obtained from the same samples showed a negative correlation (r = - 0.41 for gene promoter, r = - 0.22 for gene body regions, p < 0.05). Differential methylation analysis revealed that effects of LPS treatment were associated with methylation changes for genes involved in regulation of immune and inflammatory responses, cell adhesion, and external stimuli. Gene ontology and pathway analyses showed that most of the differentially methylated genes (DMGs) were associated with cell proliferation and apoptotic processes; and pathways such as calcium-, oxytocin- and MAPK-signaling pathways with recognized roles in innate immunity. Several DMGs were related to systemic inflammation and tissue re-modelling including HDAC4, IRAK1, AKT1, MAP3K6, Wnt7A and ADAMTS17.\n\nThe present results show that LPS altered the DNA methylation patterns of bovine endometrial epithelial cells. This information, combined with our previously reported changes in gene expression related to endometrial function, confirm that LPS activates pro-inflammatory mechanisms leading to perturbed immune balance and cell adhesion processes in the endometrium.", "doi": "10.1186/s12864-020-06777-7", "pmid": "32493210", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1186/s12864-020-06777-7"}, {"db": "pmc", "key": "PMC7268755"}], "notes": [], "created": "2020-06-09T14:54:11.383Z", "modified": "2024-01-16T13:48:42.410Z"}, {"entity": "publication", "iuid": "1e8306e370e24ba5acf2c1cba73120c4", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1e8306e370e24ba5acf2c1cba73120c4.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1e8306e370e24ba5acf2c1cba73120c4"}}, "title": "Normal Testosterone but Higher Luteinizing Hormone Plasma Levels in Men With Hypersexual Disorder.", "authors": [{"family": "Chatzittofis", "given": "Andreas", "initials": "A"}, {"family": "Bostr\u00f6m", "given": "Adrian E", "initials": "AE"}, {"family": "\u00d6berg", "given": "Katarina G\u00f6rts", "initials": "KG"}, {"family": "Flanagan", "given": "John N", "initials": "JN"}, {"family": "Schi\u00f6th", "given": "Helgi B", "initials": "HB"}, {"family": "Arver", "given": "Stefan", "initials": "S"}, {"family": "Jokinen", "given": "Jussi", "initials": "J"}], "type": "journal article", "published": "2020-06-00", "journal": {"volume": "8", "issn": "2050-1161", "issue": "2", "pages": "243-250", "title": "Sex Med", "issn-l": "2050-1161"}, "abstract": "Hypersexual disorder as suggested to be included in the Diagnostic and Statistical Manual of Mental Disorders-5 integrates aspects of sexual desire deregulation, impulsivity, and compulsivity. However, it is unknown how it affects gonadal activity and the function of the hypothalamus-pituitary-gonadal (HPG) axis.\n\nThe aim of this study was to investigate testosterone and luteinizing hormone (LH) levels in hypersexual men compared with healthy controls. Furthermore, we investigated associations between epigenetic markers and hormone levels.\n\nBasal morning plasma levels of testosterone, LH, and sex hormone-binding globulin (SHBG) were assessed in 67 hypersexual men (mean age: 39.2 years) compared with 39 age-matched healthy controls (mean age: 37.5 years). The Sexual Compulsivity Scale and the Hypersexual Disorder: Current Assessment Scale were used for assessing hypersexual behavior, the Montgomery-\u00c5sberg Depression Scale-self rating was used for depression severity, and the Childhood Trauma Questionnaire (CTQ) was used for assessing history of childhood adversity. The genome-wide methylation pattern of more than 850 K CpG sites was measured in whole blood using the Illumina Infinium Methylation EPIC BeadChip. CpG sites located within 2,000 bp of the transcriptional start site of hypothalamus pituitary adrenal (HPA) and HPG axis-coupled genes were included.\n\nTestosterone and LH plasma levels in association with clinical rating and a secondary outcome was the epigenetic profile of HPA and HPG axis-coupled CpG sites with testosterone and LH levels.\n\nLH plasma levels were significantly higher in patients with hypersexual disorder than in healthy volunteers. No significant differences in plasma testosterone, follicle stimulating hormone, prolactin, and SHBG levels were found between the groups. There were no significant associations between DNA methylation of HPA and HPG axis-coupled genes and plasma testosterone or LH levels after multiple testing corrections.\n\nSubtle dysregulation of the HPG axis, with increased LH plasma levels but no difference in testosterone levels may be present in hypersexual men. Chatzittofis A, Bostr\u00f6m AE, \u00d6berg KG, et al. Normal Testosterone but Higher Luteinizing Hormone Plasma Levels in Men With Hypersexual Disorder. Sex Med 2020;8:243-250.", "doi": "10.1016/j.esxm.2020.02.005", "pmid": "32173350", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "S2050-1161(20)30028-3"}, {"db": "pmc", "key": "PMC7261685"}], "notes": [], "created": "2020-06-09T14:54:10.628Z", "modified": "2021-11-10T12:50:36.262Z"}, {"entity": "publication", "iuid": "47c327c6229e475bad4889ad53a15767", "links": {"self": {"href": "https://publications.scilifelab.se/publication/47c327c6229e475bad4889ad53a15767.json"}, "display": {"href": "https://publications.scilifelab.se/publication/47c327c6229e475bad4889ad53a15767"}}, "title": "Mitochondrial genomes from Bronze Age Poland reveal genetic continuity from the Late Neolithic and additional genetic affinities with the steppe populations.", "authors": [{"family": "Juras", "given": "Anna", "initials": "A", "orcid": "0000-0002-2585-127X", "researcher": {"href": "https://publications.scilifelab.se/researcher/21890fe291bb4e8e913c5eb5963bcdce.json"}}, {"family": "Makarowicz", "given": "Przemys\u0142aw", "initials": "P"}, {"family": "Chyle\u0144ski", "given": "Maciej", "initials": "M"}, {"family": "Ehler", "given": "Edvard", "initials": "E", "orcid": "0000-0003-1774-0091", "researcher": {"href": "https://publications.scilifelab.se/researcher/6d5e30a4e46e47d8b800d5242e23d7de.json"}}, {"family": "Malmstr\u00f6m", "given": "Helena", "initials": "H"}, {"family": "Krzewi\u0144ska", "given": "Maja", "initials": "M"}, {"family": "Pospieszny", "given": "\u0141ukasz", "initials": "\u0141"}, {"family": "G\u00f3rski", "given": "Jacek", "initials": "J"}, {"family": "Taras", "given": "Halina", "initials": "H"}, {"family": "Szczepanek", "given": "Anita", "initials": "A"}, {"family": "Pola\u0144ska", "given": "Marta", "initials": "M"}, {"family": "W\u0142odarczak", "given": "Piotr", "initials": "P"}, {"family": "Szyca", "given": "Agnieszka", "initials": "A"}, {"family": "Lasota-Ku\u015b", "given": "Anna", "initials": "A"}, {"family": "W\u00f3jcik", "given": "Irena", "initials": "I"}, {"family": "Jakobsson", "given": "Mattias", "initials": "M", "orcid": "0000-0001-7840-7853", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a4abe0fcb20492d9ec849c9fbf58a71.json"}}, {"family": "Dabert", "given": "Miroslawa", "initials": "M"}], "type": "historical article", "published": "2020-06-00", "journal": {"title": "Am. J. Phys. Anthropol.", "issn": "1096-8644", "volume": "172", "issue": "2", "pages": "176-188", "issn-l": "0002-9483"}, "abstract": "In this work we aim to investigate the origins and genetic affinities of Bronze Age populations (2,400-1,100 BC) from the region of southern Poland and to trace maternal kinship patterns present in the burials of those populations by the use of complete mitochondrial genomes.\n\nWe performed ancient DNA analyses for Bronze Age individuals from present-day Poland associated with the Strzy\u017cow culture, the Mierzanowice culture, and the Trzciniec Cultural circle. To obtain complete mitochondrial genomes, we sequenced genomic libraries using Illumina platform. Additionally, hybridization capture was used to enrich some of the samples for mitochondrial DNA. AMS 14 C-dating was conducted for 51 individuals to verify chronological and cultural attribution of the analyzed samples.\n\nComplete ancient mitochondrial genomes were generated for 80 of the Bronze Age individuals from present-day Poland. The results of the population genetic analyses indicate close maternal genetic affinity between Mierzanowice, Trzciniec, and Corded Ware culture-associated populations. This is in contrast to the genetically more distant Strzy\u017c\u00f3w people that displayed closer maternal genetic relation to steppe populations associated with the preceding Yamnaya culture and Catacomb culture, and with later Scythians. Potential maternal kinship relations were identified in burials of Mierzanowice and Trzciniec populations analyzed in this study.\n\nResults revealed genetic continuity from the Late Neolithic Corded Ware groups to Bronze Age Mierzanowice and Trzciniec-associated populations, and possible additional genetic contribution from the steppe to the formation of the Strzy\u017c\u00f3w-associated group at the end of 3rd millennium BC. Mitochondrial patterns indicated several pairs of potentially maternally related individuals mostly in Trzciniec-associated group.", "doi": "10.1002/ajpa.24057", "pmid": "32297323", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2020-12-08T23:25:04.935Z", "modified": "2024-01-16T13:48:42.437Z"}, {"entity": "publication", "iuid": "a701a9709be141609a88a6452a664266", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a701a9709be141609a88a6452a664266.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a701a9709be141609a88a6452a664266"}}, "title": "Age-of-onset information helps identify 76 genetic variants associated with allergic disease.", "authors": [{"family": "Ferreira", "given": "Manuel A R", "initials": "MAR", "orcid": "0000-0001-9059-1825", "researcher": {"href": "https://publications.scilifelab.se/researcher/d27aef5015494b018b22352125c0225d.json"}}, {"family": "Vonk", "given": "Judith M", "initials": "JM", "orcid": "0000-0001-7531-4547", "researcher": {"href": "https://publications.scilifelab.se/researcher/e57100a0e5bc48c59590c043897a8bbd.json"}}, {"family": "Baurecht", "given": "Hansj\u00f6rg", "initials": "H", "orcid": "0000-0002-9265-5594", "researcher": {"href": "https://publications.scilifelab.se/researcher/65098dade92d4b87a691906582cc4fa9.json"}}, {"family": "Marenholz", "given": "Ingo", "initials": "I"}, {"family": "Tian", "given": "Chao", "initials": "C", "orcid": "0000-0001-7605-7175", "researcher": {"href": "https://publications.scilifelab.se/researcher/7dedf8f815b44a198f28485af5e69846.json"}}, {"family": "Hoffman", "given": "Joshua D", "initials": "JD", "orcid": "0000-0003-2823-1866", "researcher": {"href": "https://publications.scilifelab.se/researcher/a9f5e78834914d7699717e488827d616.json"}}, {"family": "Helmer", "given": "Quinta", "initials": "Q"}, {"family": "Tillander", "given": "Annika", "initials": "A", "orcid": "0000-0002-9239-9471", "researcher": {"href": "https://publications.scilifelab.se/researcher/b495409505824c8794717fd9b507a1f7.json"}}, {"family": "Ullemar", "given": "Vilhelmina", "initials": "V", "orcid": "0000-0002-8759-765X", "researcher": {"href": "https://publications.scilifelab.se/researcher/bf34fc1ddb7644edbabe552010e8754f.json"}}, {"family": "Lu", "given": "Yi", "initials": "Y", "orcid": "0000-0001-9933-3654", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a73eafe0b0e4221a77b96800883413d.json"}}, {"family": "Grosche", "given": "Sarah", "initials": "S"}, {"family": "R\u00fcschendorf", "given": "Franz", "initials": "F"}, {"family": "Granell", "given": "Raquel", "initials": "R", "orcid": "0000-0002-4890-4012", "researcher": {"href": "https://publications.scilifelab.se/researcher/44c4fdcdcf6149ba8b48366f9ba707d9.json"}}, {"family": "Brumpton", "given": "Ben M", "initials": "BM", "orcid": "0000-0002-3058-1059", "researcher": {"href": "https://publications.scilifelab.se/researcher/da9d23aaf1dc4d18a0a13e4847ea9955.json"}}, {"family": "Fritsche", "given": "Lars G", "initials": "LG", "orcid": "0000-0002-2110-1690", "researcher": {"href": "https://publications.scilifelab.se/researcher/00bea312a34a4b8f8436d00fcf799ac3.json"}}, {"family": "Bhatta", "given": "Laxmi", "initials": "L", "orcid": "0000-0002-8166-1470", "researcher": {"href": "https://publications.scilifelab.se/researcher/7833d21a70224f6da9d1b10982bb567f.json"}}, {"family": "Gabrielsen", "given": "Maiken E", "initials": "ME"}, {"family": "Nielsen", "given": "Jonas B", "initials": "JB"}, {"family": "Zhou", "given": "Wei", "initials": "W", "orcid": "0000-0001-7719-0859", "researcher": {"href": "https://publications.scilifelab.se/researcher/78c70f5da0ef414680693f1c41dcf99a.json"}}, {"family": "Hveem", "given": "Kristian", "initials": "K"}, {"family": "Langhammer", "given": "Arnulf", "initials": "A", "orcid": "0000-0001-5296-6673", "researcher": {"href": "https://publications.scilifelab.se/researcher/755b4b39d8054f2ea3e28476a7b0ae39.json"}}, {"family": "Holmen", "given": "Oddgeir L", "initials": "OL"}, {"family": "L\u00f8set", "given": "Mari", "initials": "M"}, {"family": "Abecasis", "given": "Gon\u00e7alo R", "initials": "GR"}, {"family": "Willer", "given": "Cristen J", "initials": "CJ"}, {"family": "Emami", "given": "Nima C", "initials": "NC", "orcid": "0000-0002-4296-7805", "researcher": {"href": "https://publications.scilifelab.se/researcher/4fc068c6fb6a4ca7a8e7434cb2a4b4f2.json"}}, {"family": "Cavazos", "given": "Taylor B", "initials": "TB", "orcid": "0000-0003-3537-2608", "researcher": {"href": "https://publications.scilifelab.se/researcher/9c03835393864b859639733cb2e64e09.json"}}, {"family": "Witte", "given": "John S", "initials": "JS"}, {"family": "Szwajda", "given": "Agnieszka", "initials": "A", "orcid": "0000-0003-2073-6018", "researcher": {"href": "https://publications.scilifelab.se/researcher/72343d922a0648598d53a02da82a68c8.json"}}, {"family": "23andMe Research Team", "given": "", "initials": ""}, {"family": "collaborators of the SHARE study", "given": "", "initials": ""}, {"family": "Hinds", "given": "David A", "initials": "DA", "orcid": "0000-0002-4911-803X", "researcher": {"href": "https://publications.scilifelab.se/researcher/ba56969917d14df0bd923a54ce9f911d.json"}}, {"family": "H\u00fcbner", "given": "Norbert", "initials": "N"}, {"family": "Weidinger", "given": "Stephan", "initials": "S"}, {"family": "Magnusson", "given": "Patrik Ke", "initials": "PK", "orcid": "0000-0002-7315-7899", "researcher": {"href": "https://publications.scilifelab.se/researcher/b277b6387de142bbab91fad82d9eff09.json"}}, {"family": "Jorgenson", "given": "Eric", "initials": "E", "orcid": "0000-0002-5829-8191", "researcher": {"href": "https://publications.scilifelab.se/researcher/38ef095c3de94bbc884d80c8949d16f5.json"}}, {"family": "Karlsson", "given": "Robert", "initials": "R", "orcid": "0000-0002-8949-2587", "researcher": {"href": "https://publications.scilifelab.se/researcher/9df14bf33f3342408d624caa70d45b7c.json"}}, {"family": "Paternoster", "given": "Lavinia", "initials": "L", "orcid": "0000-0003-2514-0889", "researcher": {"href": "https://publications.scilifelab.se/researcher/826f9852c56d4922ab255ab83d26faa8.json"}}, {"family": "Boomsma", "given": "Dorret I", "initials": "DI", "orcid": "0000-0002-7099-7972", "researcher": {"href": "https://publications.scilifelab.se/researcher/4b66ab2525fd4a468e7a4ad14c955cb4.json"}}, {"family": "Almqvist", "given": "Catarina", "initials": "C", "orcid": "0000-0002-1045-1898", "researcher": {"href": "https://publications.scilifelab.se/researcher/c7b0899897f046499272a916fd0c6ba5.json"}}, {"family": "Lee", "given": "Young-Ae", "initials": "Y"}, {"family": "Koppelman", "given": "Gerard H", "initials": "GH", "orcid": "0000-0001-8567-3252", "researcher": {"href": "https://publications.scilifelab.se/researcher/cd7e0158050a4ab3860e288c4eb9ae87.json"}}], "type": "journal article", "published": "2020-06-00", "journal": {"title": "PLoS Genet.", "issn": "1553-7404", "issn-l": "1553-7390", "volume": "16", "issue": "6", "pages": "e1008725"}, "abstract": "Risk factors that contribute to inter-individual differences in the age-of-onset of allergic diseases are poorly understood. The aim of this study was to identify genetic risk variants associated with the age at which symptoms of allergic disease first develop, considering information from asthma, hay fever and eczema. Self-reported age-of-onset information was available for 117,130 genotyped individuals of European ancestry from the UK Biobank study. For each individual, we identified the earliest age at which asthma, hay fever and/or eczema was first diagnosed and performed a genome-wide association study (GWAS) of this combined age-of-onset phenotype. We identified 50 variants with a significant independent association (P<3x10-8) with age-of-onset. Forty-five variants had comparable effects on the onset of the three individual diseases and 38 were also associated with allergic disease case-control status in an independent study (n = 222,484). We observed a strong negative genetic correlation between age-of-onset and case-control status of allergic disease (rg = -0.63, P = 4.5x10-61), indicating that cases with early disease onset have a greater burden of allergy risk alleles than those with late disease onset. Subsequently, a multivariate GWAS of age-of-onset and case-control status identified a further 26 associations that were missed by the univariate analyses of age-of-onset or case-control status only. Collectively, of the 76 variants identified, 18 represent novel associations for allergic disease. We identified 81 likely target genes of the 76 associated variants based on information from expression quantitative trait loci (eQTL) and non-synonymous variants, of which we highlight ADAM15, FOSL2, TRIM8, BMPR2, CD200R1, PRKCQ, NOD2, SMAD4, ABCA7 and UBE2L3. Our results support the notion that early and late onset allergic disease have partly distinct genetic architectures, potentially explaining known differences in pathophysiology between individuals.", "doi": "10.1371/journal.pgen.1008725", "pmid": "32603359", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pii", "key": "PGENETICS-D-18-02006"}, {"db": "pmc", "key": "PMC7367489"}], "notes": [], "created": "2021-01-07T17:01:52.734Z", "modified": "2021-12-07T13:51:25.031Z"}, {"entity": "publication", "iuid": "24c1864eab62411f9d39198e02fc37de", "links": {"self": {"href": "https://publications.scilifelab.se/publication/24c1864eab62411f9d39198e02fc37de.json"}, "display": {"href": "https://publications.scilifelab.se/publication/24c1864eab62411f9d39198e02fc37de"}}, "title": "Transitions in wheat endosperm metabolism upon transcriptional induction of oil accumulation by oat endosperm WRINKLED1.", "authors": [{"family": "Grimberg", "given": "\u00c5sa", "initials": "\u00c5", "orcid": "0000-0002-3083-7448", "researcher": {"href": "https://publications.scilifelab.se/researcher/e237918aef734c6b89ffa5f551d6e3a6.json"}}, {"family": "Wilkinson", "given": "Mark", "initials": "M"}, {"family": "Snell", "given": "Per", "initials": "P"}, {"family": "De Vos", "given": "Rebecca P", "initials": "RP"}, {"family": "Gonz\u00e1lez-Thuillier", "given": "Irene", "initials": "I"}, {"family": "Tawfike", "given": "Ahmed", "initials": "A"}, {"family": "Ward", "given": "Jane L", "initials": "JL"}, {"family": "Carlsson", "given": "Anders S", "initials": "AS"}, {"family": "Shewry", "given": "Peter", "initials": "P"}, {"family": "Hofvander", "given": "Per", "initials": "P"}], "type": "journal article", "published": "2020-05-25", "journal": {"title": "BMC Plant Biol.", "issn": "1471-2229", "volume": "20", "issue": "1", "pages": "235", "issn-l": "1471-2229"}, "abstract": "Cereal grains, including wheat (Triticum aestivum L.), are major sources of food and feed, with wheat being dominant in temperate zones. These end uses exploit the storage reserves in the starchy endosperm of the grain, with starch being the major storage component in most cereal species. However, oats (Avena sativa L.) differs in that the starchy endosperm stores significant amounts of oil. Understanding the control of carbon allocation between groups of storage compounds, such as starch and oil, is therefore important for understanding the composition and hence end use quality of cereals. WRINKLED1 is a transcription factor known to induce triacylglycerol (TAG; oil) accumulation in several plant storage tissues.\n\nAn oat endosperm homolog of WRI1 (AsWRI1) expressed from the endosperm-specific HMW1Dx5 promoter resulted in drastic changes in carbon allocation in wheat grains, with reduced seed weight and a wrinkled seed phenotype. The starch content of mature grain endosperms of AsWRI1-wheat was reduced compared to controls (from 62 to 22% by dry weight (dw)), TAG was increased by up to nine-fold (from 0.7 to 6.4% oil by dw) and sucrose from 1.5 to 10% by dw. Expression of AsWRI1 in wheat grains also resulted in multiple layers of elongated peripheral aleurone cells. RNA-sequencing, lipid analyses, and pulse-chase experiments using 14C-sucrose indicated that futile cycling of fatty acids could be a limitation for oil accumulation.\n\nOur data show that expression of oat endosperm WRI1 in the wheat endosperm results in changes in metabolism which could underpin the application of biotechnology to manipulate grain composition. In particular, the striking effect on starch synthesis in the wheat endosperm indicates that an important indirect role of WRI1 is to divert carbon allocation away from starch biosynthesis in plant storage tissues that accumulate oil.", "doi": "10.1186/s12870-020-02438-9", "pmid": "32450804", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1186/s12870-020-02438-9"}, {"db": "pmc", "key": "PMC7249431"}], "notes": [], "created": "2020-07-03T05:28:46.118Z", "modified": "2021-11-10T12:50:50.964Z"}, {"entity": "publication", "iuid": "d98c58bf1e6e4de9b468b52b6592fa41", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d98c58bf1e6e4de9b468b52b6592fa41.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d98c58bf1e6e4de9b468b52b6592fa41"}}, "title": "Multi-ancestry GWAS of the electrocardiographic PR interval identifies 202 loci underlying cardiac conduction.", "authors": [{"family": "Ntalla", "given": "Ioanna", "initials": "I"}, {"family": "Weng", "given": "Lu-Chen", "initials": "LC", "orcid": "0000-0003-1475-4930", "researcher": {"href": "https://publications.scilifelab.se/researcher/0e52c9c21794412bbb3750fda1fecfe0.json"}}, {"family": "Cartwright", "given": "James H", "initials": "JH"}, {"family": "Hall", "given": "Amelia Weber", "initials": "AW", "orcid": "0000-0002-7915-0313", "researcher": {"href": "https://publications.scilifelab.se/researcher/7a151b393a6c434585d4834fd32de6a4.json"}}, {"family": "Sveinbjornsson", "given": "Gardar", "initials": "G"}, {"family": "Tucker", "given": "Nathan R", "initials": "NR", "orcid": "0000-0002-5071-4218", "researcher": {"href": "https://publications.scilifelab.se/researcher/f89b1366ff014dc6a9cc5fe4bd37becf.json"}}, {"family": "Choi", "given": "Seung Hoan", "initials": "SH"}, {"family": "Chaffin", "given": "Mark D", "initials": "MD", "orcid": "0000-0002-1234-5562", "researcher": {"href": "https://publications.scilifelab.se/researcher/c73477de5ca0468ab051fd6eab7bad81.json"}}, {"family": "Roselli", "given": "Carolina", "initials": "C", "orcid": "0000-0001-5267-6756", "researcher": {"href": "https://publications.scilifelab.se/researcher/1dd28aad250f42719d505c21ed76013b.json"}}, {"family": "Barnes", "given": "Michael R", "initials": "MR", "orcid": "0000-0001-9097-7381", "researcher": {"href": "https://publications.scilifelab.se/researcher/bffbcdd5aad340b98d7da297ffc21e6b.json"}}, {"family": "Mifsud", "given": "Borbala", "initials": "B", "orcid": "0000-0003-3429-3094", "researcher": {"href": "https://publications.scilifelab.se/researcher/0105dc446d594b0bb3be38b8eb94a16b.json"}}, {"family": "Warren", "given": "Helen R", "initials": "HR"}, {"family": "Hayward", "given": "Caroline", "initials": "C", "orcid": "0000-0002-9405-9550", "researcher": {"href": "https://publications.scilifelab.se/researcher/cd49e9ad5a024c7ca2f1aa97d9e58eba.json"}}, {"family": "Marten", "given": 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"Lakatta", "given": "Edward G", "initials": "EG", "orcid": "0000-0002-4772-0035", "researcher": {"href": "https://publications.scilifelab.se/researcher/bc797241e3fa45d7b9d8438568414f2a.json"}}, {"family": "Qian", "given": "Yong", "initials": "Y"}, {"family": "Tarasov", "given": "Kirill V", "initials": "KV"}, {"family": "Levy", "given": "Daniel", "initials": "D"}, {"family": "Lin", "given": "Honghuang", "initials": "H", "orcid": "0000-0003-3043-3942", "researcher": {"href": "https://publications.scilifelab.se/researcher/9bc2f1e6bb1140dfa054376eac685d5e.json"}}, {"family": "Newton-Cheh", "given": "Christopher H", "initials": "CH"}, {"family": "Lunetta", "given": "Kathryn L", "initials": "KL", "orcid": "0000-0002-9268-810X", "researcher": {"href": "https://publications.scilifelab.se/researcher/271c9b62eb1945e99728d9bef23c909a.json"}}, {"family": "Murray", "given": "Alison D", "initials": "AD", "orcid": "0000-0003-4915-4847", "researcher": {"href": "https://publications.scilifelab.se/researcher/b302cc58c68e46f3b89019b5b6792f7f.json"}}, {"family": "Porteous", "given": "David J", "initials": "DJ", "orcid": "0000-0003-1249-6106", "researcher": {"href": "https://publications.scilifelab.se/researcher/b6e3ae11c02e4cb89e638e1e5ae0f50a.json"}}, {"family": "Smith", "given": "Blair H", "initials": "BH", "orcid": "0000-0002-5362-9430", "researcher": {"href": "https://publications.scilifelab.se/researcher/ed343544e1324911931517689ad9ba6b.json"}}, {"family": "Stricker", "given": "Bruno H", "initials": "BH"}, {"family": "Uitterlinden", "given": "Andr\u00e9", "initials": "A", "orcid": "0000-0002-7276-3387", "researcher": {"href": "https://publications.scilifelab.se/researcher/273577b238854023a9dffe34dabc3551.json"}}, {"family": "van den Berg", "given": "Marten E", "initials": "ME"}, {"family": "Haessler", "given": "Jeffrey", "initials": "J"}, {"family": "Jackson", "given": "Rebecca D", "initials": "RD"}, {"family": "Kooperberg", "given": "Charles", "initials": "C"}, {"family": "Peters", "given": "Ulrike", "initials": "U", "orcid": "0000-0001-5666-9318", "researcher": {"href": "https://publications.scilifelab.se/researcher/60e10f10b57b48bfa52f3ee2ee4e4745.json"}}, {"family": "Reiner", "given": "Alexander P", "initials": "AP"}, {"family": "Whitsel", "given": "Eric A", "initials": "EA"}, {"family": "Alonso", "given": "Alvaro", "initials": "A", "orcid": "0000-0002-2225-8323", "researcher": {"href": "https://publications.scilifelab.se/researcher/5213f2852c3e4ebb9a2c77883f46a04d.json"}}, {"family": "Arking", "given": "Dan E", "initials": "DE"}, {"family": "Boerwinkle", "given": "Eric", "initials": "E"}, {"family": "Ehret", "given": "Georg B", "initials": "GB", "orcid": "0000-0002-5730-0675", "researcher": {"href": "https://publications.scilifelab.se/researcher/b43e94a3abca4c0cbcc921f3efb828bc.json"}}, {"family": "Soliman", "given": "Elsayed Z", "initials": "EZ", "orcid": "0000-0001-5632-8150", "researcher": {"href": "https://publications.scilifelab.se/researcher/96e79156ff664c509217e8834a728c79.json"}}, {"family": "Avery", "given": "Christy L", "initials": "CL"}, {"family": "Gogarten", "given": "Stephanie M", "initials": "SM", "orcid": "0000-0002-7231-9745", "researcher": {"href": "https://publications.scilifelab.se/researcher/27741633afde4230952ee4f9016b22cd.json"}}, {"family": "Kerr", "given": "Kathleen F", "initials": "KF", "orcid": "0000-0002-6438-9583", "researcher": {"href": "https://publications.scilifelab.se/researcher/a443078bd5ac4bc7b7078b49f073db3c.json"}}, {"family": "Laurie", "given": "Cathy C", "initials": "CC"}, {"family": "Seyerle", "given": "Amanda A", "initials": "AA"}, {"family": "Stilp", "given": "Adrienne", "initials": "A"}, {"family": "Assa", "given": "Solmaz", "initials": "S"}, {"family": "Abdullah Said", "given": "M", "initials": "M", "orcid": "0000-0003-2920-7745", "researcher": {"href": "https://publications.scilifelab.se/researcher/9d897d8376084cc8905fa9177803ecba.json"}}, {"family": "Yldau van der Ende", "given": "M", "initials": "M"}, {"family": "Lambiase", "given": "Pier D", "initials": "PD"}, {"family": "Orini", "given": "Michele", "initials": "M", "orcid": "0000-0001-5773-0344", "researcher": {"href": "https://publications.scilifelab.se/researcher/ad2b6285769e43d59eaa61068cd9307d.json"}}, {"family": "Ramirez", "given": "Julia", "initials": "J", "orcid": "0000-0003-4130-5866", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff795d161ab5418ebbb32c64fc9628cf.json"}}, {"family": "Van Duijvenboden", "given": "Stefan", "initials": "S", "orcid": "0000-0001-8897-558X", "researcher": {"href": "https://publications.scilifelab.se/researcher/bedcb22e237147019c8a97c32e164456.json"}}, {"family": "Arnar", "given": "David O", "initials": "DO"}, {"family": "Gudbjartsson", "given": "Daniel F", "initials": "DF", "orcid": "0000-0002-5222-9857", "researcher": {"href": "https://publications.scilifelab.se/researcher/e41ffdc303534408aade6e4a071e4801.json"}}, {"family": "Holm", "given": "Hilma", "initials": "H"}, {"family": "Sulem", "given": "Patrick", "initials": "P", "orcid": "0000-0001-7123-6123", "researcher": {"href": "https://publications.scilifelab.se/researcher/a228963aa2c148ee82e526d07e298364.json"}}, {"family": "Thorleifsson", "given": "Gudmar", "initials": "G"}, {"family": "Thorolfsdottir", "given": "Rosa B", "initials": "RB", "orcid": "0000-0001-7475-0398", "researcher": {"href": "https://publications.scilifelab.se/researcher/e803af5742504636a2d16ae252f94af4.json"}}, {"family": "Thorsteinsdottir", "given": "Unnur", "initials": "U"}, {"family": "Benjamin", "given": "Emelia J", "initials": "EJ", "orcid": "0000-0003-4076-2336", "researcher": {"href": "https://publications.scilifelab.se/researcher/31c69bdf118d4b36ad65a6c4f780bab2.json"}}, {"family": "Tinker", "given": "Andrew", "initials": "A"}, {"family": "Stefansson", "given": "Kari", "initials": "K", "orcid": "0000-0003-1676-864X", "researcher": {"href": "https://publications.scilifelab.se/researcher/679465193fba4887a68e2aec34ccfd8e.json"}}, {"family": "Ellinor", "given": "Patrick T", "initials": "PT", "orcid": "0000-0002-2067-0533", "researcher": {"href": "https://publications.scilifelab.se/researcher/dd513dc49e0945bc8298f72d1244648d.json"}}, {"family": "Jamshidi", "given": "Yalda", "initials": "Y", "orcid": "0000-0003-0151-6482", "researcher": {"href": "https://publications.scilifelab.se/researcher/66a90ee88cbf4e9b9e782548fe4991c0.json"}}, {"family": "Lubitz", "given": "Steven A", "initials": "SA", "orcid": "0000-0002-9599-4866", "researcher": {"href": "https://publications.scilifelab.se/researcher/25bb007311104c92983dbcce80f72260.json"}}, {"family": "Munroe", "given": "Patricia B", "initials": "PB", "orcid": "0000-0002-4176-2947", "researcher": {"href": "https://publications.scilifelab.se/researcher/657544a7f921459f926aae5cd0e2065c.json"}}], "type": "journal article", "published": "2020-05-21", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "11", "issue": "1", "pages": "2542", "issn-l": "2041-1723"}, "abstract": "The electrocardiographic PR interval reflects atrioventricular conduction, and is associated with conduction abnormalities, pacemaker implantation, atrial fibrillation (AF), and cardiovascular mortality. Here we report a multi-ancestry (N = 293,051) genome-wide association meta-analysis for the PR interval, discovering 202 loci of which 141 have not previously been reported. Variants at identified loci increase the percentage of heritability explained, from 33.5% to 62.6%. We observe enrichment for cardiac muscle developmental/contractile and cytoskeletal genes, highlighting key regulation processes for atrioventricular conduction. Additionally, 8 loci not previously reported harbor genes underlying inherited arrhythmic syndromes and/or cardiomyopathies suggesting a role for these genes in cardiovascular pathology in the general population. We show that polygenic predisposition to PR interval duration is an endophenotype for cardiovascular disease, including distal conduction disease, AF, and atrioventricular pre-excitation. These findings advance our understanding of the polygenic basis of cardiac conduction, and the genetic relationship between PR interval duration and cardiovascular disease.", "doi": "10.1038/s41467-020-15706-x", "pmid": "32439900", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-020-15706-x"}, {"db": "pmc", "key": "PMC7242331"}], "notes": [], "created": "2020-05-27T13:29:26.954Z", "modified": "2021-11-10T12:50:53.503Z"}, {"entity": "publication", "iuid": "5740889604b145baac1f446821f3da8d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5740889604b145baac1f446821f3da8d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5740889604b145baac1f446821f3da8d"}}, "title": "Integrative genomics approach identifies molecular features associated with early-stage ovarian carcinoma histotypes.", "authors": [{"family": "Engqvist", "given": "Hanna", "initials": "H"}, {"family": "Parris", "given": "Toshima Z", "initials": "TZ"}, {"family": "Biermann", "given": "Jana", "initials": "J"}, {"family": "R\u00f6nnerman", "given": "Elisabeth Werner", "initials": "EW"}, {"family": "Larsson", "given": "Peter", "initials": "P"}, {"family": "Sundfeldt", "given": "Karin", "initials": "K"}, {"family": "Kov\u00e1cs", "given": "Anik\u00f3", "initials": "A"}, {"family": "Karlsson", "given": "Per", "initials": "P"}, {"family": "Helou", "given": "Khalil", "initials": "K"}], "type": "journal article", "published": "2020-05-14", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "10", "issue": "1", "pages": "7946", "issn-l": "2045-2322"}, "abstract": "Ovarian cancer comprises multiple subtypes (clear-cell (CCC), endometrioid (EC), high-grade serous (HGSC), low-grade serous (LGSC), and mucinous carcinomas (MC)) with differing molecular and clinical behavior. However, robust histotype-specific biomarkers for clinical use have yet to be identified. Here, we utilized a multi-omics approach to identify novel histotype-specific genetic markers associated with ovarian carcinoma histotypes (CCC, EC, HGSC, and MC) using DNA methylation, DNA copy number alteration and RNA sequencing data for 96 primary invasive early-stage (stage I and II) ovarian carcinomas. More specifically, the DNA methylation analysis revealed hypermethylation for CCC in comparison with the other histotypes. Moreover, copy number imbalances and novel chromothripsis-like rearrangements (n = 64) were identified in ovarian carcinoma, with the highest number of chromothripsis-like patterns in HGSC. For the 1000 most variable transcripts, underexpression was most prominent for all histotypes in comparison with normal ovarian samples. Overall, the integrative approach identified 46 putative oncogenes (overexpressed, hypomethylated and DNA gain) and three putative tumor suppressor genes (underexpressed, hypermethylated and DNA loss) when comparing the different histotypes. In conclusion, the current study provides novel insights into molecular features associated with early-stage ovarian carcinoma that may improve patient stratification and subclassification of the histotypes.", "doi": "10.1038/s41598-020-64794-8", "pmid": "32409713", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-020-64794-8"}, {"db": "pmc", "key": "PMC7224294"}], "notes": [], "created": "2020-05-27T13:29:27.972Z", "modified": "2024-01-16T13:48:42.508Z"}, {"entity": "publication", "iuid": "a67f74b1dcdf445da4ec370ee216c8d6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a67f74b1dcdf445da4ec370ee216c8d6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a67f74b1dcdf445da4ec370ee216c8d6"}}, "title": "Genetic and environmental influences on human height from infancy through adulthood at different levels of parental education.", "authors": [{"family": "Jelenkovic", "given": "Aline", "initials": "A"}, {"family": "Sund", "given": "Reijo", "initials": "R", "orcid": "0000-0002-6268-8117", "researcher": {"href": "https://publications.scilifelab.se/researcher/27f81bab545a4b158866a08fe5263e08.json"}}, {"family": "Yokoyama", "given": "Yoshie", "initials": "Y"}, {"family": "Latvala", "given": "Antti", "initials": "A", "orcid": "0000-0001-5695-117X", "researcher": {"href": "https://publications.scilifelab.se/researcher/e675261bb7354ca782cc267262fbdaba.json"}}, {"family": "Sugawara", "given": "Masumi", "initials": "M"}, {"family": "Tanaka", "given": "Mami", "initials": "M"}, {"family": "Matsumoto", "given": "Satoko", "initials": "S"}, {"family": "Freitas", "given": "Duarte L", "initials": "DL"}, {"family": "Maia", "given": "Jos\u00e9 Antonio", "initials": "JA"}, {"family": "Knafo-Noam", "given": "Ariel", "initials": "A"}, {"family": "Mankuta", "given": "David", "initials": "D"}, {"family": "Abramson", "given": "Lior", "initials": "L"}, {"family": "Ji", "given": "Fuling", "initials": "F"}, {"family": "Ning", "given": "Feng", "initials": "F"}, {"family": "Pang", "given": "Zengchang", "initials": "Z"}, {"family": "Rebato", "given": "Esther", "initials": "E"}, {"family": "Saudino", "given": "Kimberly J", "initials": "KJ"}, {"family": "Cutler", "given": "Tessa L", "initials": "TL"}, {"family": "Hopper", "given": "John L", "initials": "JL"}, {"family": "Ullemar", "given": "Vilhelmina", "initials": "V"}, {"family": "Almqvist", "given": "Catarina", "initials": "C"}, {"family": "Magnusson", "given": "Patrik K E", "initials": "PKE", "orcid": "0000-0002-7315-7899", "researcher": {"href": "https://publications.scilifelab.se/researcher/b277b6387de142bbab91fad82d9eff09.json"}}, {"family": "Cozen", "given": "Wendy", "initials": "W"}, {"family": "Hwang", "given": "Amie E", "initials": "AE"}, {"family": "Mack", "given": "Thomas M", "initials": "TM"}, {"family": "Nelson", "given": "Tracy L", "initials": "TL"}, {"family": "Whitfield", "given": "Keith E", "initials": "KE"}, {"family": "Sung", "given": "Joohon", "initials": "J"}, {"family": "Kim", "given": "Jina", "initials": "J", "orcid": "0000-0003-1684-4219", "researcher": {"href": "https://publications.scilifelab.se/researcher/869e611833bc4f6aab2f47f540f89581.json"}}, {"family": "Lee", "given": "Jooyeon", "initials": "J", "orcid": "0000-0001-5220-0950", "researcher": {"href": "https://publications.scilifelab.se/researcher/b5e4b2f4f3b34e41a3901c90f6dc0ec2.json"}}, {"family": "Lee", "given": "Sooji", "initials": "S"}, {"family": "Llewellyn", "given": "Clare H", "initials": "CH", "orcid": "0000-0002-0066-2827", "researcher": {"href": "https://publications.scilifelab.se/researcher/97213af3e4704e13b608af74637dbb2e.json"}}, {"family": "Fisher", "given": "Abigail", "initials": "A"}, {"family": "Medda", "given": "Emanuela", "initials": "E"}, {"family": "Nistic\u00f2", "given": "Lorenza", "initials": "L", "orcid": "0000-0003-1805-6240", "researcher": {"href": "https://publications.scilifelab.se/researcher/c6a2e9c1a6a34419b4661afce3e01d3e.json"}}, {"family": "Toccaceli", "given": "Virgilia", "initials": "V"}, {"family": "Baker", "given": "Laura A", "initials": "LA"}, {"family": "Tuvblad", "given": "Catherine", "initials": "C"}, {"family": "Corley", "given": "Robin P", "initials": "RP"}, {"family": "Huibregtse", "given": "Brooke M", "initials": "BM", "orcid": "0000-0003-0977-7249", "researcher": {"href": "https://publications.scilifelab.se/researcher/e9df70acb87f443eb6da650b151a679c.json"}}, {"family": "Derom", "given": "Catherine A", "initials": "CA"}, {"family": "Vlietinck", "given": "Robert F", "initials": "RF"}, {"family": "Loos", "given": "Ruth J F", "initials": "RJF", "orcid": "0000-0002-8532-5087", "researcher": {"href": "https://publications.scilifelab.se/researcher/e5b6c24c302d42828806076ded81afe1.json"}}, {"family": "Burt", "given": "S Alexandra", "initials": "SA"}, {"family": "Klump", "given": "Kelly L", "initials": "KL"}, {"family": "Silberg", "given": "Judy L", "initials": "JL"}, {"family": "Maes", "given": "Hermine H", "initials": "HH"}, {"family": "Krueger", "given": "Robert F", "initials": "RF"}, {"family": "McGue", "given": "Matt", "initials": "M"}, {"family": "Pahlen", "given": "Shandell", "initials": "S"}, {"family": "Gatz", "given": "Margaret", "initials": "M"}, {"family": "Butler", "given": "David A", "initials": "DA"}, {"family": "Harris", "given": "Jennifer R", "initials": "JR"}, {"family": "Brandt", "given": "Ingunn", "initials": "I"}, {"family": "Nilsen", "given": "Thomas S", "initials": "TS"}, {"family": "Harden", "given": "K Paige", "initials": "KP"}, {"family": "Tucker-Drob", "given": "Elliot M", "initials": "EM"}, {"family": "Franz", "given": "Carol E", "initials": "CE", "orcid": "0000-0002-8987-1755", "researcher": {"href": "https://publications.scilifelab.se/researcher/4f24c335b7f544328bca9e9e73b8560e.json"}}, {"family": "Kremen", "given": "William S", "initials": "WS"}, {"family": "Lyons", "given": "Michael J", "initials": "MJ"}, {"family": "Lichtenstein", "given": "Paul", "initials": "P", "orcid": "0000-0003-3037-5287", "researcher": {"href": "https://publications.scilifelab.se/researcher/4db67c51837b4cdfa18cacbc3fca1173.json"}}, {"family": "Bartels", "given": "Meike", "initials": "M", "orcid": "0000-0002-9667-7555", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a91c095e993411b99e81e21f40d8597.json"}}, {"family": "Beijsterveldt", "given": "Catharina E M van", "initials": "CEMV", "orcid": "0000-0002-6617-4201", "researcher": {"href": "https://publications.scilifelab.se/researcher/6c3073fc4d1e4454bfc4bc7aad11b357.json"}}, {"family": "Willemsen", "given": "Gonneke", "initials": "G"}, {"family": "\u00d6ncel", "given": "Sevgi Y", "initials": "SY"}, {"family": "Aliev", "given": "Fazil", "initials": "F", "orcid": "0000-0001-8357-4699", "researcher": {"href": "https://publications.scilifelab.se/researcher/85556629452a4054bf7228b5f7049811.json"}}, {"family": "Jeong", "given": "Hoe-Uk", "initials": "HU"}, {"family": "Hur", "given": "Yoon-Mi", "initials": "YM"}, {"family": "Turkheimer", "given": "Eric", "initials": "E"}, {"family": "Boomsma", "given": "Dorret I", "initials": "DI", "orcid": "0000-0002-7099-7972", "researcher": {"href": "https://publications.scilifelab.se/researcher/4b66ab2525fd4a468e7a4ad14c955cb4.json"}}, {"family": "S\u00f8rensen", "given": "Thorkild I A", "initials": "TIA", "orcid": "0000-0003-4821-430X", "researcher": {"href": "https://publications.scilifelab.se/researcher/3495a648342a491d9105817cc30d5d56.json"}}, {"family": "Kaprio", "given": "Jaakko", "initials": "J", "orcid": "0000-0002-3716-2455", "researcher": {"href": "https://publications.scilifelab.se/researcher/814d362333844b72a70cba9ebcf61e6f.json"}}, {"family": "Silventoinen", "given": "Karri", "initials": "K"}], "type": "journal article", "published": "2020-05-14", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "10", "issue": "1", "pages": "7974", "issn-l": "2045-2322"}, "abstract": "Genetic factors explain a major proportion of human height variation, but differences in mean stature have also been found between socio-economic categories suggesting a possible effect of environment. By utilizing a classical twin design which allows decomposing the variation of height into genetic and environmental components, we tested the hypothesis that environmental variation in height is greater in offspring of lower educated parents. Twin data from 29 cohorts including 65,978 complete twin pairs with information on height at ages 1 to 69 years and on parental education were pooled allowing the analyses at different ages and in three geographic-cultural regions (Europe, North America and Australia, and East Asia). Parental education mostly showed a positive association with offspring height, with significant associations in mid-childhood and from adolescence onwards. In variance decomposition modeling, the genetic and environmental variance components of height did not show a consistent relation to parental education. A random-effects meta-regression analysis of the aggregate-level data showed a trend towards greater shared environmental variation of height in low parental education families. In conclusion, in our very large dataset from twin cohorts around the globe, these results provide only weak evidence for the study hypothesis.", "doi": "10.1038/s41598-020-64883-8", "pmid": "32409744", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-020-64883-8"}, {"db": "pmc", "key": "PMC7224277"}], "notes": [], "created": "2020-05-27T13:29:27.487Z", "modified": "2021-11-10T12:51:04.364Z"}, {"entity": "publication", "iuid": "f4427096b88f41f3962469e06754180d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f4427096b88f41f3962469e06754180d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f4427096b88f41f3962469e06754180d"}}, "title": "A progressive and complex clinical course in two family members with ERF-related craniosynostosis: a case report.", "authors": [{"family": "K\u00f6rberg", "given": "Izabella", "initials": "I"}, {"family": "Nowinski", "given": "Daniel", "initials": "D"}, {"family": "Bondeson", "given": "Marie-Louise", "initials": "ML"}, {"family": "Melin", "given": "Malin", "initials": "M", "orcid": "0000-0002-6589-2375", "researcher": {"href": "https://publications.scilifelab.se/researcher/190c3991975c43ec952a81df72292c9a.json"}}, {"family": "K\u00f6lby", "given": "Lars", "initials": "L"}, {"family": "Stattin", "given": "Eva-Lena", "initials": "EL"}], "type": "case reports", "published": "2020-05-05", "journal": {"title": "BMC Med. Genet.", "issn": "1471-2350", "volume": "21", "issue": "1", "pages": "90", "issn-l": "1471-2350"}, "abstract": "ERF-related craniosynostosis are a rare, complex, premature trisutural fusion associated with a broad spectrum of clinical features and heterogeneous aetiology. Here we describe two cases with the same pathogenic variant and a detailed description of their clinical course.\n\nTwo subjects; a boy with a BLSS requiring repeated skull expansions and his mother who had been operated once for sagittal synostosis. Both developed intracranial hypertension at some point during the course, which was for both verified by formal invasive intracranial pressure monitoring. Exome sequencing revealed a pathogenic truncating frame shift variant in the ERF gene.\n\nHere we describe a boy and his mother with different craniosynostosis patterns, but both with verified intracranial hypertension and heterozygosity for a truncating variant of ERF c.1201_1202delAA (p.Lys401Glufs*10). Our work provides supplementary evidence in support of previous phenotypic descriptions of ERF-related craniosynostosis, particularly late presentation, an evolving synostotic pattern and variable expressivity even among affected family members.", "doi": "10.1186/s12881-020-01015-z", "pmid": "32370745", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Clinical Genomics Uppsala": "Collaborative", "Clinical Genomics": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1186/s12881-020-01015-z"}, {"db": "pmc", "key": "PMC7201657"}], "notes": [], "created": "2020-05-11T22:07:48.851Z", "modified": "2021-12-06T08:29:24.182Z"}, {"entity": "publication", "iuid": "d70da1b632d44551ac3963b1a71b3694", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d70da1b632d44551ac3963b1a71b3694.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d70da1b632d44551ac3963b1a71b3694"}}, "title": "Whole-genome sequencing of human remains to enable genealogy DNA database searches - A case report.", "authors": [{"family": "Tillmar", "given": "Andreas", "initials": "A"}, {"family": "Sj\u00f6lund", "given": "Peter", "initials": "P"}, {"family": "Lundqvist", "given": "Bo", "initials": "B"}, {"family": "Klippmark", "given": "Therese", "initials": "T"}, {"family": "\u00c4lgen\u00e4s", "given": "Cajsa", "initials": "C"}, {"family": "Green", "given": "Henrik", "initials": "H"}], "type": "case reports", "published": "2020-05-00", "journal": {"title": "Forensic Sci Int Genet", "issn": "1878-0326", "volume": "46", "issue": null, "pages": "102233", "issn-l": "1872-4973"}, "abstract": "Recently a number of high profile crime cases (e.g. the \"Golden State Killer\") have successfully been solved or given new leads with the use of genome wide DNA data in combination with pairwise matching from individuals present in genealogy DNA databases. Such databases will primarily involve distant relatives which in turn require a large amount of genetic information, in the range of several hundred thousand to millions of SNPs, to be genotyped. While it nowadays is fairly straightforward to obtain such as data from high quality and high quantity DNA, it is still a challenge for degraded DNA of low quantity such in the case of forensic samples. Here we present a successful effort in obtaining genome-wide genotype data from human remains. The goal was to get investigative leads in order to identify the remains of an unknown male (\"the Ekeby man\") that was found murdered in the south of Sweden in 2003. Whole-genome sequencing was performed on DNA originating from a bone sample. Three replicates of libraries were prepared using ThruPLEX DNA-seq Kit (Takara) which were sequenced on a HiSeq X instrument (Illumina). A mean coverage of 30X was obtained when the sequencing reads were mapped to a human reference genome. Following further bioinformatic processing, allele calling, quality checks and filtering to match the genealogy DNA database SNPs, genotypes for approximately one million SNPs were established. The resulting SNP genotypes were then used to search for relatives in the genealogy DNA database GEDmatch (www.gedmatch.com). A candidate list of relatives was obtained which was further processed using traditional genealogy methods in order to get leads about the identity of the unknown. In summary, this report shows how whole-genome sequencing successfully can be applied on forensic samples to create the SNP genotypes required for searches in genealogy DNA databases for the purpose of generating leads to identify missing or unknown persons, including perpetrators and victims.", "doi": "10.1016/j.fsigen.2020.102233", "pmid": "31981902", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "S1872-4973(20)30004-1"}], "notes": [], "created": "2020-12-08T23:48:02.849Z", "modified": "2024-01-16T13:48:42.537Z"}, {"entity": "publication", "iuid": "5ea3fa61d27c411cb95d6ae10c2cd99d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5ea3fa61d27c411cb95d6ae10c2cd99d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5ea3fa61d27c411cb95d6ae10c2cd99d"}}, "title": "SweHLA: the high confidence HLA typing bio-resource drawn from 1000 Swedish genomes.", "authors": [{"family": "Nordin", "given": "Jessika", "initials": "J", "orcid": "0000-0002-8414-2190", "researcher": {"href": "https://publications.scilifelab.se/researcher/2603df7f3ff84e6980605b9e8eef4c2f.json"}}, {"family": "Ameur", "given": "Adam", "initials": "A", "orcid": "0000-0001-6085-6749", "researcher": {"href": "https://publications.scilifelab.se/researcher/e960811513664a78b2804a00ee70f7c3.json"}}, {"family": "Lindblad-Toh", "given": "Kerstin", "initials": "K", "orcid": "0000-0001-8338-0253", "researcher": {"href": "https://publications.scilifelab.se/researcher/e0063145f7d6476f80ab42f94833f4cf.json"}}, {"family": "Gyllensten", "given": "Ulf", "initials": "U"}, {"family": "Meadows", "given": "Jennifer R S", "initials": "JRS"}], "type": "journal article", "published": "2020-05-00", "journal": {"title": "Eur. J. Hum. Genet.", "issn": "1476-5438", "issn-l": "1018-4813", "volume": "28", "issue": "5", "pages": "627-635"}, "abstract": "There is a need to accurately call human leukocyte antigen (HLA) genes from existing short-read sequencing data, however there is no single solution that matches the gold standard of Sanger sequenced lab typing. Here we aimed to combine results from available software programs, minimizing the biases of applied algorithm and HLA reference. The result is a robust HLA population resource for the published 1000 Swedish genomes, and a framework for future HLA interrogation. HLA 2nd-field alleles were called using four imputation and inference methods for the classical eight genes (class I: HLA-A, HLA-B, HLA-C; class II: HLA-DPA1, HLA-DPB1, HLA-DQA1, HLA-DQB1, HLA-DRB1). A high confidence population set (SweHLA) was determined using an n-1 concordance rule for class I (four software) and class II (three software) alleles. Results were compared across populations and individual programs benchmarked to SweHLA. Per gene, 875 to 988 of the 1000 samples were genotyped in SweHLA; 920 samples had at least seven loci called. While a small fraction of reference alleles were common to all software (class I = 1.9% and class II = 4.1%), this did not affect the overall call rate. Gene-level concordance was high compared to European populations (>0.83%), with COX and PGF the dominant SweHLA haplotypes. We noted that 15/18 discordant alleles (delta allele frequency >2) were previously reported as disease-associated. These differences could in part explain across-study genetic replication failures, reinforcing the need to use multiple software solutions. SweHLA demonstrates a way to use existing NGS data to generate a population resource agnostic to individual HLA software biases.", "doi": "10.1038/s41431-019-0559-2", "pmid": "31844174", "labels": {"National Genomics Infrastructure": "Collaborative", "NGI Uppsala (Uppsala Genome Center)": "Collaborative", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41431-019-0559-2"}, {"db": "pmc", "key": "PMC7170882"}], "notes": [], "created": "2020-02-11T10:04:25.991Z", "modified": "2021-11-10T12:51:33.748Z"}, {"entity": "publication", "iuid": "c37642986c1a4793b4f19cc918c4a9df", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c37642986c1a4793b4f19cc918c4a9df.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c37642986c1a4793b4f19cc918c4a9df"}}, "title": "Parentage and relatedness reconstruction in Pinus sylvestris using genotyping-by-sequencing.", "authors": [{"family": "Hall", "given": "David", "initials": "D"}, {"family": "Zhao", "given": "Wei", "initials": "W", "orcid": "0000-0001-9437-3198", "researcher": {"href": "https://publications.scilifelab.se/researcher/896aadb8e0dd4a82b93506003604209c.json"}}, {"family": "Wennstr\u00f6m", "given": "Ulfstand", "initials": "U"}, {"family": "Andersson Gull", "given": "Bengt", "initials": "B"}, {"family": "Wang", "given": "Xiao-Ru", "initials": "XR"}], "type": "journal article", "published": "2020-05-00", "journal": {"title": "Heredity (Edinb)", "issn": "1365-2540", "volume": "124", "issue": "5", "pages": "633-646", "issn-l": "0018-067X"}, "abstract": "Estimating kinship is fundamental for studies of evolution, conservation, and breeding. Genotyping-by-sequencing (GBS) and other restriction based genotyping methods have become widely applied in these applications in non-model organisms. However, sequencing errors, depth, and reproducibility between library preps could potentially hinder accurate genetic inferences. In this study, we tested different sets of parameters in data filtering, different reference populations and eight estimation methods to obtain a robust procedure for relatedness estimation in Scots pine (Pinus sylvestris L.). We used a seed orchard as our study system, where candidate parents are known and pedigree reconstruction can be compared with theoretical expectations. We found that relatedness estimates were lower than expected for all categories of kinship estimated if the proportion of shared SNPs was low. However, estimates reached expected values if loci showing an excess of heterozygotes were removed and genotyping error rates were considered. The genetic variance-covariance matrix (G-matrix) estimation, however, performed poorly in kinship estimation. The reduced relatedness estimates are likely due to false heterozygosity calls. We analyzed the mating structure in the seed orchard and identified a selfing rate of 3% (including crosses between clone mates) and external pollen contamination of 33.6%. Little genetic structure was observed in the sampled Scots pine natural populations, and the degree of inbreeding in the orchard seed crop is comparable to natural stands. We illustrate that under our optimized data processing procedure, relatedness, and genetic composition, including level of pollen contamination within a seed orchard crop, can be established consistently by different estimators.", "doi": "10.1038/s41437-020-0302-3", "pmid": "32123330", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41437-020-0302-3"}, {"db": "pmc", "key": "PMC7171117"}, {"db": "Dryad", "key": "10.5061/dryad.h44j0zpg5"}], "notes": [], "created": "2021-12-08T13:46:13.578Z", "modified": "2021-12-08T13:46:13.626Z"}, {"entity": "publication", "iuid": "bab887d8bdcd4298b21a1edc1dca962e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/bab887d8bdcd4298b21a1edc1dca962e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/bab887d8bdcd4298b21a1edc1dca962e"}}, "title": "Genetic identification of cell types underlying brain complex traits yields insights into the etiology of Parkinson's disease.", "authors": [{"family": "Bryois", "given": "Julien", "initials": "J"}, {"family": "Skene", "given": "Nathan G", "initials": "NG"}, {"family": "Hansen", "given": "Thomas Folkmann", "initials": "TF", "orcid": "0000-0001-6703-7762", "researcher": {"href": "https://publications.scilifelab.se/researcher/56994131a2ef4278b802dc55c838d88a.json"}}, {"family": "Kogelman", "given": "Lisette J A", "initials": "LJA"}, {"family": "Watson", "given": "Hunna J", "initials": "HJ", "orcid": "0000-0001-8405-381X", "researcher": {"href": "https://publications.scilifelab.se/researcher/8fd919535931490ba39b80b794349c49.json"}}, {"family": "Liu", "given": "Zijing", "initials": "Z"}, {"family": "Eating Disorders Working Group of the Psychiatric Genomics Consortium", "given": "", "initials": ""}, {"family": "International Headache Genetics Consortium", "given": "", "initials": ""}, {"family": "23andMe Research Team", "given": "", "initials": ""}, {"family": "Brueggeman", "given": "Leo", "initials": "L"}, {"family": "Breen", "given": "Gerome", "initials": "G", "orcid": "0000-0003-2053-1792", "researcher": {"href": "https://publications.scilifelab.se/researcher/e25b495fde8d4e1d9f26779c2af6a541.json"}}, {"family": "Bulik", "given": "Cynthia M", "initials": "CM"}, {"family": "Arenas", "given": "Ernest", "initials": "E", "orcid": "0000-0003-0197-6577", "researcher": {"href": "https://publications.scilifelab.se/researcher/a3bb18ad1c4b4dae99b60ab0ae13e36a.json"}}, {"family": "Hjerling-Leffler", "given": "Jens", "initials": "J", "orcid": "0000-0002-4539-1776", "researcher": {"href": "https://publications.scilifelab.se/researcher/51675f0ff9aa47d89d6b2eb84a14820a.json"}}, {"family": "Sullivan", "given": "Patrick F", "initials": "PF", "orcid": "0000-0002-6619-873X", "researcher": {"href": "https://publications.scilifelab.se/researcher/4d95de0b5ab14586980a6a13c8299346.json"}}], "type": "journal article", "published": "2020-05-00", "journal": {"title": "Nat. Genet.", "issn": "1546-1718", "issn-l": "1061-4036", "volume": "52", "issue": "5", "pages": "482-493"}, "abstract": "Genome-wide association studies have discovered hundreds of loci associated with complex brain disorders, but it remains unclear in which cell types these loci are active. Here we integrate genome-wide association study results with single-cell transcriptomic data from the entire mouse nervous system to systematically identify cell types underlying brain complex traits. We show that psychiatric disorders are predominantly associated with projecting excitatory and inhibitory neurons. Neurological diseases were associated with different cell types, which is consistent with other lines of evidence. Notably, Parkinson's disease was genetically associated not only with cholinergic and monoaminergic neurons (which include dopaminergic neurons) but also with enteric neurons and oligodendrocytes. Using post-mortem brain transcriptomic data, we confirmed alterations in these cells, even at the earliest stages of disease progression. Our study provides an important framework for understanding the cellular basis of complex brain maladies, and reveals an unexpected role of oligodendrocytes in Parkinson's disease.", "doi": "10.1038/s41588-020-0610-9", "pmid": "32341526", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41588-020-0610-9"}, {"db": "pmc", "key": "PMC7930801"}, {"db": "mid", "key": "NIHMS1672179"}], "notes": [], "created": "2020-05-06T12:23:56.414Z", "modified": "2024-01-16T13:48:42.561Z"}, {"entity": "publication", "iuid": "e62dab54473a4923903e72399e97dbdd", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e62dab54473a4923903e72399e97dbdd.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e62dab54473a4923903e72399e97dbdd"}}, "title": "Effect of Cobalt, Nickel, and Selenium/Tungsten Deficiency on Mesophilic Anaerobic Digestion of Chemically Defined Soluble Organic Compounds.", "authors": [{"family": "\u0160afari\u010d", "given": "Luka", "initials": "L", "orcid": "0000-0003-3274-0372", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a6e23745266454996cd0a93d9ffedac.json"}}, {"family": "Yekta", "given": "Sepehr Shakeri", "initials": "SS"}, {"family": "Svensson", "given": "Bo H", "initials": "BH"}, {"family": "Schn\u00fcrer", "given": "Anna", "initials": "A", "orcid": "0000-0003-0038-553X", "researcher": {"href": "https://publications.scilifelab.se/researcher/0f81992bc8ed48318f8197fc8caabb4f.json"}}, {"family": "Bastviken", "given": "David", "initials": "D"}, {"family": "Bj\u00f6rn", "given": "Annika", "initials": "A"}], "type": "journal article", "published": "2020-04-20", "journal": {"title": "Microorganisms", "issn": "2076-2607", "volume": "8", "issue": "4", "pages": "598", "issn-l": "2076-2607"}, "abstract": "Trace elements (TEs) are vital for anaerobic digestion (AD), due to their role as cofactors in many key enzymes. The aim of this study was to evaluate the effects of specific TE deficiencies on mixed microbial communities during AD of soluble polymer-free substrates, thus focusing on AD after hydrolysis. Three mesophilic (37 \u00b0C) continuous stirred-tank biogas reactors were depleted either of Co, Ni, or a combination of Se and W, respectively, by discontinuing their supplementation. Ni and Se/W depletion led to changes in methane kinetics, linked to progressive volatile fatty acid (VFA) accumulation, eventually resulting in process failure. No significant changes occurred in the Co-depleted reactor, indicating that the amount of Co present in the substrate in absence of supplementation was sufficient to maintain process stability. Archaeal communities remained fairly stable independent of TE concentrations, while bacterial communities gradually changed with VFA accumulation in Ni- and Se-/W-depleted reactors. Despite this, the communities remained relatively similar between these two reactors, suggesting that the major shifts in composition likely occurred due to the accumulating VFAs. Overall, the results indicate that Ni and Se/W depletion primarily lead to slower metabolic activities of methanogenic archaea and their syntrophic partners, which then has a ripple effect throughout the microbial community due to a gradual accumulation of intermediate fermentation products.", "doi": "10.3390/microorganisms8040598", "pmid": "32326100", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "microorganisms8040598"}, {"db": "pmc", "key": "PMC7232481"}], "notes": [], "created": "2020-12-08T23:46:05.594Z", "modified": "2021-11-10T12:51:56.324Z"}, {"entity": "publication", "iuid": "0501e4e6d44c4a8c947ef756d0262288", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0501e4e6d44c4a8c947ef756d0262288.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0501e4e6d44c4a8c947ef756d0262288"}}, "title": "Increased burden of ultra-rare structural variants localizing to boundaries of topologically associated domains in schizophrenia.", "authors": [{"family": "Halvorsen", "given": "Matthew", "initials": "M"}, {"family": "Huh", "given": "Ruth", "initials": "R"}, {"family": "Oskolkov", "given": "Nikolay", "initials": "N", "orcid": "0000-0001-5326-8893", "researcher": {"href": "https://publications.scilifelab.se/researcher/1a556bc2e89c457fb1e45cfcd7b567e9.json"}}, {"family": "Wen", "given": "Jia", "initials": "J", "orcid": "0000-0003-3273-7704", "researcher": {"href": "https://publications.scilifelab.se/researcher/872570fb0f94464d988fd5b2d3a8b7e7.json"}}, {"family": "Netotea", "given": "Sergiu", "initials": "S"}, {"family": "Giusti-Rodriguez", "given": "Paola", "initials": "P", "orcid": "0000-0002-1921-1305", "researcher": {"href": "https://publications.scilifelab.se/researcher/e6594f03c6c344d69b08234fd751ab23.json"}}, {"family": "Karlsson", "given": "Robert", "initials": "R", "orcid": "0000-0002-8949-2587", "researcher": {"href": "https://publications.scilifelab.se/researcher/9df14bf33f3342408d624caa70d45b7c.json"}}, {"family": "Bryois", "given": "Julien", "initials": "J"}, {"family": "Nystedt", "given": "Bj\u00f6rn", "initials": "B", "orcid": "0000-0001-7809-7664", "researcher": {"href": "https://publications.scilifelab.se/researcher/f0af5a168baa4b00a6fab8d3447ebfb4.json"}}, {"family": "Ameur", "given": "Adam", "initials": "A", "orcid": "0000-0001-6085-6749", "researcher": {"href": "https://publications.scilifelab.se/researcher/e960811513664a78b2804a00ee70f7c3.json"}}, {"family": "K\u00e4hler", "given": "Anna K", "initials": "AK"}, {"family": "Ancalade", "given": "NaEshia", "initials": "N"}, {"family": "Farrell", "given": "Martilias", "initials": "M", "orcid": "0000-0002-9520-6209", "researcher": {"href": "https://publications.scilifelab.se/researcher/20be04f56c474537ad8fa07cb17241cf.json"}}, {"family": "Crowley", "given": "James J", "initials": "JJ"}, {"family": "Li", "given": "Yun", "initials": "Y"}, {"family": "Magnusson", "given": "Patrik K E", "initials": "PKE", "orcid": "0000-0002-7315-7899", "researcher": {"href": "https://publications.scilifelab.se/researcher/b277b6387de142bbab91fad82d9eff09.json"}}, {"family": "Gyllensten", "given": "Ulf", "initials": "U"}, {"family": "Hultman", "given": "Christina M", "initials": "CM"}, {"family": "Sullivan", "given": "Patrick F", "initials": "PF"}, {"family": "Szatkiewicz", "given": "Jin P", "initials": "JP", "orcid": "0000-0002-4898-7401", "researcher": {"href": "https://publications.scilifelab.se/researcher/eb39edd3c6c14938a47f1e22ecfea080.json"}}], "type": "journal article", "published": "2020-04-15", "journal": {"title": "Nat Commun", "issn": "2041-1723", "issn-l": "2041-1723", "volume": "11", "issue": "1", "pages": "1842"}, "abstract": "Despite considerable progress in schizophrenia genetics, most findings have been for large rare structural variants and common variants in well-imputed regions with few genes implicated from exome sequencing. Whole genome sequencing (WGS) can potentially provide a more complete enumeration of etiological genetic variation apart from the exome and regions of high linkage disequilibrium. We analyze high-coverage WGS data from 1162 Swedish schizophrenia cases and 936 ancestry-matched population controls. Our main objective is to evaluate the contribution to schizophrenia etiology from a variety of genetic variants accessible to WGS but not by previous technologies. Our results suggest that ultra-rare structural variants that affect the boundaries of topologically associated domains (TADs) increase risk for schizophrenia. Alterations in TAD boundaries may lead to dysregulation of gene expression. Future mechanistic studies will be needed to determine the precise functional effects of these variants on biology.", "doi": "10.1038/s41467-020-15707-w", "pmid": "32296054", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "NGI Uppsala (Uppsala Genome Center)": "Collaborative", "Systems Biology": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-020-15707-w"}, {"db": "pmc", "key": "PMC7160146"}], "notes": [], "created": "2020-04-20T06:46:04.706Z", "modified": "2024-01-16T13:48:42.613Z"}, {"entity": "publication", "iuid": "b8409eb1124c41258c01b678e729e7e6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b8409eb1124c41258c01b678e729e7e6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b8409eb1124c41258c01b678e729e7e6"}}, "title": "The conifer root rot pathogens Heterobasidion irregulare and Heterobasidion occidentale employ different strategies to infect Norway spruce.", "authors": [{"family": "Hu", "given": "Yang", "initials": "Y"}, {"family": "Elfstrand", "given": "Malin", "initials": "M"}, {"family": "Stenlid", "given": "Jan", "initials": "J"}, {"family": "Durling", "given": "Mikael Brandstr\u00f6m", "initials": "MB", "orcid": "0000-0001-6485-197X", "researcher": {"href": "https://publications.scilifelab.se/researcher/7be72d0dcc48489495509b23c7ad3d38.json"}}, {"family": "Olson", "given": "\u00c5ke", "initials": "\u00c5", "orcid": "0000-0001-8998-6096", "researcher": {"href": "https://publications.scilifelab.se/researcher/83a79139c2b94d9f97cf038e1cab8c03.json"}}], "type": "journal article", "published": "2020-04-03", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "10", "issue": "1", "pages": "5884", "issn-l": "2045-2322"}, "abstract": "Heterobasidion irregulare and H. occidentale are two closely related conifer root rot pathogens in the H. annosum sensu lato (s.l.) species complex. The two species H. irregulare and H. occidentale have different host preference with pine and non-pine tree species favored, respectively. The comparison of transcriptomes of H. irregulare and H. occidentale growing in Norway spruce bark, a susceptible host non-native to North America, showed large differences in gene expression. Heterobasidion irregulare induced more genes involved in detoxification of host compounds and in production of secondary metabolites, while the transcriptome induced in H. occidentale was more oriented towards carbohydrate degradation. Along with their separated evolutionary history, the difference might be driven by their host preferences as indicated by the differentially expressed genes enriched in particular Gene Ontology terms.", "doi": "10.1038/s41598-020-62521-x", "pmid": "32246017", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-020-62521-x"}, {"db": "pmc", "key": "PMC7125170"}], "notes": [], "created": "2020-07-03T05:24:05.280Z", "modified": "2024-01-16T13:48:42.649Z"}, {"entity": "publication", "iuid": "2b6302172b5c4073976116e40f945d60", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2b6302172b5c4073976116e40f945d60.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2b6302172b5c4073976116e40f945d60"}}, "title": "Polymerase IV Plays a Crucial Role in Pollen Development in Capsella.", "authors": [{"family": "Wang", "given": "Zhenxing", "initials": "Z", "orcid": "0000-0001-5102-7121", "researcher": {"href": "https://publications.scilifelab.se/researcher/4b6c9f88c65d4fbc94da6d7598102335.json"}}, {"family": "Butel", "given": "Nicolas", "initials": "N", "orcid": "0000-0003-2484-4980", "researcher": {"href": "https://publications.scilifelab.se/researcher/f05a8316c3504f84abcc8cc66e770879.json"}}, {"family": "Santos-Gonz\u00e1lez", "given": "Juan", "initials": "J", "orcid": "0000-0002-8712-9776", "researcher": {"href": "https://publications.scilifelab.se/researcher/d26cc8b837e64875aa2226cb9a8b8da3.json"}}, {"family": "Borges", "given": "Filipe", "initials": "F", "orcid": "0000-0002-7388-2118", "researcher": {"href": "https://publications.scilifelab.se/researcher/08f47b282fc04126bb3359ec05ba9d02.json"}}, {"family": "Yi", "given": "Jun", "initials": "J", "orcid": "0000-0001-5539-0016", "researcher": {"href": "https://publications.scilifelab.se/researcher/c3fd9fa6dfce4a76996f52f7a8611b87.json"}}, {"family": "Martienssen", "given": "Robert A", "initials": "RA", "orcid": "0000-0003-1285-9608", "researcher": {"href": "https://publications.scilifelab.se/researcher/d40eed1e991b4eb08d5756886f50da55.json"}}, {"family": "Martinez", "given": "German", "initials": "G", "orcid": "0000-0002-5215-0866", "researcher": {"href": "https://publications.scilifelab.se/researcher/591f629ea8ed44c2bd9cd417dcebd8bc.json"}}, {"family": "K\u00f6hler", "given": "Claudia", "initials": "C", "orcid": "0000-0002-2619-4857", "researcher": {"href": "https://publications.scilifelab.se/researcher/accd3f9307614c8ab67154dd5e50cdac.json"}}], "type": "journal article", "published": "2020-04-00", "journal": {"title": "Plant Cell", "issn": "1532-298X", "issn-l": "1040-4651", "volume": "32", "issue": "4", "pages": "950-966"}, "abstract": "In Arabidopsis (Arabidopsis thaliana), DNA-dependent RNA polymerase IV (Pol IV) is required for the formation of transposable element (TE)-derived small RNA transcripts. These transcripts are processed by DICER-LIKE3 into 24-nucleotide small interfering RNAs (siRNAs) that guide RNA-directed DNA methylation. In the pollen grain, Pol IV is also required for the accumulation of 21/22-nucleotide epigenetically activated siRNAs, which likely silence TEs via post-transcriptional mechanisms. Despite this proposed role of Pol IV, its loss of function in Arabidopsis does not cause a discernible pollen defect. Here, we show that the knockout of NRPD1, encoding the largest subunit of Pol IV, in the Brassicaceae species Capsella (Capsella rubella), caused postmeiotic arrest of pollen development at the microspore stage. As in Arabidopsis, all TE-derived siRNAs were depleted in Capsella nrpd1 microspores. In the wild-type background, the same TEs produced 21/22-nucleotide and 24-nucleotide siRNAs; these processes required Pol IV activity. Arrest of Capsella nrpd1 microspores was accompanied by the deregulation of genes targeted by Pol IV-dependent siRNAs. TEs were much closer to genes in Capsella compared with Arabidopsis, perhaps explaining the essential role of Pol IV in pollen development in Capsella. Our discovery that Pol IV is functionally required in Capsella microspores emphasizes the relevance of investigating different plant models.", "doi": "10.1105/tpc.19.00938", "pmid": "31988265", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "tpc.19.00938"}, {"db": "pmc", "key": "PMC7145478"}], "notes": [], "created": "2020-12-08T23:35:28.348Z", "modified": "2021-11-10T12:52:33.683Z"}, {"entity": "publication", "iuid": "524e673c4b9048aea0126ac55a98c663", "links": {"self": {"href": "https://publications.scilifelab.se/publication/524e673c4b9048aea0126ac55a98c663.json"}, "display": {"href": "https://publications.scilifelab.se/publication/524e673c4b9048aea0126ac55a98c663"}}, "title": "A Multi-Omics Approach to Liver Diseases: Integration of Single Nuclei Transcriptomics with Proteomics and HiCap Bulk Data in Human Liver.", "authors": [{"family": "Cavalli", "given": "Marco", "initials": "M"}, {"family": "Diamanti", "given": "Klev", "initials": "K"}, {"family": "Pan", "given": "Gang", "initials": "G"}, {"family": "Spalinskas", "given": "Rapolas", "initials": "R"}, {"family": "Kumar", "given": "Chanchal", "initials": "C"}, {"family": "Deshmukh", "given": "Atul Shahaji", "initials": "AS"}, {"family": "Mann", "given": "Matthias", "initials": "M"}, {"family": "Sahl\u00e9n", "given": "Pelin", "initials": "P"}, {"family": "Komorowski", "given": "Jan", "initials": "J"}, {"family": "Wadelius", "given": "Claes", "initials": "C"}], "type": "journal article", "published": "2020-04-00", "journal": {"title": "OMICS", "issn": "1557-8100", "volume": "24", "issue": "4", "pages": "180-194", "issn-l": "1536-2310"}, "abstract": "The liver is the largest solid organ and a primary metabolic hub. In recent years, intact cell nuclei were used to perform single-nuclei RNA-seq (snRNA-seq) for tissues difficult to dissociate and for flash-frozen archived tissue samples to discover unknown and rare cell subpopulations. In this study, we performed snRNA-seq of a liver sample to identify subpopulations of cells based on nuclear transcriptomics. In 4282 single nuclei, we detected, on average, 1377 active genes and we identified seven major cell types. We integrated data from 94,286 distal interactions (p < 0.05) for 7682 promoters from a targeted chromosome conformation capture technique (HiCap) and mass spectrometry proteomics for the same liver sample. We observed a reasonable correlation between proteomics and in silico bulk snRNA-seq (r = 0.47) using tissue-independent gene-specific protein abundancy estimation factors. We specifically looked at genes of medical importance. The DPYD gene is involved in the pharmacogenetics of fluoropyrimidine toxicity and some of its variants are analyzed for clinical purposes. We identified a new putative polymorphic regulatory element, which may contribute to variation in toxicity. Hepatocellular carcinoma (HCC) is the most common type of primary liver cancer and we investigated all known risk genes. We identified a complex regulatory landscape for the SLC2A2 gene with 16 candidate enhancers. Three of them harbor somatic motif breaking and other mutations in HCC in the Pan Cancer Analysis of Whole Genomes dataset and are candidates to contribute to malignancy. Our results highlight the potential of a multi-omics approach in the study of human diseases.", "doi": "10.1089/omi.2019.0215", "pmid": "32181701", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC7185313"}], "notes": [], "created": "2020-11-16T09:10:16.494Z", "modified": "2024-01-16T13:48:42.722Z"}, {"entity": "publication", "iuid": "3d27ad2c075348029d3f5ac0be8dd349", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3d27ad2c075348029d3f5ac0be8dd349.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3d27ad2c075348029d3f5ac0be8dd349"}}, "title": "Antimicrobial peptide and sequence variation along a latitudinal gradient in two anurans.", "authors": [{"family": "Cort\u00e1zar-Chinarro", "given": "Maria", "initials": "M"}, {"family": "Meyer-Lucht", "given": "Yvonne", "initials": "Y"}, {"family": "Van der Valk", "given": "Tom", "initials": "T"}, {"family": "Richter-Boix", "given": "Alex", "initials": "A"}, {"family": "Laurila", "given": "Anssi", "initials": "A"}, {"family": "H\u00f6glund", "given": "Jacob", "initials": "J"}], "type": "journal article", "published": "2020-03-30", "journal": {"title": "BMC Genet.", "issn": "1471-2156", "volume": "21", "issue": "1", "pages": "38", "issn-l": "1471-2156"}, "abstract": "While there is evidence of both purifying and balancing selection in immune defense genes, large-scale genetic diversity in antimicrobial peptides (AMPs), an important part of the innate immune system released from dermal glands in the skin, has remained uninvestigated. Here we describe genetic diversity at three AMP loci (Temporin, Brevinin and Palustrin) in two ranid frogs (Rana arvalis and R. temporaria) along a 2000 km latitudinal gradient. We amplified and sequenced part of the Acidic Propiece domain and the hypervariable Mature Peptide domain (~ 150-200 bp) in the three genes using Illumina Miseq and expected to find decreased AMP genetic variation towards the northern distribution limit of the species similarly to studies on MHC genetic patterns.\n\nWe found multiple loci for each AMP and relatively high gene diversity, but no clear pattern of geographic genetic structure along the latitudinal gradient. We found evidence of trans-specific polymorphism in the two species, indicating a common evolutionary origin of the alleles. Temporin and Brevinin did not form monophyletic clades suggesting that they belong to the same gene family. By implementing codon evolution models we found evidence of strong positive selection acting on the Mature Peptide. We also found evidence of diversifying selection as indicated by divergent allele frequencies among populations and high Theta k values.\n\nOur results suggest that AMPs are an important source of adaptive diversity, minimizing the chance of microorganisms developing resistance to individual peptides.", "doi": "10.1186/s12863-020-00839-1", "pmid": "32228443", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1186/s12863-020-00839-1"}, {"db": "pmc", "key": "PMC7106915"}], "notes": [], "created": "2020-07-03T05:23:05.872Z", "modified": "2024-01-16T13:48:42.737Z"}, {"entity": "publication", "iuid": "7964577bf0bb4f2f8925eb1bb6111278", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7964577bf0bb4f2f8925eb1bb6111278.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7964577bf0bb4f2f8925eb1bb6111278"}}, "title": "Marine Sediments Illuminate Chlamydiae Diversity and Evolution.", "authors": [{"family": "Dharamshi", "given": "Jennah E", "initials": "JE"}, {"family": "Tamarit", "given": "Daniel", "initials": "D"}, {"family": "Eme", "given": "Laura", "initials": "L"}, {"family": "Stairs", "given": "Courtney W", "initials": "CW"}, {"family": "Martijn", "given": "Joran", "initials": "J"}, {"family": "Homa", "given": "Felix", "initials": "F"}, {"family": "J\u00f8rgensen", "given": "Steffen L", "initials": "SL"}, {"family": "Spang", "given": "Anja", "initials": "A"}, {"family": "Ettema", "given": "Thijs J G", "initials": "TJG"}], "type": "journal article", "published": "2020-03-23", "journal": {"title": "Curr. Biol.", "issn": "1879-0445", "issn-l": "0960-9822", "volume": "30", "issue": "6", "pages": "1032-1048.e7"}, "abstract": "The bacterial phylum Chlamydiae is so far composed of obligate symbionts of eukaryotic hosts. Well known for Chlamydiaceae, pathogens of humans and other animals, Chlamydiae also include so-called environmental lineages that primarily infect microbial eukaryotes. Environmental surveys indicate that Chlamydiae are found in a wider range of environments than anticipated previously. However, the vast majority of this chlamydial diversity has been underexplored, biasing our current understanding of their biology, ecological importance, and evolution. Here, we report that previously undetected and active chlamydial lineages dominate microbial communities in deep anoxic marine sediments taken from the Arctic Mid-Ocean Ridge. Reaching relative abundances of up to 43% of the bacterial community, and a maximum diversity of 163 different species-level taxonomic units, these Chlamydiae represent important community members. Using genome-resolved metagenomics, we reconstructed 24 draft chlamydial genomes, expanding by over a third the known genomic diversity in this phylum. Phylogenomic analyses revealed several novel clades across the phylum, including a previously unknown sister lineage of the Chlamydiaceae, providing new insights into the origin of pathogenicity in this family. We were unable to identify putative eukaryotic hosts for these marine sediment chlamydiae, despite identifying genomic features that may be indicative of host-association. The high abundance and genomic diversity of Chlamydiae in these anoxic marine sediments indicate that some members could play an important, and thus far overlooked, ecological role in such environments and may indicate alternate lifestyle strategies.", "doi": "10.1016/j.cub.2020.02.016", "pmid": "32142706", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "S0960-9822(20)30189-5"}, {"db": "figshare", "key": "10.6084/m9.figshare.11413008"}], "notes": [], "created": "2020-12-08T23:17:14.367Z", "modified": "2024-01-16T13:48:42.752Z"}, {"entity": "publication", "iuid": "2b5977da5b3448489e1540bbccf6f890", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2b5977da5b3448489e1540bbccf6f890.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2b5977da5b3448489e1540bbccf6f890"}}, "title": "Immune Profiling of Human Gut-Associated Lymphoid Tissue Identifies a Role for Isolated Lymphoid Follicles in Priming of Region-Specific Immunity.", "authors": [{"family": "Fenton", "given": "Thomas M", "initials": "TM"}, {"family": "J\u00f8rgensen", "given": "Peter B", "initials": "PB"}, {"family": "Niss", "given": "Kristoffer", "initials": "K"}, {"family": "Rubin", "given": "Samuel J S", "initials": "SJS"}, {"family": "M\u00f6rbe", "given": "Urs M", "initials": "UM"}, {"family": "Riis", "given": "Lene B", "initials": "LB"}, {"family": "Da Silva", "given": "Cl\u00e9ment", "initials": "C"}, {"family": "Plumb", "given": "Adam", "initials": "A"}, {"family": "Vandamme", "given": "Julien", "initials": "J"}, {"family": "Jakobsen", "given": "Henrik L", "initials": "HL"}, {"family": "Brunak", "given": "S\u00f8ren", "initials": "S"}, {"family": "Habtezion", "given": "Aida", "initials": "A"}, {"family": "Nielsen", "given": "Ole H", "initials": "OH"}, {"family": "Johansson-Lindbom", "given": "Bengt", "initials": "B"}, {"family": "Agace", "given": "William W", "initials": "WW"}], "type": "journal article", "published": "2020-03-17", "journal": {"title": "Immunity", "issn": "1097-4180", "volume": "52", "issue": "3", "pages": "557-570.e6", "issn-l": "1074-7613"}, "abstract": "The intestine contains some of the most diverse and complex immune compartments in the body. Here we describe a method for isolating human gut-associated lymphoid tissues (GALTs) that allows unprecedented profiling of the adaptive immune system in submucosal and mucosal isolated lymphoid follicles (SM-ILFs and M-ILFs, respectively) as well as in GALT-free intestinal lamina propria (LP). SM-ILF and M-ILF showed distinct patterns of distribution along the length of the intestine, were linked to the systemic circulation through MAdCAM-1+ high endothelial venules and efferent lymphatics, and had immune profiles consistent with immune-inductive sites. IgA sequencing analysis indicated that human ILFs are sites where intestinal adaptive immune responses are initiated in an anatomically restricted manner. Our findings position ILFs as key inductive hubs for regional immunity in the human intestine, and the methods presented will allow future assessment of these compartments in health and disease.", "doi": "10.1016/j.immuni.2020.02.001", "pmid": "32160523", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "S1074-7613(20)30072-8"}, {"db": "pmc", "key": "PMC7155934"}, {"db": "mid", "key": "NIHMS1568648"}], "notes": [], "created": "2020-07-03T05:24:52.368Z", "modified": "2021-11-10T12:53:00.374Z"}, {"entity": "publication", "iuid": "9467415b5d16477fbd0e52bb300c393b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9467415b5d16477fbd0e52bb300c393b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9467415b5d16477fbd0e52bb300c393b"}}, "title": "Effects of acute sleep loss on diurnal plasma dynamics of CNS health biomarkers in young men.", "authors": [{"family": "Benedict", "given": "Christian", "initials": "C", "orcid": "0000-0002-8911-4068", "researcher": {"href": "https://publications.scilifelab.se/researcher/fe597b41566a4042a73152771650a0cc.json"}}, {"family": "Blennow", "given": "Kaj", "initials": "K"}, {"family": "Zetterberg", "given": "Henrik", "initials": "H"}, {"family": "Cedernaes", "given": "Jonathan", "initials": "J", "orcid": "0000-0002-9052-8372", "researcher": {"href": "https://publications.scilifelab.se/researcher/46549a2cffc84c0b97e388ab09b977bc.json"}}], "type": "journal article", "published": "2020-03-17", "journal": {"title": "Neurology", "issn": "1526-632X", "issn-l": "0028-3878", "volume": "94", "issue": "11", "pages": "e1181-e1189"}, "abstract": "Disrupted sleep increases CSF levels of tau and \u03b2-amyloid (A\u03b2) and is associated with an increased risk of Alzheimer disease (AD). Our aim was to determine whether acute sleep loss alters diurnal profiles of plasma-based AD-associated biomarkers.\r\n\r\nIn a 2-condition crossover study, 15 healthy young men participated in 2 standardized sedentary in-laboratory conditions in randomized order: normal sleep vs overnight sleep loss. Plasma levels of total tau (t-tau), A\u03b240, A\u03b242, neurofilament light chain (NfL), and glial fibrillary acidic protein (GFAP) were assessed using ultrasensitive single molecule array assays or ELISAs, in the fasted state in the evening prior to, and in the morning after, each intervention.\r\n\r\nIn response to sleep loss (+17.2%), compared with normal sleep (+1.8%), the evening to morning ratio was increased for t-tau (p = 0.035). No changes between the sleep conditions were seen for levels of A\u03b240, A\u03b242, NfL, or GFAP (all p > 0.10). The AD risk genotype rs4420638 did not significantly interact with sleep loss-related diurnal changes in plasma levels of A\u03b240 or A\u03b242 (p > 0.10). Plasma levels of A\u03b242 (-17.1%) and GFAP (-12.1%) exhibited an evening to morning decrease across conditions (p < 0.05).\r\n\r\nOur exploratory study suggests that acute sleep loss results in increased blood levels of t-tau. These changes provide further evidence that sleep loss may have detrimental effects on brain health even in younger individuals. Larger cohorts are warranted to delineate sleep vs circadian mechanisms, implications for long-term recurrent conditions (e.g., in shift workers), as well as interactions with other lifestyle and genetic factors.", "doi": "10.1212/WNL.0000000000008866", "pmid": "31915189", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "WNL.0000000000008866"}, {"db": "pmc", "key": "PMC7220231"}], "notes": [], "created": "2021-01-07T17:01:48.786Z", "modified": "2024-01-16T13:48:42.759Z"}, {"entity": "publication", "iuid": "a5ffc222ff2f4848955dbd9ffdb38a85", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a5ffc222ff2f4848955dbd9ffdb38a85.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a5ffc222ff2f4848955dbd9ffdb38a85"}}, "title": "Genome-wide Association Analysis in Humans Links Nucleotide Metabolism to Leukocyte Telomere Length.", "authors": [{"family": "Li", "given": "Chen", "initials": "C"}, {"family": "Stoma", "given": "Svetlana", "initials": "S"}, {"family": "Lotta", "given": "Luca A", "initials": "LA"}, {"family": "Warner", "given": "Sophie", "initials": "S"}, {"family": "Albrecht", "given": "Eva", "initials": "E"}, {"family": "Allione", "given": "Alessandra", "initials": "A"}, {"family": "Arp", "given": "Pascal P", "initials": "PP"}, {"family": "Broer", "given": "Linda", "initials": "L"}, {"family": "Buxton", "given": "Jessica L", "initials": "JL"}, {"family": "Da Silva Couto Alves", "given": "Alexessander", "initials": "A"}, {"family": "Deelen", "given": "Joris", "initials": "J"}, {"family": "Fedko", "given": "Iryna O", "initials": "IO"}, {"family": "Gordon", "given": "Scott D", "initials": "SD"}, {"family": "Jiang", "given": "Tao", "initials": "T"}, {"family": "Karlsson", "given": "Robert", "initials": "R"}, {"family": "Kerrison", "given": "Nicola", "initials": "N"}, {"family": "Loe", "given": "Taylor K", "initials": "TK"}, {"family": "Mangino", "given": "Massimo", "initials": "M"}, {"family": "Milaneschi", "given": "Yuri", "initials": "Y"}, {"family": "Miraglio", "given": "Benjamin", "initials": "B"}, {"family": "Pervjakova", "given": "Natalia", "initials": "N"}, {"family": "Russo", "given": "Alessia", "initials": "A"}, {"family": "Surakka", "given": "Ida", "initials": "I"}, {"family": "van der Spek", "given": "Ashley", "initials": "A"}, {"family": "Verhoeven", "given": "Josine E", "initials": "JE"}, {"family": "Amin", "given": "Najaf", "initials": "N"}, {"family": "Beekman", "given": "Marian", "initials": "M"}, {"family": "Blakemore", "given": "Alexandra I", "initials": "AI"}, {"family": "Canzian", "given": "Federico", "initials": "F"}, {"family": "Hamby", "given": "Stephen E", "initials": "SE"}, {"family": "Hottenga", "given": "Jouke-Jan", "initials": "JJ"}, {"family": "Jones", "given": "Peter D", "initials": "PD"}, {"family": "Jousilahti", "given": "Pekka", "initials": "P"}, {"family": "M\u00e4gi", "given": "Reedik", "initials": "R"}, {"family": "Medland", "given": "Sarah E", "initials": "SE"}, {"family": "Montgomery", "given": "Grant W", "initials": "GW"}, {"family": "Nyholt", "given": "Dale R", "initials": "DR"}, {"family": "Perola", "given": "Markus", "initials": "M"}, {"family": "Pietil\u00e4inen", "given": "Kirsi H", "initials": "KH"}, {"family": "Salomaa", "given": "Veikko", "initials": "V"}, {"family": "Sillanp\u00e4\u00e4", "given": "Elina", "initials": "E"}, {"family": "Suchiman", "given": "H Eka", "initials": "HE"}, {"family": "van Heemst", "given": "Diana", "initials": "D"}, {"family": "Willemsen", "given": "Gonneke", "initials": "G"}, {"family": "Agudo", "given": "Antonio", "initials": "A"}, {"family": "Boeing", "given": "Heiner", "initials": "H"}, {"family": "Boomsma", "given": "Dorret I", "initials": "DI"}, {"family": "Chirlaque", "given": "Maria-Dolores", "initials": "MD"}, {"family": "Fagherazzi", "given": "Guy", "initials": "G"}, {"family": "Ferrari", "given": "Pietro", "initials": "P"}, {"family": "Franks", "given": "Paul", "initials": "P"}, {"family": "Gieger", "given": "Christian", "initials": "C"}, {"family": "Eriksson", "given": "Johan Gunnar", "initials": "JG"}, {"family": "Gunter", "given": "Marc", "initials": "M"}, {"family": "H\u00e4gg", "given": "Sara", "initials": "S"}, {"family": "Hovatta", "given": "Iiris", "initials": "I"}, {"family": "Imaz", "given": "Liher", "initials": "L"}, {"family": "Kaprio", "given": "Jaakko", "initials": "J"}, {"family": "Kaaks", "given": "Rudolf", "initials": "R"}, {"family": "Key", "given": "Timothy", "initials": "T"}, {"family": "Krogh", "given": "Vittorio", "initials": "V"}, {"family": "Martin", "given": "Nicholas G", "initials": "NG"}, {"family": "Melander", "given": "Olle", "initials": "O"}, {"family": "Metspalu", "given": "Andres", "initials": "A"}, {"family": "Moreno", "given": "Concha", "initials": "C"}, {"family": "Onland-Moret", "given": "N Charlotte", "initials": "NC"}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}, {"family": "Ong", "given": "Ken K", "initials": "KK"}, {"family": "Overvad", "given": "Kim", "initials": "K"}, {"family": "Palli", "given": "Domenico", "initials": "D"}, {"family": "Panico", "given": "Salvatore", "initials": "S"}, {"family": "Pedersen", "given": "Nancy L", "initials": "NL"}, {"family": "Penninx", "given": "Brenda W J H", "initials": "BWJH"}, {"family": "Quir\u00f3s", "given": "J Ram\u00f3n", "initials": "JR"}, {"family": "Jarvelin", "given": "Marjo Riitta", "initials": "MR"}, {"family": "Rodr\u00edguez-Barranco", "given": "Miguel", "initials": "M"}, {"family": "Scott", "given": "Robert A", "initials": "RA"}, {"family": "Severi", "given": "Gianluca", "initials": "G"}, {"family": "Slagboom", "given": "P Eline", "initials": "PE"}, {"family": "Spector", "given": "Tim D", "initials": "TD"}, {"family": "Tjonneland", "given": "Anne", "initials": "A"}, {"family": "Trichopoulou", "given": "Antonia", "initials": "A"}, {"family": "Tumino", "given": "Rosario", "initials": "R"}, {"family": "Uitterlinden", "given": "Andr\u00e9 G", "initials": "AG"}, {"family": "van der Schouw", "given": "Yvonne T", "initials": "YT"}, {"family": "van Duijn", "given": "Cornelia M", "initials": "CM"}, {"family": "Weiderpass", "given": "Elisabete", "initials": "E"}, {"family": "Denchi", "given": "Eros Lazzerini", "initials": "EL"}, {"family": "Matullo", "given": "Giuseppe", "initials": "G"}, {"family": "Butterworth", "given": "Adam S", "initials": "AS"}, {"family": "Danesh", "given": "John", "initials": "J"}, {"family": "Samani", "given": "Nilesh J", "initials": "NJ"}, {"family": "Wareham", "given": "Nicholas J", "initials": "NJ"}, {"family": "Nelson", "given": "Christopher P", "initials": "CP"}, {"family": "Langenberg", "given": "Claudia", "initials": "C"}, {"family": "Codd", "given": "Veryan", "initials": "V"}], "type": "journal article", "published": "2020-03-05", "journal": {"title": "Am. J. Hum. Genet.", "issn": "1537-6605", "volume": "106", "issue": "3", "pages": "389-404", "issn-l": "0002-9297"}, "abstract": "Leukocyte telomere length (LTL) is a heritable biomarker of genomic aging. In this study, we perform a genome-wide meta-analysis of LTL by pooling densely genotyped and imputed association results across large-scale European-descent studies including up to 78,592 individuals. We identify 49 genomic regions at a false dicovery rate (FDR) < 0.05 threshold and prioritize genes at 31, with five highlighting nucleotide metabolism as an important regulator of LTL. We report six genome-wide significant loci in or near SENP7, MOB1B, CARMIL1, PRRC2A, TERF2, and RFWD3, and our results support recently identified PARP1, POT1, ATM, and MPHOSPH6 loci. Phenome-wide analyses in >350,000 UK Biobank participants suggest that genetically shorter telomere length increases the risk of hypothyroidism and decreases the risk of thyroid cancer, lymphoma, and a range of proliferative conditions. Our results replicate previously reported associations with increased risk of coronary artery disease and lower risk for multiple cancer types. Our findings substantially expand current knowledge on genes that regulate LTL and their impact on human health and disease.", "doi": "10.1016/j.ajhg.2020.02.006", "pmid": "32109421", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "S0002-9297(20)30048-3"}, {"db": "pmc", "key": "PMC7058826"}], "notes": [], "created": "2020-03-03T12:57:27.050Z", "modified": "2021-11-10T12:53:17.953Z"}, {"entity": "publication", "iuid": "67b440a208864ecea283f09dd7ca7f80", "links": {"self": {"href": "https://publications.scilifelab.se/publication/67b440a208864ecea283f09dd7ca7f80.json"}, "display": {"href": "https://publications.scilifelab.se/publication/67b440a208864ecea283f09dd7ca7f80"}}, "title": "Transcriptomic resources for evolutionary studies in flat periwinkles and related species.", "authors": [{"family": "Marques", "given": "Jo\u00e3o P", "initials": "JP", "orcid": "0000-0001-9834-1361", "researcher": {"href": "https://publications.scilifelab.se/researcher/7bb0a67732e44e108fe1f58f86ce4ef2.json"}}, {"family": "Sotelo", "given": "Graciela", "initials": "G"}, {"family": "Galindo", "given": "Juan", "initials": "J"}, {"family": "Chaube", "given": "Pragya", "initials": "P"}, {"family": "Costa", "given": "Diana", "initials": "D"}, {"family": "Afonso", "given": "Sandra", "initials": "S"}, {"family": "Panova", "given": "Marina", "initials": "M"}, {"family": "Nowick", "given": "Katja", "initials": "K"}, {"family": "Butlin", "given": "Roger", "initials": "R", "orcid": "0000-0003-4736-0954", "researcher": {"href": "https://publications.scilifelab.se/researcher/e510a963ebeb4e8c8af68b10a001a326.json"}}, {"family": "Hollander", "given": "Johan", "initials": "J"}, {"family": "Faria", "given": "Rui", "initials": "R"}], "type": "dataset", "published": "2020-03-03", "journal": {"title": "Sci Data", "issn": "2052-4463", "volume": "7", "issue": "1", "pages": "73", "issn-l": "2052-4463"}, "abstract": "The flat periwinkles, Littorina fabalis and L. obtusata, comprise two sister gastropod species that have an enormous potential to elucidate the mechanisms involved in ecological speciation in the marine realm. However, the molecular resources currently available for these species are still scarce. In order to circumvent this limitation, we used RNA-seq data to characterize the transcriptome of four individuals from each species sampled in different locations across the Iberian Peninsula. Four de novo transcriptome assemblies were generated, as well as a pseudo-reference using the L. saxatilis reference transcriptome as backbone. After transcripts' annotation, variant calling resulted in the identification of 19,072 to 45,340 putatively species-diagnostic SNPs. The discriminatory power of a subset of these SNPs was validated by implementing an independent genotyping assay to characterize reference populations, resulting in an accurate classification of individuals into each species and in the identification of hybrids between the two. These data comprise valuable genomic resources for a wide range of evolutionary and conservation studies in flat periwinkles and related taxa.", "doi": "10.1038/s41597-020-0408-8", "pmid": "32127542", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41597-020-0408-8"}, {"db": "pmc", "key": "PMC7054417"}], "notes": [], "created": "2020-03-16T09:47:51.783Z", "modified": "2021-11-10T12:53:19.043Z"}, {"entity": "publication", "iuid": "fc7a25ffb3114b019ba788d35be80ecc", "links": {"self": {"href": "https://publications.scilifelab.se/publication/fc7a25ffb3114b019ba788d35be80ecc.json"}, "display": {"href": "https://publications.scilifelab.se/publication/fc7a25ffb3114b019ba788d35be80ecc"}}, "title": "Oral Microbiota Profile Associates with Sugar Intake and Taste Preference Genes.", "authors": [{"family": "Esberg", "given": "Anders", "initials": "A", "orcid": "0000-0002-4430-8125", "researcher": {"href": "https://publications.scilifelab.se/researcher/a6610f154ad749a49a8f5d89382c6b1b.json"}}, {"family": "Haworth", "given": "Simon", "initials": "S", "orcid": "0000-0001-7793-7326", "researcher": {"href": "https://publications.scilifelab.se/researcher/43fa9fb331c849b58d4ac4b14f04fbda.json"}}, {"family": "Hassl\u00f6f", "given": "Pamela", "initials": "P"}, {"family": "Lif Holgerson", "given": "Pernilla", "initials": "P", "orcid": "0000-0002-2779-5865", "researcher": {"href": "https://publications.scilifelab.se/researcher/90cb42e842044260888df6e0a10afdd1.json"}}, {"family": "Johansson", "given": "Ingegerd", "initials": "I", "orcid": "0000-0002-9227-8434", "researcher": {"href": "https://publications.scilifelab.se/researcher/ee3e20587b664a42a880870f1648160a.json"}}], "type": "clinical trial", "published": "2020-03-03", "journal": {"title": "Nutrients", "issn": "2072-6643", "volume": "12", "issue": "3", "pages": "681", "issn-l": "2072-6643"}, "abstract": "Oral microbiota ecology is influenced by environmental and host conditions, but few studies have evaluated associations between untargeted measures of the entire oral microbiome and potentially relevant environmental and host factors. This study aimed to identify salivary microbiota cluster groups using hierarchical cluster analyses (Wards method) based on 16S rRNA gene amplicon sequencing, and identify lifestyle and host factors which were associated with these groups. Group members (n = 175) were distinctly separated by microbiota profiles and differed in reported sucrose intake and allelic variation in the taste-preference-associated genes TAS1R1 (rs731024) and GNAT3 (rs2074673). Groups with higher sucrose intake were either characterized by a wide panel of species or phylotypes with fewer aciduric species, or by a narrower profile that included documented aciduric- and caries-associated species. The inferred functional profiles of the latter type were dominated by metabolic pathways associated with the carbohydrate metabolism with enrichment of glycosidase functions. In conclusion, this study supported in vivo associations between sugar intake and oral microbiota ecology, but it also found evidence for a variable microbiota response to sugar, highlighting the importance of modifying host factors and microbes beyond the commonly targeted acidogenic and acid-tolerant species. The results should be confirmed under controlled settings with comprehensive phenotypic and genotypic data.", "doi": "10.3390/nu12030681", "pmid": "32138214", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "nu12030681"}, {"db": "pmc", "key": "PMC7146170"}], "notes": [], "created": "2020-03-16T09:47:51.000Z", "modified": "2021-11-10T12:53:20.230Z"}, {"entity": "publication", "iuid": "804fe367d4ba45b59d3d3ed95177e766", "links": {"self": {"href": "https://publications.scilifelab.se/publication/804fe367d4ba45b59d3d3ed95177e766.json"}, "display": {"href": "https://publications.scilifelab.se/publication/804fe367d4ba45b59d3d3ed95177e766"}}, "title": "Overexpression of chromatin remodeling and tyrosine kinase genes in iAMP21-positive acute lymphoblastic leukemia.", "authors": [{"family": "Ivanov \u00d6fverholm", "given": "Ingegerd", "initials": "I", "orcid": "0000-0002-6907-8004", "researcher": {"href": "https://publications.scilifelab.se/researcher/0ba94eeea4d24e9c8c354fe1256fd0ce.json"}}, {"family": "Zachariadis", "given": "Vasilios", "initials": "V", "orcid": "0000-0001-9360-9859", "researcher": {"href": "https://publications.scilifelab.se/researcher/0607f2b65c12492cb30fb7a445d37937.json"}}, {"family": "Taylan", "given": "Fulya", "initials": "F", "orcid": "0000-0002-2907-0235", "researcher": {"href": "https://publications.scilifelab.se/researcher/c250909cc40f42ff9d6e2f640d12451b.json"}}, {"family": "Marincevic-Zuniga", "given": "Yanara", "initials": "Y", "orcid": "0000-0001-5576-2115", "researcher": {"href": "https://publications.scilifelab.se/researcher/eb045b70f16140b6b6e69476d701012c.json"}}, {"family": "Tran", "given": "Anh Nhi", "initials": "AN"}, {"family": "Saft", "given": "Leonie", "initials": "L"}, {"family": "Nilsson", "given": "Daniel", "initials": "D", "orcid": "0000-0001-5831-385X", "researcher": {"href": "https://publications.scilifelab.se/researcher/9b3f854e51704270831e155518265ea6.json"}}, {"family": "Syv\u00e4nen", "given": "Ann-Christine", "initials": "AC", "orcid": "0000-0002-9681-9146", "researcher": {"href": "https://publications.scilifelab.se/researcher/f7012e35025543379380cb90efd71243.json"}}, {"family": "L\u00f6nnerholm", "given": "Gudmar", "initials": "G"}, {"family": "Harila-Saari", "given": "Arja", "initials": "A"}, {"family": "Nordenskj\u00f6ld", "given": "Magnus", "initials": "M", "orcid": "0000-0002-4974-425X", "researcher": {"href": "https://publications.scilifelab.se/researcher/9f9dec008f1b42868dd133e9a396c968.json"}}, {"family": "Heyman", "given": "Mats", "initials": "M"}, {"family": "Nordgren", "given": "Ann", "initials": "A", "orcid": "0000-0003-3285-4281", "researcher": {"href": "https://publications.scilifelab.se/researcher/08e74c6ddc27493696beca0883027cdd.json"}}, {"family": "Nordlund", "given": "Jessica", "initials": "J", "orcid": "0000-0001-8699-9959", "researcher": {"href": "https://publications.scilifelab.se/researcher/ddf48c9262134821bcc6ce1180049753.json"}}, {"family": "Barbany", "given": "Gisela", "initials": "G"}], "type": "journal article", "published": "2020-03-00", "journal": {"title": "Leuk. Lymphoma", "issn": "1029-2403", "issn-l": "1026-8022", "volume": "61", "issue": "3", "pages": "604-613"}, "abstract": "Intrachromosomal amplification of chromosome 21 (iAMP21) is a cytogenetic subtype associated with relapse and poor prognosis in pediatric B-cell precursor acute lymphoblastic leukemia (BCP ALL). The biology behind the high relapse risk is unknown and the aim of this study was to further characterize the genomic and transcriptional landscape of iAMP21. Using DNA arrays and sequencing, we could identify rearrangements and aberrations characteristic for iAMP21. RNA sequencing revealed that only half of the genes in the minimal region of amplification (20/45) were differentially expressed in iAMP21. Among them were the top overexpressed genes (p < 0.001) in iAMP21 vs. BCP ALL without iAMP21 and three candidate genes could be identified, the tyrosine kinase gene DYRK1A and chromatin remodeling genes CHAF1B and SON. While overexpression of DYRK1A and CHAF1B is associated with poor prognosis in malignant diseases including myeloid leukemia, this is the first study to show significant correlation with iAMP21-positive ALL.", "doi": "10.1080/10428194.2019.1678153", "pmid": "31640433", "labels": {"National Genomics Infrastructure": "Collaborative", "NGI Uppsala (SNP&SEQ Technology Platform)": "Collaborative", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2019-12-03T10:45:21.445Z", "modified": "2024-01-16T13:48:42.841Z"}, {"entity": "publication", "iuid": "b5443abd00b749b6ae6e72151a971b87", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b5443abd00b749b6ae6e72151a971b87.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b5443abd00b749b6ae6e72151a971b87"}}, "title": "Longitudinal changes in the frequency of mosaic chromosome Y loss in peripheral blood cells of aging men varies profoundly between individuals.", "authors": [{"family": "Danielsson", "given": "Marcus", "initials": "M", "orcid": "0000-0003-4418-0165", "researcher": {"href": "https://publications.scilifelab.se/researcher/d6b237ce613e4ef8a6d7ab2654c2c41e.json"}}, {"family": "Halvardson", "given": "Jonatan", "initials": "J"}, {"family": "Davies", "given": "Hanna", "initials": "H"}, {"family": "Torabi Moghadam", "given": "Behrooz", "initials": "B"}, {"family": "Mattisson", "given": "Jonas", "initials": "J", "orcid": "0000-0002-4456-9667", "researcher": {"href": "https://publications.scilifelab.se/researcher/2672b9fa599b44a395d1a2f8f59a5949.json"}}, {"family": "Rychlicka-Buniowska", "given": "Edyta", "initials": "E"}, {"family": "Jaszczy\u0144ski", "given": "Janusz", "initials": "J"}, {"family": "Heintz", "given": "Julia", "initials": "J"}, {"family": "Lannfelt", "given": "Lars", "initials": "L"}, {"family": "Giedraitis", "given": "Vilmantas", "initials": "V"}, {"family": "Ingelsson", "given": "Martin", "initials": "M"}, {"family": "Dumanski", "given": "Jan P", "initials": "JP"}, {"family": "Forsberg", "given": "Lars A", "initials": "LA", "orcid": "0000-0002-1701-755X", "researcher": {"href": "https://publications.scilifelab.se/researcher/9ac2d8e983764a82982118b6db84029e.json"}}], "type": "journal article", "published": "2020-03-00", "journal": {"title": "Eur. J. Hum. Genet.", "issn": "1476-5438", "issn-l": "1018-4813", "volume": "28", "issue": "3", "pages": "349-357"}, "abstract": "Mosaic loss of chromosome Y (LOY) is the most common somatic genetic aberration and is associated with increased risk for all-cause mortality, various forms of cancer and Alzheimer's disease, as well as other common human diseases. By tracking LOY frequencies in subjects from which blood samples have been serially collected up to five times during up to 22 years, we observed a pronounced intra-individual variation of changes in the frequency of LOY within individual men over time. We observed that in some individuals the frequency of LOY in blood clearly progressed over time and that in other men, the frequency was constant or showed other types of longitudinal development. The predominant method used for estimating LOY is calculation of the median Log R Ratio of probes located in the male specific part of chromosome Y (mLRRY) from intensity data generated by SNP-arrays, which is difficult to interpret due to its logarithmic and inversed scale. We present here a formula to transform mLRRY-values to percentage of LOY that is a more comprehensible unit. The formula was derived using measurements of LOY from matched samples analysed using SNP-array, whole genome sequencing and a new AMELX/AMELY-based assay for droplet digital PCR. The methods described could be applied for analyses of the vast amount of SNP-array data already generated in the scientific community, allowing further discoveries of LOY associated diseases and outcomes.", "doi": "10.1038/s41431-019-0533-z", "pmid": "31654039", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41431-019-0533-z"}, {"db": "pmc", "key": "PMC7028735"}], "notes": [], "created": "2019-10-30T13:13:11.626Z", "modified": "2024-01-16T13:48:42.853Z"}, {"entity": "publication", "iuid": "a5dc2e45a1f5491ca43a9380cf38b99a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a5dc2e45a1f5491ca43a9380cf38b99a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a5dc2e45a1f5491ca43a9380cf38b99a"}}, "title": "High genetic risk score is associated with early disease onset, damage accrual and decreased survival in systemic lupus erythematosus.", "authors": [{"family": "Reid", "given": "Sarah", "initials": "S", "orcid": "0000-0003-4065-6875", "researcher": {"href": "https://publications.scilifelab.se/researcher/689ab046bc19433483d502284d2c51c4.json"}}, {"family": "Alexsson", "given": "Andrei", "initials": "A"}, {"family": "Frodlund", "given": "Martina", "initials": "M"}, {"family": "Morris", "given": "David", "initials": "D"}, {"family": "Sandling", "given": "Johanna K", "initials": "JK"}, {"family": "Bolin", "given": "Karin", "initials": "K"}, {"family": "Svenungsson", "given": "Elisabet", "initials": "E", "orcid": "0000-0003-3396-3244", "researcher": {"href": "https://publications.scilifelab.se/researcher/0ab5989c3c604a96bf42b1b6f90434a0.json"}}, {"family": "J\u00f6nsen", "given": "Andreas", "initials": "A"}, {"family": "Bengtsson", "given": "Christine", "initials": "C"}, {"family": "Gunnarsson", "given": "Iva", "initials": "I"}, {"family": "Illescas Rodriguez", "given": "Vera", "initials": "V"}, {"family": "Bengtsson", "given": "Anders", "initials": "A"}, {"family": "Arve", "given": "Sabine", "initials": "S", "orcid": "0000-0002-3347-5550", "researcher": {"href": "https://publications.scilifelab.se/researcher/b64a9ba6c7d344d0a47ef99532a347ab.json"}}, {"family": "Rantap\u00e4\u00e4-Dahlqvist", "given": "Solbritt", "initials": "S", "orcid": "0000-0001-8259-3863", "researcher": {"href": "https://publications.scilifelab.se/researcher/dfca4bfdcf3946fda64397d3b7debc59.json"}}, {"family": "Eloranta", "given": "Maija-Leena", "initials": "ML"}, {"family": "Syv\u00e4nen", "given": "Ann-Christine", "initials": "AC", "orcid": "0000-0002-9681-9146", "researcher": {"href": "https://publications.scilifelab.se/researcher/f7012e35025543379380cb90efd71243.json"}}, {"family": "Sj\u00f6wall", "given": "Christopher", "initials": "C", "orcid": "0000-0003-0900-2048", "researcher": {"href": "https://publications.scilifelab.se/researcher/fe4dd47b8ca1436e8a26fdea33f5e7f6.json"}}, {"family": "Vyse", "given": "Timothy James", "initials": "TJ"}, {"family": "R\u00f6nnblom", "given": "Lars", "initials": "L", "orcid": "0000-0001-9403-6503", "researcher": {"href": "https://publications.scilifelab.se/researcher/053ed3b657124a1bab3a78dc685556e6.json"}}, {"family": "Leonard", "given": "Dag", "initials": "D", "orcid": "0000-0002-6275-7282", "researcher": {"href": "https://publications.scilifelab.se/researcher/42ed25c2f495484db4757f4fef51abae.json"}}], "type": "journal article", "published": "2020-03-00", "journal": {"title": "Ann. Rheum. Dis.", "issn": "1468-2060", "issn-l": "0003-4967", "volume": "79", "issue": "3", "pages": "363-369"}, "abstract": "To investigate associations between a high genetic disease risk and disease severity in patients with systemic lupus erythematosus (SLE).\n\nPatients with SLE (n=1001, discovery cohort and n=5524, replication cohort) and healthy controls (n=2802 and n=9859) were genotyped using a 200K Immunochip single nucleotide polymorphism array. A genetic risk score (GRS) was assigned to each individual based on 57 SLE risk loci.\n\nSLE was more prevalent in the high, compared with the low, GRS-quartile (OR 12.32 (9.53 to 15.71), p=7.9\u00d710-86 and OR 7.48 (6.73 to 8.32), p=2.2\u00d710-304 for the discovery and the replication cohorts, respectively). In the discovery cohort, patients in the high GRS-quartile had a 6-year earlier mean disease onset (HR 1.47 (1.22 to 1.75), p=4.3\u00d710-5), displayed higher prevalence of damage accrual (OR 1.47 (1.06 to 2.04), p=2.0\u00d710-2), renal disorder (OR 2.22 (1.50 to 3.27), p=5.9\u00d710-5), anti-dsDNA (OR 1.83 (1.19 to 2.81), p=6.1\u00d710-3), end-stage renal disease (ESRD) (OR 5.58 (1.50 to 20.79), p=1.0\u00d710-2), proliferative nephritis (OR 2.42 (1.30 to 4.49), p=5.1\u00d710-3), anti-cardiolipin-IgG (OR 1.89 (1.13 to 3.18), p=1.6\u00d710-2), anti-\u03b22-glycoprotein-I-IgG (OR 2.29 (1.29 to 4.06), p=4.8\u00d710-3) and positive lupus anticoagulant test (OR 2.12 (1.16 to 3.89), p=1.5\u00d710-2) compared with patients in the low GRS-quartile. Survival analysis showed earlier onset of the first organ damage (HR 1.51 (1.04 to 2.25), p=3.7\u00d710-2), first cardiovascular event (HR 1.65 (1.03 to 2.64), p=2.6\u00d710-2), nephritis (HR 2.53 (1.72 to 3.71), p=9.6\u00d710-7), ESRD (HR 6.78 (1.78 to 26.86), p=6.5\u00d710-3) and decreased overall survival (HR 1.83 (1.02 to 3.30), p=4.3\u00d710-2) in high to low quartile comparison.\n\nA high GRS is associated with increased risk of organ damage, renal dysfunction and all-cause mortality. Our results indicate that genetic profiling may be useful for predicting outcomes in patients with SLE.", "doi": "10.1136/annrheumdis-2019-216227", "pmid": "31826855", "labels": {"National Genomics Infrastructure": "Collaborative", "NGI Uppsala (SNP&SEQ Technology Platform)": "Collaborative", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "annrheumdis-2019-216227"}, {"db": "pmc", "key": "PMC7034364"}], "notes": [], "created": "2019-12-18T16:32:05.276Z", "modified": "2024-01-16T13:48:42.863Z"}, {"entity": "publication", "iuid": "66acb228c0fe4207af5b7c2a2b3ad412", "links": {"self": {"href": "https://publications.scilifelab.se/publication/66acb228c0fe4207af5b7c2a2b3ad412.json"}, "display": {"href": "https://publications.scilifelab.se/publication/66acb228c0fe4207af5b7c2a2b3ad412"}}, "title": "Heritability of Caries Scores, Trajectories, and Disease Subtypes.", "authors": [{"family": "Haworth", "given": "S", "initials": "S", "orcid": "0000-0001-7793-7326", "researcher": {"href": "https://publications.scilifelab.se/researcher/43fa9fb331c849b58d4ac4b14f04fbda.json"}}, {"family": "Esberg", "given": "A", "initials": "A", "orcid": "0000-0002-4430-8125", "researcher": {"href": "https://publications.scilifelab.se/researcher/a6610f154ad749a49a8f5d89382c6b1b.json"}}, {"family": "Lif Holgerson", "given": "P", "initials": "P"}, {"family": "Kuja-Halkola", "given": "R", "initials": "R"}, {"family": "Timpson", "given": "N J", "initials": "NJ"}, {"family": "Magnusson", "given": "P K E", "initials": "PKE"}, {"family": "Franks", "given": "P W", "initials": "PW"}, {"family": "Johansson", "given": "I", "initials": "I"}], "type": "journal article", "published": "2020-03-00", "journal": {"title": "J Dent Res", "issn": "0022-0345", "volume": "99", "issue": "3", "pages": "264-270", "issn-l": null}, "abstract": "Previous studies report that dental caries is partially heritable, but there is uncertainty in the magnitude of genetic effects and little understanding of how genetic factors might influence caries progression or caries subtypes. This study aimed to estimate the relative importance of genetic and environmental factors in the etiology of different caries outcomes using a twin-based design. Analysis included up to 41,678 twins in the Swedish Twin Register aged 7 to 97 y, and dental data were obtained from preexisting dental records. The outcome measures were 1) summary indices of caries experience, 2) parameters representing trajectory in caries progression derived from longitudinal modeling, and 3) caries scores in groups of biologically similar tooth surfaces derived from hierarchical clustering of tooth surfaces (termed caries clusters). Additive genetic factors explained between 49.1% and 62.7% of variation in caries scores and between 50.0% and 60.5% of variation in caries trajectories. Seven caries clusters were identified, which had estimates of heritability lying between 41.9% and 54.3%. Shared environmental factors were important for only some of these clusters and explained 16% of variation in fissure caries in molar teeth but little variation in other clusters of caries presentation. The genetic factors influencing these clusters were only partially overlapping, suggesting that different biological processes are important in different groups of tooth surfaces and that innate liability to some patterns of caries presentation may partially explain why groups of tooth surfaces form clusters within the mouth. These results provide 1) improved quantification of genetic factors in the etiology of caries and 2) new data about the role of genetics in terms of longitudinal changes in caries status and specific patterns of disease presentation, and they may help lay the foundations for personalized interventions in the future.", "doi": "10.1177/0022034519897910", "pmid": "31905308", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC7036480"}], "notes": [], "created": "2021-01-07T17:01:45.040Z", "modified": "2021-12-07T13:55:12.669Z"}, {"entity": "publication", "iuid": "801a1c8a83fa4b0183e5729b84f7a003", "links": {"self": {"href": "https://publications.scilifelab.se/publication/801a1c8a83fa4b0183e5729b84f7a003.json"}, "display": {"href": "https://publications.scilifelab.se/publication/801a1c8a83fa4b0183e5729b84f7a003"}}, "title": "PCSK6 Is a Key Protease in the Control of Smooth Muscle Cell Function in Vascular Remodeling.", "authors": [{"family": "Rykaczewska", "given": "Urszula", "initials": "U"}, {"family": "Suur", "given": "Bianca E", "initials": "BE"}, {"family": "R\u00f6hl", "given": "Samuel", "initials": "S"}, {"family": "Razuvaev", "given": "Anton", "initials": "A"}, {"family": "Lengquist", "given": "Mariette", "initials": "M"}, {"family": "Sabater-Lleal", "given": "Maria", "initials": "M"}, {"family": "van der Laan", "given": "Sander W", "initials": "SW"}, {"family": "Miller", "given": "Clint L", "initials": "CL"}, {"family": "Wirka", "given": "Robert C", "initials": "RC"}, {"family": "Kronqvist", "given": "Malin", "initials": "M"}, {"family": "Gonzalez Diez", "given": "Maria", "initials": "M"}, {"family": "Vesterlund", "given": "Mattias", "initials": "M"}, {"family": "Gillgren", "given": "Peter", "initials": "P"}, {"family": "Odeberg", "given": "Jacob", "initials": "J"}, {"family": "Lindeman", "given": "Jan H", "initials": "JH"}, {"family": "Veglia", "given": "Fabrizio", "initials": "F"}, {"family": "Humphries", "given": "Steve E", "initials": "SE"}, {"family": "de Faire", "given": "Ulf", "initials": "U"}, {"family": "Baldassarre", "given": "Damiano", "initials": "D"}, {"family": "Tremoli", "given": "Elena", "initials": "E"}, {"family": "IMPROVE study group", "given": "", "initials": ""}, {"family": "Lehti\u00f6", "given": "Janne", "initials": "J", "orcid": "0000-0002-8100-9562", "researcher": {"href": "https://publications.scilifelab.se/researcher/8406a97bac744a59b1bc951978994581.json"}}, {"family": "Hansson", "given": "G\u00f6ran K", "initials": "GK"}, {"family": "Paulsson-Berne", "given": "Gabrielle", "initials": "G"}, {"family": "Pasterkamp", "given": "Gerard", "initials": "G"}, {"family": "Quertermous", "given": "Thomas", "initials": "T"}, {"family": "Hamsten", "given": "Anders", "initials": "A"}, {"family": "Eriksson", "given": "Per", "initials": "P"}, {"family": "Hedin", "given": "Ulf", "initials": "U"}, {"family": "Matic", "given": "Ljubica", "initials": "L"}], "type": "journal article", "published": "2020-02-28", "journal": {"volume": "126", "issn": "1524-4571", "issue": "5", "title": "Circ. Res.", "pages": "571-585", "issn-l": "0009-7330"}, "abstract": "PCSKs (Proprotein convertase subtilisins/kexins) are a protease family with unknown functions in vasculature. Previously, we demonstrated PCSK6 upregulation in human atherosclerotic plaques associated with smooth muscle cells (SMCs), inflammation, extracellular matrix remodeling, and mitogens.\n\nHere, we applied a systems biology approach to gain deeper insights into the PCSK6 role in normal and diseased vessel wall.\n\nGenetic analyses revealed association of intronic PCSK6 variant rs1531817 with maximum internal carotid intima-media thickness progression in high-cardiovascular risk subjects. This variant was linked with PCSK6 mRNA expression in healthy aortas and plaques but also with overall plaque SMA+ cell content and pericyte fraction. Increased PCSK6 expression was found in several independent human cohorts comparing atherosclerotic lesions versus healthy arteries, using transcriptomic and proteomic datasets. By immunohistochemistry, PCSK6 was localized to fibrous cap SMA+ cells and neovessels in plaques. In human, rat, and mouse intimal hyperplasia, PCSK6 was expressed by proliferating SMA+ cells and upregulated after 5 days in rat carotid balloon injury model, with positive correlation to PDGFB (platelet-derived growth factor subunit B) and MMP (matrix metalloprotease) 2/MMP14. Here, PCSK6 was shown to colocalize and cointeract with MMP2/MMP14 by in situ proximity ligation assay. Microarrays of carotid arteries from Pcsk6-/- versus control mice revealed suppression of contractile SMC markers, extracellular matrix remodeling enzymes, and cytokines/receptors. Pcsk6-/- mice showed reduced intimal hyperplasia response upon carotid ligation in vivo, accompanied by decreased MMP14 activation and impaired SMC outgrowth from aortic rings ex vivo. PCSK6 silencing in human SMCs in vitro leads to downregulation of contractile markers and increase in MMP2 expression. Conversely, PCSK6 overexpression increased PDGFBB (platelet-derived growth factor BB)-induced cell proliferation and particularly migration.\n\nPCSK6 is a novel protease that induces SMC migration in response to PDGFB, mechanistically via modulation of contractile markers and MMP14 activation. This study establishes PCSK6 as a key regulator of SMC function in vascular remodeling. Visual Overview: An online visual overview is available for this article.", "doi": "10.1161/CIRCRESAHA.119.316063", "pmid": "31893970", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Global Proteomics and Proteogenomics": "Collaborative"}, "xrefs": [], "notes": [], "created": "2020-01-14T10:04:55.756Z", "modified": "2021-11-10T12:53:44.074Z"}, {"entity": "publication", "iuid": "f9c089828e5f4a3dac5e5eb778b7f3c2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f9c089828e5f4a3dac5e5eb778b7f3c2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f9c089828e5f4a3dac5e5eb778b7f3c2"}}, "title": "The Relationship Between Polygenic Risk Scores and Cognition in Schizophrenia.", "authors": [{"family": "Richards", "given": "Alexander L", "initials": "AL", "orcid": "0000-0003-3218-7247", "researcher": {"href": "https://publications.scilifelab.se/researcher/d6a0551c61bc4754a742df8b26ef40db.json"}}, {"family": "Pardi\u00f1as", "given": "Antonio F", "initials": "AF"}, {"family": "Frizzati", "given": "Aura", "initials": "A"}, {"family": "Tansey", "given": "Katherine E", "initials": "KE"}, {"family": "Lynham", "given": "Amy J", "initials": "AJ", "orcid": "0000-0002-3189-6888", "researcher": {"href": "https://publications.scilifelab.se/researcher/2c789b2e9aa24bd6ad212dc0a1ddbb96.json"}}, {"family": "Holmans", "given": "Peter", "initials": "P"}, {"family": "Legge", "given": "Sophie E", "initials": "SE"}, {"family": "Savage", "given": "Jeanne E", "initials": "JE"}, {"family": "Agartz", "given": "Ingrid", "initials": "I"}, {"family": "Andreassen", "given": "Ole A", "initials": "OA"}, {"family": "Blokland", "given": "Gabriella A M", "initials": "GAM"}, {"family": "Corvin", "given": "Aiden", "initials": "A"}, {"family": "Cosgrove", "given": "Donna", "initials": "D"}, {"family": "Degenhardt", "given": "Franziska", "initials": "F"}, {"family": "Djurovic", "given": "Srdjan", "initials": "S"}, {"family": "Espeseth", "given": "Thomas", "initials": "T"}, {"family": "Ferraro", "given": "Laura", "initials": "L"}, {"family": "Gayer-Anderson", "given": "Charlotte", "initials": "C"}, {"family": "Giegling", "given": "Ina", "initials": "I"}, {"family": "van Haren", "given": "Neeltje E", "initials": "NE"}, {"family": "Hartmann", "given": "Annette M", "initials": "AM"}, {"family": "Hubert", "given": "John J", "initials": "JJ"}, {"family": "J\u00f6nsson", "given": "Erik G", "initials": "EG"}, {"family": "Konte", "given": "Bettina", "initials": "B"}, {"family": "Lennertz", "given": "Leonhard", "initials": "L"}, {"family": "Olde Loohuis", "given": "Loes M", "initials": "LM"}, {"family": "Melle", "given": "Ingrid", "initials": "I"}, {"family": "Morgan", "given": "Craig", "initials": "C"}, {"family": "Morris", "given": "Derek W", "initials": "DW"}, {"family": "Murray", "given": "Robin M", "initials": "RM"}, {"family": "Nyman", "given": "H\u00e5kan", "initials": "H"}, {"family": "Ophoff", "given": "Roel A", "initials": "RA"}, {"family": "GROUP Investigators", "given": "", "initials": ""}, {"family": "van Os", "given": "Jim", "initials": "J"}, {"family": "EUGEI WP2 Group", "given": "", "initials": ""}, {"family": "Schizophrenia Working Group of the Psychiatric Genomics Consortium", "given": "", "initials": ""}, {"family": "Petryshen", "given": "Tracey L", "initials": "TL"}, {"family": "Quattrone", "given": "Diego", "initials": "D"}, {"family": "Rietschel", "given": "Marcella", "initials": "M"}, {"family": "Rujescu", "given": "Dan", "initials": "D"}, {"family": "Rutten", "given": "Bart P F", "initials": "BPF"}, {"family": "Streit", "given": "Fabian", "initials": "F"}, {"family": "Strohmaier", "given": "Jana", "initials": "J"}, {"family": "Sullivan", "given": "Patrick F", "initials": "PF"}, {"family": "Sundet", "given": "Kjetil", "initials": "K"}, {"family": "Wagner", "given": "Michael", "initials": "M"}, {"family": "Escott-Price", "given": "Valentina", "initials": "V"}, {"family": "Owen", "given": "Michael J", "initials": "MJ"}, {"family": "Donohoe", "given": "Gary", "initials": "G"}, {"family": "O'Donovan", "given": "Michael C", "initials": "MC"}, {"family": "Walters", "given": "James T R", "initials": "JTR"}], "type": "journal article", "published": "2020-02-26", "journal": {"title": "Schizophr Bull", "issn": "1745-1701", "volume": "46", "issue": "2", "pages": "336-344", "issn-l": "0586-7614"}, "abstract": "Cognitive impairment is a clinically important feature of schizophrenia. Polygenic risk score (PRS) methods have demonstrated genetic overlap between schizophrenia, bipolar disorder (BD), major depressive disorder (MDD), educational attainment (EA), and IQ, but very few studies have examined associations between these PRS and cognitive phenotypes within schizophrenia cases.\n\nWe combined genetic and cognitive data in 3034 schizophrenia cases from 11 samples using the general intelligence factor g as the primary measure of cognition. We used linear regression to examine the association between cognition and PRS for EA, IQ, schizophrenia, BD, and MDD. The results were then meta-analyzed across all samples. A genome-wide association studies (GWAS) of cognition was conducted in schizophrenia cases.\n\nPRS for both population IQ (P = 4.39 \u00d7 10-28) and EA (P = 1.27 \u00d7 10-26) were positively correlated with cognition in those with schizophrenia. In contrast, there was no association between cognition in schizophrenia cases and PRS for schizophrenia (P = .39), BD (P = .51), or MDD (P = .49). No individual variant approached genome-wide significance in the GWAS.\n\nCognition in schizophrenia cases is more strongly associated with PRS that index cognitive traits in the general population than PRS for neuropsychiatric disorders. This suggests the mechanisms of cognitive variation within schizophrenia are at least partly independent from those that predispose to schizophrenia diagnosis itself. Our findings indicate that this cognitive variation arises at least in part due to genetic factors shared with cognitive performance in populations and is not solely due to illness or treatment-related factors, although our findings are consistent with important contributions from these factors.", "doi": "10.1093/schbul/sbz061", "pmid": "31206164", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "5519548"}, {"db": "pmc", "key": "PMC7442352"}], "notes": [], "created": "2020-02-27T09:21:00.659Z", "modified": "2021-11-10T12:53:46.726Z"}, {"entity": "publication", "iuid": "22a173ef02f045c28253c98404dcdc0a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/22a173ef02f045c28253c98404dcdc0a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/22a173ef02f045c28253c98404dcdc0a"}}, "title": "Patterns of African and Asian admixture in the Afrikaner population of South Africa.", "authors": [{"family": "Hollfelder", "given": "N", "initials": "N"}, {"family": "Erasmus", "given": "J C", "initials": "JC"}, {"family": "Hammaren", "given": "R", "initials": "R"}, {"family": "Vicente", "given": "M", "initials": "M"}, {"family": "Jakobsson", "given": "M", "initials": "M", "orcid": "0000-0001-7840-7853", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a4abe0fcb20492d9ec849c9fbf58a71.json"}}, {"family": "Greeff", "given": "J M", "initials": "JM"}, {"family": "Schlebusch", "given": "C M", "initials": "CM", "orcid": "0000-0002-8160-9621", "researcher": {"href": "https://publications.scilifelab.se/researcher/682f10853c1145649b8c76680605dd9b.json"}}], "type": "journal article", "published": "2020-02-24", "journal": {"title": "BMC Biol.", "issn": "1741-7007", "volume": "18", "issue": "1", "pages": "16", "issn-l": "1741-7007"}, "abstract": "The Afrikaner population of South Africa is the descendants of European colonists who started to colonize the Cape of Good Hope in the 1600s. In the early days of the colony, mixed unions between European males and non-European females gave rise to admixed children who later became incorporated into either the Afrikaner or the Coloured populations of South Africa. Differences in ancestry, social class, culture, sex ratio and geographic structure led to distinct and characteristic admixture patterns in the Afrikaner and Coloured populations. The Afrikaner population has a predominant European composition, whereas the Coloured population has more diverse ancestries. Genealogical records previously estimated the contribution of non-Europeans into the Afrikaners to be between 5.5 and 7.2%.\n\nTo investigate the genetic ancestry of the Afrikaner population today (11-13 generations after initial colonization), we genotyped approximately five million genome-wide markers in 77 Afrikaner individuals and compared their genotypes to populations across the world to determine parental source populations and admixture proportions. We found that the majority of Afrikaner ancestry (average 95.3%) came from European populations (specifically northwestern European populations), but that almost all Afrikaners had admixture from non-Europeans. The non-European admixture originated mostly from people who were brought to South Africa as slaves and, to a lesser extent, from local Khoe-San groups. Furthermore, despite a potentially small founding population, there is no sign of a recent bottleneck in the Afrikaner compared to other European populations. Admixture amongst diverse groups from Europe and elsewhere during early colonial times might have counterbalanced the effects of a small founding population.\n\nWhile Afrikaners have an ancestry predominantly from northwestern Europe, non-European admixture signals are ubiquitous in the Afrikaner population. Interesting patterns and similarities could be observed between genealogical predictions and our genetic inferences. Afrikaners today have comparable inbreeding levels to current-day European populations.", "doi": "10.1186/s12915-020-0746-1", "pmid": "32089133", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1186/s12915-020-0746-1"}, {"db": "pmc", "key": "PMC7038537"}], "notes": [], "created": "2020-02-28T12:44:13.878Z", "modified": "2024-01-16T13:48:42.894Z"}, {"entity": "publication", "iuid": "334f24d1e0724ca99b3736c82f798484", "links": {"self": {"href": "https://publications.scilifelab.se/publication/334f24d1e0724ca99b3736c82f798484.json"}, "display": {"href": "https://publications.scilifelab.se/publication/334f24d1e0724ca99b3736c82f798484"}}, "title": "rs953413 Regulates Polyunsaturated Fatty Acid Metabolism by Modulating ELOVL2 Expression.", "authors": [{"family": "Pan", "given": "Gang", "initials": "G"}, {"family": "Cavalli", "given": "Marco", "initials": "M"}, {"family": "Carlsson", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Skrtic", "given": "Stanko", "initials": "S"}, {"family": "Kumar", "given": "Chanchal", "initials": "C"}, {"family": "Wadelius", "given": "Claes", "initials": "C", "orcid": "0000-0002-2033-7829", "researcher": {"href": "https://publications.scilifelab.se/researcher/2ec5ca1122024da4893b61e329a5ece5.json"}}], "type": "journal article", "published": "2020-02-21", "journal": {"title": "iScience", "issn": "2589-0042", "volume": "23", "issue": "2", "pages": "100808", "issn-l": "2589-0042"}, "abstract": "Long-chain polyunsaturated fatty acids (LC-PUFAs) influence human health in several areas, including cardiovascular disease, diabetes, fatty liver disease, and cancer. ELOVL2 encodes one of the key enzymes in the in vivo synthesis of LC-PUFAs from their precursors. Variants near ELOVL2 have repeatedly been associated with levels of LC-PUFA-derived metabolites in genome-wide association studies (GWAS), but the mechanisms behind these observations remain poorly defined. In this study, we found that rs953413, located in the first intron of ELOVL2, lies within a functional FOXA and HNF4\u03b1 cooperative binding site. The G allele of rs953413 increases binding of FOXA1/FOXA2 and HNF4\u03b1 to an evolutionarily conserved enhancer element, conferring allele-specific upregulation of the rs953413-associated gene ELOVL2. The expression of ELOVL2 was significantly downregulated by both FOXA1 and HNF4\u03b1 knockdown and CRISPR/Cas9-mediated direct mutation to the enhancer element. Our results suggest that rs953413 regulates LC-PUFAs metabolism by altering ELOVL2 expression through FOXA1/FOXA2 and HNF4\u03b1 cooperation.", "doi": "10.1016/j.isci.2019.100808", "pmid": "31928966", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "S2589-0042(19)30554-1"}, {"db": "pmc", "key": "PMC7033636"}], "notes": [], "created": "2020-11-16T09:09:06.978Z", "modified": "2024-01-16T13:48:42.901Z"}, {"entity": "publication", "iuid": "5d45e246a4a448159af62be64061ffaa", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5d45e246a4a448159af62be64061ffaa.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5d45e246a4a448159af62be64061ffaa"}}, "title": "Dominance of Mating Type A1 and Indication of Epigenetic Effects During Early Stages of Mating in Phytophthora infestans.", "authors": [{"family": "Tzelepis", "given": "Georgios", "initials": "G"}, {"family": "Hod\u00e9n", "given": "Kristian Persson", "initials": "KP"}, {"family": "Fogelqvist", "given": "Johan", "initials": "J"}, {"family": "\u00c5sman", "given": "Anna K M", "initials": "AKM"}, {"family": "Vetukuri", "given": "Ramesh R", "initials": "RR"}, {"family": "Dixelius", "given": "Christina", "initials": "C"}], "type": "journal article", "published": "2020-02-21", "journal": {"title": "Front Microbiol", "issn": "1664-302X", "volume": "11", "issue": null, "pages": "252", "issn-l": "1664-302X"}, "abstract": "The potato late blight pathogen Phytophthora infestans has both an asexual and a sexual mode of reproduction. In Scandinavia, the pathogen is reproducing sexually on a regular basis, whereas clonal lineages dominate in other geographical regions. This study aimed at elucidating events or key genes underlying this difference in sexual behavior. First, the transcriptomes of eight strains, known as either clonal or sexual, were compared during early stages of mating. Principal component analysis (PCA) divided the samples in two clusters A and B and a clear grouping of the mating samples together with the A1 mating type parents was observed. Induction of genes encoding DNA adenine N6-methylation (6mA) methyl-transferases clearly showed a bias toward the cluster A. In contrast, the Avrblb2 effector gene family was highly induced in most of the mating samples and was associated with cluster B in the PCA, similarly to genes coding for acetyl-transferases, which play an important role in RXLR modification prior to secretion. Avrblb2 knock-down strains displayed a reduction in virulence and oospore formation, suggesting a role during the mating process. In conclusion, a number of gene candidates important for the reproductive processes were revealed. The results suggest a possible epigenetic influence and involvement of specific RXLR effectors in mating-related processes.", "doi": "10.3389/fmicb.2020.00252", "pmid": "32153537", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC7046690"}], "notes": [], "created": "2020-07-08T13:04:13.663Z", "modified": "2021-11-10T12:53:51.325Z"}, {"entity": "publication", "iuid": "c1de8d695c1944ae8db24b9a04b4ab8a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c1de8d695c1944ae8db24b9a04b4ab8a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c1de8d695c1944ae8db24b9a04b4ab8a"}}, "title": "Refined detection and phasing of structural aberrations in pediatric acute lymphoblastic leukemia by linked-read whole-genome sequencing.", "authors": [{"family": "Nordlund", "given": "Jessica", "initials": "J", "orcid": "0000-0001-8699-9959", "researcher": {"href": "https://publications.scilifelab.se/researcher/ddf48c9262134821bcc6ce1180049753.json"}}, {"family": "Marincevic-Zuniga", "given": "Yanara", "initials": "Y"}, {"family": "Cavelier", "given": "Lucia", "initials": "L", "orcid": "0009-0003-8195-370X", "researcher": {"href": "https://publications.scilifelab.se/researcher/f01226edb140436da0c9d166c1f5fe51.json"}}, {"family": "Raine", "given": "Amanda", "initials": "A"}, {"family": "Martin", "given": "Tom", "initials": "T"}, {"family": "Lundmark", "given": "Anders", "initials": "A"}, {"family": "Abrahamsson", "given": "Jonas", "initials": "J"}, {"family": "Nor\u00e9n-Nystr\u00f6m", "given": "Ulrika", "initials": "U"}, {"family": "L\u00f6nnerholm", "given": "Gudmar", "initials": "G"}, {"family": "Syv\u00e4nen", "given": "Ann-Christine", "initials": "AC", "orcid": "0000-0002-9681-9146", "researcher": {"href": "https://publications.scilifelab.se/researcher/f7012e35025543379380cb90efd71243.json"}}], "type": "journal article", "published": "2020-02-13", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "10", "issue": "1", "pages": "2512", "issn-l": "2045-2322"}, "abstract": "Structural chromosomal rearrangements that can lead to in-frame gene-fusions are a leading source of information for diagnosis, risk stratification, and prognosis in pediatric acute lymphoblastic leukemia (ALL). Traditional methods such as karyotyping and FISH struggle to accurately identify and phase such large-scale chromosomal aberrations in ALL genomes. We therefore evaluated linked-read WGS for detecting chromosomal rearrangements in primary samples of from 12 patients diagnosed with ALL. We assessed the effect of input DNA quality on phased haplotype block size and the detectability of copy number aberrations and structural variants in the ALL genomes. We found that biobanked DNA isolated by standard column-based extraction methods was sufficient to detect chromosomal rearrangements even at low 10x sequencing coverage. Linked-read WGS enabled precise, allele-specific, digital karyotyping at a base-pair resolution for a wide range of structural variants including complex rearrangements and aneuploidy assessment. With use of haplotype information from the linked-reads, we also identified previously unknown structural variants, such as a compound heterozygous deletion of ERG in a patient with the DUX4-IGH fusion gene. We conclude that linked-read WGS allows detection of important pathogenic variants in ALL genomes at a resolution beyond that of traditional karyotyping and FISH.", "doi": "10.1038/s41598-020-59214-w", "pmid": "32054878", "labels": {"National Genomics Infrastructure": "Collaborative", "NGI Uppsala (SNP&SEQ Technology Platform)": "Collaborative", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-020-59214-w"}, {"db": "pmc", "key": "PMC7018692"}], "notes": [], "created": "2020-11-05T12:22:11.615Z", "modified": "2024-01-16T13:48:42.944Z"}, {"entity": "publication", "iuid": "e5f1bff2a04840b1a4bde038251fa843", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e5f1bff2a04840b1a4bde038251fa843.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e5f1bff2a04840b1a4bde038251fa843"}}, "title": "Using null models to compare bacterial and microeukaryotic metacommunity assembly under shifting environmental conditions.", "authors": [{"family": "Vass", "given": "M\u00e1t\u00e9", "initials": "M", "orcid": "0000-0003-0718-7659", "researcher": {"href": "https://publications.scilifelab.se/researcher/6fed30af96e540269edcb565cb34bc39.json"}}, {"family": "Sz\u00e9kely", "given": "Anna J", "initials": "AJ", "orcid": "0000-0001-8063-7156", "researcher": {"href": "https://publications.scilifelab.se/researcher/c9b2d69cfd6a4f41a978b38ddf66c8d5.json"}}, {"family": "Lindstr\u00f6m", "given": "Eva S", "initials": "ES", "orcid": "0000-0001-8920-3071", "researcher": {"href": "https://publications.scilifelab.se/researcher/9290d334ce5a4488b8afd2af511e02ad.json"}}, {"family": "Langenheder", "given": "Silke", "initials": "S", "orcid": "0000-0002-5245-9935", "researcher": {"href": "https://publications.scilifelab.se/researcher/efa9e8f2174a4c7cb903b0f9b895a183.json"}}], "type": "journal article", "published": "2020-02-12", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "10", "issue": "1", "pages": "2455", "issn-l": "2045-2322"}, "abstract": "Temporal variations in microbial metacommunity structure and assembly processes in response to shifts in environmental conditions are poorly understood. Hence, we conducted a temporal field study by sampling rock pools in four-day intervals during a 5-week period that included strong changes in environmental conditions due to intensive rain. We characterized bacterial and microeukaryote communities by 16S and 18S rRNA gene sequencing, respectively. Using a suite of null model approaches (elements of metacommunity structure, Raup-Crick beta-diversity and quantitative process estimates) to assess dynamics in community assembly, we found that strong changes in environmental conditions induced small but significant temporal changes in assembly processes and triggered different responses in bacterial and microeukaryotic metacommunities, promoting distinct selection processes. Incidence-based approaches showed that the assemblies of both communities were mainly governed by stochastic processes. In contrast, abundance-based methods indicated the dominance of historical contingency and unmeasured factors in the case of bacteria and microeukaryotes, respectively. We distinguished these processes from dispersal-related processes using additional tests. Regardless of the applied null model, our study highlights that community assembly processes are not static, and the relative importance of different assembly processes can vary under different conditions and between different microbial groups.", "doi": "10.1038/s41598-020-59182-1", "pmid": "32051469", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-020-59182-1"}, {"db": "pmc", "key": "PMC7016149"}], "notes": [], "created": "2020-12-08T23:47:42.006Z", "modified": "2024-01-16T13:48:42.952Z"}, {"entity": "publication", "iuid": "7d10557c49554f21b70aaf8ab173723b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7d10557c49554f21b70aaf8ab173723b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7d10557c49554f21b70aaf8ab173723b"}}, "title": "Longitudinal trajectories, correlations and mortality associations of nine biological ages across 20-years follow-up.", "authors": [{"family": "Li", "given": "Xia", "initials": "X", "orcid": "0000-0003-1922-7152", "researcher": {"href": "https://publications.scilifelab.se/researcher/862fd8b41938458f9105c5bb73c35294.json"}}, {"family": "Ploner", "given": "Alexander", "initials": "A", "orcid": "0000-0002-5042-8326", "researcher": {"href": "https://publications.scilifelab.se/researcher/6f1b8cb5cffa4b69b057e2f94ac08d3b.json"}}, {"family": "Wang", "given": "Yunzhang", "initials": "Y"}, {"family": "Magnusson", "given": "Patrik Ke", "initials": "PK"}, {"family": "Reynolds", "given": "Chandra", "initials": "C"}, {"family": "Finkel", "given": "Deborah", "initials": "D"}, {"family": "Pedersen", "given": "Nancy L", "initials": "NL"}, {"family": "Jylh\u00e4v\u00e4", "given": "Juulia", "initials": "J"}, {"family": "H\u00e4gg", "given": "Sara", "initials": "S", "orcid": "0000-0002-2452-1500", "researcher": {"href": "https://publications.scilifelab.se/researcher/e1d010dfe5d84a33b6a6c7ec815ca3dc.json"}}], "type": "journal article", "published": "2020-02-11", "journal": {"title": "Elife", "issn": "2050-084X", "volume": "9", "issue": null, "issn-l": "2050-084X"}, "abstract": "Biological age measurements (BAs) assess aging-related physiological change and predict health risks among individuals of the same chronological age (CA). Multiple BAs have been proposed and are well studied individually but not jointly. We included 845 individuals and 3973 repeated measurements from a Swedish population-based cohort and examined longitudinal trajectories, correlations, and mortality associations of nine BAs across 20 years follow-up. We found the longitudinal growth of functional BAs accelerated around age 70; average levels of BA curves differed by sex across the age span (50-90 years). All BAs were correlated to varying degrees; correlations were mostly explained by CA. Individually, all BAs except for telomere length were associated with mortality risk independently of CA. The largest effects were seen for methylation age estimators (GrimAge) and the frailty index (FI). In joint models, two methylation age estimators (Horvath and GrimAge) and FI remained predictive, suggesting they are complementary in predicting mortality.", "doi": "10.7554/eLife.51507", "pmid": "32041686", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "51507"}, {"db": "pmc", "key": "PMC7012595"}], "notes": [], "created": "2020-02-27T09:21:02.553Z", "modified": "2024-01-16T13:48:42.960Z"}, {"entity": "publication", "iuid": "bb7a04bc18cd4f11adcb9f73addb3cc5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/bb7a04bc18cd4f11adcb9f73addb3cc5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/bb7a04bc18cd4f11adcb9f73addb3cc5"}}, "title": "Clinicopathological features and prognostic value of SOX11 in childhood acute lymphoblastic leukemia.", "authors": [{"family": "Gr\u00f6nroos", "given": "Toni", "initials": "T"}, {"family": "M\u00e4kinen", "given": "Artturi", "initials": "A"}, {"family": "Laukkanen", "given": "Saara", "initials": "S"}, {"family": "Mehtonen", "given": "Juha", "initials": "J", "orcid": "0000-0003-0554-4667", "researcher": {"href": "https://publications.scilifelab.se/researcher/d7a49312223a458dbb35c809f20372af.json"}}, {"family": "Nikkil\u00e4", "given": "Atte", "initials": "A"}, {"family": "Oksa", "given": "Laura", "initials": "L"}, {"family": "Rounioja", "given": "Samuli", "initials": "S"}, {"family": "Marincevic-Zuniga", "given": "Yanara", "initials": "Y"}, {"family": "Nordlund", "given": "Jessica", "initials": "J", "orcid": "0000-0001-8699-9959", "researcher": {"href": "https://publications.scilifelab.se/researcher/ddf48c9262134821bcc6ce1180049753.json"}}, {"family": "Pohjolainen", "given": "Virva", "initials": "V"}, {"family": "Paavonen", "given": "Timo", "initials": "T"}, {"family": "Hein\u00e4niemi", "given": "Merja", "initials": "M"}, {"family": "Lohi", "given": "Olli", "initials": "O"}], "type": "journal article", "published": "2020-02-06", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "10", "issue": "1", "pages": "2043", "issn-l": "2045-2322"}, "abstract": "Acute lymphoblastic leukemia is marked by aberrant transcriptional features that alter cell differentiation, self-renewal, and proliferative features. We sought to identify the transcription factors exhibiting altered and subtype-specific expression patterns in B-ALL and report here that SOX11, a developmental and neuronal transcription factor, is aberrantly expressed in the ETV6-RUNX1 and TCF3-PBX1 subtypes of acute B-cell leukemias. We show that a high expression of SOX11 leads to alterations of gene expression that are typically associated with cell adhesion, migration, and differentiation. A high expression is associated with DNA hypomethylation at the SOX11 locus and a favorable outcome. The results indicate that SOX11 expression marks a group of patients with good outcomes and thereby prompts further study of its use as a biomarker.", "doi": "10.1038/s41598-020-58970-z", "pmid": "32029838", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-020-58970-z"}, {"db": "pmc", "key": "PMC7005266"}], "notes": [], "created": "2020-02-20T11:30:30.655Z", "modified": "2021-11-10T12:54:08.673Z"}, {"entity": "publication", "iuid": "ae00dd95619c4b038d34abdb141a1384", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ae00dd95619c4b038d34abdb141a1384.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ae00dd95619c4b038d34abdb141a1384"}}, "title": "Convergent Evolution of Hydrogenosomes from Mitochondria by Gene Transfer and Loss.", "authors": [{"family": "Lewis", "given": "William H", "initials": "WH"}, {"family": "Lind", "given": "Anders E", "initials": "AE"}, {"family": "Sendra", "given": "Kacper M", "initials": "KM"}, {"family": "Onsbring", "given": "Henning", "initials": "H"}, {"family": "Williams", "given": "Tom A", "initials": "TA"}, {"family": "Esteban", "given": "Genoveva F", "initials": "GF"}, {"family": "Hirt", "given": "Robert P", "initials": "RP"}, {"family": "Ettema", "given": "Thijs J G", "initials": "TJG"}, {"family": "Embley", "given": "T Martin", "initials": "TM"}], "type": "journal article", "published": "2020-02-01", "journal": {"title": "Mol. Biol. Evol.", "issn": "1537-1719", "issn-l": "0737-4038", "volume": "37", "issue": "2", "pages": "524-539"}, "abstract": "Hydrogenosomes are H2-producing mitochondrial homologs found in some anaerobic microbial eukaryotes that provide a rare intracellular niche for H2-utilizing endosymbiotic archaea. Among ciliates, anaerobic and aerobic lineages are interspersed, demonstrating that the switch to an anaerobic lifestyle with hydrogenosomes has occurred repeatedly and independently. To investigate the molecular details of this transition, we generated genomic and transcriptomic data sets from anaerobic ciliates representing three distinct lineages. Our data demonstrate that hydrogenosomes have evolved from ancestral mitochondria in each case and reveal different degrees of independent mitochondrial genome and proteome reductive evolution, including the first example of complete mitochondrial genome loss in ciliates. Intriguingly, the FeFe-hydrogenase used for generating H2 has a unique domain structure among eukaryotes and appears to have been present, potentially through a single lateral gene transfer from an unknown donor, in the common aerobic ancestor of all three lineages. The early acquisition and retention of FeFe-hydrogenase helps to explain the facility whereby mitochondrial function can be so radically modified within this diverse and ecologically important group of microbial eukaryotes.", "doi": "10.1093/molbev/msz239", "pmid": "31647561", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "5606724"}, {"db": "pmc", "key": "PMC6993867"}], "notes": [], "created": "2020-12-08T23:16:45.895Z", "modified": "2021-11-10T12:54:16.742Z"}, {"entity": "publication", "iuid": "bcb394512c2e411aa9ce831cde4aa7d9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/bcb394512c2e411aa9ce831cde4aa7d9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/bcb394512c2e411aa9ce831cde4aa7d9"}}, "title": "Dynamic architecture and regulatory implications of the miRNA network underlying the response to stress in melon.", "authors": [{"family": "Sanz-Carbonell", "given": "Alejandro", "initials": "A", "orcid": "0000-0002-1969-5557", "researcher": {"href": "https://publications.scilifelab.se/researcher/2132a132afcd44ba909dbbb86df6b23a.json"}}, {"family": "Marques", "given": "Maria Carmen", "initials": "MC", "orcid": "0000-0001-8392-453X", "researcher": {"href": "https://publications.scilifelab.se/researcher/e5022479d8564ebb8f59739d5073deb7.json"}}, {"family": "Martinez", "given": "German", "initials": "G", "orcid": "0000-0002-5215-0866", "researcher": {"href": "https://publications.scilifelab.se/researcher/591f629ea8ed44c2bd9cd417dcebd8bc.json"}}, {"family": "Gomez", "given": "Gustavo", "initials": "G", "orcid": "0000-0003-3715-7792", "researcher": {"href": "https://publications.scilifelab.se/researcher/157cf3e864e5415886f9cb9d7f9544c1.json"}}], "type": "journal article", "published": "2020-02-00", "journal": {"title": "RNA Biol", "issn": "1555-8584", "volume": "17", "issue": "2", "pages": "292-308", "issn-l": "1547-6286"}, "abstract": "miRNAs are small RNAs that regulate mRNAs at both transcriptional and posttranscriptional level. In plants, miRNAs are involved in the regulation of different processes including development and stress-response. Elucidating how stress-responsive miRNAs are regulated is key to understand the global response to stress but also to develop efficient biotechnological tools that could help to cope with stress. Here, we describe a computational approach based on sRNA sequencing, transcript quantification and degradome data to analyse the accumulation, function and structural organization of melon miRNAs reactivated under seven biotic and abiotic stress conditions at two and four days post-treatment. Our pipeline allowed us to identify fourteen stress-responsive miRNAs (including evolutionary conserved such as miR156, miR166, miR172, miR319, miR398, miR399, miR894 and miR408) at both analysed times. According to our analysis miRNAs were categorized in three groups showing a broad-, intermediate- or narrow- response range. miRNAs reactive to a broad range of environmental cues appear as central components in the stress-response network. The strictly coordinated response of miR398 and miR408 (broad response-range) to the seven stress treatments during the period analysed here reinforces this notion. Although both, the amplitude and diversity of the miRNA-related response to stress changes during the exposition time, the architecture of the miRNA-network is conserved. This organization of miRNA response to stress is also conserved in rice and soybean supporting the conservation of miRNA-network organization in other crops. Overall, our work sheds light into how miRNA networks in plants organize and function during stress.", "doi": "10.1080/15476286.2019.1697487", "pmid": "31766933", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC6973316"}], "notes": [], "created": "2020-12-08T23:34:40.772Z", "modified": "2021-11-10T12:54:27.181Z"}, {"entity": "publication", "iuid": "2a0ff5d5278f4f43a312d4a527ebc89f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2a0ff5d5278f4f43a312d4a527ebc89f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2a0ff5d5278f4f43a312d4a527ebc89f"}}, "title": "Analysis of the genetic variants associated with circulating levels of sgp130. Results from the IMPROVE study.", "authors": [{"family": "Bonomi", "given": "Alice", "initials": "A"}, {"family": "Veglia", "given": "Fabrizio", "initials": "F"}, {"family": "Baldassarre", "given": "Damiano", "initials": "D"}, {"family": "Strawbridge", "given": "Rona J", "initials": "RJ", "orcid": "0000-0001-8506-3585", "researcher": {"href": "https://publications.scilifelab.se/researcher/8ac5060a3b37466dae002d4ad8f4d0ac.json"}}, {"family": "Golabkesh", "given": "Zahra", "initials": "Z"}, {"family": "Sennblad", "given": "Bengt", "initials": "B", "orcid": "0000-0002-4360-8003", "researcher": {"href": "https://publications.scilifelab.se/researcher/1c991150beec46ba8886379193d6037b.json"}}, {"family": "Leander", "given": "Karin", "initials": "K"}, {"family": "Smit", "given": "Andries J", "initials": "AJ"}, {"family": "Giral", "given": "Philippe", "initials": "P"}, {"family": "Humphries", "given": "Steve E", "initials": "SE"}, {"family": "Tremoli", "given": "Elena", "initials": "E"}, {"family": "Hamsten", "given": "Anders", "initials": "A"}, {"family": "de Faire", "given": "Ulf", "initials": "U"}, {"family": "Gigante", "given": "Bruna", "initials": "B", "orcid": "0000-0003-4508-7990", "researcher": {"href": "https://publications.scilifelab.se/researcher/3ac1bdc52e3241ea9eb5645f603229a3.json"}}, {"family": " on behalf of the IMPROVE study group", "given": "", "initials": ""}], "type": "journal article", "published": "2020-02-00", "journal": {"volume": "21", "issn": "1476-5470", "issue": "2", "title": "Genes Immun.", "pages": "100-108", "issn-l": "1466-4879"}, "abstract": "The genes regulating circulating levels of soluble gp130 (sgp130), the antagonist of the inflammatory response in atherosclerosis driven by interleukin 6, are largely unknown. Aims of the present study were to identify genetic loci associated with circulating sgp130 and to explore the potential association between variants associated with sgp130 and markers of subclinical atherosclerosis. The study is based on IMPROVE (n = 3703), a cardiovascular multicentre study designed to investigate the determinants of carotid intima media thickness, a measure of subclinical atherosclerosis. Genomic DNA was genotyped by the CardioMetaboChip and ImmunoChip. About 360,842 SNPs were tested for association with log-transformed sgp130, using linear regression adjusted for age, gender, and population stratification using PLINK v1.07. A p value of 1 \u00d7 10-5 was chosen as threshold for significance value. In an exploratory analysis, SNPs associated with sgp130 were tested for association with c-IMT measures. We identified two SNPs significantly associated with sgp130 levels and 24 showing suggestive association with sgp130 levels. One SNP (rs17688225) on chromosome 14 was positively associated with sgp130 serum levels (\u03b2 = 0.03 SE = 0.007, p = 4.77 \u00d7 10-5) and inversely associated with c-IMT (c-IMTmean-max \u03b2 = -0.001 SE = 0.005, p = 0.0342). Our data indicate that multiple loci regulate sgp130 levels and suggest a possible common pathway between sgp130 and c-IMT measures.", "doi": "10.1038/s41435-019-0090-z", "pmid": "31932740", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41435-019-0090-z"}, {"db": "pmc", "key": "PMC7182533"}], "notes": [], "created": "2020-01-17T08:12:24.951Z", "modified": "2021-11-10T12:54:53.393Z"}, {"entity": "publication", "iuid": "796149f9eb4f4e3980d73a2969461850", "links": {"self": {"href": "https://publications.scilifelab.se/publication/796149f9eb4f4e3980d73a2969461850.json"}, "display": {"href": "https://publications.scilifelab.se/publication/796149f9eb4f4e3980d73a2969461850"}}, "title": "Building de novo reference genome assemblies of complex eukaryotic microorganisms from single nuclei.", "authors": [{"family": "Montoliu-Nerin", "given": "Merce", "initials": "M", "orcid": "0000-0002-5200-0411", "researcher": {"href": "https://publications.scilifelab.se/researcher/7f89e94a04c6429db7e706b4d8d6626a.json"}}, {"family": "S\u00e1nchez-Garc\u00eda", "given": "Marisol", "initials": "M", "orcid": "0000-0002-0635-6281", "researcher": {"href": "https://publications.scilifelab.se/researcher/5ccb3584fa144e178750ff2fc4666cfe.json"}}, {"family": "Bergin", "given": "Claudia", "initials": "C"}, {"family": "Grabherr", "given": "Manfred", "initials": "M"}, {"family": "Ellis", "given": "Barbara", "initials": "B"}, {"family": "Kutschera", "given": "Verena Esther", "initials": "VE", "orcid": "0000-0002-8930-534X", "researcher": {"href": "https://publications.scilifelab.se/researcher/4f80fb4d234c4f2fa2179ad1e7c6a6db.json"}}, {"family": "Kierczak", "given": "Marcin", "initials": "M"}, {"family": "Johannesson", "given": "Hanna", "initials": "H"}, {"family": "Rosling", "given": "Anna", "initials": "A", "orcid": "0000-0002-7003-5941", "researcher": {"href": "https://publications.scilifelab.se/researcher/c4c4bbb9e6c343808e8fa9345b7c05b2.json"}}], "type": "journal article", "published": "2020-01-28", "journal": {"title": "Sci Rep", "issn": "2045-2322", "issn-l": "2045-2322", "volume": "10", "issue": "1", "pages": "1303"}, "abstract": "The advent of novel sequencing techniques has unraveled a tremendous diversity on Earth. Genomic data allow us to understand ecology and function of organisms that we would not otherwise know existed. However, major methodological challenges remain, in particular for multicellular organisms with large genomes. Arbuscular mycorrhizal (AM) fungi are important plant symbionts with cryptic and complex multicellular life cycles, thus representing a suitable model system for method development. Here, we report a novel method for large scale, unbiased nuclear sorting, sequencing, and de novo assembling of AM fungal genomes. After comparative analyses of three assembly workflows we discuss how sequence data from single nuclei can best be used for different downstream analyses such as phylogenomics and comparative genomics of single nuclei. Based on analysis of completeness, we conclude that comprehensive de novo genome assemblies can be produced from six to seven nuclei. The method is highly applicable for a broad range of taxa, and will greatly improve our ability to study multicellular eukaryotes with complex life cycles.", "doi": "10.1038/s41598-020-58025-3", "pmid": "31992756", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Microbial Single Cell Genomics": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-020-58025-3"}, {"db": "pmc", "key": "PMC6987183"}], "notes": [], "created": "2020-02-03T10:35:42.153Z", "modified": "2024-01-16T13:48:43.036Z"}, {"entity": "publication", "iuid": "bea2a6c152d74b7a8b9703f4e41bfb79", "links": {"self": {"href": "https://publications.scilifelab.se/publication/bea2a6c152d74b7a8b9703f4e41bfb79.json"}, "display": {"href": "https://publications.scilifelab.se/publication/bea2a6c152d74b7a8b9703f4e41bfb79"}}, "title": "Population Pharmacokinetics and Pharmacogenetics of Ethambutol in Adult Patients Coinfected with Tuberculosis and HIV.", "authors": [{"family": "Sundell", "given": "Jesper", "initials": "J", "orcid": "0000-0002-5395-9819", "researcher": {"href": "https://publications.scilifelab.se/researcher/8dba5ed8dd254a5b9f09cb89f3dda721.json"}}, {"family": "Bienvenu", "given": "Emile", "initials": "E"}, {"family": "Birgersson", "given": "Sofia", "initials": "S"}, {"family": "\u00c4bel\u00f6", "given": "Angela", "initials": "A"}, {"family": "Ashton", "given": "Michael", "initials": "M"}], "type": "journal article", "published": "2020-01-27", "journal": {"title": "Antimicrob. Agents Chemother.", "issn": "1098-6596", "issn-l": "0066-4804", "volume": "64", "issue": "2", "pages": null}, "abstract": "This study aimed to characterize the population pharmacokinetics and pharmacogenetics of ethambutol in tuberculosis-HIV-coinfected adult patients. Ethambutol plasma concentrations, determined by liquid chromatography-tandem mass spectrometry, in 63 patients receiving ethambutol as part of rifampin-based fixed-dose combination therapy for tuberculosis were analyzed using nonlinear mixed-effects modeling. A one-compartment disposition model with first-order elimination and four transit compartments prior to first-order absorption was found to adequately describe the concentration-time profiles of ethambutol in plasma. Body weight was implemented as an allometric function on the clearance and volume parameters. Estimates of oral clearance and volume of distribution were 77.4 liters/h and 76.2 liters, respectively. A G/A mutation with regard to CYP1A2 2159 G>A was associated with a 50% reduction in relative bioavailability. Simulations revealed that doses of 30 mg/kg of body weight and 50 mg/kg for G/G and G/A carriers, respectively, would result in clinically adequate exposure. The results presented here suggest that CYP1A2 polymorphism affects ethambutol exposure in this population and that current treatment guidelines may result in underexposure in patients coinfected with tuberculosis and HIV. Based on simulations, a dose increase from15 to 20 mg/kg to 30 mg/kg is suggested. However, the 50-mg/kg dose required to reach therapeutic exposure in G/A carriers may be inappropriate due to the dose-dependent toxicity of ethambutol. Additional studies are required to further investigate CYP450 polymorphism effects on ethambutol pharmacokinetics.", "doi": "10.1128/AAC.01583-19", "pmid": "31712201", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pii", "key": "AAC.01583-19"}, {"db": "pmc", "key": "PMC6985744"}], "notes": [], "created": "2021-01-14T11:59:21.203Z", "modified": "2021-12-07T13:56:13.923Z"}, {"entity": "publication", "iuid": "ab3cc4d0906f402b8e0f5a5fecb6f0a0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ab3cc4d0906f402b8e0f5a5fecb6f0a0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ab3cc4d0906f402b8e0f5a5fecb6f0a0"}}, "title": "CREBBP and WDR 24 Identified as Candidate Genes for Quantitative Variation in Red-Brown Plumage Colouration in the Chicken.", "authors": [{"family": "Fogelholm", "given": "J", "initials": "J"}, {"family": "Henriksen", "given": "R", "initials": "R"}, {"family": "H\u00f6glund", "given": "A", "initials": "A"}, {"family": "Huq", "given": "N", "initials": "N"}, {"family": "Johnsson", "given": "M", "initials": "M"}, {"family": "Lenz", "given": "R", "initials": "R"}, {"family": "Jensen", "given": "P", "initials": "P"}, {"family": "Wright", "given": "D", "initials": "D"}], "type": "journal article", "published": "2020-01-24", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "10", "issue": "1", "pages": "1161", "issn-l": "2045-2322"}, "abstract": "Plumage colouration in birds is important for a plethora of reasons, ranging from camouflage, sexual signalling, and species recognition. The genes underlying colour variation have been vital in understanding how genes can affect a phenotype. Multiple genes have been identified that affect plumage variation, but research has principally focused on major-effect genes (such as those causing albinism, barring, and the like), rather than the smaller effect modifier loci that more subtly influence colour. By utilising a domestic \u00d7 wild advanced intercross with a combination of classical QTL mapping of red colouration as a quantitative trait and a targeted genetical genomics approach, we have identified five separate candidate genes (CREBBP, WDR24, ARL8A, PHLDA3, LAD1) that putatively influence quantitative variation in red-brown colouration in chickens. By treating colour as a quantitative rather than qualitative trait, we have identified both QTL and genes of small effect. Such small effect loci are potentially far more prevalent in wild populations, and can therefore potentially be highly relevant to colour evolution.", "doi": "10.1038/s41598-020-57710-7", "pmid": "31980681", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-020-57710-7"}, {"db": "pmc", "key": "PMC6981141"}], "notes": [], "created": "2020-02-04T11:55:41.471Z", "modified": "2024-01-16T13:48:43.050Z"}, {"entity": "publication", "iuid": "8e7d434d65094896b5c0c4f4328ae62e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8e7d434d65094896b5c0c4f4328ae62e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8e7d434d65094896b5c0c4f4328ae62e"}}, "title": "Transcriptome analysis of fibroblasts from schizophrenia patients reveals differential expression of schizophrenia-related genes.", "authors": [{"family": "Etemadikhah", "given": "Mitra", "initials": "M", "orcid": "0000-0001-5795-9085", "researcher": {"href": "https://publications.scilifelab.se/researcher/7e68ca63254a4b5697188bb87087852f.json"}}, {"family": "Niazi", "given": "Adnan", "initials": "A", "orcid": "0000-0003-0311-5279", "researcher": {"href": "https://publications.scilifelab.se/researcher/c9e07c9891804a60980eb07956a7cd0d.json"}}, {"family": "Wetterberg", "given": "Lennart", "initials": "L"}, {"family": "Feuk", "given": "Lars", "initials": "L", "orcid": "0000-0003-2355-2919", "researcher": {"href": "https://publications.scilifelab.se/researcher/3eb2f826b3554d4b9971bf0766b275c4.json"}}], "type": "journal article", "published": "2020-01-20", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "10", "issue": "1", "pages": "630", "issn-l": "2045-2322"}, "abstract": "Schizophrenia is a complex neurodevelopmental disorder with high rate of morbidity and mortality. While the heritability rate is high, the precise etiology is still unknown. Although schizophrenia is a central nervous system disorder, studies using peripheral tissues have also been established to search for patient specific biomarkers and to increase understanding of schizophrenia etiology. Among all peripheral tissues, fibroblasts stand out as they are easy to obtain and culture. Furthermore, they keep genetic stability for long period and exhibit molecular similarities to cells from nervous system. Using a unique set of fibroblast samples from a genetically isolated population in northern Sweden, we performed whole transcriptome sequencing to compare differentially expressed genes in seven controls and nine patients. We found differential fibroblast expression between cases and controls for 48 genes, including eight genes previously implicated in schizophrenia or schizophrenia related pathways; HGF, PRRT2, EGR1, EGR3, C11orf87, TLR3, PLEKHH2 and PIK3CD. Weighted gene correlation network analysis identified three differentially co-expressed networks of genes significantly-associated with schizophrenia. All three modules were significantly suppressed in patients compared to control, with one module highly enriched in genes involved in synaptic plasticity, behavior and synaptic transmission. In conclusion, our results support the use of fibroblasts for identification of differentially expressed genes in schizophrenia and highlight dysregulation of synaptic networks as an important mechanism in schizophrenia.", "doi": "10.1038/s41598-020-57467-z", "pmid": "31959813", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-020-57467-z"}, {"db": "pmc", "key": "PMC6971273"}], "notes": [], "created": "2020-07-03T05:23:47.172Z", "modified": "2024-01-16T13:48:43.065Z"}, {"entity": "publication", "iuid": "7ece5c90f5a84512a7eef65aed76aed2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7ece5c90f5a84512a7eef65aed76aed2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7ece5c90f5a84512a7eef65aed76aed2"}}, "title": "Genome-wide association and Mendelian 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"https://publications.scilifelab.se/researcher/e529a40052644d83bdef588a3e4f4e99.json"}}, {"family": "Voors", "given": "Adriaan A", "initials": "AA"}, {"family": "Wang", "given": "Xiaosong", "initials": "X"}, {"family": "Wareham", "given": "Nicholas J", "initials": "NJ"}, {"family": "Waterworth", "given": "Dawn", "initials": "D"}, {"family": "Weeke", "given": "Peter E", "initials": "PE"}, {"family": "Weiss", "given": "Raul", "initials": "R"}, {"family": "Wiggins", "given": "Kerri L", "initials": "KL", "orcid": "0000-0003-2749-1279", "researcher": {"href": "https://publications.scilifelab.se/researcher/a9d1f9cb10ef4038abb10fb6ee289504.json"}}, {"family": "Xing", "given": "Heming", "initials": "H"}, {"family": "Yerges-Armstrong", "given": "Laura M", "initials": "LM"}, {"family": "Yu", "given": "Bing", "initials": "B"}, {"family": "Zannad", "given": "Faiez", "initials": "F"}, {"family": "Zhao", "given": "Jing Hua", "initials": "JH"}, {"family": "Hemingway", "given": "Harry", "initials": "H", "orcid": "0000-0003-2279-0624", "researcher": {"href": "https://publications.scilifelab.se/researcher/0bc6b343a8ab4b4c9ff6380d8d4aa626.json"}}, {"family": "Samani", "given": "Nilesh J", "initials": "NJ"}, {"family": "McMurray", "given": "John J V", "initials": "JJV"}, {"family": "Yang", "given": "Jian", "initials": "J", "orcid": "0000-0003-2001-2474", "researcher": {"href": "https://publications.scilifelab.se/researcher/99b6239b59ad42248e8f18583b40777a.json"}}, {"family": "Visscher", "given": "Peter M", "initials": "PM", "orcid": "0000-0002-2143-8760", "researcher": {"href": "https://publications.scilifelab.se/researcher/dcdb41d4720b436494304f74e33206ae.json"}}, {"family": "Newton-Cheh", "given": "Christopher", "initials": "C"}, {"family": "Malarstig", "given": "Anders", "initials": "A"}, {"family": "Holm", "given": "Hilma", "initials": "H"}, {"family": "Lubitz", "given": "Steven A", "initials": "SA", "orcid": "0000-0002-9599-4866", "researcher": {"href": "https://publications.scilifelab.se/researcher/25bb007311104c92983dbcce80f72260.json"}}, {"family": "Sattar", "given": "Naveed", "initials": "N", "orcid": "0000-0002-1604-2593", "researcher": {"href": "https://publications.scilifelab.se/researcher/80fbc7cdcfc444acb066449f80f87181.json"}}, {"family": "Holmes", "given": "Michael V", "initials": "MV"}, {"family": "Cappola", "given": "Thomas P", "initials": "TP", "orcid": "0000-0002-9630-7204", "researcher": {"href": "https://publications.scilifelab.se/researcher/6cc50d241ad14477b91f83e012918181.json"}}, {"family": "Asselbergs", "given": "Folkert W", "initials": "FW", "orcid": "0000-0002-1692-8669", "researcher": {"href": "https://publications.scilifelab.se/researcher/7037429ef1304bdaabd837d242b1e6f5.json"}}, {"family": "Hingorani", "given": "Aroon D", "initials": "AD"}, {"family": "Kuchenbaecker", "given": "Karoline", "initials": "K", "orcid": "0000-0001-9726-603X", "researcher": {"href": "https://publications.scilifelab.se/researcher/4e142157c79648ce96b258ea78019829.json"}}, {"family": "Ellinor", "given": "Patrick T", "initials": "PT", "orcid": "0000-0002-2067-0533", "researcher": {"href": "https://publications.scilifelab.se/researcher/dd513dc49e0945bc8298f72d1244648d.json"}}, {"family": "Lang", "given": "Chim C", "initials": "CC"}, {"family": "Stefansson", "given": "Kari", "initials": "K"}, {"family": "Smith", "given": "J Gustav", "initials": "JG"}, {"family": "Vasan", "given": "Ramachandran S", "initials": "RS", "orcid": "0000-0001-7357-5970", "researcher": {"href": "https://publications.scilifelab.se/researcher/50ceef6f00ea4251a5e1e83cd379a506.json"}}, {"family": "Swerdlow", "given": "Daniel I", "initials": "DI"}, {"family": "Lumbers", "given": "R Thomas", "initials": "RT", "orcid": "0000-0002-9077-4741", "researcher": {"href": "https://publications.scilifelab.se/researcher/a53e4d6591db481f881ec6046d54535b.json"}}], "type": "journal article", "published": "2020-01-09", "journal": {"volume": "11", "issn": "2041-1723", "issue": "1", "pages": "163", "title": "Nat Commun", "issn-l": "2041-1723"}, "abstract": "Heart failure (HF) is a leading cause of morbidity and mortality worldwide. A small proportion of HF cases are attributable to monogenic cardiomyopathies and existing genome-wide association studies (GWAS) have yielded only limited insights, leaving the observed heritability of HF largely unexplained. We report results from a GWAS meta-analysis of HF comprising 47,309 cases and 930,014 controls. Twelve independent variants at 11 genomic loci are associated with HF, all of which demonstrate one or more associations with coronary artery disease (CAD), atrial fibrillation, or reduced left ventricular function, suggesting shared genetic aetiology. Functional analysis of non-CAD-associated loci implicate genes involved in cardiac development (MYOZ1, SYNPO2L), protein homoeostasis (BAG3), and cellular senescence (CDKN1A). Mendelian randomisation analysis supports causal roles for several HF risk factors, and demonstrates CAD-independent effects for atrial fibrillation, body mass index, and hypertension. These findings extend our knowledge of the pathways underlying HF and may inform new therapeutic strategies.", "doi": "10.1038/s41467-019-13690-5", "pmid": "31919418", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC6952380"}, {"db": "pii", "key": "10.1038/s41467-019-13690-5"}], "notes": [], "created": "2020-01-14T10:04:57.921Z", "modified": "2023-06-19T13:01:57.741Z"}, {"entity": "publication", "iuid": "61cb2c382f5b4954ae79250a61c45daa", "links": {"self": {"href": "https://publications.scilifelab.se/publication/61cb2c382f5b4954ae79250a61c45daa.json"}, "display": {"href": "https://publications.scilifelab.se/publication/61cb2c382f5b4954ae79250a61c45daa"}}, "title": "DNA methylation changes in Down syndrome derived neural iPSCs uncover co-dysregulation of ZNF and HOX3 families of transcription factors.", "authors": [{"family": "Laan", "given": "Loora", "initials": "L"}, {"family": "Klar", "given": "Joakim", "initials": "J"}, {"family": "Sobol", "given": "Maria", "initials": "M"}, {"family": "Hoeber", "given": "Jan", "initials": "J"}, {"family": "Shahsavani", "given": "Mansoureh", "initials": "M"}, {"family": "Kele", "given": "Malin", "initials": "M"}, {"family": "Fatima", "given": "Ambrin", "initials": "A"}, {"family": "Zakaria", "given": "Muhammad", "initials": "M"}, {"family": "Anner\u00e9n", "given": "G\u00f6ran", "initials": "G"}, {"family": "Falk", "given": "Anna", "initials": "A"}, {"family": "Schuster", "given": "Jens", "initials": "J"}, {"family": "Dahl", "given": "Niklas", "initials": "N", "orcid": "0000-0002-8122-0800", "researcher": {"href": "https://publications.scilifelab.se/researcher/689e06ddc001490a8cb891050ba5a732.json"}}], "type": "comparative study", "published": "2020-01-08", "journal": {"volume": "12", "issn": "1868-7083", "issue": "1", "pages": "9", "title": "Clin Epigenetics", "issn-l": "1868-7075"}, "abstract": "Down syndrome (DS) is characterized by neurodevelopmental abnormalities caused by partial or complete trisomy of human chromosome 21 (T21). Analysis of Down syndrome brain specimens has shown global epigenetic and transcriptional changes but their interplay during early neurogenesis remains largely unknown. We differentiated induced pluripotent stem cells (iPSCs) established from two DS patients with complete T21 and matched euploid donors into two distinct neural stages corresponding to early- and mid-gestational ages.\n\nUsing the Illumina Infinium 450K array, we assessed the DNA methylation pattern of known CpG regions and promoters across the genome in trisomic neural iPSC derivatives, and we identified a total of 500 stably and differentially methylated CpGs that were annotated to CpG islands of 151 genes. The genes were enriched within the DNA binding category, uncovering 37 factors of importance for transcriptional regulation and chromatin structure. In particular, we observed regional epigenetic changes of the transcription factor genes ZNF69, ZNF700 and ZNF763 as well as the HOXA3, HOXB3 and HOXD3 genes. A similar clustering of differential methylation was found in the CpG islands of the HIST1 genes suggesting effects on chromatin remodeling.\n\nThe study shows that early established differential methylation in neural iPSC derivatives with T21 are associated with a set of genes relevant for DS brain development, providing a novel framework for further studies on epigenetic changes and transcriptional dysregulation during T21 neurogenesis.", "doi": "10.1186/s13148-019-0803-1", "pmid": "31915063", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Long-term Support WABI": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1186/s13148-019-0803-1"}, {"db": "pmc", "key": "PMC6950999"}], "notes": [], "created": "2020-01-14T10:04:59.643Z", "modified": "2021-11-10T12:55:02.672Z"}, {"entity": "publication", "iuid": "f591fb00201c499e85e74b11ee304e39", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f591fb00201c499e85e74b11ee304e39.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f591fb00201c499e85e74b11ee304e39"}}, "title": "The Genome of the Endangered Dryas Monkey Provides New Insights into the Evolutionary History of the Vervets.", "authors": [{"family": "van der Valk", "given": "Tom", "initials": "T", "orcid": "0000-0001-6582-3452", "researcher": {"href": "https://publications.scilifelab.se/researcher/f56ca19cfa4f4909be996b2c99ec24f1.json"}}, {"family": "Gonda", "given": "Catalina M", "initials": "CM"}, {"family": "Silegowa", "given": "Henri", "initials": "H"}, {"family": "Almanza", "given": "Sandra", "initials": "S"}, {"family": "Sifuentes-Romero", "given": "Itzel", "initials": "I"}, {"family": "Hart", "given": "Terese B", "initials": "TB"}, {"family": "Hart", "given": "John A", "initials": "JA"}, {"family": "Detwiler", "given": "Kate M", "initials": "KM"}, {"family": "Guschanski", "given": "Katerina", "initials": "K"}], "type": "journal article", "published": "2020-01-01", "journal": {"title": "Mol. Biol. Evol.", "issn": "1537-1719", "volume": "37", "issue": "1", "pages": "183-194", "issn-l": "0737-4038"}, "abstract": "Genomic data can be a powerful tool for inferring ecology, behavior, and conservation needs of highly elusive species, particularly, when other sources of information are hard to come by. Here, we focus on the Dryas monkey (Cercopithecus dryas), an endangered primate endemic to the Congo Basin with cryptic behavior and possibly <250 remaining adult individuals. Using whole-genome sequencing data, we show that the Dryas monkey represents a sister lineage to the vervets (Chlorocebus sp.) and has diverged from them \u223c1.4 Ma with additional bidirectional gene flow \u223c750,000-\u223c500,000 years ago that has likely involved the crossing of the Congo River. Together with evidence of gene flow across the Congo River in bonobos and okapis, our results suggest that the fluvial topology of the Congo River might have been more dynamic than previously recognized. Despite the presence of several homozygous loss-of-function mutations in genes associated with sperm mobility and immunity, we find high genetic diversity and low levels of inbreeding and genetic load in the studied Dryas monkey individual. This suggests that the current population carries sufficient genetic variability for long-term survival and might be larger than currently recognized. We thus provide an example of how genomic data can directly improve our understanding of highly elusive species.", "doi": "10.1093/molbev/msz213", "pmid": "31529046", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "5570178"}, {"db": "pmc", "key": "PMC6984364"}], "notes": [], "created": "2020-02-12T07:40:44.973Z", "modified": "2024-01-16T13:48:43.100Z"}, {"entity": "publication", "iuid": "b113002942174b6b8c2f67907d1d2182", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b113002942174b6b8c2f67907d1d2182.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b113002942174b6b8c2f67907d1d2182"}}, "title": "Discovery of Novel Sequences in 1,000 Swedish Genomes.", "authors": [{"family": "Eisfeldt", "given": "Jesper", "initials": "J", "orcid": "0000-0003-3716-4917", "researcher": {"href": "https://publications.scilifelab.se/researcher/32a701ee07674785b48b047665e18ee6.json"}}, {"family": "M\u00e5rtensson", "given": "Gustaf", "initials": "G"}, {"family": "Ameur", "given": "Adam", "initials": "A", "orcid": "0000-0001-6085-6749", "researcher": {"href": "https://publications.scilifelab.se/researcher/e960811513664a78b2804a00ee70f7c3.json"}}, {"family": "Nilsson", "given": "Daniel", "initials": "D", "orcid": "0000-0001-5831-385X", "researcher": {"href": "https://publications.scilifelab.se/researcher/9b3f854e51704270831e155518265ea6.json"}}, {"family": "Lindstrand", "given": "Anna", "initials": "A", "orcid": "0000-0003-0806-5602", "researcher": {"href": "https://publications.scilifelab.se/researcher/07f3e6152da043d38c7a81974fcf8c23.json"}}], "type": "journal article", "published": "2020-01-01", "journal": {"volume": "37", "issn": "1537-1719", "issue": "1", "pages": "18-30", "title": "Mol. Biol. Evol.", "issn-l": "0737-4038"}, "abstract": "Novel sequences (NSs), not present in the human reference genome, are abundant and remain largely unexplored. Here, we utilize de novo assembly to study NS in 1,000 Swedish individuals first sequenced as part of the SweGen project revealing a total of 46 Mb in 61,044 distinct contigs of sequences not present in GRCh38. The contigs were aligned to recently published catalogs of Icelandic and Pan-African NSs, as well as the chimpanzee genome, revealing a great diversity of shared sequences. Analyzing the positioning of NS across the chimpanzee genome, we find that 2,807 NS align confidently within 143 chimpanzee orthologs of human genes. Aligning the whole genome sequencing data to the chimpanzee genome, we discover ancestral NS common throughout the Swedish population. The NSs were searched for repeats and repeat elements: revealing a majority of repetitive sequence (56%), and enrichment of simple repeats (28%) and satellites (15%). Lastly, we align the unmappable reads of a subset of the thousand genomes data to our collection of NS, as well as the previously published Pan-African NS: revealing that both the Swedish and Pan-African NS are widespread, and that the Swedish NSs are largely a subset of the Pan-African NS. Overall, these results highlight the importance of creating a more diverse reference genome and illustrate that significant amounts of the NS may be of ancestral origin.", "doi": "10.1093/molbev/msz176", "pmid": "31560401", "labels": {"NGI Stockholm (Genomics Production)": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Uppsala (Uppsala Genome Center)": "Collaborative", "National Genomics Infrastructure": "Collaborative", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "5555682"}, {"db": "pmc", "key": "PMC6984370"}], "notes": [], "created": "2019-10-30T08:45:30.942Z", "modified": "2024-01-16T13:48:43.107Z"}, {"entity": "publication", "iuid": "72a503969cf644bfb111a0651557793a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/72a503969cf644bfb111a0651557793a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/72a503969cf644bfb111a0651557793a"}}, "title": "Whole genome sequencing of apparently mutation-negative MEN1 patients.", "authors": [{"family": "Backman", "given": "Samuel", "initials": "S"}, {"family": "Bajic", "given": "Duska", "initials": "D"}, {"family": "Crona", "given": "Joakim", "initials": "J"}, {"family": "Hellman", "given": "Per", "initials": "P"}, {"family": "Skogseid", "given": "Britt", "initials": "B"}, {"family": "St\u00e5lberg", "given": "Peter", "initials": "P"}], "type": "journal article", "published": "2020-01-00", "journal": {"title": "Eur. J. Endocrinol.", "issn": "1479-683X", "issn-l": "0804-4643", "volume": "182", "issue": "1", "pages": "35-45"}, "abstract": "Multiple endocrine neoplasia type 1 (MEN1) is an autosomal dominant syndrome usually caused by loss-of-function mutations in the MEN1 gene. However, a minority of patients who fulfill the criteria for MEN1 are not found to harbor MEN1 mutations. Besides, some of these individuals, present with a subtly different phenotype suggestive of sporadic disease. The aim of the present study was to investigate the genetic architecture of mutation-negative MEN1.\n\nFourteen patients with a clinical diagnosis (n = 13) or suspicion (n = 1) of MEN1 who had negative genetic screening of the MEN1 gene were included.\n\nConstitutional DNA from the included patients, as well as tumor DNA from six of the patients, was subjected to whole genome sequencing. Constitutional variants were filtered against population databases and somatic variants were studied under a tumor-suppressor model.\n\nThree patients carried pathogenic variants (two splice-site variants, one missense variant) in MEN1 that had not been detected during routine clinical sequencing, one patient carried a pathogenic variant in CASR and one patient carried a gross deletion on chromosome 1q which included the CDC73 gene. Analysis of matched tumor DNA from six patients without mutations did not detect any recurrent genes fulfilling Knudson's two-hit model.\n\nThese results highlight the possibility of germline mutations being missed in routine screening, the importance of considering phenocopies in atypical or mutation-negative cases. The absence of apparent disease-causing mutations suggests that a fraction of MEN1 mutation-negative MEN1 cases may be due to the chance occurrence of several endocrine tumors in one patient.", "doi": "10.1530/EJE-19-0522", "pmid": "31658439", "labels": {"Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support and Infrastructure": "Service", "National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pii", "key": "EJE-19-0522"}], "notes": [], "created": "2020-01-08T14:27:31.627Z", "modified": "2024-01-16T13:48:43.114Z"}, {"entity": "publication", "iuid": "6096e926f8b84db291d25f029ecd581c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6096e926f8b84db291d25f029ecd581c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6096e926f8b84db291d25f029ecd581c"}}, "title": "Variable neurodevelopmental and morphological phenotypes of carriers with 12q12 duplications.", "authors": [{"family": "Myers", "given": "Lynnea", "initials": "L"}, {"family": "Blyth", "given": "Moira", "initials": "M"}, {"family": "Moradkhani", "given": "Kamran", "initials": "K"}, {"family": "Hranilovi\u0107", "given": "Dubravka", "initials": "D"}, {"family": "Polesie", "given": "Sam", "initials": "S"}, {"family": "Isaksson", "given": "Johan", "initials": "J"}, {"family": "Nordgren", "given": "Ann", "initials": "A"}, {"family": "Bucan", "given": "Maja", "initials": "M"}, {"family": "Vincent", "given": "Marie", "initials": "M"}, {"family": "B\u00f6lte", "given": "Sven", "initials": "S"}, {"family": "Anderlid", "given": "Britt-Marie", "initials": "BM"}, {"family": "Tammimies", "given": "Kristiina", "initials": "K", "orcid": "0000-0002-8324-4697", "researcher": {"href": "https://publications.scilifelab.se/researcher/ba19ec07147743c6942ea10c9a92482a.json"}}], "type": "case reports", "published": "2020-01-00", "journal": {"title": "Mol Genet Genomic Med", "issn": "2324-9269", "volume": "8", "issue": "1", "pages": "e1013", "issn-l": "2324-9269"}, "abstract": "Variable size deletions affecting 12q12 have been found in individuals with neurodevelopmental disorders (NDDs) and distinct facial and physical features. For many genetic loci affected by deletions in individuals with NDDs, reciprocal duplications have been described. However, for the 12q12 region, there are no detailed descriptions of duplication cases in the literature.\n\nWe report a phenotypic description of a family with monozygotic twins diagnosed with NDDs, carrying a 9 Mb duplication at 12q12, and five other individuals with overlapping duplications ranging from 4.54 Mb up to 15.16 Mb.\n\nThe duplication carriers had language delays, cognitive delays, and were diagnosed with autism spectrum disorder. Additionally, distinct facial features (e.g., high foreheads, deeply set eyes, short palpebral fissures, small ears, high nasal bridges, abnormalities of the nose tip, thin lips), large feet, and abnormalities in the digits were noted. We also describe incomplete penetrance of the NDD phenotypes among the individuals with 12q12 duplication.\n\nThis case series expands our knowledge on this rare genetic aberration and suggests that large 12q12 duplications may increase the risk for developing NDDs.", "doi": "10.1002/mgg3.1013", "pmid": "31730283", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC6978403"}], "notes": [], "created": "2020-03-03T12:57:26.226Z", "modified": "2024-01-16T13:48:43.121Z"}, {"entity": "publication", "iuid": "5eb47205592b4eb78cfff50bb2fde093", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5eb47205592b4eb78cfff50bb2fde093.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5eb47205592b4eb78cfff50bb2fde093"}}, "title": "Protein and DNA methylation-based scores as surrogate markers for interferon system activation in patients with primary Sj\u00f6gren's syndrome.", "authors": [{"family": "Bj\u00f6rk", "given": "Albin", "initials": "A"}, {"family": "Richardsdotter Andersson", "given": "Elina", "initials": "E"}, {"family": "Imgenberg-Kreuz", "given": "Juliana", "initials": "J"}, {"family": "Thorlacius", "given": "Gudny Ella", "initials": "GE"}, {"family": "Mofors", "given": "Johannes", "initials": "J"}, {"family": "Syv\u00e4nen", "given": "Ann-Christine", "initials": "AC", "orcid": "0000-0002-9681-9146", "researcher": {"href": "https://publications.scilifelab.se/researcher/f7012e35025543379380cb90efd71243.json"}}, {"family": "Kvarnstr\u00f6m", "given": "Marika", "initials": "M"}, {"family": "Nordmark", "given": "Gunnel", "initials": "G", "orcid": "0000-0002-3829-7431", "researcher": {"href": "https://publications.scilifelab.se/researcher/188fda53498740dbb007441cc94bb1ad.json"}}, {"family": "Wahren-Herlenius", "given": "Marie", "initials": "M", "orcid": "0000-0002-0915-7245", "researcher": {"href": "https://publications.scilifelab.se/researcher/a8451e7f5e6e4e4da0bace3dfafaeb38.json"}}], "type": "journal article", "published": "2020-01-00", "journal": {"title": "RMD Open", "issn": "2056-5933", "issn-l": "2056-5933", "volume": "6", "issue": "1", "pages": "e000995"}, "abstract": "Standard assessment of interferon (IFN) system activity in systemic rheumatic diseases depends on the availability of RNA samples. In this study, we describe and evaluate alternative methods using plasma, serum and DNA samples, exemplified in the IFN-driven disease primary Sj\u00f6gren's syndrome (pSS).\n\nPatients with pSS seropositive or negative for anti-SSA/SSB and controls were included. Protein-based IFN (pIFN) scores were calculated from levels of PD-1, CXCL9 and CXCL10. DNA methylation-based (DNAm) IFN scores were calculated from DNAm levels at RSAD2, IFIT1 and IFI44L . Scores were compared with mRNA-based IFN scores measured by quantitative PCR (qPCR), Nanostring or RNA sequencing (RNAseq).\n\nmRNA-based IFN scores displayed strong correlations between B cells and monocytes (r=0.93 and 0.95, p<0.0001) and between qPCR and Nanostring measurements (r=0.92 and 0.92, p<0.0001). The pIFN score in plasma and serum was higher in patients compared with controls (p<0.0001) and correlated well with mRNA-based IFN scores (r=0.62-0.79, p<0.0001), as well as with each other (r=0.94, p<0.0001). Concordance of classification as 'high' or 'low' IFN signature between the pIFN score and mRNA-based IFN scores ranged from 79.5% to 88.6%, and the pIFN score was effective at classifying patients and controls (area under the curve, AUC=0.89-0.93, p<0.0001). The DNAm IFN score showed strong correlation to the RNAseq IFN score (r=0.84, p<0.0001) and performed well in classifying patients and controls (AUC=0.96, p<0.0001).\n\nWe describe novel methods of assessing IFN system activity in plasma, serum or DNA samples, which may prove particularly valuable in studies where RNA samples are not available.", "doi": "10.1136/rmdopen-2019-000995", "pmid": "31958277", "labels": {"National Genomics Infrastructure": "Service", "Clinical Biomarkers": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "PLA and Single Cell Proteomics": "Service", "Affinity Proteomics Uppsala": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "rmdopen-2019-000995"}, {"db": "pmc", "key": "PMC7046975"}], "notes": [], "created": "2020-01-23T16:05:43.255Z", "modified": "2024-01-16T13:48:43.143Z"}, {"entity": "publication", "iuid": "65e4b1d80b394c3cac3245642f6292c9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/65e4b1d80b394c3cac3245642f6292c9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/65e4b1d80b394c3cac3245642f6292c9"}}, "title": "Association of genetic variants related to plasma fatty acids with type 2 diabetes mellitus and glycaemic traits: a Mendelian randomisation study.", "authors": [{"family": "Yuan", "given": "Shuai", "initials": "S"}, {"family": "Larsson", "given": "Susanna C", "initials": "SC"}], "type": "journal article", "published": "2020-01-00", "journal": {"volume": "63", "issn": "1432-0428", "issue": "1", "pages": "116-123", "title": "Diabetologia", "issn-l": "0012-186X"}, "abstract": "Epidemiological data on the associations of circulating fatty acid levels with type 2 diabetes are inconsistent. We conducted a two-sample Mendelian randomisation study to explore the causal associations of plasma levels of ten fatty acids with type 2 diabetes and glycaemic traits.\n\nThirteen SNPs associated with circulating levels of ten individual fatty acids at the genome-wide significance level (p < 5 \u00d7 10-8) were selected as instrumental variables for the exposures. For the outcomes, summary-level data were obtained from the DIAbetes Genetics Replication And Meta-analysis (DIAGRAM) consortium for type 2 diabetes (898,130 individuals) and from the Meta-Analyses of Glucose and Insulin-related traits Consortium (MAGIC) for the glycaemic traits (up to 46,186 non-diabetic individuals). The inverse-variance weighted method was used for analyses.\n\nGenetic predisposition to higher plasma levels of eight of the ten fatty acids were statistically significantly associated with lower or higher odds of type 2 diabetes. The OR per one SD increment of each fatty acid was 0.93 (95% CI 0.90, 0.96; p = 2.21 \u00d7 10-5) for \u03b1-linolenic acid, 0.96 (95% CI 0.94, 0.98; p = 1.85 \u00d7 10-4) for linoleic acid, 0.86 (95% CI 0.81, 0.91; p = 6.68 \u00d7 10-7) for palmitoleic acid, 0.87 (95% CI 0.81, 0.93; p = 2.21 \u00d7 10-5) for oleic acid, 1.08 (95% CI 1.03, 1.12; p = 0.002) for eicosapentaenoic acid, 1.04 (95% CI 1.02, 1.07; p = 0.001) for docosapentaenoic acid, 1.03 (95% CI 1.02, 1.05; p = 2.51 \u00d7 10-5) for arachidonic acid and 1.09 (95% CI 1.03, 1.15; p = 0.003) for stearic acid. The same eight fatty acids were also associated with fasting glucose levels and HOMA-B. The associations, except that for palmitoleic acid, were driven by variants in FADS1/2.\n\nGenetic predisposition to higher circulating levels of eight out of ten fatty acids was associated with type 2 diabetes, fasting glucose and islet beta cell function. However, the associations, except that for palmitoleic acid, were driven by variants in FADS1/2, which encode enzymes with a key role in fatty acid metabolism.", "doi": "10.1007/s00125-019-05019-0", "pmid": "31690987", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1007/s00125-019-05019-0"}, {"db": "pmc", "key": "PMC6890658"}], "notes": [], "created": "2020-01-14T10:04:58.804Z", "modified": "2024-01-16T13:48:43.229Z"}, {"entity": "publication", "iuid": "a7bc4b57504c4cc99ed928474b6819bc", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a7bc4b57504c4cc99ed928474b6819bc.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a7bc4b57504c4cc99ed928474b6819bc"}}, "title": "Gene transfer across species boundaries in bryophytes: evidence from major life cycle stages in Homalothecium lutescens and H. sericeum.", "authors": [{"family": "Sawangproh", "given": "W", "initials": "W"}, {"family": "Heden\u00e4s", "given": "L", "initials": "L"}, {"family": "Lang", "given": "A S", "initials": "AS"}, {"family": "Hansson", "given": "B", "initials": "B"}, {"family": "Cronberg", "given": "N", "initials": "N"}], "type": "journal article", "published": "2019-12-24", "journal": {"volume": null, "issn": "1095-8290", "issue": null, "pages": null, "title": "Ann. Bot.", "issn-l": "0305-7364"}, "abstract": "The mosses Homalothecium lutescens and H. sericeum are genetically, morphologically and ecologically differentiated, mixed populations sometimes occur. In sympatric populations, intermediate character states among gametophytes and sporophytes have been observed, suggesting hybridization and introgression in such populations.\r\n\r\nWe determined genotypes using bi-allelic co-dominant single nucleotide polymorphism (SNP) markers, specific to either H. lutescens or H. sericeum, to estimate the degree of genetic mixing in 449 moss samples collected from seven sympatric and five allopatric populations on the island of \u00d6land, south Sweden. The samples represented three generations: haploid maternal gametophytes, diploid sporophytes, and haploid sporelings.\r\n\r\nAdmixture analyses of SNP genotypes identified a majority as pure H. lutescens or H. sericeum, but 76 samples were identified as mildly admixed (17%) and 17 samples (3.8%) as strongly admixed. Admixed samples were represented in all three generations in several populations. Hybridization and introgression was bidirectional.\r\n\r\nOur results demonstrate that admixed genomes are transferred between the generations, so that the populations behave as true hybrid zones. Earlier studies of sympatric bryophyte populations with admixed individuals have not been able to show that admixed alleles are transferred beyond the first generation. The presence of true hybrid zones has strong evolutionary implications because genetic material transferred across species boundaries can be directly exposed to selection in the long-lived haploid generation of the bryophyte life cycle, and contribute to local adaptation, long-time survival and speciation.", "doi": "10.1093/aob/mcz209", "pmid": "31872857", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support and Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pii", "key": "5686322"}], "notes": [], "created": "2020-01-07T14:39:04.363Z", "modified": "2024-01-16T13:48:43.252Z"}, {"entity": "publication", "iuid": "6e3550f1cdd44f318ef25c27e183be41", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6e3550f1cdd44f318ef25c27e183be41.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6e3550f1cdd44f318ef25c27e183be41"}}, "title": "Inoculum Source Determines Acetate and Lactate Production during Anaerobic Digestion of Sewage Sludge and Food Waste.", "authors": [{"family": "Moestedt", "given": "Jan", "initials": "J"}, {"family": "Westerholm", "given": "Maria", "initials": "M"}, {"family": "Isaksson", "given": "Simon", "initials": "S"}, {"family": "Schn\u00fcrer", "given": "Anna", "initials": "A", "orcid": "0000-0003-0038-553X", "researcher": {"href": "https://publications.scilifelab.se/researcher/0f81992bc8ed48318f8197fc8caabb4f.json"}}], "type": "journal article", "published": "2019-12-23", "journal": {"volume": "7", "issn": "2306-5354", "issue": "1", "pages": "3", "title": "Bioengineering", "issn-l": "2306-5354"}, "abstract": "Acetate production from food waste or sewage sludge was evaluated in four semi-continuous anaerobic digestion processes. To examine the importance of inoculum and substrate for acid production, two different inoculum sources (a wastewater treatment plant (WWTP) and a co-digestion plant treating food and industry waste) and two common substrates (sewage sludge and food waste) were used in process operations. The processes were evaluated with regard to the efficiency of hydrolysis, acidogenesis, acetogenesis, and methanogenesis and the microbial community structure was determined. Feeding sewage sludge led to mixed acid fermentation and low total acid yield, whereas feeding food waste resulted in the production of high acetate and lactate yields. Inoculum from WWTP with sewage sludge substrate resulted in maintained methane production, despite a low hydraulic retention time. For food waste, the process using inoculum from WWTP produced high levels of lactate (30 g/L) and acetate (10 g/L), while the process initiated with inoculum from the co-digestion plant had higher acetate (25 g/L) and lower lactate (15 g/L) levels. The microbial communities developed during acid production consisted of the major genera Lactobacillus (92-100%) with food waste substrate, and Roseburia (44-45%) and Fastidiosipila (16-36%) with sewage sludge substrate. Use of the outgoing material (hydrolysates) in a biogas production system resulted in a non-significant increase in bio-methane production (+5-20%) compared with direct biogas production from food waste and sewage sludge.", "doi": "10.3390/bioengineering7010003", "pmid": "31877953", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "bioengineering7010003"}, {"db": "pmc", "key": "PMC7175179"}], "notes": [], "created": "2020-01-08T12:45:09.420Z", "modified": "2021-06-16T14:38:42.675Z"}, {"entity": "publication", "iuid": "5ad7cb65e5e24baca7b6999875f3d1e9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5ad7cb65e5e24baca7b6999875f3d1e9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5ad7cb65e5e24baca7b6999875f3d1e9"}}, "title": "Genetic Screening of Plasticity Regulating Nogo-Type Signaling Genes in Migraine.", "authors": [{"family": "Smedfors", "given": "Gabriella", "initials": "G"}, {"family": "Liesecke", "given": "Franziska", "initials": "F"}, {"family": "Ran", "given": "Caroline", "initials": "C"}, {"family": "Olson", "given": "Lars", "initials": "L"}, {"family": "Karlsson", "given": "Tobias E", "initials": "TE"}, {"family": "Carmine Belin", "given": "Andrea", "initials": "A"}], "type": "journal article", "published": "2019-12-20", "journal": {"volume": "10", "issn": "2076-3425", "issue": "1", "title": "Brain Sci", "issn-l": "2076-3425"}, "abstract": "Migraine is the sixth most prevalent disease in the world and a substantial number of experiments have been conducted to analyze potential differences between the migraine brain and the healthy brain. Results from these investigations point to the possibility that development and aggravation of migraine may include grey matter plasticity. Nogo-type signaling is a potent plasticity regulating system in the CNS and consists of ligands, receptors, co-receptors and modulators with a dynamic age- and activity-related expression in cortical and subcortical regions. Here we investigated a potential link between migraine and five key Nogo-type signaling genes: RTN4, OMGP, MAG, RTN4R and LINGO1, by screening 15 single nucleotide polymorphisms (SNPs) within these genes. In a large Swedish migraine cohort (749 migraine patients and 4032 controls), using a logistic regression with sex as covariate, we found that there was no such association. In addition, a haplotype analysis was performed which revealed three haplotype blocks. These blocks had no significant association with migraine. However, to robustly conclude that Nogo-type genotypes signaling do not influence the prevalence of migraine, further studies are encouraged.", "doi": "10.3390/brainsci10010005", "pmid": "31861860", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "brainsci10010005"}], "notes": [], "created": "2020-01-07T14:39:05.132Z", "modified": "2024-01-16T13:48:43.267Z"}, {"entity": "publication", "iuid": "50298673c29845b082e21ec46b31ce6c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/50298673c29845b082e21ec46b31ce6c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/50298673c29845b082e21ec46b31ce6c"}}, "title": "Tissue-specific transposon-associated small RNAs in the gymnosperm tree, Norway spruce.", "authors": [{"family": "Nakamura", "given": "Miyuki", "initials": "M", "orcid": "0000-0002-8153-7293", "researcher": {"href": "https://publications.scilifelab.se/researcher/fa9f227109b54fa9a1457a1f7af197af.json"}}, {"family": "K\u00f6hler", "given": "Claudia", "initials": "C"}, {"family": "Hennig", "given": "Lars", "initials": "L"}], "type": "journal article", "published": "2019-12-19", "journal": {"volume": "20", "issn": "1471-2164", "issue": "1", "pages": "997", "title": "BMC Genomics", "issn-l": "1471-2164"}, "abstract": "Small RNAs (sRNAs) are regulatory molecules impacting on gene expression and transposon activity. MicroRNAs (miRNAs) are responsible for tissue-specific and environmentally-induced gene repression. Short interfering RNAs (siRNA) are constitutively involved in transposon silencing across different type of tissues. The male gametophyte in angiosperms has a unique set of sRNAs compared to vegetative tissues, including phased siRNAs from intergenic or genic regions, or epigenetically activated siRNAs. This is contrasted by a lack of knowledge about the sRNA profile of the male gametophyte of gymnosperms.\n\nHere, we isolated mature pollen from male cones of Norway spruce and investigated its sRNA profiles. While 21-nt sRNAs is the major size class of sRNAs in needles, in pollen 21-nt and 24-nt sRNAs are the most abundant size classes. Although the 24-nt sRNAs were exclusively derived from TEs in pollen, both 21-nt and 24-nt sRNAs were associated with TEs. We also investigated sRNAs from somatic embryonic callus, which has been reported to contain 24-nt sRNAs. Our data show that the 24-nt sRNA profiles are tissue-specific and differ between pollen and cell culture.\n\nOur data reveal that gymnosperm pollen, like angiosperm pollen, has a unique sRNA profile, differing from vegetative leaf tissue. Thus, our results reveal that angiosperm and gymnosperm pollen produce new size classes not present in vegetative tissues; while in angiosperm pollen 21-nt sRNAs are generated, in the gymnosperm Norway spruce 24-nt sRNAs are generated. The tissue-specific production of distinct TE-derived sRNAs in angiosperms and gymnosperms provides insights into the diversification process of sRNAs in TE silencing pathways between the two groups of seed plants.", "doi": "10.1186/s12864-019-6385-7", "pmid": "31856707", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1186/s12864-019-6385-7"}, {"db": "pmc", "key": "PMC6923980"}], "notes": [], "created": "2020-01-08T12:42:35.674Z", "modified": "2021-06-16T14:53:11.254Z"}, {"entity": "publication", "iuid": "ad8084cfea9d4cbfb73fec4819833186", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ad8084cfea9d4cbfb73fec4819833186.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ad8084cfea9d4cbfb73fec4819833186"}}, "title": "Longitudinal DNA methylation changes at MET may alter HGF/c-MET signalling in adolescents at risk for depression.", "authors": [{"family": "Ciuculete", "given": "Diana M", "initials": "DM", "orcid": "0000-0001-6377-0270", "researcher": {"href": "https://publications.scilifelab.se/researcher/1facf036e83a4fd1934204cc1dc7ee4d.json"}}, {"family": "Voisin", "given": "Sarah", "initials": "S", "orcid": "0000-0002-4074-7083", "researcher": {"href": "https://publications.scilifelab.se/researcher/3c6eab1a09084c1499c442d89bd2ff83.json"}}, {"family": "Kular", "given": "Lara", "initials": "L"}, {"family": "Welihinda", "given": "Nipuni", "initials": "N"}, {"family": "Jonsson", "given": "J\u00f6rgen", "initials": "J"}, {"family": "Jagodic", "given": "Maja", "initials": "M"}, {"family": "Mwinyi", "given": "Jessica", "initials": "J"}, {"family": "Schi\u00f6th", "given": "Helgi B", "initials": "HB"}], "type": "journal article", "published": "2019-12-19", "journal": {"volume": "15", "issn": "1559-2308", "issue": "6-7", "pages": "646-663", "title": "Epigenetics", "issn-l": "1559-2294"}, "abstract": "Unrecognized depression during adolescence can result in adult suicidal behaviour. The aim of this study was to identify, replicate and characterize DNA methylation (DNAm) shifts in depression aetiology, using a longitudinal, multi-tissue (blood and brain) and multi-layered (genetics, epigenetics, transcriptomics) approach. We measured genome-wide blood DNAm data at baseline and one-year follow-up, and imputed genetic variants, in 59 healthy adolescents comprising the discovery cohort. Depression and suicidal symptoms were determined using the Development and Well-Being Assessment (DAWBA) depression band, Montgomery-\u00c5sberg Depression Rating Scale-Self (MADRS-S) and SUicide Assessment Scale (SUAS). DNAm levels at follow-up were regressed against depression scores, adjusting for sex, age and the DNAm residuals at baseline. Higher methylation levels of 5% and 13% at cg24627299 within the MET gene were associated with higher depression scores (praw<1e-4) and susceptibility for suicidal symptoms (padj.<0.005). The nearby rs39748 was discovered to be a methylation and expression quantitative trait locus in blood cells. mRNA levels of hepatocyte growth factor (HGF) expression, known to strongly interact with MET, were inversely associated with methylation levels at cg24627299, in an independent cohort of 1180 CD14+ samples. In an open-access dataset of brain tissue, lower methylation at cg24627299 was found in 45 adults diagnosed with major depressive disorder compared with matched controls (padj.<0.05). Furthermore, lower MET expression was identified in the hippocampus of depressed individuals compared with controls in a fourth, independent cohort. Our findings reveal methylation changes at MET in the pathology of depression, possibly involved in downregulation of HGF/c-MET signalling the hippocampal region.", "doi": "10.1080/15592294.2019.1700628", "pmid": "31852353", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC7574381"}], "notes": [], "created": "2020-01-07T14:39:03.531Z", "modified": "2024-01-16T13:48:43.281Z"}, {"entity": "publication", "iuid": "6f47cb083bf04be7965bf777c7caf27a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6f47cb083bf04be7965bf777c7caf27a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6f47cb083bf04be7965bf777c7caf27a"}}, "title": "Comprehensive longitudinal study of epigenetic mutations in aging.", "authors": [{"family": "Wang", "given": "Yunzhang", "initials": "Y"}, {"family": "Karlsson", "given": "Robert", "initials": "R"}, {"family": "Jylh\u00e4v\u00e4", "given": "Juulia", "initials": "J"}, {"family": "Hedman", "given": "\u00c5sa K", "initials": "\u00c5K"}, {"family": "Almqvist", "given": "Catarina", "initials": "C"}, {"family": "Karlsson", "given": "Ida K", "initials": "IK"}, {"family": "Pedersen", "given": "Nancy L", "initials": "NL"}, {"family": "Almgren", "given": "Malin", "initials": "M"}, {"family": "H\u00e4gg", "given": "Sara", "initials": "S"}], "type": "journal article", "published": "2019-12-09", "journal": {"volume": "11", "issn": "1868-7075", "issue": "1", "pages": "187", "title": "Clin Epigenetics", "issn-l": null}, "abstract": "The role of DNA methylation in aging has been widely studied. However, epigenetic mutations, here defined as aberrant methylation levels compared to the distribution in a population, are less understood. Hence, we investigated longitudinal accumulation of epigenetic mutations, using 994 blood samples collected at up to five time points from 375 individuals in old ages.\n\nWe verified earlier cross-sectional evidence on the increase of epigenetic mutations with age, and identified important contributing factors including sex, CD19+ B cells, genetic background, cancer diagnosis, and technical artifacts. We further classified epigenetic mutations into High/Low Methylation Outliers (HMO/LMO) according to their changes in methylation, and specifically studied methylation sites (CpGs) that were prone to mutate (frequently mutated CpGs). We validated four epigenetically mutated CpGs using pyrosequencing in 93 samples. Furthermore, by using twins, we concluded that the age-related accumulation of epigenetic mutations was not related to genetic factors, hence driven by stochastic or environmental effects.\n\nHere we conducted a comprehensive study of epigenetic mutation and highlighted its important role in aging process and cancer development.", "doi": "10.1186/s13148-019-0788-9", "pmid": "31818313", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1186/s13148-019-0788-9"}], "notes": [], "created": "2019-12-12T08:51:07.118Z", "modified": "2024-01-16T13:48:43.296Z"}, {"entity": "publication", "iuid": "fa14c3d7e65e4526a320df7f80d7ef60", "links": {"self": {"href": "https://publications.scilifelab.se/publication/fa14c3d7e65e4526a320df7f80d7ef60.json"}, "display": {"href": "https://publications.scilifelab.se/publication/fa14c3d7e65e4526a320df7f80d7ef60"}}, "title": "A Gene-Environment Interaction Between Smoking and Gene polymorphisms Provides a High Risk of Two Subgroups of Sarcoidosis.", "authors": [{"family": "Rivera", "given": "Natalia V", "initials": "NV"}, {"family": "Patasova", "given": "Karina", "initials": "K"}, {"family": "Kullberg", "given": "Susanna", "initials": "S"}, {"family": "Diaz-Gallo", "given": "Lina Marcela", "initials": "LM"}, {"family": "Iseda", "given": "Tomoko", "initials": "T"}, {"family": "Bengtsson", "given": "Camilla", "initials": "C"}, {"family": "Alfredsson", "given": "Lars", "initials": "L"}, {"family": "Eklund", "given": "Anders", "initials": "A"}, {"family": "Kockum", "given": "Ingrid", "initials": "I"}, {"family": "Grunewald", "given": "Johan", "initials": "J"}, {"family": "Padyukov", "given": "Leonid", "initials": "L"}], "type": "journal article", "published": "2019-12-09", "journal": {"volume": "9", "issn": "2045-2322", "issue": "1", "pages": "18633", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "The influence and effect of cigarette smoking in sarcoidosis is unclear. Here, we evaluated gene-environment interaction between multiple genetic variants including HLA genes and smoking in sarcoidosis defined by two clinical phenotypes, L\u00f6fgren's syndrome (LS) and patients without L\u00f6fgren's syndrome (non-LS). To quantify smoking effects in sarcoidosis, we performed a gene-environment interaction study in a Swedish population-based case-control study consisting of 3,713 individuals. Cases and controls were classified according to their cigarette smoking status and genotypes by Immunochip platform. Gene-smoking interactions were quantified by an additive interaction model using a logistic regression adjusted by sex, age and first two principal components. The estimated attributable proportion (AP) was used to quantify the interaction effect. Assessment of smoking effects with inclusion of genetic information revealed 53 (in LS) and 34 (in non-LS) SNP-smoking additive interactions at false discovery rate (FDR) below 5%. The lead signals interacting with smoking were rs12132140 (AP = 0.56, 95% CI = 0.22-0.90), p = 1.28e-03) in FCRL1 for LS and rs61780312 (AP = 0.62, 95% CI = 0.28-0.90), p = 3e-04) in IL23R for non-LS. We further identified 16 genomic loci (in LS) and 13 (in non-LS) that interact with cigarette smoking. These findings suggest that sarcoidosis risk is modulated by smoking due to genetic susceptibility. Therefore, patients having certain gene variants, are at a higher risk for the disease. Consideration of individual's genetic predisposition is crucial to quantify effects of smoking in sarcoidosis.", "doi": "10.1038/s41598-019-54612-1", "pmid": "31819081", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-019-54612-1"}], "notes": [], "created": "2019-12-16T13:39:42.295Z", "modified": "2024-01-16T13:48:43.304Z"}, {"entity": "publication", "iuid": "8fefd871b5d64a629a618eeb2a501689", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8fefd871b5d64a629a618eeb2a501689.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8fefd871b5d64a629a618eeb2a501689"}}, "title": "Epigenome-wide meta-analysis of blood DNA methylation and its association with subcortical volumes: findings from the ENIGMA Epigenetics Working Group.", "authors": [{"family": "Jia", "given": "Tianye", "initials": "T"}, {"family": "Chu", "given": "Congying", "initials": "C"}, {"family": "Liu", "given": "Yun", "initials": "Y"}, {"family": "van Dongen", "given": "Jenny", "initials": "J"}, {"family": "Papastergios", "given": "Evangelos", "initials": "E"}, {"family": "Armstrong", "given": "Nicola J", "initials": "NJ"}, {"family": "Bastin", "given": "Mark E", "initials": "ME"}, {"family": "Carrillo-Roa", "given": "Tania", "initials": "T"}, {"family": "den Braber", "given": "Anouk", "initials": "A"}, {"family": "Harris", "given": "Mathew", "initials": "M"}, {"family": "Jansen", "given": "Rick", "initials": "R"}, {"family": "Liu", "given": "Jingyu", "initials": "J"}, {"family": "Luciano", "given": "Michelle", "initials": "M"}, {"family": "Ori", "given": "Anil P S", "initials": "APS"}, {"family": "Roiz Santia\u00f1ez", "given": "Roberto", "initials": "R"}, {"family": "Ruggeri", "given": "Barbara", "initials": "B"}, {"family": "Sarkisyan", "given": "Daniil", "initials": "D"}, {"family": "Shin", "given": "Jean", "initials": "J"}, {"family": "Sungeun", "given": "Kim", "initials": "K"}, {"family": "Tordesillas Guti\u00e9rrez", "given": "Diana", "initials": "D"}, {"family": "Van't Ent", "given": "Dennis", "initials": "D"}, {"family": "Ames", "given": "David", "initials": "D"}, {"family": "Artiges", "given": "Eric", "initials": "E"}, {"family": "Bakalkin", "given": "Georgy", "initials": "G"}, {"family": "Banaschewski", "given": "Tobias", "initials": "T"}, {"family": "Bokde", "given": "Arun L W", "initials": "ALW"}, {"family": "Brodaty", "given": "Henry", "initials": "H"}, {"family": "Bromberg", "given": "Uli", "initials": "U"}, {"family": "Brouwer", "given": "Rachel", "initials": "R"}, {"family": "B\u00fcchel", "given": "Christian", "initials": "C"}, {"family": "Burke Quinlan", "given": "Erin", "initials": "E"}, {"family": "Cahn", "given": "Wiepke", "initials": "W"}, {"family": "de Zubicaray", "given": "Greig I", "initials": "GI"}, {"family": "Ehrlich", "given": "Stefan", "initials": "S"}, {"family": "Ekstr\u00f6m", "given": "Tomas J", "initials": "TJ"}, {"family": "Flor", "given": "Herta", "initials": "H"}, {"family": "Fr\u00f6hner", "given": "Juliane H", "initials": "JH"}, {"family": "Frouin", "given": "Vincent", "initials": "V"}, {"family": "Garavan", "given": "Hugh", "initials": "H"}, {"family": "Gowland", "given": "Penny", "initials": "P"}, {"family": "Heinz", "given": "Andreas", "initials": "A"}, {"family": "Hoare", "given": "Jacqueline", "initials": "J"}, {"family": "Ittermann", "given": "Bernd", "initials": "B"}, {"family": "Jahanshad", "given": "Neda", "initials": "N"}, {"family": "Jiang", "given": "Jiyang", "initials": "J"}, {"family": "Kwok", "given": "John B", "initials": "JB"}, {"family": "Martin", "given": "Nicholas G", "initials": "NG"}, {"family": "Martinot", "given": "Jean-Luc", "initials": "JL"}, {"family": "Mather", "given": "Karen A", "initials": "KA"}, {"family": "McMahon", "given": "Katie L", "initials": "KL"}, {"family": "McRae", "given": "Allan F", "initials": "AF"}, {"family": "Nees", "given": "Frauke", "initials": "F"}, {"family": "Papadopoulos Orfanos", "given": "Dimitri", "initials": "D"}, {"family": "Paus", "given": "Tom\u00e1\u0161", "initials": "T"}, {"family": "Poustka", "given": "Luise", "initials": "L"}, {"family": "S\u00e4mann", "given": "Philipp G", "initials": "PG"}, {"family": "Schofield", "given": "Peter R", "initials": "PR"}, {"family": "Smolka", "given": "Michael N", "initials": "MN"}, {"family": "Stein", "given": "Dan J", "initials": "DJ"}, {"family": "Strike", "given": "Lachlan T", "initials": "LT"}, {"family": "Teeuw", "given": "Jalmar", "initials": "J"}, {"family": "Thalamuthu", "given": "Anbupalam", "initials": "A"}, {"family": "Trollor", "given": "Julian", "initials": "J"}, {"family": "Walter", "given": "Henrik", "initials": "H"}, {"family": "Wardlaw", "given": "Joanna M", "initials": "JM"}, {"family": "Wen", "given": "Wei", "initials": "W"}, {"family": "Whelan", "given": "Robert", "initials": "R"}, {"family": "Apostolova", "given": "Liana G", "initials": "LG"}, {"family": "Binder", "given": "Elisabeth B", "initials": "EB"}, {"family": "Boomsma", "given": "Dorret I", "initials": "DI"}, {"family": "Calhoun", "given": "Vince", "initials": "V"}, {"family": "Crespo-Facorro", "given": "Benedicto", "initials": "B"}, {"family": "Deary", "given": "Ian J", "initials": "IJ"}, {"family": "Hulshoff Pol", "given": "Hilleke", "initials": "H"}, {"family": "Ophoff", "given": "Roel A", "initials": "RA"}, {"family": "Pausova", "given": "Zdenka", "initials": "Z"}, {"family": "Sachdev", "given": "Perminder S", "initials": "PS"}, {"family": "Saykin", "given": "Andrew", "initials": "A"}, {"family": "Wright", "given": "Margaret J", "initials": "MJ"}, {"family": "Thompson", "given": "Paul M", "initials": "PM"}, {"family": "Schumann", "given": "Gunter", "initials": "G"}, {"family": "Desrivi\u00e8res", "given": "Sylvane", "initials": "S"}], "type": "journal article", "published": "2019-12-06", "journal": {"volume": null, "issn": "1476-5578", "issue": null, "title": "Mol. Psychiatry", "issn-l": "1359-4184"}, "abstract": "DNA methylation, which is modulated by both genetic factors and environmental exposures, may offer a unique opportunity to discover novel biomarkers of disease-related brain phenotypes, even when measured in other tissues than brain, such as blood. A few studies of small sample sizes have revealed associations between blood DNA methylation and neuropsychopathology, however, large-scale epigenome-wide association studies (EWAS) are needed to investigate the utility of DNA methylation profiling as a peripheral marker for the brain. Here, in an analysis of eleven international cohorts, totalling 3337 individuals, we report epigenome-wide meta-analyses of blood DNA methylation with volumes of the hippocampus, thalamus and nucleus accumbens (NAcc)-three subcortical regions selected for their associations with disease and heritability and volumetric variability. Analyses of individual CpGs revealed genome-wide significant associations with hippocampal volume at two loci. No significant associations were found for analyses of thalamus and nucleus accumbens volumes. Cluster-based analyses revealed additional differentially methylated regions (DMRs) associated with hippocampal volume. DNA methylation at these loci affected expression of proximal genes involved in learning and memory, stem cell maintenance and differentiation, fatty acid metabolism and type-2 diabetes. These DNA methylation marks, their interaction with genetic variants and their impact on gene expression offer new insights into the relationship between epigenetic variation and brain structure and may provide the basis for biomarker discovery in neurodegeneration and neuropsychiatric conditions.", "doi": "10.1038/s41380-019-0605-z", "pmid": "31811260", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41380-019-0605-z"}], "notes": [], "created": "2019-12-18T16:32:06.247Z", "modified": "2024-01-16T13:48:43.316Z"}, {"entity": "publication", "iuid": "9e5622f51ee24776be28a7e9a266fb7e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9e5622f51ee24776be28a7e9a266fb7e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9e5622f51ee24776be28a7e9a266fb7e"}}, "title": "Replicating associations between DNA methylation and body mass index in a longitudinal sample of older twins.", "authors": [{"family": "Karlsson", "given": "Ida K", "initials": "IK"}, {"family": "Ericsson", "given": "Malin", "initials": "M"}, {"family": "Wang", "given": "Yunzhang", "initials": "Y"}, {"family": "Jylh\u00e4v\u00e4", "given": "Juulia", "initials": "J"}, {"family": "H\u00e4gg", "given": "Sara", "initials": "S"}, {"family": "Pedersen", "given": "Nancy L", "initials": "NL"}, {"family": "Reynolds", "given": "Chandra A", "initials": "CA"}, {"family": "Dahl Aslan", "given": "Anna K", "initials": "AK"}], "type": "journal article", "published": "2019-12-04", "journal": {"volume": null, "issn": "1476-5497", "issue": null, "title": "Int J Obes (Lond)", "issn-l": "0307-0565"}, "abstract": "There is an important interplay between epigenetic factors and body weight, and previous work has identified ten sites where DNA methylation is robustly associated with body mass index (BMI) cross-sectionally. However, interpretation of the associations is complicated by the substantial changes in BMI often occurring in late-life, and the fact that methylation is often driven by genetic variation. This study therefore investigated the longitudinal association between these ten sites and BMI from midlife to late-life, and whether associations persist after controlling for genetic factors.\n\nWe used data from 535 individuals (mean age 68) in the Swedish Adoption/Twin Study of Aging (SATSA) with longitudinal measures of both DNA methylation from blood samples and BMI, spanning up to 20 years. Methylation levels were measured with the Infinium Human Methylation 450K or Infinium MethylationEpic array, with seven of the ten sites passing quality control. Latent growth curve models were applied to investigate longitudinal associations between methylation and BMI, and between-within models to study associations within twin pairs, thus adjusting for genetic factors.\n\nBaseline DNA methylation levels at five of the seven sites were associated with BMI level at age 65 (cg00574958 [CPT1A]; cg11024682 [SREBF1]), and/or change (cg06192883 [MYO5C]; cg06946797 [RMI2]; cg08857797 [VPS25]). For four of the five sites, the associations remained comparable within twin pairs. However, the effects of cg06192883 were substantially attenuated within pairs. No change in DNA methylation was detected for any of the seven evaluated sites.\n\nFive of the seven sites investigated were associated with late-life level and/or change in BMI. The effects for four of the sites remained similar when examined within twin pairs, indicating that the associations are mainly environmentally driven. However, the substantial attenuation in the association between cg06192883 and late-life BMI within pairs points to the importance of genetic factors in this association.", "doi": "10.1038/s41366-019-0498-6", "pmid": "31801962", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41366-019-0498-6"}], "notes": [], "created": "2019-12-12T08:51:06.058Z", "modified": "2024-01-16T13:48:43.346Z"}, {"entity": "publication", "iuid": "8f3a5c256e104f959dd462fe6d7ec82c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8f3a5c256e104f959dd462fe6d7ec82c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8f3a5c256e104f959dd462fe6d7ec82c"}}, "title": "The MADS-box transcription factor PHERES1 controls imprinting in the endosperm by binding to domesticated transposons.", "authors": [{"family": "Batista", "given": "Rita A", "initials": "RA", "orcid": "0000-0002-2083-4622", "researcher": {"href": "https://publications.scilifelab.se/researcher/e29741f654544bb6a03a3c1b49481f7b.json"}}, {"family": "Moreno-Romero", "given": "Jordi", "initials": "J"}, {"family": "Qiu", "given": "Yichun", "initials": "Y"}, {"family": "van Boven", "given": "Joram", "initials": "J"}, {"family": "Santos-Gonz\u00e1lez", "given": "Juan", "initials": "J"}, {"family": "Figueiredo", "given": "Duarte D", "initials": "DD", "orcid": "0000-0001-7990-3592", "researcher": {"href": "https://publications.scilifelab.se/researcher/c390239e3c6949d3af266f5dee344d5b.json"}}, {"family": "K\u00f6hler", "given": "Claudia", "initials": "C", "orcid": "0000-0002-2619-4857", "researcher": {"href": "https://publications.scilifelab.se/researcher/accd3f9307614c8ab67154dd5e50cdac.json"}}], "type": "journal article", "published": "2019-12-02", "journal": {"volume": "8", "issn": "2050-084X", "issue": null, "pages": null, "title": "Elife", "issn-l": "2050-084X"}, "abstract": "MADS-box transcription factors (TFs) are ubiquitous in eukaryotic organisms and play major roles during plant development. Nevertheless, their function in seed development remains largely unknown. Here, we show that the imprinted Arabidopsis thaliana MADS-box TF PHERES1 (PHE1) is a master regulator of paternally expressed imprinted genes, as well as of non-imprinted key regulators of endosperm development. PHE1 binding sites show distinct epigenetic modifications on maternal and paternal alleles, correlating with parental-specific transcriptional activity. Importantly, we show that the CArG-box-like DNA-binding motifs that are bound by PHE1 have been distributed by RC/Helitron transposable elements. Our data provide an example of the molecular domestication of these elements which, by distributing PHE1 binding sites throughout the genome, have facilitated the recruitment of crucial endosperm regulators into a single transcriptional network.", "doi": "10.7554/eLife.50541", "pmid": "31789592", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "50541"}, {"db": "pmc", "key": "PMC6914339"}, {"db": "GEO", "key": "GSE129744"}, {"db": "GEO", "key": "GSE66585"}, {"db": "GEO", "key": "GSE84122"}, {"db": "GEO", "key": "GSE53642"}, {"db": "GEO", "key": "GSE119915"}, {"db": "GEO", "key": "GSE12404"}], "notes": [], "created": "2020-01-08T12:45:42.774Z", "modified": "2021-06-16T14:39:46.058Z"}, {"entity": "publication", "iuid": "75c0d2a11d08485782437af9dc2ef53a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/75c0d2a11d08485782437af9dc2ef53a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/75c0d2a11d08485782437af9dc2ef53a"}}, "title": "Population history and genetic adaptation of the Fulani nomads: inferences from genome-wide data and the lactase persistence trait.", "authors": [{"family": "Vicente", "given": "M\u00e1rio", "initials": "M"}, {"family": "Priehodov\u00e1", "given": "Edita", "initials": "E"}, {"family": "Diallo", "given": "Issa", "initials": "I"}, {"family": "Podgorn\u00e1", "given": "Eli\u0161ka", "initials": "E"}, {"family": "Poloni", "given": "Estella S", "initials": "ES"}, {"family": "\u010cern\u00fd", "given": "Viktor", "initials": "V"}, {"family": "Schlebusch", "given": "Carina M", "initials": "CM"}], "type": "journal article", "published": "2019-12-02", "journal": {"volume": "20", "issn": "1471-2164", "issue": "1", "pages": "915", "title": "BMC Genomics", "issn-l": "1471-2164"}, "abstract": "Human population history in the Holocene was profoundly impacted by changes in lifestyle following the invention and adoption of food-production practices. These changes triggered significant increases in population sizes and expansions over large distances. Here we investigate the population history of the Fulani, a pastoral population extending throughout the African Sahel/Savannah belt.\n\nBased on genome-wide analyses we propose that ancestors of the Fulani population experienced admixture between a West African group and a group carrying both European and North African ancestries. This admixture was likely coupled with newly adopted herding practices, as it resulted in signatures of genetic adaptation in contemporary Fulani genomes, including the control element of the LCT gene enabling carriers to digest lactose throughout their lives. The lactase persistence (LP) trait in the Fulani is conferred by the presence of the allele T-13910, which is also present at high frequencies in Europe. We establish that the T-13910 LP allele in Fulani individuals analysed in this study lies on a European haplotype background thus excluding parallel convergent evolution. We furthermore directly link the T-13910 haplotype with the Lactase Persistence phenotype through a Genome Wide Association study (GWAS) and identify another genomic region in the vicinity of the SPRY2 gene associated with glycaemic measurements after lactose intake.\n\nOur findings suggest that Eurasian admixture and the European LP allele was introduced into the Fulani through contact with a North African population/s. We furthermore confirm the link between the lactose digestion phenotype in the Fulani to the MCM6/LCT locus by reporting the first GWAS of the lactase persistence trait. We also explored other signals of recent adaptation in the Fulani and identified additional candidates for selection to adapt to herding life-styles.", "doi": "10.1186/s12864-019-6296-7", "pmid": "31791255", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1186/s12864-019-6296-7"}], "notes": [], "created": "2019-12-04T15:15:34.229Z", "modified": "2024-01-16T13:48:43.354Z"}, {"entity": "publication", "iuid": "ca73dd7b26da44ba81bd7bcb0e8847ff", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ca73dd7b26da44ba81bd7bcb0e8847ff.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ca73dd7b26da44ba81bd7bcb0e8847ff"}}, "title": "DNA methylation profiles in chronic lymphocytic leukemia patients treated with chemoimmunotherapy.", "authors": [{"family": "Tsagiopoulou", "given": "Maria", "initials": "M"}, {"family": "Papakonstantinou", "given": "Nikos", "initials": "N"}, {"family": "Moysiadis", "given": "Theodoros", "initials": "T"}, {"family": "Mansouri", "given": "Larry", "initials": "L"}, {"family": "Ljungstr\u00f6m", "given": "Viktor", "initials": "V"}, {"family": "Duran-Ferrer", "given": "Mart\u00ed", "initials": "M"}, {"family": "Malousi", "given": "Andigoni", "initials": "A"}, {"family": "Queir\u00f3s", "given": "Ana C", "initials": "AC"}, {"family": "Plevova", "given": "Karla", "initials": "K"}, {"family": "Bhoi", "given": "Sujata", "initials": "S"}, {"family": "Kollia", "given": "Panagoula", "initials": "P"}, {"family": "Oscier", "given": "David", "initials": "D"}, {"family": "Anagnostopoulos", "given": "Achilles", "initials": "A"}, {"family": "Trentin", "given": "Livio", "initials": "L"}, {"family": "Ritgen", "given": "Matthias", "initials": "M"}, {"family": "Pospisilova", "given": "Sarka", "initials": "S"}, {"family": "Stavroyianni", "given": "Niki", "initials": "N"}, {"family": "Ghia", "given": "Paolo", "initials": "P"}, {"family": "Martin-Subero", "given": "Jose I", "initials": "JI"}, {"family": "Pott", "given": "Christiane", "initials": "C"}, {"family": "Rosenquist", "given": "Richard", "initials": "R"}, {"family": "Stamatopoulos", "given": "Kostas", "initials": "K"}], "type": "journal article", "published": "2019-12-02", "journal": {"volume": "11", "issn": "1868-7075", "issue": "1", "pages": "177", "title": "Clin Epigenetics", "issn-l": null}, "abstract": "In order to gain insight into the contribution of DNA methylation to disease progression of chronic lymphocytic leukemia (CLL), using 450K Illumina arrays, we determined the DNA methylation profiles in paired pre-treatment/relapse samples from 34 CLL patients treated with chemoimmunotherapy, mostly (n = 31) with the fludarabine-cyclophosphamide-rituximab (FCR) regimen.\n\nThe extent of identified changes in CLL cells versus memory B cells from healthy donors was termed \"epigenetic burden\" (EB) whereas the number of changes between the pre-treatment versus the relapse sample was termed \"relapse changes\" (RC). Significant (p < 0.05) associations were identified between (i) high EB and short time-to-first-treatment (TTFT); and, (ii) few RCs and short time-to-relapse. Both the EB and the RC clustered in specific genomic regions and chromatin states, including regulatory regions containing binding sites of transcription factors implicated in B cell and CLL biology.\n\nOverall, we show that DNA methylation in CLL follows different dynamics in response to chemoimmunotherapy. These epigenetic alterations were linked with specific clinical and biological features.", "doi": "10.1186/s13148-019-0783-1", "pmid": "31791414", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1186/s13148-019-0783-1"}], "notes": [], "created": "2019-12-09T10:09:05.829Z", "modified": "2020-01-21T13:56:15.999Z"}, {"entity": "publication", "iuid": "31af97f3e7794e698898124e67568507", "links": {"self": {"href": "https://publications.scilifelab.se/publication/31af97f3e7794e698898124e67568507.json"}, "display": {"href": "https://publications.scilifelab.se/publication/31af97f3e7794e698898124e67568507"}}, "title": "Arteria: An automation system for a sequencing core facility.", "authors": [{"family": "Dahlberg", "given": "Johan", "initials": "J"}, {"family": "Hermansson", "given": "Johan", "initials": "J"}, {"family": "Sturlaugsson", "given": "Steinar", "initials": "S"}, {"family": "Lysenkova", "given": "Mariya", "initials": "M"}, {"family": "Smeds", "given": "Patrik", "initials": "P"}, {"family": "Ladenvall", "given": "Claes", "initials": "C"}, {"family": "Guimera", "given": "Roman Valls", "initials": "RV"}, {"family": "Reisinger", "given": "Florian", "initials": "F"}, {"family": "Hofmann", "given": "Oliver", "initials": "O"}, {"family": "Larsson", "given": "Pontus", "initials": "P"}], "type": "journal article", "published": "2019-12-01", "journal": {"volume": "8", "issn": "2047-217X", "issue": "12", "pages": null, "title": "Gigascience", "issn-l": "2047-217X"}, "abstract": "In recent years, nucleotide sequencing has become increasingly instrumental in both research and clinical settings. This has led to an explosive growth in sequencing data produced worldwide. As the amount of data increases, so does the need for automated solutions for data processing and analysis. The concept of workflows has gained favour in the bioinformatics community, but there is little in the scientific literature describing end-to-end automation systems. Arteria is an automation system that aims at providing a solution to the data-related operational challenges that face sequencing core facilities.\n\nArteria is built on existing open source technologies, with a modular design allowing for a community-driven effort to create plug-and-play micro-services. In this article we describe the system, elaborate on the underlying conceptual framework, and present an example implementation. Arteria can be reduced to 3 conceptual levels: orchestration (using an event-based model of automation), process (the steps involved in processing sequencing data, modelled as workflows), and execution (using a series of RESTful micro-services). This creates a system that is both flexible and scalable. Arteria-based systems have been successfully deployed at 3 sequencing core facilities. The Arteria Project code, written largely in Python, is available as open source software, and more information can be found at https://arteria-project.github.io/ .\n\nWe describe the Arteria system and the underlying conceptual framework, demonstrating how this model can be used to automate data handling and analysis in the context of a sequencing core facility.", "doi": "10.1093/gigascience/giz135", "pmid": "31825479", "labels": {"National Genomics Infrastructure": "Technology development", "NGI Uppsala (SNP&SEQ Technology Platform)": "Technology development", "Clinical Genomics Uppsala": "Technology development", "Clinical Genomics": "Technology development"}, "xrefs": [{"db": "pii", "key": "5673459"}, {"db": "pmc", "key": "PMC6905352"}], "notes": [], "created": "2020-01-08T12:39:25.028Z", "modified": "2021-07-08T12:39:20.845Z"}, {"entity": "publication", "iuid": "1352e2277ea64042b7223339b4060434", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1352e2277ea64042b7223339b4060434.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1352e2277ea64042b7223339b4060434"}}, "title": "Transmission dynamics study of tuberculosis isolates with whole genome sequencing in southern Sweden", "authors": [{"family": "Alaridah", "given": "Nader", "initials": "N"}, {"family": "Hallb\u00e4ck", "given": "Erika T\u00e5ng", "initials": "ET"}, {"family": "T\u00e5ngrot", "given": "Jeanette", "initials": "J"}, {"family": "Winqvist", "given": "Niclas", "initials": "N"}, {"family": "Stureg\u00e5rd", "given": "Erik", "initials": "E"}, {"family": "Flor\u00e9n-Johansson", "given": "Kerstin", "initials": "K"}, {"family": "J\u00f6nsson", "given": "Bodil", "initials": "B"}, {"family": "Tenland", "given": "Erik", "initials": "E"}, {"family": "Welinder-Olsson", "given": "Christina", "initials": "C"}, {"family": "Medstrand", "given": "Patrik", "initials": "P"}, {"family": "Kaijser", "given": "Bertil", "initials": "B"}, {"family": "Godaly", "given": "Gabriela", "initials": "G"}], "type": "journal-article", "published": "2019-12-00", "journal": {"volume": "9", "issn": "2045-2322", "issue": "1", "pages": null, "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "Epidemiological contact tracing complemented with genotyping of clinical Mycobacterium tuberculosis isolates is important for understanding disease transmission. In Sweden, tuberculosis (TB) is mostly reported in migrant and homeless where epidemiologic contact tracing could pose a problem. This study compared epidemiologic linking with genotyping in a low burden country. Mycobacterium tuberculosis isolates (n = 93) collected at Scania University Hospital in Southern Sweden were analysed with the standard genotyping method mycobacterial interspersed repetitive units-variable number tandem repeats (MIRU-VNTR) and the results were compared with whole genome sequencing (WGS). Using a maximum of twelve single nucleotide polymorphisms (SNPs) as the upper threshold of genomic relatedness noted among hosts, we identified 18 clusters with WGS comprising 52 patients with overall pairwise genetic maximum distances ranging from zero to nine SNPs. MIRU-VNTR and WGS clustered the same isolates, although the distribution differed depending on MIRU-VNTR limitations. Both genotyping techniques identified clusters where epidemiologic linking was insufficient, although WGS had higher correlation with epidemiologic data. To summarize, WGS provided better resolution of transmission than MIRU-VNTR in a setting with low TB incidence. WGS predicted epidemiologic links better which could consolidate and correct the epidemiologically linked cases, avoiding thus false clustering.", "doi": "10.1038/s41598-019-39971-z", "pmid": "30894568", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support and Infrastructure": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [], "notes": [], "created": "2019-04-23T15:06:38.395Z", "modified": "2020-01-21T13:56:17.604Z"}, {"entity": "publication", "iuid": "1a1d372b9e16494cbd68b5793f731edf", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1a1d372b9e16494cbd68b5793f731edf.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1a1d372b9e16494cbd68b5793f731edf"}}, "title": "Transcriptomes of Dravet syndrome iPSC derived GABAergic cells reveal dysregulated pathways for chromatin remodeling and neurodevelopment.", "authors": [{"family": "Schuster", "given": "Jens", "initials": "J", "orcid": "0000-0002-4383-9880", "researcher": {"href": "https://publications.scilifelab.se/researcher/a194d037b21c47a2926b082e9e79de31.json"}}, {"family": "Laan", "given": "Loora", "initials": "L"}, {"family": "Klar", "given": "Joakim", "initials": "J"}, {"family": "Jin", "given": "Zhe", "initials": "Z"}, {"family": "Huss", "given": "Mikael", "initials": "M"}, {"family": "Korol", "given": "Sergiy", "initials": "S"}, {"family": "Noraddin", "given": "Feria Hikmet", "initials": "FH"}, {"family": "Sobol", "given": "Maria", "initials": "M"}, {"family": "Birnir", "given": "Bryndis", "initials": "B"}, {"family": "Dahl", "given": "Niklas", "initials": "N", "orcid": "0000-0002-8122-0800", "researcher": {"href": "https://publications.scilifelab.se/researcher/689e06ddc001490a8cb891050ba5a732.json"}}], "type": "journal article", "published": "2019-12-00", "journal": {"volume": "132", "issn": "1095-953X", "issue": null, "pages": "104583", "title": "Neurobiol. Dis.", "issn-l": "0969-9961"}, "abstract": "Dravet syndrome (DS) is an early onset refractory epilepsy typically caused by de novo heterozygous variants in SCN1A encoding the \u03b1-subunit of the neuronal sodium channel Na v1.1. The syndrome is characterized by age-related progression of seizures, cognitive decline and movement disorders. We hypothesized that the distinct neurodevelopmental features in DS are caused by the disruption of molecular pathways in Nav1.1 haploinsufficient cells resulting in perturbed neural differentiation and maturation. Here, we established DS-patient and control induced pluripotent stem cell derived neural progenitor cells (iPSC NPC) and GABAergic inter-neuronal (iPSC GABA) cells. The DS-patient iPSC GABA cells showed a shift in sodium current activation and a perturbed response to induced oxidative stress. Transcriptome analysis revealed specific dysregulations of genes for chromatin structure, mitotic progression, neural plasticity and excitability in DS-patient iPSC NPCs and DS-patient iPSC GABA cells versus controls. The transcription factors FOXM1 and E2F1, positive regulators of the disrupted pathways for histone modification and cell cycle regulation, were markedly up-regulated in DS-iPSC GABA lines. Our study highlights transcriptional changes and disrupted pathways of chromatin remodeling in Nav1.1 haploinsufficient GABAergic cells, providing a molecular framework that overlaps with that of neurodevelopmental disorders and other epilepsies.", "doi": "10.1016/j.nbd.2019.104583", "pmid": "31445158", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "S0969-9961(19)30251-7"}], "notes": [], "created": "2019-11-20T15:33:02.190Z", "modified": "2024-01-16T13:48:43.380Z"}, {"entity": "publication", "iuid": "ddddcada24bb4fd693b02a2124cff7ca", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ddddcada24bb4fd693b02a2124cff7ca.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ddddcada24bb4fd693b02a2124cff7ca"}}, "title": "The genomic footprint of sexual conflict.", "authors": [{"family": "Sayadi", "given": "Ahmed", "initials": "A"}, {"family": "Martinez Barrio", "given": "Alvaro", "initials": "A"}, {"family": "Immonen", "given": "Elina", "initials": "E"}, {"family": "Dainat", "given": "Jacques", "initials": "J"}, {"family": "Berger", "given": "David", "initials": "D"}, {"family": "Tellgren-Roth", "given": "Christian", "initials": "C"}, {"family": "Nystedt", "given": "Bj\u00f6rn", "initials": "B", "orcid": "0000-0001-7809-7664", "researcher": {"href": "https://publications.scilifelab.se/researcher/f0af5a168baa4b00a6fab8d3447ebfb4.json"}}, {"family": "Arnqvist", "given": "G\u00f6ran", "initials": "G"}], "type": "journal article", "published": "2019-12-00", "journal": {"volume": "3", "issn": "2397-334X", "issue": "12", "pages": "1725-1730", "title": "Nat Ecol Evol", "issn-l": "2397-334X"}, "abstract": "Genes with sex-biased expression show a number of unique properties and this has been seen as evidence for conflicting selection pressures in males and females, forming a genetic 'tug-of-war' between the sexes. However, we lack studies of taxa where an understanding of conflicting phenotypic selection in the sexes has been linked with studies of genomic signatures of sexual conflict. Here, we provide such a link. We used an insect where sexual conflict is unusually well understood, the seed beetle Callosobruchus maculatus, to test for molecular genetic signals of sexual conflict across genes with varying degrees of sex-bias in expression. We sequenced, assembled and annotated its genome and performed population resequencing of three divergent populations. Sex-biased genes showed increased levels of genetic diversity and bore a remarkably clear footprint of relaxed purifying selection. Yet, segregating genetic variation was also affected by balancing selection in weakly female-biased genes, while male-biased genes showed signs of overall purifying selection. Female-biased genes contributed disproportionally to shared polymorphism across populations, while male-biased genes, male seminal fluid protein genes and sex-linked genes did not. Genes showing genomic signatures consistent with sexual conflict generally matched life-history phenotypes known to experience sexually antagonistic selection in this species. Our results highlight metabolic and reproductive processes, confirming the key role of general life-history traits in sexual conflict.", "doi": "10.1038/s41559-019-1041-9", "pmid": "31740847", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support and Infrastructure": "Service", "NGI Uppsala (Uppsala Genome Center)": "Collaborative", "National Genomics Infrastructure": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1038/s41559-019-1041-9"}], "notes": [], "created": "2019-12-05T15:30:07.525Z", "modified": "2024-01-16T13:48:43.388Z"}, {"entity": "publication", "iuid": "a5ab01a5bde945bfb283a90ca30e3fb5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a5ab01a5bde945bfb283a90ca30e3fb5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a5ab01a5bde945bfb283a90ca30e3fb5"}}, "title": "Studies of liver tissue identify functional gene regulatory elements associated to gene expression, type 2 diabetes, and other metabolic diseases", "authors": [{"family": "Cavalli", "given": "Marco", "initials": "M"}, {"family": "Baltzer", "given": "Nicholas", "initials": "N"}, {"family": "Pan", "given": "Gang", "initials": "G"}, {"family": "B\u00e1rcenas Walls", "given": "Jos\u00e9 Ram\u00f3n", "initials": "JR"}, {"family": "Smolinska Garbulowska", "given": "Karolina", "initials": "K"}, {"family": "Kumar", "given": "Chanchal", "initials": "C"}, {"family": "Skrtic", "given": "Stanko", "initials": "S"}, {"family": "Komorowski", "given": "Jan", "initials": "J"}, {"family": "Wadelius", "given": "Claes", "initials": "C"}], "type": "journal-article", "published": "2019-12-00", "journal": {"volume": "13", "issn": "1479-7364", "issue": "1", "pages": "20", "title": "Hum Genomics", "issn-l": "1473-9542"}, "abstract": "Genome-wide association studies (GWAS) of diseases and traits have found associations to gene regions but not the functional SNP or the gene mediating the effect. Difference in gene regulatory signals can be detected using chromatin immunoprecipitation and next-gen sequencing (ChIP-seq) of transcription factors or histone modifications by aligning reads to known polymorphisms in individual genomes. The aim was to identify such regulatory elements in the human liver to understand the genetics behind type 2 diabetes and metabolic diseases.\n\nThe genome of liver tissue was sequenced using 10X Genomics technology to call polymorphic positions. Using ChIP-seq for two histone modifications, H3K4me3 and H3K27ac, and the transcription factor CTCF, and our established bioinformatics pipeline, we detected sites with significant difference in signal between the alleles.\n\nWe detected 2329 allele-specific SNPs (AS-SNPs) including 25 associated to GWAS SNPs linked to liver biology, e.g., 4 AS-SNPs at two type 2 diabetes loci. Two hundred ninety-two AS-SNPs were associated to liver gene expression in GTEx, and 134 AS-SNPs were located on 166 candidate functional motifs and most of them in EGR1-binding sites.\n\nThis study provides a valuable collection of candidate liver regulatory elements for further experimental validation.", "doi": "10.1186/s40246-019-0204-8", "pmid": "31036066", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1186/s40246-019-0204-8"}, {"db": "pmc", "key": "PMC6489362"}], "notes": [], "created": "2020-01-08T12:42:51.378Z", "modified": "2021-06-16T14:44:36.175Z"}, {"entity": "publication", "iuid": "7d00b2f694174425a4e820b73f5c248b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7d00b2f694174425a4e820b73f5c248b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7d00b2f694174425a4e820b73f5c248b"}}, "title": "Insight into the biology of Mycobacterium mucogenicum and Mycobacterium neoaurum clade members", "authors": [{"family": "Behra", "given": "Phani Rama Krishna", "initials": "PRK"}, {"family": "Pettersson", "given": "B M Fredrik", "initials": "BMF"}, {"family": "Ramesh", "given": "Malavika", "initials": "M"}, {"family": "Dasgupta", "given": "Santanu", "initials": "S"}, {"family": "Kirsebom", "given": "Leif A", "initials": "LA", "orcid": "0000-0002-5092-512X", "researcher": {"href": "https://publications.scilifelab.se/researcher/e80849a89d0043b0b4daff9804c67332.json"}}], "type": "journal-article", "published": "2019-12-00", "journal": {"volume": "9", "issn": "2045-2322", "issue": "1", "pages": "19259", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "Nontuberculous mycobacteria, NTM, are of growing concern and among these members of the Mycobacterium mucogenicum (Mmuc) and Mycobacterium neoaurum (Mneo) clades can cause infections in humans and they are resistant to first-line anti-tuberculosis drugs. They can be isolated from different ecological niches such as soil, tap water and ground water. Mycobacteria, such as Mmuc and Mneo, are classified as rapid growing mycobacteria, RGM, while the most familiar, Mycobacterium tuberculosis, belongs to the slow growing mycobacteria, SGM. Modern \"omics\" approaches have provided new insights into our understanding of the biology and evolution of this group of bacteria. Here we present comparative genomics data for seventeen NTM of which sixteen belong to the Mmuc- and Mneo-clades. Focusing on virulence genes, including genes encoding sigma/anti-sigma factors, serine threonine protein kinases (STPK), type VII (ESX genes) secretion systems and mammalian cell entry (Mce) factors we provide insight into their presence as well as phylogenetic relationship in the case of the sigma/anti-sigma factors and STPKs. Our data further suggest that these NTM lack ESX-5 and Mce2 genes, which are known to affect virulence. In this context, Mmuc- and Mneo-clade members lack several of the genes in the glycopeptidolipid (GLP) locus, which have roles in colony morphotype appearance and virulence. For the M. mucogenicum type strain, Mmuc T, we provide RNASeq data focusing on mRNA levels for sigma factors, STPK, ESX proteins and Mce proteins. These data are discussed and compared to in particular the SGM and fish pathogen Mycobacterium marinum. Finally, we provide insight into as to why members of the Mmuc- and Mneo-clades show resistance to rifampin and isoniazid, and why MmucT forms a rough colony morphotype.", "doi": "10.1038/s41598-019-55464-5", "pmid": "31848383", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-019-55464-5"}, {"db": "pmc", "key": "PMC6917791"}], "notes": [], "created": "2020-01-08T12:38:20.448Z", "modified": "2021-06-16T14:51:44.614Z"}, {"entity": "publication", "iuid": "b1c8e445bafa421699e0ca5d311d02b9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b1c8e445bafa421699e0ca5d311d02b9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b1c8e445bafa421699e0ca5d311d02b9"}}, "title": "Improved power and precision with whole genome sequencing data in genome-wide association studies of inflammatory biomarkers", "authors": [{"family": "H\u00f6glund", "given": "Julia", "initials": "J"}, {"family": "Rafati", "given": "Nima", "initials": "N"}, {"family": "Rask-Andersen", "given": "Mathias", "initials": "M"}, {"family": "Enroth", "given": "Stefan", "initials": "S"}, {"family": "Karlsson", "given": "Torgny", "initials": "T"}, {"family": "Ek", "given": "Weronica E", "initials": "WE"}, {"family": "Johansson", "given": "\u00c5sa", "initials": "\u00c5"}], "type": "journal-article", "published": "2019-12-00", "journal": {"volume": "9", "issn": "2045-2322", "issue": "1", "pages": null, "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "Genome-wide association studies (GWAS) have identified associations between thousands of common genetic variants and human traits. However, common variants usually explain a limited fraction of the heritability of a trait. A powerful resource for identifying trait-associated variants is whole genome sequencing (WGS) data in cohorts comprised of families or individuals from a limited geographical area. To evaluate the power of WGS compared to imputations, we performed GWAS on WGS data for 72 inflammatory biomarkers, in a kinship-structured cohort. When using WGS data, we identified 18 novel associations that were not detected when analyzing the same biomarkers with genotyped or imputed SNPs. Five of the novel top variants were low frequency variants with a minor allele frequency (MAF) of <5%. Our results suggest that, even when applying a GWAS approach, we gain power and precision using WGS data, presumably due to more accurate determination of genotypes. The lack of a comparable dataset for replication of our results is a limitation in our study. However, this further highlights that there is a need for more genetic epidemiological studies based on WGS data.", "doi": "10.1038/s41598-019-53111-7", "pmid": "31727947", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Long-term Support WABI": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [], "notes": [], "created": "2019-11-29T12:36:47.798Z", "modified": "2024-01-16T13:48:43.415Z"}, {"entity": "publication", "iuid": "67cc504ce8344efe89d794909aabc482", "links": {"self": {"href": "https://publications.scilifelab.se/publication/67cc504ce8344efe89d794909aabc482.json"}, "display": {"href": "https://publications.scilifelab.se/publication/67cc504ce8344efe89d794909aabc482"}}, "title": "Genetic Prediction of Serum 25-Hydroxyvitamin D, Calcium, and Parathyroid Hormone Levels in Relation to Development of Type 2 Diabetes: A Mendelian Randomization Study.", "authors": [{"family": "Yuan", "given": "Shuai", "initials": "S"}, {"family": "Jiang", "given": "Xia", "initials": "X"}, {"family": "Micha\u00eblsson", "given": "Karl", "initials": "K"}, {"family": "Larsson", "given": "Susanna C", "initials": "SC"}], "type": "journal article", "published": "2019-12-00", "journal": {"volume": "42", "issn": "1935-5548", "issue": "12", "pages": "2197-2203", "title": "Diabetes Care", "issn-l": "0149-5992"}, "abstract": "We conducted a Mendelian randomization study to investigate the associations of genetically predicted serum 25-hydroxyvitamin D (S-25OHD), calcium (S-Ca), and parathyroid hormone (S-PTH) levels with type 2 diabetes (T2DM).\n\nSeven, six, and five single nucleotide polymorphisms (SNPs) associated with S-25OHD, S-Ca, and S-PTH levels, respectively, were used as instrumental variables. Data on T2DM were available for 74,124 case subjects with T2DM and 824,006 control subjects. The inverse variance-weighted method was used for the primary analyses, and the weighted median and Mendelian randomization (MR)-Egger methods were used for supplementary analyses.\n\nGenetically predicted S-25OHD but not S-Ca and S-PTH levels were associated with T2DM in the primary analyses. For 1 SD increment of S-25OHD levels, the odds ratio (OR) of T2DM was 0.94 (95% CI 0.88-0.99; P = 0.029) in an analysis based on all seven SNPs and 0.90 (95% CI 0.83-0.98; P = 0.011) in an analysis based on three SNPs within or near genes involved in vitamin D synthesis. Only the association based on the SNPs involved in vitamin D synthesis remained in the weighted median analysis, and no pleiotropy was detected (P = 0.153). Pleiotropy was detected in the analysis of S-Ca (P = 0.013). After correcting for this bias using MR-Egger regression, the OR of T2DM per 1 SD increment of S-Ca levels was 1.41 (95% CI 1.12-1.77; P = 0.003).\n\nModest lifelong higher S-25OHD levels were associated with reduced odds of T2DM, but the association was only robust for SNPs in the vitamin D synthesis pathway. The possible role of S-Ca levels for T2DM development requires further research.", "doi": "10.2337/dc19-1247", "pmid": "31548248", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "dc19-1247"}], "notes": [], "created": "2019-11-28T07:41:32.083Z", "modified": "2024-01-16T13:48:43.440Z"}, {"entity": "publication", "iuid": "ba86a46c687f4ce7bb5fae6d07683dfd", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ba86a46c687f4ce7bb5fae6d07683dfd.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ba86a46c687f4ce7bb5fae6d07683dfd"}}, "title": "Epigenetic signatures associated with imprinted paternally expressed genes in the Arabidopsis endosperm", "authors": [{"family": "Moreno-Romero", "given": "Jordi", "initials": "J"}, {"family": "Del Toro-De Le\u00f3n", "given": "Gerardo", "initials": "G"}, {"family": "Yadav", "given": "Vikash Kumar", "initials": "VK"}, {"family": "Santos-Gonz\u00e1lez", "given": "Juan", "initials": "J"}, {"family": "K\u00f6hler", "given": "Claudia", "initials": "C"}], "type": "journal-article", "published": "2019-12-00", "journal": {"volume": "20", "issn": "1474-760X", "issue": "1", "pages": null, "title": "Genome Biol.", "issn-l": "1474-7596"}, "abstract": "Imprinted genes are epigenetically modified during gametogenesis and maintain the established epigenetic signatures after fertilization, causing parental-specific gene expression.\n\nIn this study, we show that imprinted paternally expressed genes (PEGs) in the Arabidopsis endosperm are marked by an epigenetic signature of Polycomb Repressive Complex2 (PRC2)-mediated H3K27me3 together with heterochromatic H3K9me2 and CHG methylation, which specifically mark the silenced maternal alleles of PEGs. The co-occurrence of H3K27me3 and H3K9me2 on defined loci in the endosperm drastically differs from the strict separation of both pathways in vegetative tissues, revealing tissue-specific employment of repressive epigenetic pathways in plants. Based on the presence of this epigenetic signature on maternal alleles, we are able to predict known PEGs at high accuracy and identify several new PEGs that we confirm using INTACT-based transcriptomes generated in this study.\n\nThe presence of the three repressive epigenetic marks, H3K27me3, H3K9me2, and CHG methylation on the maternal alleles in the endosperm serves as a specific epigenetic signature that allows prediction of genes with parental-specific gene expression. Our study reveals that there are substantially more PEGs than previously identified, indicating that paternal-specific gene expression is of higher functional relevance than currently estimated. The combined activity of PRC2-mediated H3K27me3 together with the heterochromatic H3K9me3 has also been reported to silence the maternal Xist locus in mammalian preimplantation embryos, suggesting convergent employment of both pathways during the evolution of genomic imprinting.", "doi": "10.1186/s13059-019-1652-0", "pmid": "30791924", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service"}, "xrefs": [], "notes": [], "created": "2019-11-25T14:50:26.905Z", "modified": "2020-01-21T13:56:16.670Z"}, {"entity": "publication", "iuid": "4a17548e14a9443faef15b5e0f5a9e78", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4a17548e14a9443faef15b5e0f5a9e78.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4a17548e14a9443faef15b5e0f5a9e78"}}, "title": "The Swedish Twin Registry: Content and Management as a Research Infrastructure.", "authors": [{"family": "Zagai", "given": "Ulrika", "initials": "U"}, {"family": "Lichtenstein", "given": "Paul", "initials": "P"}, {"family": "Pedersen", "given": "Nancy L", "initials": "NL"}, {"family": "Magnusson", "given": "Patrik K E", "initials": "PKE"}], "type": "journal article", "published": "2019-11-21", "journal": {"volume": null, "issn": "1832-4274", "issue": null, "pages": "1-9", "title": "Twin Res Hum Genet", "issn-l": null}, "abstract": "The Swedish Twin Registry functions as research infrastructure containing information on 216,258 twins born between 1886 and 2015, of whom 86,199 pairs have zygosity determined by DNA, an intrapair similarity algorithm, or being of opposite sex. In essence, practically all twins alive and currently 9 years or older have been invited for participation and donation of DNA on which genomewide single nucleotide polymorphisms array genotyping has been performed. Content, management and alternatives for future improvements are discussed.", "doi": "10.1017/thg.2019.99", "pmid": "31747977", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "S1832427419000999"}], "notes": [], "created": "2019-11-28T07:41:35.824Z", "modified": "2024-01-16T13:48:43.476Z"}, {"entity": "publication", "iuid": "d04554a222c64b18b5a4907124fce362", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d04554a222c64b18b5a4907124fce362.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d04554a222c64b18b5a4907124fce362"}}, "title": "Evidence that genes involved in hedgehog signaling are associated with both bipolar disorder and high BMI.", "authors": [{"family": "Pisanu", "given": "Claudia", "initials": "C"}, {"family": "Williams", "given": "Michael J", "initials": "MJ"}, {"family": "Ciuculete", "given": "Diana M", "initials": "DM"}, {"family": "Olivo", "given": "Gaia", "initials": "G"}, {"family": "Del Zompo", "given": "Maria", "initials": "M"}, {"family": "Squassina", "given": "Alessio", "initials": "A"}, {"family": "Schi\u00f6th", "given": "Helgi B", "initials": "HB"}], "type": "journal article", "published": "2019-11-21", "journal": {"volume": "9", "issn": "2158-3188", "issue": "1", "pages": "315", "title": "Transl Psychiatry", "issn-l": "2158-3188"}, "abstract": "Patients with bipolar disorder (BD) show higher frequency of obesity and type 2 diabetes (T2D), but the underlying genetic determinants and molecular pathways are not well studied. Using large publicly available datasets, we (1) conducted a gene-based analysis using MAGMA to identify genes associated with BD and body mass index (BMI) or T2D and investigated their functional enrichment; and (2) performed two meta-analyses between BD and BMI, as well as BD and T2D using Metasoft. Target druggability was assessed using the Drug Gene Interaction Database (DGIdb). We identified 518 and 390 genes significantly associated with BD and BMI or BD and T2D, respectively. A total of 52 and 12 genes, respectively, were significant after multiple testing correction. Pathway analyses conducted on nominally significant targets showed that genes associated with BD and BMI were enriched for the Neuronal cell body Gene Ontology (GO) term (p = 1.0E-04; false discovery rate (FDR) = 0.025) and different pathways, including the Signaling by Hedgehog pathway (p = 4.8E-05, FDR = 0.02), while genes associated with BD and T2D showed no specific enrichment. The meta-analysis between BD and BMI identified 64 relevant single nucleotide polymorphisms (SNPs). While the majority of these were located in intergenic regions or in a locus on chromosome 16 near and in the NPIPL1 and SH2B1 genes (best SNP: rs4788101, p = 2.1E-24), five were located in the ETV5 gene (best SNP: rs1516725, p = 1E-24), which was previously associated with both BD and obesity, and one in the RPGRIP1L gene (rs1477199, p = 5.7E-09), which was also included in the Signaling by Hedgehog pathway. The meta-analysis between BD and T2D identified six significant SNPs, three of which were located in ALAS1 (best SNP: rs352165, p = 3.4E-08). Thirteen SNPs associated with BD and BMI, and one with BD and T2D, were located in genes which are part of the druggable genome. Our results support the hypothesis of shared genetic determinants between BD and BMI and point to genes involved in Hedgehog signaling as promising targets.", "doi": "10.1038/s41398-019-0652-x", "pmid": "31754094", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41398-019-0652-x"}], "notes": [], "created": "2019-11-28T07:41:33.694Z", "modified": "2024-01-16T13:48:43.483Z"}, {"entity": "publication", "iuid": "9636a3d2b2d54eaaa019ac0da7105d74", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9636a3d2b2d54eaaa019ac0da7105d74.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9636a3d2b2d54eaaa019ac0da7105d74"}}, "title": "Genotype-dependent epigenetic regulation of DLGAP2 in alcohol use and dependence.", "authors": [{"family": "Meng", "given": "Weida", "initials": "W"}, {"family": "Sj\u00f6holm", "given": "Louise K", "initials": "LK"}, {"family": "Kononenko", "given": "Olga", "initials": "O"}, {"family": "Tay", "given": "Nicole", "initials": "N"}, {"family": "Zhang", "given": "Dandan", "initials": "D"}, {"family": "Sarkisyan", "given": "Daniil", "initials": "D"}, {"family": "Geske", "given": "Jennifer R", "initials": "JR"}, {"family": "Ing", "given": "Alex", "initials": "A"}, {"family": "Qiu", "given": "Wenqing", "initials": "W"}, {"family": "Watanabe", "given": "Hiroyuki", "initials": "H"}, {"family": "Almamoun", "given": "Radwa", "initials": "R"}, {"family": "Frieling", "given": "Helge", "initials": "H"}, {"family": "Bleich", "given": "Stefan", "initials": "S"}, {"family": "Cui", "given": "Donghong", "initials": "D"}, {"family": "Biernacka", "given": "Joanna M", "initials": "JM"}, {"family": "Mayfield", "given": "R Dayne", "initials": "RD"}, {"family": "Dang", "given": "Yongjun", "initials": "Y"}, {"family": "Karpyak", "given": "Victor M", "initials": "VM"}, {"family": "Schumann", "given": "Gunter", "initials": "G"}, {"family": "IMAGEN Consortium", "given": "", "initials": ""}, {"family": "Bakalkin", "given": "Georgy", "initials": "G"}, {"family": "Ekstr\u00f6m", "given": "Tomas J", "initials": "TJ"}, {"family": "R\u00fcegg", "given": "Joelle", "initials": "J"}, {"family": "Liu", "given": "Yun", "initials": "Y"}], "type": "journal article", "published": "2019-11-19", "journal": {"volume": null, "issn": "1476-5578", "issue": null, "title": "Mol. Psychiatry", "issn-l": "1359-4184"}, "abstract": "Alcohol misuse is a major public health problem originating from genetic and environmental risk factors. Alterations in the brain epigenome may orchestrate changes in gene expression that lead to alcohol misuse and dependence. Through epigenome-wide association analysis of DNA methylation from human brain tissues, we identified a differentially methylated region, DMR-DLGAP2, associated with alcohol dependence. Methylation within DMR-DLGAP2 was found to be genotype-dependent, allele-specific and associated with reward processing in brain. Methylation at the DMR-DLGAP2 regulated expression of DLGAP2 in vitro, and Dlgap2-deficient mice showed reduced alcohol consumption compared with wild-type controls. These results suggest that DLGAP2 may be an interface for genetic and epigenetic factors controlling alcohol use and dependence.", "doi": "10.1038/s41380-019-0588-9", "pmid": "31745236", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41380-019-0588-9"}], "notes": [], "created": "2019-11-28T07:41:32.986Z", "modified": "2024-01-16T13:48:43.518Z"}, {"entity": "publication", "iuid": "6ee8890ae41c4865a9558a5cc934c0f4", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6ee8890ae41c4865a9558a5cc934c0f4.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6ee8890ae41c4865a9558a5cc934c0f4"}}, "title": "Genetic regulation of gene expression and splicing during a 10-year period of human aging.", "authors": [{"family": "Balliu", "given": "Brunilda", "initials": "B"}, {"family": "Durrant", "given": "Matthew", "initials": "M"}, {"family": "Goede", "given": "Olivia de", "initials": "O"}, {"family": "Abell", "given": "Nathan", "initials": "N"}, {"family": "Li", "given": "Xin", "initials": "X"}, {"family": "Liu", "given": "Boxiang", "initials": "B"}, {"family": "Gloudemans", "given": "Michael J", "initials": "MJ"}, {"family": "Cook", "given": "Naomi L", "initials": "NL"}, {"family": "Smith", "given": "Kevin S", "initials": "KS"}, {"family": "Knowles", "given": "David A", "initials": "DA"}, {"family": "Pala", "given": "Mauro", "initials": "M"}, {"family": "Cucca", "given": "Francesco", "initials": "F"}, {"family": "Schlessinger", "given": "David", "initials": "D"}, {"family": "Jaiswal", "given": "Siddhartha", "initials": "S"}, {"family": "Sabatti", "given": "Chiara", "initials": "C"}, {"family": "Lind", "given": "Lars", "initials": "L"}, {"family": "Ingelsson", "given": "Erik", "initials": "E"}, {"family": "Montgomery", "given": "Stephen B", "initials": "SB"}], "type": "journal article", "published": "2019-11-04", "journal": {"volume": "20", "issn": "1474-760X", "issue": "1", "pages": "230", "title": "Genome Biol.", "issn-l": "1474-7596"}, "abstract": "Molecular and cellular changes are intrinsic to aging and age-related diseases. Prior cross-sectional studies have investigated the combined effects of age and genetics on gene expression and alternative splicing; however, there has been no long-term, longitudinal characterization of these molecular changes, especially in older age.\n\nWe perform RNA sequencing in whole blood from the same individuals at ages 70 and 80 to quantify how gene expression, alternative splicing, and their genetic regulation are altered during this 10-year period of advanced aging at a population and individual level. We observe that individuals are more similar to their own expression profiles later in life than profiles of other individuals their own age. We identify 1291 and 294 genes differentially expressed and alternatively spliced with age, as well as 529 genes with outlying individual trajectories. Further, we observe a strong correlation of genetic effects on expression and splicing between the two ages, with a small subset of tested genes showing a reduction in genetic associations with expression and splicing in older age.\n\nThese findings demonstrate that, although the transcriptome and its genetic regulation is mostly stable late in life, a small subset of genes is dynamic and is characterized by a reduction in genetic regulation, most likely due to increasing environmental variance with age.", "doi": "10.1186/s13059-019-1840-y", "pmid": "31684996", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1186/s13059-019-1840-y"}, {"db": "pmc", "key": "PMC6827221"}], "notes": [], "created": "2019-11-28T07:41:31.414Z", "modified": "2020-01-21T13:56:15.153Z"}, {"entity": "publication", "iuid": "de1bfea65dfe46d5bbe9caf4a2eb2305", "links": {"self": {"href": "https://publications.scilifelab.se/publication/de1bfea65dfe46d5bbe9caf4a2eb2305.json"}, "display": {"href": "https://publications.scilifelab.se/publication/de1bfea65dfe46d5bbe9caf4a2eb2305"}}, "title": "Sulfide level in municipal sludge digesters affects microbial community response to long-chain fatty acid loads.", "authors": [{"family": "Shakeri Yekta", "given": "Sepehr", "initials": "S"}, {"family": "Liu", "given": "Tong", "initials": "T"}, {"family": "Axelsson Bjerg", "given": "Mette", "initials": "M"}, {"family": "\u0160afari\u010d", "given": "Luka", "initials": "L"}, {"family": "Karlsson", "given": "Anna", "initials": "A"}, {"family": "Bj\u00f6rn", "given": "Annika", "initials": "A"}, {"family": "Schn\u00fcrer", "given": "Anna", "initials": "A"}], "type": "journal article", "published": "2019-11-02", "journal": {"volume": "12", "issn": "1754-6834", "issue": "1", "pages": "259", "title": "Biotechnol Biofuels", "issn-l": "1754-6834"}, "abstract": "Waste lipids are attractive substrates for co-digestion with primary and activated sewage sludge (PASS) to improve biogas production at wastewater treatment plants. However, slow conversion rates of long-chain fatty acids (LCFA), produced during anaerobic digestion (AD), limit the applicability of waste lipids as co-substrates for PASS. Previous observations indicate that the sulfide level in PASS digesters affects the capacity of microbial communities to convert LCFA to biogas. This study assessed the microbial community response to LCFA loads in relation to sulfide level during AD of PASS by investigating process performance and microbial community dynamics upon addition of oleate (C 18:1) and stearate (C18:0) to PASS digesters at ambient and elevated sulfide levels.\n\nConversion of LCFA to biogas was limited (30% of theoretical biogas potential) during continuous co-digestion with PASS, which resulted in further LCFA accumulation. However, the accumulated LCFA were converted to biogas (up to 66% of theoretical biogas potential) during subsequent batch-mode digestion, performed without additional substrate load. Elevated sulfide level stimulated oleate (but not stearate) conversion to acetate, but oleate and sulfide imposed a synergistic limiting effect on acetoclastic methanogenesis and biogas formation. Next-generation sequencing of 16S rRNA gene amplicons of bacteria and archaea showed that differences in sulfide level and LCFA type resulted in microbial community alterations with distinctly different patterns. Taxonomic profiling of the sequencing data revealed that the phylum Cloacimonetes is likely a key group during LCFA degradation in PASS digesters, where different members take part in degradation of saturated and unsaturated LCFA; genus W5 (family Cloacimonadaceae) and family W27 (order Cloacimonadales), respectively. In addition, LCFA-degrading Syntrophomonas, which is commonly present in lipid-fed digesters, increased in relative abundance after addition of oleate at elevated sulfide level, but not without sulfide or after stearate addition. Stearate conversion to biogas was instead associated with increasing abundance of hydrogen-producing Smithella and hydrogenotrophic Methanobacterium.\n\nLong-chain fatty acid chain saturation and sulfide level are selective drivers for establishment of LCFA-degrading microbial communities in municipal sludge digesters.", "doi": "10.1186/s13068-019-1598-1", "pmid": "31700542", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "1598"}, {"db": "pmc", "key": "PMC6825336"}], "notes": [], "created": "2019-12-03T10:45:03.087Z", "modified": "2021-06-16T14:40:57.121Z"}, {"entity": "publication", "iuid": "74be35950eca40edbc43a331133fbb7d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/74be35950eca40edbc43a331133fbb7d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/74be35950eca40edbc43a331133fbb7d"}}, "title": "Serum Parathyroid Hormone and Risk of Coronary Artery Disease: Exploring Causality Using Mendelian Randomization.", "authors": [{"family": "Melhus", "given": "H\u00e5kan", "initials": "H"}, {"family": "Micha\u00eblsson", "given": "Karl", "initials": "K"}, {"family": "Larsson", "given": "Susanna C", "initials": "SC"}], "type": "journal article", "published": "2019-11-01", "journal": {"volume": "104", "issn": "1945-7197", "issue": "11", "pages": "5595-5600", "title": "J. Clin. Endocrinol. Metab.", "issn-l": "0021-972X"}, "abstract": "Elevated circulating parathyroid hormone concentrations have been associated with increased risk of cardiovascular disease in observational studies, but whether the association is causal is unknown.\n\nWe used the Mendelian randomization design to test whether genetically increased serum parathyroid hormone (S-PTH) concentrations are associated with coronary artery disease (CAD).\n\nFive single-nucleotide polymorphisms robustly associated with S-PTH concentrations were used as instrumental variables to estimate the association of genetically higher S-PTH concentrations with CAD. Summary statistics data for CAD were obtained from a genetic consortium with data from 184,305 individuals (60,801 CAD cases and 123,504 noncases).\n\nOR of CAD per genetically predicted one SD increase of S-PTH concentrations.\n\nGenetically higher S-PTH concentration was not associated with CAD as a whole or myocardial infarction specifically (\u223c70% of total cases). The ORs per genetically predicted one SD increase in S-PTH concentration were 1.01 (95% CI: 0.93 to 1.09; P = 0.88) for CAD and 1.02 (95% CI: 0.94 to 1.10; P = 0.64) for myocardial infarction. The lack of association remained in various sensitivity analyses.\n\nGenetic predisposition to higher S-PTH concentrations does not appear to be an independent risk factor for CAD.", "doi": "10.1210/jc.2019-01063", "pmid": "31310319", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "5532038"}], "notes": [], "created": "2019-10-11T10:29:28.429Z", "modified": "2024-01-16T13:48:43.588Z"}, {"entity": "publication", "iuid": "0c62a08ad3364fb49240b4399d1c6a17", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0c62a08ad3364fb49240b4399d1c6a17.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0c62a08ad3364fb49240b4399d1c6a17"}}, "title": "A genomic inference of the White Plymouth Rock genealogy.", "authors": [{"family": "Guo", "given": "Y", "initials": "Y"}, {"family": "Lillie", "given": "M", "initials": "M"}, {"family": "Zan", "given": "Y", "initials": "Y"}, {"family": "Beranger", "given": "J", "initials": "J"}, {"family": "Martin", "given": "A", "initials": "A"}, {"family": "Honaker", "given": "C F", "initials": "CF"}, {"family": "Siegel", "given": "P B", "initials": "PB"}, {"family": "Carlborg", "given": "\u00d6", "initials": "\u00d6", "orcid": "0000-0002-2722-5264", "researcher": {"href": "https://publications.scilifelab.se/researcher/4efb0861e6144f00b8b4f5dd8a83c75b.json"}}], "type": "journal article", "published": "2019-11-01", "journal": {"volume": "98", "issn": "1525-3171", "issue": "11", "pages": "5272-5280", "title": "Poult. Sci.", "issn-l": "0032-5791"}, "abstract": "Crossing of populations has been, and still is, a central component in domestication and breed and variety formation. It is a way for breeders to utilize heterosis and to introduce new genetic variation into existing plant and livestock populations. During the mid-19th century, several chicken breeds that had been introduced to America from Europe and Asia became the founders for those formed in the USA. Historical records about the genealogy of these populations are often unclear and inconsistent. Here, we used genomics in an attempt to describe the ancestry of the White Plymouth Rock (WPR) chicken. In total, 150 chickens from the WPR and 8 other stocks that historical records suggested contributed to its formation were whole-genome re-sequenced. The admixture analyses of the autosomal and sex chromosomes showed that the WPR was likely founded as a cross between a paternal lineage that was primarily Dominique, and a maternal lineage where Black Java and Cochin contributed in essentially equal proportions. These results were consistent and provided quantification with the historical records that they were the main contributors to the WPR. The genomic analyses also revealed genome-wide contributions (<10% each) by Brahma, Langshan, and Black Minorca. When viewed on an individual chromosomal basis, contributions varied considerably among stocks.", "doi": "10.3382/ps/pez411", "pmid": "31309227", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "S0032-5791(19)45728-3"}, {"db": "pmc", "key": "PMC6863967"}], "notes": [], "created": "2020-01-08T12:44:55.485Z", "modified": "2021-06-16T16:21:12.189Z"}, {"entity": "publication", "iuid": "3a47c5fc960c4076accd675041affc60", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3a47c5fc960c4076accd675041affc60.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3a47c5fc960c4076accd675041affc60"}}, "title": "In search of causal pathways in diabetes: a study using proteomics and genotyping data from a cross-sectional study.", "authors": [{"family": "Beijer", "given": "Kristina", "initials": "K"}, {"family": "Nowak", "given": "Christoph", "initials": "C"}, {"family": "Sundstr\u00f6m", "given": "Johan", "initials": "J"}, {"family": "\u00c4rnl\u00f6v", "given": "Johan", "initials": "J"}, {"family": "Fall", "given": "Tove", "initials": "T"}, {"family": "Lind", "given": "Lars", "initials": "L"}], "type": "journal article", "published": "2019-11-00", "journal": {"title": "Diabetologia", "issn": "1432-0428", "issn-l": "0012-186X", "volume": "62", "issue": "11", "pages": "1998-2006"}, "abstract": "The pathogenesis of type 2 diabetes is not fully understood. We investigated whether circulating levels of preselected proteins were associated with the outcome 'diabetes' and whether these associations were causal.\n\nIn 2467 individuals of the population-based, cross-sectional EpiHealth study (45-75 years, 50% women), 249 plasma proteins were analysed by the proximity extension assay technique. DNA was genotyped using the Illumina HumanCoreExome-12 v1.0 BeadChip. Diabetes was defined as taking glucose-lowering treatment or having a fasting plasma glucose of \u22657.0 mmol/l. The associations between proteins and diabetes were assessed using logistic regression. To investigate causal relationships between proteins and diabetes, a bidirectional two-sample Mendelian randomisation was performed based on large, genome-wide association studies belonging to the DIAGRAM and MAGIC consortia, and a genome-wide association study in the EpiHealth study.\n\nTwenty-six proteins were positively associated with diabetes, including cathepsin D, retinal dehydrogenase 1, \u03b1-L-iduronidase, hydroxyacid oxidase 1 and galectin-4 (top five findings). Three proteins, lipoprotein lipase, IGF-binding protein 2 and paraoxonase 3 (PON-3), were inversely associated with diabetes. Fourteen of the proteins are novel discoveries. The Mendelian randomisation study did not disclose any significant causal effects between the proteins and diabetes in either direction that were consistent with the relationships found between the protein levels and diabetes.\n\nThe 29 proteins associated with diabetes are involved in several physiological pathways, but given the power of the study no causal link was identified for those proteins tested in Mendelian randomisation. Therefore, the identified proteins are likely to be biomarkers for type 2 diabetes, rather than representing causal pathways.", "doi": "10.1007/s00125-019-4960-8", "pmid": "31446444", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Clinical Biomarkers": "Service", "PLA and Single Cell Proteomics": "Service", "Affinity Proteomics Uppsala": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1007/s00125-019-4960-8"}, {"db": "pmc", "key": "PMC6805963"}], "notes": [], "created": "2019-09-05T12:01:54.527Z", "modified": "2024-01-16T13:48:43.603Z"}, {"entity": "publication", "iuid": "211a813209dd4aea84b0d15626f9044a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/211a813209dd4aea84b0d15626f9044a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/211a813209dd4aea84b0d15626f9044a"}}, "title": "Genetic predisposition to mosaic Y chromosome loss in blood.", "authors": [{"family": "Thompson", "given": "Deborah J", "initials": "DJ"}, {"family": "Genovese", "given": "Giulio", "initials": "G"}, {"family": "Halvardson", "given": "Jonatan", "initials": "J"}, {"family": "Ulirsch", "given": "Jacob C", "initials": "JC"}, {"family": "Wright", "given": "Daniel J", "initials": "DJ"}, {"family": "Terao", "given": "Chikashi", "initials": "C"}, {"family": "Davidsson", "given": "Olafur B", "initials": "OB"}, {"family": "Day", "given": "Felix R", "initials": "FR"}, {"family": "Sulem", "given": "Patrick", "initials": "P"}, {"family": "Jiang", "given": "Yunxuan", "initials": "Y"}, {"family": "Danielsson", "given": "Marcus", "initials": "M"}, {"family": "Davies", "given": "Hanna", "initials": "H"}, {"family": "Dennis", "given": "Joe", "initials": "J"}, {"family": "Dunlop", "given": "Malcolm G", "initials": "MG"}, {"family": "Easton", "given": "Douglas F", "initials": "DF"}, {"family": "Fisher", "given": "Victoria A", "initials": "VA"}, {"family": "Zink", "given": "Florian", "initials": "F"}, {"family": "Houlston", "given": "Richard S", "initials": "RS"}, {"family": "Ingelsson", "given": "Martin", "initials": "M"}, {"family": "Kar", "given": "Siddhartha", "initials": "S"}, {"family": "Kerrison", "given": "Nicola D", "initials": "ND"}, {"family": "Kinnersley", "given": "Ben", "initials": "B"}, {"family": "Kristjansson", "given": "Ragnar P", "initials": "RP"}, {"family": "Law", "given": "Philip J", "initials": "PJ"}, {"family": "Li", "given": "Rong", "initials": "R"}, {"family": "Loveday", "given": "Chey", "initials": "C"}, {"family": "Mattisson", "given": "Jonas", "initials": "J"}, {"family": "McCarroll", "given": "Steven A", "initials": "SA"}, {"family": "Murakami", "given": "Yoshinori", "initials": "Y"}, {"family": "Murray", "given": "Anna", "initials": "A"}, {"family": "Olszewski", "given": "Pawel", "initials": "P"}, {"family": "Rychlicka-Buniowska", "given": "Edyta", "initials": "E"}, {"family": "Scott", "given": "Robert A", "initials": "RA"}, {"family": "Thorsteinsdottir", "given": "Unnur", "initials": "U"}, {"family": "Tomlinson", "given": "Ian", "initials": "I"}, {"family": "Moghadam", "given": "Behrooz Torabi", "initials": "BT"}, {"family": "Turnbull", "given": "Clare", "initials": "C"}, {"family": "Wareham", "given": "Nicholas J", "initials": "NJ"}, {"family": "Gudbjartsson", "given": "Daniel F", "initials": "DF"}, {"family": "International Lung Cancer Consortium (INTEGRAL-ILCCO)", "given": "", "initials": ""}, {"family": "Breast Cancer Association Consortium", "given": "", "initials": ""}, {"family": "Consortium of Investigators of Modifiers of BRCA1/2", "given": "", "initials": ""}, {"family": "Endometrial Cancer Association Consortium", "given": "", "initials": ""}, {"family": "Ovarian Cancer Association Consortium", "given": "", "initials": ""}, {"family": "Prostate Cancer Association Group to Investigate Cancer Associated Alterations in the Genome (PRACTICAL) Consortium", "given": "", "initials": ""}, {"family": "Kidney Cancer GWAS Meta-Analysis Project", "given": "", "initials": ""}, {"family": "eQTLGen Consortium", "given": "", "initials": ""}, {"family": "Biobank-based Integrative Omics Study (BIOS) Consortium", "given": "", "initials": ""}, {"family": "23andMe Research Team", "given": "", "initials": ""}, {"family": "Kamatani", "given": "Yoichiro", "initials": "Y"}, {"family": "Hoffmann", "given": "Eva R", "initials": "ER"}, {"family": "Jackson", "given": "Steve P", "initials": "SP"}, {"family": "Stefansson", "given": "Kari", "initials": "K"}, {"family": "Auton", "given": "Adam", "initials": "A"}, {"family": "Ong", "given": "Ken K", "initials": "KK"}, {"family": "Machiela", "given": "Mitchell J", "initials": "MJ"}, {"family": "Loh", "given": "Po-Ru", "initials": "PR"}, {"family": "Dumanski", "given": "Jan P", "initials": "JP"}, {"family": "Chanock", "given": "Stephen J", "initials": "SJ"}, {"family": "Forsberg", "given": "Lars A", "initials": "LA"}, {"family": "Perry", "given": "John R B", "initials": "JRB"}], "type": "journal article", "published": "2019-11-00", "journal": {"title": "Nature", "issn": "1476-4687", "issn-l": "0028-0836", "volume": "575", "issue": "7784", "pages": "652-657"}, "abstract": "Mosaic loss of chromosome Y (LOY) in circulating white blood cells is the most common form of clonal mosaicism 1-5, yet our knowledge of the causes and consequences of this is limited. Here, using a computational approach, we estimate that 20% of the male population represented in the UK Biobank study (n = 205,011) has detectable LOY. We identify 156 autosomal genetic determinants of LOY, which we replicate in 757,114 men of European and Japanese ancestry. These loci highlight genes that are involved in cell-cycle regulation and cancer susceptibility, as well as somatic drivers of tumour growth and targets of cancer therapy. We demonstrate that genetic susceptibility to LOY is associated with non-haematological effects on health in both men and women, which supports the hypothesis that clonal haematopoiesis is a biomarker of genomic instability in other tissues. Single-cell RNA sequencing identifies dysregulated expression of autosomal genes in leukocytes with LOY and provides insights into why clonal expansion of these cells may occur. Collectively, these data highlight the value of studying clonal mosaicism to uncover fundamental mechanisms that underlie cancer and other ageing-related diseases.", "doi": "10.1038/s41586-019-1765-3", "pmid": "31748747", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41586-019-1765-3"}, {"db": "pmc", "key": "PMC6887549"}, {"db": "mid", "key": "EMS84547"}], "notes": [], "created": "2019-11-22T13:52:02.522Z", "modified": "2021-06-16T16:16:31.191Z"}, {"entity": "publication", "iuid": "7fe0a03b3cf040bc9efcd73174997a3d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7fe0a03b3cf040bc9efcd73174997a3d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7fe0a03b3cf040bc9efcd73174997a3d"}}, "title": "Genetic architecture of subcortical brain structures in 38,851 individuals.", "authors": [{"family": "Satizabal", "given": "Claudia L", "initials": "CL", "orcid": "0000-0002-1115-4430", "researcher": {"href": "https://publications.scilifelab.se/researcher/4fef87b562c74168ba8b9acbc9048eb9.json"}}, {"family": "Adams", "given": "Hieab H H", "initials": "HHH", "orcid": "0000-0003-3687-2508", "researcher": {"href": "https://publications.scilifelab.se/researcher/ab5c4744d60d4290a3a8a6b80c107f42.json"}}, {"family": "Hibar", "given": "Derrek P", "initials": "DP"}, {"family": "White", "given": "Charles C", "initials": "CC"}, {"family": "Knol", "given": "Maria J", "initials": "MJ", "orcid": "0000-0002-3597-1531", "researcher": {"href": "https://publications.scilifelab.se/researcher/0edb736bd840429bbb57ecd1b2924561.json"}}, {"family": "Stein", "given": "Jason L", "initials": "JL"}, {"family": "Scholz", "given": "Markus", "initials": "M", "orcid": "0000-0002-4059-1779", "researcher": {"href": "https://publications.scilifelab.se/researcher/53d7b0e2dcdb4361b54016cb1550c5fe.json"}}, {"family": "Sargurupremraj", "given": "Muralidharan", "initials": "M"}, {"family": "Jahanshad", "given": "Neda", "initials": "N"}, {"family": "Roshchupkin", "given": "Gennady V", "initials": "GV", "orcid": "0000-0002-3403-2313", "researcher": {"href": "https://publications.scilifelab.se/researcher/414f2c13b88d47c7b9c7a68a3116eeef.json"}}, {"family": "Smith", "given": "Albert V", "initials": "AV"}, {"family": "Bis", "given": "Joshua C", "initials": "JC"}, {"family": "Jian", "given": "Xueqiu", "initials": "X"}, {"family": "Luciano", "given": "Michelle", "initials": "M", "orcid": "0000-0002-7306-3008", "researcher": {"href": "https://publications.scilifelab.se/researcher/b6b709773257475da679b1b918a99af9.json"}}, {"family": "Hofer", "given": "Edith", "initials": "E"}, {"family": "Teumer", "given": "Alexander", "initials": "A", "orcid": "0000-0002-8309-094X", "researcher": {"href": "https://publications.scilifelab.se/researcher/dc9c2667a55b47a6a08aea764fab0946.json"}}, {"family": "van der Lee", "given": "Sven J", "initials": "SJ", "orcid": "0000-0003-1606-8643", "researcher": {"href": "https://publications.scilifelab.se/researcher/9a34a1b7b98b4360b48dafe3f0d5dcb2.json"}}, {"family": "Yang", "given": "Jingyun", "initials": "J"}, {"family": "Yanek", "given": "Lisa R", "initials": "LR", "orcid": "0000-0001-7117-1075", "researcher": {"href": "https://publications.scilifelab.se/researcher/4ccbe54244ce407bb4361f52f02e3b59.json"}}, {"family": "Lee", "given": "Tom V", "initials": "TV"}, {"family": "Li", "given": "Shuo", "initials": "S", "orcid": "0000-0003-2331-2448", "researcher": {"href": "https://publications.scilifelab.se/researcher/68e60fab4eab4ca1a84dac5f77511a5b.json"}}, {"family": "Hu", "given": "Yanhui", "initials": "Y"}, {"family": "Koh", "given": "Jia Yu", "initials": "JY", "orcid": "0000-0001-8772-8392", "researcher": {"href": "https://publications.scilifelab.se/researcher/a298813f69bc4134bb894f514bdb38af.json"}}, {"family": "Eicher", "given": "John D", "initials": "JD"}, {"family": "Desrivi\u00e8res", "given": "Sylvane", "initials": "S", "orcid": "0000-0002-9120-7060", "researcher": {"href": "https://publications.scilifelab.se/researcher/f7874c28697a419ea0360afd9d3f6b16.json"}}, {"family": "Arias-Vasquez", "given": "Alejandro", "initials": "A"}, {"family": "Chauhan", "given": "Ganesh", "initials": "G"}, {"family": "Athanasiu", "given": "Lavinia", "initials": "L"}, {"family": "Renter\u00eda", "given": "Miguel E", "initials": "ME", "orcid": "0000-0003-4626-7248", "researcher": {"href": "https://publications.scilifelab.se/researcher/9324d6a0142e4e94a780f4acab229b11.json"}}, {"family": "Kim", "given": "Sungeun", "initials": "S"}, {"family": "Hoehn", "given": "David", "initials": "D"}, {"family": "Armstrong", "given": "Nicola J", "initials": "NJ"}, {"family": "Chen", "given": "Qiang", "initials": "Q"}, {"family": "Holmes", "given": "Avram J", "initials": "AJ"}, {"family": "den Braber", "given": "Anouk", "initials": "A"}, {"family": "Kloszewska", "given": "Iwona", "initials": "I"}, {"family": "Andersson", "given": "Micael", "initials": "M"}, {"family": "Espeseth", "given": "Thomas", "initials": "T"}, {"family": "Grimm", "given": "Oliver", "initials": "O"}, {"family": "Abramovic", "given": "Lucija", "initials": "L"}, {"family": "Alhusaini", "given": "Saud", "initials": "S"}, {"family": "Milaneschi", "given": "Yuri", "initials": "Y"}, {"family": "Papmeyer", "given": "Martina", "initials": "M"}, {"family": "Axelsson", "given": "Tomas", "initials": "T"}, {"family": "Ehrlich", "given": "Stefan", "initials": "S"}, {"family": "Roiz-Santia\u00f1ez", "given": "Roberto", "initials": "R", "orcid": "0000-0002-5176-2983", "researcher": {"href": "https://publications.scilifelab.se/researcher/490c7f20337d4a07a121476a50286251.json"}}, {"family": "Kraemer", "given": "Bernd", "initials": "B"}, {"family": "H\u00e5berg", "given": "Asta K", "initials": "AK"}, {"family": "Jones", "given": "Hannah J", "initials": "HJ", "orcid": "0000-0002-5883-9605", "researcher": {"href": "https://publications.scilifelab.se/researcher/6105d35c1a9d4f96a24a0c1d6d124528.json"}}, {"family": "Pike", "given": "G Bruce", "initials": "GB", "orcid": "0000-0001-8924-683X", "researcher": {"href": "https://publications.scilifelab.se/researcher/8fc0bc043868454f8f93e88651f07bf0.json"}}, {"family": "Stein", "given": "Dan J", "initials": "DJ", "orcid": "0000-0001-7218-7810", "researcher": {"href": "https://publications.scilifelab.se/researcher/645116cff97744fd99f4563edef43a72.json"}}, {"family": "Stevens", "given": "Allison", "initials": "A"}, {"family": "Bralten", "given": "Janita", "initials": "J"}, {"family": "Vernooij", "given": "Meike W", "initials": "MW"}, {"family": "Harris", "given": "Tamara B", "initials": "TB"}, {"family": "Filippi", "given": "Irina", "initials": "I"}, {"family": "Witte", "given": "A Veronica", "initials": "AV"}, {"family": "Guadalupe", "given": "Tulio", "initials": "T"}, {"family": "Wittfeld", "given": "Katharina", "initials": "K", "orcid": "0000-0003-4383-5043", "researcher": {"href": "https://publications.scilifelab.se/researcher/6830477685ec42aebf4348d0475d329d.json"}}, {"family": "Mosley", "given": "Thomas H", "initials": "TH"}, {"family": "Becker", "given": "James T", "initials": "JT", "orcid": "0000-0003-4425-4726", "researcher": {"href": "https://publications.scilifelab.se/researcher/b2a380c26b7f457bb938894cab2957d3.json"}}, {"family": "Doan", "given": "Nhat Trung", "initials": "NT"}, {"family": "Hagenaars", "given": "Saskia P", "initials": "SP"}, {"family": "Saba", "given": "Yasaman", "initials": "Y"}, {"family": "Cuellar-Partida", "given": "Gabriel", "initials": "G"}, {"family": "Amin", "given": "Najaf", "initials": "N"}, {"family": "Hilal", "given": "Saima", "initials": "S"}, {"family": "Nho", "given": "Kwangsik", "initials": "K"}, {"family": "Mirza-Schreiber", "given": "Nazanin", "initials": "N", "orcid": "0000-0003-0836-8267", "researcher": {"href": "https://publications.scilifelab.se/researcher/a341a91f4bf24662a3996cb2d9470205.json"}}, {"family": "Arfanakis", "given": "Konstantinos", "initials": "K"}, {"family": "Becker", "given": "Diane M", "initials": "DM"}, {"family": "Ames", "given": "David", "initials": "D"}, {"family": "Goldman", "given": "Aaron L", "initials": "AL"}, {"family": "Lee", "given": "Phil H", "initials": "PH"}, {"family": "Boomsma", "given": "Dorret I", "initials": "DI", "orcid": "0000-0002-7099-7972", "researcher": {"href": "https://publications.scilifelab.se/researcher/4b66ab2525fd4a468e7a4ad14c955cb4.json"}}, {"family": "Lovestone", "given": "Simon", "initials": "S"}, {"family": "Giddaluru", "given": "Sudheer", "initials": "S"}, {"family": "Le Hellard", "given": "Stephanie", "initials": "S"}, {"family": "Mattheisen", "given": "Manuel", "initials": "M", "orcid": "0000-0002-8442-493X", "researcher": {"href": "https://publications.scilifelab.se/researcher/c38fef539c2c4cebb81eff917aa3d4ef.json"}}, {"family": "Bohlken", "given": "Marc M", "initials": "MM"}, {"family": "Kasperaviciute", "given": "Dalia", "initials": "D"}, {"family": "Schmaal", "given": "Lianne", "initials": "L"}, {"family": "Lawrie", "given": "Stephen M", "initials": "SM", "orcid": "0000-0002-2444-5675", "researcher": {"href": "https://publications.scilifelab.se/researcher/6bc515d4baf14d04ba9725397e617fdd.json"}}, {"family": "Agartz", "given": "Ingrid", "initials": "I"}, {"family": "Walton", "given": "Esther", "initials": "E"}, {"family": "Tordesillas-Gutierrez", "given": "Diana", "initials": "D"}, {"family": "Davies", "given": "Gareth E", "initials": "GE"}, {"family": "Shin", "given": "Jean", "initials": "J", "orcid": "0000-0001-7353-5178", "researcher": {"href": "https://publications.scilifelab.se/researcher/d83d5f2b94154e25b4b606adf74d3606.json"}}, {"family": "Ipser", "given": "Jonathan C", "initials": "JC"}, {"family": "Vinke", "given": "Louis N", "initials": "LN"}, {"family": "Hoogman", "given": "Martine", "initials": "M"}, {"family": "Jia", "given": "Tianye", "initials": "T", "orcid": "0000-0001-5399-2953", "researcher": {"href": "https://publications.scilifelab.se/researcher/50180570d807436595c5b66cc1df8ed6.json"}}, {"family": "Burkhardt", "given": "Ralph", "initials": "R", "orcid": "0000-0003-1924-1202", "researcher": {"href": "https://publications.scilifelab.se/researcher/abe3ddd140b3478485f44119d18926b7.json"}}, {"family": "Klein", "given": "Marieke", "initials": "M", "orcid": "0000-0001-8784-5679", "researcher": {"href": "https://publications.scilifelab.se/researcher/a7481a7b70b6411b98c77e27e0de9b2f.json"}}, {"family": "Crivello", "given": "Fabrice", "initials": "F", "orcid": "0000-0001-6950-984X", "researcher": {"href": "https://publications.scilifelab.se/researcher/93a891e406494360a578ec556906f256.json"}}, {"family": "Janowitz", "given": "Deborah", "initials": "D", "orcid": "0000-0003-4324-9298", "researcher": {"href": "https://publications.scilifelab.se/researcher/02996a0a859f411da889b9826d26dc5a.json"}}, {"family": "Carmichael", "given": "Owen", "initials": "O"}, {"family": "Haukvik", "given": "Unn K", "initials": "UK"}, {"family": "Aribisala", "given": "Benjamin S", "initials": "BS"}, {"family": "Schmidt", "given": "Helena", "initials": "H"}, {"family": "Strike", "given": "Lachlan T", "initials": "LT"}, {"family": "Cheng", "given": "Ching-Yu", "initials": "CY"}, {"family": "Risacher", "given": "Shannon L", "initials": "SL"}, {"family": "P\u00fctz", "given": "Benno", "initials": "B", "orcid": "0000-0002-2208-209X", "researcher": {"href": "https://publications.scilifelab.se/researcher/a1520fd3be154860bf7370498d840ba9.json"}}, {"family": "Fleischman", "given": "Debra A", "initials": "DA"}, {"family": "Assareh", "given": "Amelia A", "initials": "AA"}, {"family": "Mattay", "given": "Venkata S", "initials": "VS"}, {"family": "Buckner", "given": "Randy L", "initials": "RL", "orcid": "0000-0001-6422-8037", "researcher": {"href": "https://publications.scilifelab.se/researcher/ad82b5a898ae467a80bab699148baa91.json"}}, {"family": "Mecocci", "given": "Patrizia", "initials": "P"}, {"family": "Dale", "given": "Anders M", "initials": "AM"}, {"family": "Cichon", "given": "Sven", "initials": "S"}, {"family": "Boks", "given": "Marco P", "initials": "MP", "orcid": "0000-0001-6163-7484", "researcher": {"href": "https://publications.scilifelab.se/researcher/329c0bdc09434418a9dd8fab2da410c2.json"}}, {"family": "Matarin", "given": "Mar", "initials": "M"}, {"family": "Penninx", "given": "Brenda W J H", "initials": "BWJH"}, {"family": "Calhoun", "given": "Vince D", "initials": "VD", "orcid": "0000-0001-9058-0747", "researcher": {"href": "https://publications.scilifelab.se/researcher/f972685fe81a42d896f855f961984feb.json"}}, {"family": "Chakravarty", "given": "M Mallar", "initials": "MM"}, {"family": "Marquand", "given": "Andre F", "initials": "AF"}, {"family": "Macare", "given": 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"initials": "CA"}, {"family": "DeStefano", "given": "Anita L", "initials": "AL"}, {"family": "Heslenfeld", "given": "Dirk J", "initials": "DJ"}, {"family": "Weiner", "given": "Michael W", "initials": "MW"}, {"family": "Walter", "given": "Henrik", "initials": "H", "orcid": "0000-0002-9403-6121", "researcher": {"href": "https://publications.scilifelab.se/researcher/2fb8400c66af486bae4c0d8b56c38316.json"}}, {"family": "Hoekstra", "given": "Pieter J", "initials": "PJ"}, {"family": "Nyquist", "given": "Paul A", "initials": "PA"}, {"family": "Franke", "given": "Barbara", "initials": "B", "orcid": "0000-0003-4375-6572", "researcher": {"href": "https://publications.scilifelab.se/researcher/105f0131cfc34a668ed840e622e4f902.json"}}, {"family": "Bennett", "given": "David A", "initials": "DA"}, {"family": "Grabe", "given": "Hans J", "initials": "HJ", "orcid": "0000-0003-3684-4208", "researcher": {"href": "https://publications.scilifelab.se/researcher/d660f9169e6c4c8485041382ebf71e3d.json"}}, {"family": "Johnson", "given": "Andrew D", "initials": "AD"}, {"family": "Chen", "given": "Christopher", "initials": "C"}, {"family": "van Duijn", "given": "Cornelia M", "initials": "CM"}, {"family": "Lopez", "given": "Oscar L", "initials": "OL"}, {"family": "Fornage", "given": "Myriam", "initials": "M"}, {"family": "Wardlaw", "given": "Joanna M", "initials": "JM", "orcid": "0000-0002-9812-6642", "researcher": {"href": "https://publications.scilifelab.se/researcher/5fd13301b0e34ae88b49d5d40145bb74.json"}}, {"family": "Schmidt", "given": "Reinhold", "initials": "R"}, {"family": "DeCarli", "given": "Charles", "initials": "C"}, {"family": "De Jager", "given": "Philip L", "initials": "PL", "orcid": "0000-0002-8057-2505", "researcher": {"href": "https://publications.scilifelab.se/researcher/6fb514edc45a46b688ef0fa75250a322.json"}}, {"family": "Villringer", "given": "Arno", "initials": "A"}, {"family": "Debette", "given": "St\u00e9phanie", "initials": "S"}, {"family": "Gudnason", "given": "Vilmundur", "initials": "V", "orcid": "0000-0001-5696-0084", "researcher": {"href": "https://publications.scilifelab.se/researcher/d18327939c1541acba054b2340ac174f.json"}}, {"family": "Medland", "given": "Sarah E", "initials": "SE", "orcid": "0000-0003-1382-380X", "researcher": {"href": "https://publications.scilifelab.se/researcher/da1f0230a912425c9237830be85aa642.json"}}, {"family": "Shulman", "given": "Joshua M", "initials": "JM"}, {"family": "Thompson", "given": "Paul M", "initials": "PM"}, {"family": "Seshadri", "given": "Sudha", "initials": "S"}, {"family": "Ikram", "given": "M Arfan", "initials": "MA", "orcid": "0000-0003-0372-8585", "researcher": {"href": "https://publications.scilifelab.se/researcher/2ec81571f4a94af682b4e23526f87385.json"}}], "type": "journal article", "published": "2019-11-00", "journal": {"volume": "51", "issn": "1546-1718", "issue": "11", "pages": "1624-1636", "title": "Nat. Genet.", "issn-l": "1061-4036"}, "abstract": "Subcortical brain structures are integral to motion, consciousness, emotions and learning. We identified common genetic variation related to the volumes of the nucleus accumbens, amygdala, brainstem, caudate nucleus, globus pallidus, putamen and thalamus, using genome-wide association analyses in almost 40,000 individuals from CHARGE, ENIGMA and UK Biobank. We show that variability in subcortical volumes is heritable, and identify 48 significantly associated loci (40 novel at the time of analysis). Annotation of these loci by utilizing gene expression, methylation and neuropathological data identified 199 genes putatively implicated in neurodevelopment, synaptic signaling, axonal transport, apoptosis, inflammation/infection and susceptibility to neurological disorders. This set of genes is significantly enriched for Drosophila orthologs associated with neurodevelopmental phenotypes, suggesting evolutionarily conserved mechanisms. Our findings uncover novel biology and potential drug targets underlying brain development and disease.", "doi": "10.1038/s41588-019-0511-y", "pmid": "31636452", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41588-019-0511-y"}, {"db": "pmc", "key": "PMC7055269"}, {"db": "mid", "key": "NIHMS1553652"}], "notes": [], "created": "2019-10-22T06:26:22.885Z", "modified": "2021-06-18T13:55:45.367Z"}, {"entity": "publication", "iuid": "5e70d33879bb4e06877cb055d7c9c062", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5e70d33879bb4e06877cb055d7c9c062.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5e70d33879bb4e06877cb055d7c9c062"}}, "title": "EZH2 upregulates the PI3K/AKT pathway through IGF1R and MYC in clinically aggressive chronic lymphocytic leukaemia.", "authors": [{"family": "Kosalai", "given": "Subazini Thankaswamy", "initials": "ST"}, {"family": "Morsy", "given": "Mohammad Hamdy Abdelrazak", "initials": "MHA"}, {"family": "Papakonstantinou", "given": "Nikos", "initials": "N"}, {"family": "Mansouri", "given": "Larry", "initials": "L"}, {"family": "Stavroyianni", "given": "Niki", "initials": "N"}, {"family": "Kanduri", "given": "Chandrasekhar", "initials": "C"}, {"family": "Stamatopoulos", "given": "Kostas", "initials": "K"}, {"family": "Rosenquist", "given": "Richard", "initials": "R"}, {"family": "Kanduri", "given": "Meena", "initials": "M"}], "type": "journal article", "published": "2019-11-00", "journal": {"volume": "14", "issn": "1559-2308", "issue": "11", "pages": "1125-1140", "title": "Epigenetics", "issn-l": "1559-2294"}, "abstract": "EZH2 is overexpressed in poor-prognostic chronic lymphocytic leukaemia (CLL) cases, acting as an oncogene; however, thus far, the EZH2 target genes in CLL have not been disclosed. In this study, using ChIP-sequencing, we identified EZH2 and H3K27me3 target genes in two prognostic subgroups of CLL with distinct prognosis and outcome, i.e., cases with unmutated (U-CLL, n = 6) or mutated IGHV genes (M-CLL, n = 6). While the majority of oncogenic pathways were equally enriched for EZH2 target genes in both prognostic subgroups, PI3K pathway genes were differentially bound by EZH2 in U-CLL versus M-CLL. The occupancy of EZH2 for selected PI3K pathway target genes was validated in additional CLL samples (n = 16) and CLL cell lines using siRNA-mediated EZH2 downregulation and ChIP assays. Intriguingly, we found that EZH2 directly binds to the IGF1R promoter along with MYC and upregulates IGF1R expression in U-CLL, leading to downstream PI3K activation. By investigating an independent CLL cohort (n = 96), a positive correlation was observed between EZH2 and IGF1R expression with higher levels in U-CLL compared to M-CLL. Accordingly, siRNA-mediated downregulation of either EZH2, MYC or IGF1R and treatment with EZH2 and MYC pharmacological inhibitors in the HG3 CLL cell line induced a significant reduction in PI3K pathway activation. In conclusion, we characterize for the first time EZH2 target genes in CLL revealing a hitherto unknown implication of EZH2 in modulating the PI3K pathway in a non-canonical, PRC2-independent way, with potential therapeutic implications considering that PI3K inhibitors are effective therapeutic agents for CLL.", "doi": "10.1080/15592294.2019.1633867", "pmid": "31216925", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC6773411"}], "notes": [], "created": "2019-12-03T10:47:45.011Z", "modified": "2024-01-16T13:48:43.618Z"}, {"entity": "publication", "iuid": "d1701aa9b9c94da0bd7e1177f39c9fe6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d1701aa9b9c94da0bd7e1177f39c9fe6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d1701aa9b9c94da0bd7e1177f39c9fe6"}}, "title": "Characterization of Bacterial Communities in Breeding Waters of Anopheles darlingi in Manaus in the Amazon Basin Malaria-Endemic Area.", "authors": [{"family": "Nilsson", "given": "Louise K J", "initials": "LKJ", "orcid": "0000-0001-6314-3357", "researcher": {"href": "https://publications.scilifelab.se/researcher/48ab7696dfb849ee8ca076527d84bdd6.json"}}, {"family": "de Oliveira", "given": "Marta Rodrigues", "initials": "MR"}, {"family": "Marinotti", "given": "Osvaldo", "initials": "O"}, {"family": "Rocha", "given": "Elerson Matos", "initials": "EM"}, {"family": "H\u00e5kansson", "given": "Sebastian", "initials": "S"}, {"family": "Tadei", "given": "Wanderli P", "initials": "WP"}, {"family": "de Souza", "given": "Antonia Queiroz Lima", "initials": "AQL"}, {"family": "Terenius", "given": "Olle", "initials": "O"}], "type": "journal article", "published": "2019-11-00", "journal": {"volume": "78", "issn": "1432-184X", "issue": "4", "pages": "781-791", "title": "Microb. Ecol.", "issn-l": "0095-3628"}, "abstract": "The microbiota in mosquito breeding waters can affect ovipositing mosquitoes, have effects on larval development, and can modify adult mosquito-gut bacterial composition. This, in turn, can affect transmission of human pathogens such as malaria parasites. Here, we explore the microbiota of four breeding sites for Anopheles darlingi, the most important malaria vector in Latin America. The sites are located in Manaus in the Amazon basin in Brazil, an area of active malaria transmission. Using 16S rRNA gene sequencing by MiSeq, we found that all sites were dominated by Proteobacteria and Firmicutes and that 94% of the total number of reads belonged to 36 operational taxonomic units (OTUs) identified in all sites. Of these, the most common OTUs belonged to Escherichia/Shigella, Staphylococcus, and Pseudomonas. Of the remaining 6% of the reads, the OTUs found to differentiate between the four sites belonged to the orders Burkholderiales, Actinomycetales, and Clostridiales. We conclude that An. darlingi can develop in breeding waters with different surface-water bacteria, but that the common microbiota found in all breeding sites might indicate or contribute to a suitable habitat for this important malaria vector.", "doi": "10.1007/s00248-019-01369-9", "pmid": "30989355", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1007/s00248-019-01369-9"}, {"db": "pmc", "key": "PMC6842340"}], "notes": [], "created": "2019-12-03T10:25:36.108Z", "modified": "2024-01-16T13:48:43.625Z"}, {"entity": "publication", "iuid": "89c87476555544e39ef6bf6717603f84", "links": {"self": {"href": "https://publications.scilifelab.se/publication/89c87476555544e39ef6bf6717603f84.json"}, "display": {"href": "https://publications.scilifelab.se/publication/89c87476555544e39ef6bf6717603f84"}}, "title": "Associations of autozygosity with a broad range of human phenotypes.", "authors": [{"family": "Clark", "given": "David W", "initials": "DW", "orcid": "0000-0002-1025-9185", "researcher": {"href": "https://publications.scilifelab.se/researcher/a71ee9badf4f458d9b04ebf89f5f16c9.json"}}, {"family": "Okada", "given": "Yukinori", "initials": "Y", "orcid": "0000-0002-0311-8472", "researcher": {"href": "https://publications.scilifelab.se/researcher/40b13860bfef41959c29be2de853b456.json"}}, {"family": "Moore", "given": "Kristjan H S", "initials": "KHS", "orcid": "0000-0002-9579-4362", "researcher": {"href": "https://publications.scilifelab.se/researcher/38a8eaf6f23c4dd9a90cda85b0a998b5.json"}}, {"family": "Mason", "given": "Dan", "initials": "D", "orcid": "0000-0002-0026-9216", "researcher": {"href": "https://publications.scilifelab.se/researcher/3e9d969adc0849ab83d0080430bb6758.json"}}, {"family": "Pirastu", "given": "Nicola", "initials": "N", "orcid": "0000-0002-5363-3886", "researcher": {"href": "https://publications.scilifelab.se/researcher/badf4678d37546ce993bccb3880d4f12.json"}}, {"family": "Gandin", "given": "Ilaria", "initials": "I", "orcid": "0000-0003-3196-2491", "researcher": {"href": "https://publications.scilifelab.se/researcher/ee19a08d128d40cf8bffcff35e37481d.json"}}, {"family": "Mattsson", "given": "Hannele", "initials": "H"}, {"family": "Barnes", "given": "Catriona L K", "initials": "CLK"}, {"family": "Lin", "given": "Kuang", "initials": "K"}, {"family": "Zhao", "given": "Jing Hua", "initials": "JH"}, {"family": "Deelen", "given": "Patrick", "initials": "P", "orcid": "0000-0002-5654-3966", "researcher": {"href": "https://publications.scilifelab.se/researcher/29b4f65a7b6e454d92315f99841f0e70.json"}}, {"family": "Rohde", "given": "Rebecca", "initials": "R"}, {"family": "Schurmann", "given": "Claudia", "initials": "C", "orcid": "0000-0003-4158-9192", "researcher": {"href": "https://publications.scilifelab.se/researcher/357aae1711d34a0e993b10c93c73cfb4.json"}}, {"family": "Guo", "given": "Xiuqing", "initials": "X"}, {"family": "Giulianini", "given": "Franco", "initials": "F"}, {"family": "Zhang", "given": "Weihua", "initials": "W"}, {"family": "Medina-Gomez", "given": "Carolina", "initials": "C", "orcid": "0000-0001-7999-5538", "researcher": {"href": "https://publications.scilifelab.se/researcher/c1f97914d1c34f1f8190738c2d2e27b0.json"}}, {"family": "Karlsson", "given": "Robert", "initials": "R", "orcid": "0000-0002-8949-2587", "researcher": {"href": "https://publications.scilifelab.se/researcher/9df14bf33f3342408d624caa70d45b7c.json"}}, {"family": "Bao", "given": "Yanchun", "initials": "Y", "orcid": "0000-0002-6102-5098", "researcher": {"href": "https://publications.scilifelab.se/researcher/edd80af47df24a508164d6b550093563.json"}}, {"family": "Bartz", "given": "Traci M", "initials": "TM"}, {"family": "Baumbach", "given": "Clemens", "initials": "C"}, {"family": "Biino", "given": "Ginevra", "initials": "G", "orcid": "0000-0002-9936-946X", "researcher": {"href": "https://publications.scilifelab.se/researcher/791ca64b8e7c4930a8727ea9a52a5c15.json"}}, {"family": "Bixley", "given": "Matthew J", "initials": "MJ"}, {"family": "Brumat", "given": "Marco", "initials": "M", "orcid": "0000-0003-3268-039X", "researcher": {"href": "https://publications.scilifelab.se/researcher/422e5540e38047cfaa64708b0b118760.json"}}, {"family": "Chai", "given": "Jin-Fang", "initials": "JF", "orcid": "0000-0003-3770-1137", "researcher": {"href": "https://publications.scilifelab.se/researcher/7cac060e59cd405b94a588203b5955ca.json"}}, {"family": "Corre", "given": "Tanguy", "initials": "T"}, {"family": "Cousminer", "given": "Diana L", "initials": "DL"}, {"family": "Dekker", "given": "Annelot M", "initials": "AM"}, {"family": "Eccles", "given": "David A", "initials": "DA", "orcid": "0000-0003-4634-4995", "researcher": {"href": "https://publications.scilifelab.se/researcher/94670fee34be4f47ab7cf5c46a054fa4.json"}}, {"family": "van Eijk", "given": "Kristel R", "initials": "KR"}, {"family": "Fuchsberger", "given": "Christian", "initials": "C"}, {"family": "Gao", "given": "He", "initials": "H"}, {"family": "Germain", "given": "Marine", "initials": "M"}, {"family": "Gordon", "given": "Scott D", "initials": "SD", "orcid": "0000-0001-7623-328X", "researcher": {"href": "https://publications.scilifelab.se/researcher/8815739662214e75b60f71f0b1ca58a6.json"}}, {"family": "de Haan", "given": "Hugoline G", "initials": "HG"}, {"family": "Harris", "given": "Sarah E", "initials": "SE", "orcid": "0000-0002-4941-5106", "researcher": {"href": "https://publications.scilifelab.se/researcher/1bbd06383e594035ab80af3bcdb29f91.json"}}, {"family": "Hofer", "given": "Edith", "initials": "E"}, {"family": "Huerta-Chagoya", "given": "Alicia", "initials": "A"}, {"family": "Igartua", "given": "Catherine", "initials": "C"}, {"family": "Jansen", "given": "Iris E", "initials": "IE"}, {"family": "Jia", "given": "Yucheng", "initials": "Y"}, {"family": "Kacprowski", "given": "Tim", "initials": "T", "orcid": "0000-0002-5393-2413", "researcher": {"href": "https://publications.scilifelab.se/researcher/a5e640df1f184777a3066805d02a67c7.json"}}, {"family": "Karlsson", "given": "Torgny", "initials": "T", "orcid": "0000-0001-8095-6149", "researcher": {"href": "https://publications.scilifelab.se/researcher/691d6823b8e04c5abf1613513da32b08.json"}}, {"family": "Kleber", "given": "Marcus E", "initials": "ME", "orcid": "0000-0003-0663-7275", "researcher": {"href": "https://publications.scilifelab.se/researcher/a51175112cfb4721b8c9fbfdc71c4307.json"}}, {"family": "Li", "given": "Shengchao Alfred", "initials": "SA"}, {"family": "Li-Gao", "given": "Ruifang", "initials": "R"}, {"family": "Mahajan", "given": "Anubha", "initials": "A", "orcid": "0000-0001-5585-3420", "researcher": {"href": "https://publications.scilifelab.se/researcher/194be8a851164e2ea4d004dd2febc9be.json"}}, {"family": "Matsuda", "given": "Koichi", "initials": "K", "orcid": "0000-0001-7292-2686", "researcher": {"href": "https://publications.scilifelab.se/researcher/016c48eb6c8341b7b593c4b1c9e39266.json"}}, {"family": "Meidtner", "given": "Karina", "initials": "K"}, {"family": "Meng", "given": "Weihua", "initials": "W", "orcid": "0000-0001-5388-8494", "researcher": {"href": "https://publications.scilifelab.se/researcher/cdb05cc4a7554f4d8fdc57ec60b542d2.json"}}, {"family": "Montasser", "given": "May E", "initials": "ME"}, {"family": "van der Most", "given": "Peter J", "initials": "PJ", "orcid": "0000-0001-8450-3518", "researcher": {"href": "https://publications.scilifelab.se/researcher/17cd11842111490ba5460f3093a366f3.json"}}, {"family": "Munz", "given": "Matthias", "initials": "M", "orcid": "0000-0002-4728-3357", "researcher": {"href": "https://publications.scilifelab.se/researcher/715a85c9e5794eac8d55860014a3e407.json"}}, {"family": "Nutile", "given": "Teresa", "initials": "T"}, {"family": "Palviainen", "given": "Teemu", "initials": "T", "orcid": "0000-0002-7847-8384", "researcher": {"href": "https://publications.scilifelab.se/researcher/bcbc4c92052b4819b5d7d821c0c421b0.json"}}, {"family": "Prasad", "given": "Gauri", "initials": "G"}, {"family": "Prasad", "given": "Rashmi B", "initials": "RB", "orcid": "0000-0002-4400-6741", "researcher": {"href": "https://publications.scilifelab.se/researcher/313aa9ded0c946c3b986e856a62ae85a.json"}}, {"family": "Priyanka", "given": "Tallapragada Divya Sri", "initials": "TDS"}, {"family": "Rizzi", "given": "Federica", "initials": "F"}, {"family": "Salvi", "given": "Erika", "initials": "E", "orcid": "0000-0002-2724-2291", "researcher": {"href": "https://publications.scilifelab.se/researcher/c5119a5a894746dc92bb484e0d5cc4a3.json"}}, {"family": "Sapkota", "given": "Bishwa R", "initials": "BR"}, {"family": "Shriner", "given": "Daniel", "initials": "D"}, {"family": "Skotte", "given": "Line", "initials": "L", "orcid": "0000-0002-7398-1271", "researcher": {"href": "https://publications.scilifelab.se/researcher/8078f2481d644ec8a53c28570e9af119.json"}}, {"family": "Smart", "given": "Melissa C", "initials": "MC"}, {"family": "Smith", "given": "Albert Vernon", "initials": "AV"}, {"family": "van der Spek", "given": "Ashley", "initials": "A", "orcid": "0000-0001-7136-0159", "researcher": {"href": "https://publications.scilifelab.se/researcher/85d1ebe3cc5d4ff89d89a4dbead121de.json"}}, {"family": "Spracklen", "given": "Cassandra N", "initials": "CN", "orcid": "0000-0003-3590-7182", "researcher": {"href": "https://publications.scilifelab.se/researcher/132c3af299ef430294d5d2091f135e90.json"}}, {"family": "Strawbridge", "given": "Rona J", "initials": "RJ", "orcid": "0000-0001-8506-3585", "researcher": {"href": "https://publications.scilifelab.se/researcher/8ac5060a3b37466dae002d4ad8f4d0ac.json"}}, {"family": "Tajuddin", "given": "Salman M", "initials": "SM", "orcid": "0000-0002-7919-8528", "researcher": {"href": "https://publications.scilifelab.se/researcher/609b3374c75b4f16b7d9272de4f2a2aa.json"}}, {"family": "Trompet", "given": "Stella", "initials": "S"}, {"family": "Turman", "given": "Constance", "initials": "C"}, {"family": "Verweij", "given": "Niek", "initials": "N", "orcid": "0000-0002-4303-7685", "researcher": {"href": "https://publications.scilifelab.se/researcher/7306319d42a640a483b937de588a17a4.json"}}, {"family": "Viberti", "given": "Clara", "initials": "C"}, {"family": "Wang", "given": "Lihua", "initials": "L"}, {"family": "Warren", "given": "Helen R", "initials": "HR"}, {"family": "Wootton", "given": "Robyn E", "initials": "RE"}, {"family": "Yanek", "given": "Lisa R", "initials": "LR", "orcid": "0000-0001-7117-1075", "researcher": {"href": "https://publications.scilifelab.se/researcher/4ccbe54244ce407bb4361f52f02e3b59.json"}}, {"family": "Yao", "given": "Jie", "initials": "J"}, {"family": "Yousri", "given": "Noha A", "initials": "NA"}, {"family": "Zhao", "given": "Wei", "initials": "W", "orcid": "0000-0001-7388-0692", "researcher": {"href": "https://publications.scilifelab.se/researcher/a0c2246e69494086bab7ead8e6f1f717.json"}}, {"family": "Adeyemo", "given": "Adebowale A", "initials": "AA"}, {"family": "Afaq", "given": "Saima", "initials": "S"}, {"family": "Aguilar-Salinas", "given": "Carlos Alberto", "initials": "CA"}, {"family": "Akiyama", "given": "Masato", "initials": "M"}, {"family": "Albert", "given": "Matthew L", "initials": "ML", "orcid": "0000-0001-7285-6973", "researcher": {"href": "https://publications.scilifelab.se/researcher/0653a389768947abafecf0bd010afc6c.json"}}, {"family": "Allison", "given": "Matthew A", "initials": "MA"}, {"family": "Alver", "given": "Maris", "initials": "M"}, {"family": "Aung", "given": "Tin", "initials": "T"}, {"family": "Azizi", "given": "Fereidoun", "initials": "F"}, {"family": "Bentley", "given": "Amy R", "initials": "AR", "orcid": "0000-0002-0827-9101", "researcher": {"href": 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{"family": "Tregouet", "given": "David-Alexandre", "initials": "DA"}, {"family": "Tuomi", "given": "Tiinamaija", "initials": "T", "orcid": "0000-0002-8306-6202", "researcher": {"href": "https://publications.scilifelab.se/researcher/19f5ce9936ca454c85f0af966acac5c0.json"}}, {"family": "Vollenweider", "given": "Peter", "initials": "P"}, {"family": "Wang", "given": "Carol A", "initials": "CA", "orcid": "0000-0002-4301-3974", "researcher": {"href": "https://publications.scilifelab.se/researcher/bf99a43c27034a68976e978b104a91d7.json"}}, {"family": "Weir", "given": "David R", "initials": "DR", "orcid": "0000-0002-1661-2402", "researcher": {"href": "https://publications.scilifelab.se/researcher/f90b7cfe829845fb8cbea9558a5c82a7.json"}}, {"family": "Whitfield", "given": "John B", "initials": "JB", "orcid": "0000-0002-1103-0876", "researcher": {"href": "https://publications.scilifelab.se/researcher/e0f61a914f9748ee9047301da8026bd7.json"}}, {"family": "Wijmenga", "given": "Cisca", "initials": "C"}, {"family": "Wong", "given": "Tien-Yin", "initials": "TY"}, {"family": "Wright", "given": "John", "initials": "J"}, {"family": "Yang", "given": "Jingyun", "initials": "J"}, {"family": "Yu", "given": "Lei", "initials": "L"}, {"family": "Zemel", "given": "Babette S", "initials": "BS"}, {"family": "Zonderman", "given": "Alan B", "initials": "AB"}, {"family": "Perola", "given": "Markus", "initials": "M"}, {"family": "Magnusson", "given": "Patrik K E", "initials": "PKE", "orcid": "0000-0002-7315-7899", "researcher": {"href": "https://publications.scilifelab.se/researcher/b277b6387de142bbab91fad82d9eff09.json"}}, {"family": "Uitterlinden", "given": "Andr\u00e9 G", "initials": "AG", "orcid": "0000-0002-7276-3387", "researcher": {"href": "https://publications.scilifelab.se/researcher/273577b238854023a9dffe34dabc3551.json"}}, {"family": "Kooner", "given": "Jaspal S", "initials": "JS"}, {"family": "Chasman", "given": "Daniel I", "initials": "DI"}, {"family": "Loos", "given": "Ruth J F", "initials": "RJF", "orcid": "0000-0002-8532-5087", "researcher": {"href": "https://publications.scilifelab.se/researcher/e5b6c24c302d42828806076ded81afe1.json"}}, {"family": "Franceschini", "given": "Nora", "initials": "N"}, {"family": "Franke", "given": "Lude", "initials": "L", "orcid": "0000-0002-5159-8802", "researcher": {"href": "https://publications.scilifelab.se/researcher/ee63161f78274a53b615c05555b81a10.json"}}, {"family": "Haley", "given": "Chris S", "initials": "CS", "orcid": "0000-0002-9811-0210", "researcher": {"href": "https://publications.scilifelab.se/researcher/c4fee769cfe84186abbc285881e0529c.json"}}, {"family": "Hayward", "given": "Caroline", "initials": "C", "orcid": "0000-0002-9405-9550", "researcher": {"href": "https://publications.scilifelab.se/researcher/cd49e9ad5a024c7ca2f1aa97d9e58eba.json"}}, {"family": "Walters", "given": "Robin G", "initials": "RG", "orcid": "0000-0002-9179-0321", "researcher": {"href": "https://publications.scilifelab.se/researcher/f36254611faa44b782b76da870e89bd3.json"}}, {"family": "Perry", "given": "John R B", "initials": "JRB"}, {"family": "Esko", "given": "T\u014dnu", "initials": "T"}, {"family": "Helgason", "given": "Agnar", "initials": "A"}, {"family": "Stefansson", "given": "Kari", "initials": "K"}, {"family": "Joshi", "given": "Peter K", "initials": "PK", "orcid": "0000-0002-6361-5059", "researcher": {"href": "https://publications.scilifelab.se/researcher/46050ddec8f64054b3bab46c5016aebf.json"}}, {"family": "Kubo", "given": "Michiaki", "initials": "M"}, {"family": "Wilson", "given": "James F", "initials": "JF", "orcid": "0000-0001-5751-9178", "researcher": {"href": "https://publications.scilifelab.se/researcher/b39e6e0f7210494cb4f80be0f7413b6f.json"}}], "type": "journal article", "published": "2019-10-31", "journal": {"volume": "10", "issn": "2041-1723", "issue": "1", "pages": "4957", "title": "Nat Commun", "issn-l": "2041-1723"}, "abstract": "In many species, the offspring of related parents suffer reduced reproductive success, a phenomenon known as inbreeding depression. In humans, the importance of this effect has remained unclear, partly because reproduction between close relatives is both rare and frequently associated with confounding social factors. Here, using genomic inbreeding coefficients (FROH) for >1.4 million individuals, we show that FROH is significantly associated (p < 0.0005) with apparently deleterious changes in 32 out of 100 traits analysed. These changes are associated with runs of homozygosity (ROH), but not with common variant homozygosity, suggesting that genetic variants associated with inbreeding depression are predominantly rare. The effect on fertility is striking: FROH equivalent to the offspring of first cousins is associated with a 55% decrease [95% CI 44-66%] in the odds of having children. Finally, the effects of FROH are confirmed within full-sibling pairs, where the variation in FROH is independent of all environmental confounding.", "doi": "10.1038/s41467-019-12283-6", "pmid": "31673082", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC6823371"}, {"db": "pii", "key": "10.1038/s41467-019-12283-6"}], "notes": [], "created": "2019-11-28T07:41:34.797Z", "modified": "2023-06-19T13:09:10.356Z"}, {"entity": "publication", "iuid": "4789f60251ef4a938877b3e98f35fb49", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4789f60251ef4a938877b3e98f35fb49.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4789f60251ef4a938877b3e98f35fb49"}}, "title": "doepipeline: a systematic approach to optimizing multi-level and multi-step data processing workflows.", "authors": [{"family": "Svensson", "given": "Daniel", "initials": "D"}, {"family": "Sj\u00f6gren", "given": "Rickard", "initials": "R"}, {"family": "Sundell", "given": "David", "initials": "D"}, {"family": "Sj\u00f6din", "given": "Andreas", "initials": "A"}, {"family": "Trygg", "given": "Johan", "initials": "J", "orcid": "0000-0003-3799-6094", "researcher": {"href": "https://publications.scilifelab.se/researcher/7df02186ac1a4a60952737b1690363b7.json"}}], "type": "journal article", "published": "2019-10-15", "journal": {"volume": "20", "issn": "1471-2105", "issue": "1", "pages": "498", "title": "BMC Bioinformatics", "issn-l": "1471-2105"}, "abstract": "Selecting the proper parameter settings for bioinformatic software tools is challenging. Not only will each parameter have an individual effect on the outcome, but there are also potential interaction effects between parameters. Both of these effects may be difficult to predict. To make the situation even more complex, multiple tools may be run in a sequential pipeline where the final output depends on the parameter configuration for each tool in the pipeline. Because of the complexity and difficulty of predicting outcomes, in practice parameters are often left at default settings or set based on personal or peer experience obtained in a trial and error fashion. To allow for the reliable and efficient selection of parameters for bioinformatic pipelines, a systematic approach is needed.\n\nWe present doepipeline, a novel approach to optimizing bioinformatic software parameters, based on core concepts of the Design of Experiments methodology and recent advances in subset designs. Optimal parameter settings are first approximated in a screening phase using a subset design that efficiently spans the entire search space, then optimized in the subsequent phase using response surface designs and OLS modeling. Doepipeline was used to optimize parameters in four use cases; 1) de-novo assembly, 2) scaffolding of a fragmented genome assembly, 3) k-mer taxonomic classification of Oxford Nanopore Technologies MinION reads, and 4) genetic variant calling. In all four cases, doepipeline found parameter settings that produced a better outcome with respect to the characteristic measured when compared to using default values. Our approach is implemented and available in the Python package doepipeline.\n\nOur proposed methodology provides a systematic and robust framework for optimizing software parameter settings, in contrast to labor- and time-intensive manual parameter tweaking. Implementation in doepipeline makes our methodology accessible and user-friendly, and allows for automatic optimization of tools in a wide range of cases. The source code of doepipeline is available at https://github.com/clicumu/doepipeline and it can be installed through conda-forge.", "doi": "10.1186/s12859-019-3091-z", "pmid": "31615395", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1186/s12859-019-3091-z"}, {"db": "pmc", "key": "PMC6794737"}], "notes": [], "created": "2019-12-03T10:42:58.012Z", "modified": "2024-01-16T13:48:43.684Z"}, {"entity": "publication", "iuid": "8db3fd392e7444cb8500e993c162495c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8db3fd392e7444cb8500e993c162495c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8db3fd392e7444cb8500e993c162495c"}}, "title": "Associations Between Attention-Deficit/Hyperactivity Disorder and Various Eating Disorders: A Swedish Nationwide Population Study Using Multiple Genetically Informative Approaches.", "authors": [{"family": "Yao", "given": "Shuyang", "initials": "S"}, {"family": "Kuja-Halkola", "given": "Ralf", "initials": "R"}, {"family": "Martin", "given": "Joanna", "initials": "J"}, {"family": "Lu", "given": "Yi", "initials": "Y"}, {"family": "Lichtenstein", "given": "Paul", "initials": "P"}, {"family": "Norring", "given": "Claes", "initials": "C"}, {"family": "Birgeg\u00e5rd", "given": "Andreas", "initials": "A"}, {"family": "Yilmaz", "given": "Zeynep", "initials": "Z"}, {"family": "H\u00fcbel", "given": "Christopher", "initials": "C"}, {"family": "Watson", "given": "Hunna", "initials": "H"}, {"family": "Baker", "given": "Jessica", "initials": "J"}, {"family": "Almqvist", "given": "Catarina", "initials": "C"}, {"family": "Eating Disorders Working Group of the Psychiatric Genomics Consortium", "given": "", "initials": ""}, {"family": "Thornton", "given": "Laura M", "initials": "LM"}, {"family": "Magnusson", "given": "Patrik K", "initials": "PK"}, {"family": "Bulik", "given": "Cynthia M", "initials": "CM"}, {"family": "Larsson", "given": "Henrik", "initials": "H"}], "type": "journal article", "published": "2019-10-15", "journal": {"volume": "86", "issn": "1873-2402", "issue": "8", "pages": "577-586", "title": "Biol. Psychiatry", "issn-l": "0006-3223"}, "abstract": "Although attention-deficit/hyperactivity disorder (ADHD) and eating disorders (EDs) frequently co-occur, little is known about the shared etiology. In this study, we comprehensively investigated the genetic association between ADHD and various EDs, including anorexia nervosa (AN) and other EDs such as bulimia nervosa.\n\nWe applied different genetically informative designs to register-based information of a Swedish nationwide population (N\u00a0= 3,550,118). We first examined the familial coaggregation of clinically diagnosed ADHD and EDs across multiple types of relatives. We then applied quantitative genetic modeling in full-sisters and maternal half-sisters to estimate the genetic correlations between ADHD and EDs. We further tested the associations between ADHD polygenic risk scores and ED symptoms, and between AN polygenic risk scores and ADHD symptoms, in a genotyped population-based sample (N\u00a0= 13,472).\n\nIncreased risk of all types of EDs was found in individuals with ADHD (any ED: odds ratio [OR]\u00a0= 3.97, 95% confidence interval [CI]\u00a0= 3.81, 4.14; AN: OR\u00a0= 2.68, 95% CI\u00a0= 2.15, 2.86; other EDs: OR\u00a0= 4.66, 95% CI\u00a0= 4.47, 4.87; bulimia nervosa: OR\u00a0= 5.01, 95% CI\u00a0= 4.63, 5.41) and their relatives compared with individuals without ADHD and their relatives. The magnitude of the associations decreased as the degree of relatedness decreased, suggesting shared familial liability between ADHD and EDs. Quantitative genetic models revealed stronger genetic correlation of ADHD with other EDs (.37, 95% CI\u00a0= .31, .42) than with AN (.14, 95% CI\u00a0= .05, .22). ADHD polygenic risk scores correlated positively with ED symptom measures overall and with the subscales Drive for Thinness and Body Dissatisfaction despite small effect sizes.\n\nWe observed stronger genetic association with ADHD for non-AN EDs than for AN, highlighting specific genetic correlation beyond a general genetic factor across psychiatric disorders.", "doi": "10.1016/j.biopsych.2019.04.036", "pmid": "31301758", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "S0006-3223(19)31371-X"}], "notes": [], "created": "2019-10-02T13:48:00.089Z", "modified": "2020-01-21T13:56:14.614Z"}, {"entity": "publication", "iuid": "588ea50294e0470cbaa20fdebb9123e4", "links": {"self": {"href": "https://publications.scilifelab.se/publication/588ea50294e0470cbaa20fdebb9123e4.json"}, "display": {"href": "https://publications.scilifelab.se/publication/588ea50294e0470cbaa20fdebb9123e4"}}, "title": "The genomic ancestry of the Scandinavian Battle Axe Culture people and their relation to the broader Corded Ware horizon.", "authors": [{"family": "Malmstr\u00f6m", "given": "Helena", "initials": "H"}, {"family": "G\u00fcnther", "given": "Torsten", "initials": "T"}, {"family": "Svensson", "given": "Emma M", "initials": "EM"}, {"family": "Juras", "given": "Anna", "initials": "A"}, {"family": "Fraser", "given": "Magdalena", "initials": "M"}, {"family": "Munters", "given": "Arielle R", "initials": "AR"}, {"family": "Pospieszny", "given": "\u0141ukasz", "initials": "\u0141"}, {"family": "T\u00f5rv", "given": "Mari", "initials": "M"}, {"family": "Lindstr\u00f6m", "given": "Jonathan", "initials": "J"}, {"family": "G\u00f6therstr\u00f6m", "given": "Anders", "initials": "A", "orcid": "0000-0001-6307-8188", "researcher": {"href": "https://publications.scilifelab.se/researcher/2a1a0a680ab8456cbf5a941e9718fd5a.json"}}, {"family": "Stor\u00e5", "given": "Jan", "initials": "J"}, {"family": "Jakobsson", "given": "Mattias", "initials": "M", "orcid": "0000-0001-7840-7853", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a4abe0fcb20492d9ec849c9fbf58a71.json"}}], "type": "historical article", "published": "2019-10-09", "journal": {"volume": "286", "issn": "1471-2954", "issue": "1912", "pages": "20191528", "title": "Proc. Biol. Sci.", "issn-l": "0962-8452"}, "abstract": "The Neolithic period is characterized by major cultural transformations and human migrations, with lasting effects across Europe. To understand the population dynamics in Neolithic Scandinavia and the Baltic Sea area, we investigate the genomes of individuals associated with the Battle Axe Culture (BAC), a Middle Neolithic complex in Scandinavia resembling the continental Corded Ware Culture (CWC). We sequenced 11 individuals (dated to 3330-1665 calibrated before common era (cal BCE)) from modern-day Sweden, Estonia, and Poland to 0.26-3.24\u00d7 coverage. Three of the individuals were from CWC contexts and two from the central-Swedish BAC burial 'Bergsgraven'. By analysing these genomes together with the previously published data, we show that the BAC represents a group different from other Neolithic populations in Scandinavia, revealing stratification among cultural groups. Similar to continental CWC, the BAC-associated individuals display ancestry from the Pontic-Caspian steppe herders, as well as smaller components originating from hunter-gatherers and Early Neolithic farmers. Thus, the steppe ancestry seen in these Scandinavian BAC individuals can be explained only by migration into Scandinavia. Furthermore, we highlight the reuse of megalithic tombs of the earlier Funnel Beaker Culture (FBC) by people related to BAC. The BAC groups likely mixed with resident middle Neolithic farmers (e.g. FBC) without substantial contributions from Neolithic foragers.", "doi": "10.1098/rspb.2019.1528", "pmid": "31594508", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC6790770"}, {"db": "figshare", "key": "10.6084/m9.figshare.c.4682318"}], "notes": [], "created": "2020-01-08T12:39:39.334Z", "modified": "2021-07-07T10:46:20.330Z"}, {"entity": "publication", "iuid": "5226f490816647da97024c77ff20ed95", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5226f490816647da97024c77ff20ed95.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5226f490816647da97024c77ff20ed95"}}, "title": "Along the Indian Ocean coast: genomic variation in Mozambique provides new insights into the Bantu expansion.", "authors": [{"family": "Semo", "given": "Armando", "initials": "A"}, {"family": "Gay\u00e0-Vidal", "given": "Magdalena", "initials": "M"}, {"family": "Fortes-Lima", "given": "Cesar", "initials": "C"}, {"family": "Alard", "given": "B\u00e9r\u00e9nice", "initials": "B"}, {"family": "Oliveira", "given": "Sandra", "initials": "S"}, {"family": "Almeida", "given": "Jo\u00e3o", "initials": "J"}, {"family": "Prista", "given": "Ant\u00f3nio", "initials": "A"}, {"family": "Damasceno", "given": "Albertino", "initials": "A"}, {"family": "Fehn", "given": "Anne-Maria", "initials": "AM"}, {"family": "Schlebusch", "given": "Carina", "initials": "C"}, {"family": "Rocha", "given": "Jorge", "initials": "J"}], "type": "journal article", "published": "2019-10-08", "journal": {"volume": null, "issn": "1537-1719", "issue": null, "title": "Mol. Biol. Evol.", "issn-l": "0737-4038"}, "abstract": "The Bantu expansion, which started in West Central Africa around 5,000\u2009BP, constitutes a major migratory movement involving the joint spread of peoples and languages across sub-Saharan Africa. Despite the rich linguistic and archaeological evidence available, the genetic relationships between different Bantu-speaking populations and the migratory routes they followed during various phases of the expansion remain poorly understood. Here, we analyze the genetic profiles of southwestern and southeastern Bantu-speaking peoples located at the edges of the Bantu expansion by generating genome-wide data for 200 individuals from 12 Mozambican and 3 Angolan populations using \u223c1.9 million autosomal single nucleotide polymorphisms. Incorporating a wide range of available genetic data, our analyses confirm previous results favoring a \"late split\" between West and East Bantu speakers, following a joint passage through the rainforest. In addition, we find that Bantu speakers from eastern Africa display genetic substructure, with Mozambican populations forming a gradient of relatedness along a North-South cline stretching from the coastal border between Kenya and Tanzania to South Africa. This gradient is further associated with a southward increase in genetic homogeneity, and involved minimum admixture with resident populations. Together, our results provide the first genetic evidence in support of a rapid North-South dispersal of Bantu peoples along the Indian Ocean Coast, as inferred from the distribution and antiquity of Early Iron Age assemblages associated with the Kwale archaeological tradition.", "doi": "10.1093/molbev/msz224", "pmid": "31593238", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "5583770"}], "notes": [], "created": "2019-10-14T10:12:47.372Z", "modified": "2024-01-16T13:48:43.699Z"}, {"entity": "publication", "iuid": "9c85b04495334bb0817ec3e19a5e0aee", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9c85b04495334bb0817ec3e19a5e0aee.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9c85b04495334bb0817ec3e19a5e0aee"}}, "title": "Target genes, variants, tissues and transcriptional pathways influencing human serum urate levels.", "authors": [{"family": "Tin", "given": "Adrienne", "initials": "A"}, {"family": "Marten", "given": "Jonathan", "initials": "J"}, {"family": "Halperin Kuhns", "given": "Victoria L", "initials": "VL"}, {"family": "Li", "given": "Yong", "initials": "Y"}, {"family": "Wuttke", "given": "Matthias", "initials": "M"}, {"family": "Kirsten", "given": "Holger", "initials": "H"}, {"family": "Sieber", "given": "Karsten B", "initials": "KB"}, {"family": "Qiu", "given": "Chengxiang", "initials": "C"}, {"family": "Gorski", "given": "Mathias", "initials": "M"}, {"family": "Yu", "given": "Zhi", "initials": "Z"}, {"family": "Giri", "given": "Ayush", "initials": "A"}, {"family": "Sveinbjornsson", "given": "Gardar", "initials": "G"}, {"family": "Li", "given": "Man", "initials": "M"}, {"family": "Chu", "given": "Audrey Y", "initials": "AY"}, {"family": "Hoppmann", "given": "Anselm", "initials": "A"}, {"family": "O'Connor", "given": "Luke J", "initials": "LJ"}, {"family": "Prins", "given": "Bram", "initials": "B"}, {"family": "Nutile", "given": "Teresa", "initials": "T"}, {"family": "Noce", "given": "Damia", "initials": "D"}, {"family": "Akiyama", "given": "Masato", "initials": "M"}, {"family": "Cocca", "given": "Massimiliano", "initials": "M"}, {"family": "Ghasemi", "given": "Sahar", "initials": "S"}, {"family": "van der Most", "given": "Peter J", "initials": "PJ"}, {"family": "Horn", "given": "Katrin", "initials": "K"}, {"family": "Xu", "given": "Yizhe", "initials": "Y"}, {"family": "Fuchsberger", "given": "Christian", "initials": "C"}, {"family": "Sedaghat", "given": "Sanaz", "initials": "S"}, {"family": "Afaq", "given": "Saima", "initials": "S"}, {"family": "Amin", "given": "Najaf", "initials": "N"}, {"family": "\u00c4rnl\u00f6v", "given": "Johan", "initials": "J"}, {"family": "Bakker", "given": "Stephan J L", "initials": "SJL"}, {"family": "Bansal", "given": "Nisha", "initials": "N"}, {"family": "Baptista", "given": 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"given": "Simona", "initials": "S"}, {"family": "van der Harst", "given": "Pim", "initials": "P"}, {"family": "van Duijn", "given": "Cornelia M", "initials": "CM"}, {"family": "Verweij", "given": "Niek", "initials": "N"}, {"family": "V\u00f6lker", "given": "Uwe", "initials": "U"}, {"family": "Vollenweider", "given": "Peter", "initials": "P"}, {"family": "Waeber", "given": "Gerard", "initials": "G"}, {"family": "Waldenberger", "given": "Melanie", "initials": "M"}, {"family": "Whitfield", "given": "John B", "initials": "JB"}, {"family": "Wild", "given": "Sarah H", "initials": "SH"}, {"family": "Wilson", "given": "James F", "initials": "JF"}, {"family": "Yang", "given": "Qiong", "initials": "Q"}, {"family": "Zhang", "given": "Weihua", "initials": "W"}, {"family": "Zonderman", "given": "Alan B", "initials": "AB"}, {"family": "Bochud", "given": "Murielle", "initials": "M"}, {"family": "Wilson", "given": "James G", "initials": "JG"}, {"family": "Pendergrass", "given": "Sarah A", "initials": "SA"}, {"family": "Ho", "given": "Kevin", "initials": "K"}, {"family": "Parsa", "given": "Afshin", "initials": "A"}, {"family": "Pramstaller", "given": "Peter P", "initials": "PP"}, {"family": "Psaty", "given": "Bruce M", "initials": "BM"}, {"family": "B\u00f6ger", "given": "Carsten A", "initials": "CA"}, {"family": "Snieder", "given": "Harold", "initials": "H"}, {"family": "Butterworth", "given": "Adam S", "initials": "AS"}, {"family": "Okada", "given": "Yukinori", "initials": "Y"}, {"family": "Edwards", "given": "Todd L", "initials": "TL"}, {"family": "Stefansson", "given": "Kari", "initials": "K"}, {"family": "Susztak", "given": "Katalin", "initials": "K"}, {"family": "Scholz", "given": "Markus", "initials": "M"}, {"family": "Heid", "given": "Iris M", "initials": "IM"}, {"family": "Hung", "given": "Adriana M", "initials": "AM"}, {"family": "Teumer", "given": "Alexander", "initials": "A"}, {"family": "Pattaro", "given": "Cristian", "initials": "C"}, {"family": "Woodward", "given": "Owen M", "initials": "OM"}, {"family": "Vitart", "given": "Veronique", "initials": "V"}, {"family": "K\u00f6ttgen", "given": "Anna", "initials": "A"}], "type": "journal article", "published": "2019-10-02", "journal": {"volume": null, "issn": "1546-1718", "issue": null, "title": "Nat. Genet.", "issn-l": "1061-4036"}, "abstract": "Elevated serum urate levels cause gout and correlate with cardiometabolic diseases via poorly understood mechanisms. We performed a trans-ancestry genome-wide association study of serum urate in 457,690 individuals, identifying 183 loci (147 previously unknown) that improve the prediction of gout in an independent cohort of 334,880 individuals. Serum urate showed significant genetic correlations with many cardiometabolic traits, with genetic causality analyses supporting a substantial role for pleiotropy. Enrichment analysis, fine-mapping of urate-associated loci and colocalization with gene expression in 47 tissues implicated the kidney and liver as the main target organs and prioritized potentially causal genes and variants, including the transcriptional master regulators in the liver and kidney, HNF1A and HNF4A. Experimental validation showed that HNF4A transactivated the promoter of ABCG2, encoding a major urate transporter, in kidney cells, and that HNF4A p.Thr139Ile is a functional variant. Transcriptional coregulation within and across organs may be a general mechanism underlying the observed pleiotropy between urate and cardiometabolic traits.", "doi": "10.1038/s41588-019-0504-x", "pmid": "31578528", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41588-019-0504-x"}], "notes": [], "created": "2019-10-08T08:43:46.521Z", "modified": "2020-01-21T13:56:14.626Z"}, {"entity": "publication", "iuid": "896c9ba71a5a4bc8a9a93699bd1f5df7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/896c9ba71a5a4bc8a9a93699bd1f5df7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/896c9ba71a5a4bc8a9a93699bd1f5df7"}}, "title": "Transcriptome and Proteome Profiling of Neural Induced Pluripotent Stem Cells from Individuals with Down Syndrome Disclose Dynamic Dysregulations of Key Pathways and Cellular Functions.", "authors": [{"family": "Sobol", "given": "Maria", "initials": "M"}, {"family": "Klar", "given": "Joakim", "initials": "J"}, {"family": "Laan", "given": "Loora", "initials": "L"}, {"family": "Shahsavani", "given": "Mansoureh", "initials": "M"}, {"family": "Schuster", "given": "Jens", "initials": "J"}, {"family": "Anner\u00e9n", "given": "G\u00f6ran", "initials": "G"}, {"family": "Konzer", "given": "Anne", "initials": "A"}, {"family": "Mi", "given": "Jia", "initials": "J"}, {"family": "Bergquist", "given": "Jonas", "initials": "J"}, {"family": "Nordlund", "given": "Jessica", "initials": "J", "orcid": "0000-0001-8699-9959", "researcher": {"href": "https://publications.scilifelab.se/researcher/ddf48c9262134821bcc6ce1180049753.json"}}, {"family": "Hoeber", "given": "Jan", "initials": "J"}, {"family": "Huss", "given": "Mikael", "initials": "M"}, {"family": "Falk", "given": "Anna", "initials": "A"}, {"family": "Dahl", "given": "Niklas", "initials": "N", "orcid": "0000-0002-8122-0800", "researcher": {"href": "https://publications.scilifelab.se/researcher/689e06ddc001490a8cb891050ba5a732.json"}}], "type": "journal article", "published": "2019-10-00", "journal": {"volume": "56", "issn": "1559-1182", "issue": "10", "pages": "7113-7127", "title": "Mol Neurobiol", "issn-l": "0893-7648"}, "abstract": "Down syndrome (DS) or trisomy 21 (T21) is a leading genetic cause of intellectual disability. To gain insights into dynamics of molecular perturbations during neurogenesis in DS, we established a model using induced pluripotent stem cells (iPSC) with transcriptome profiles comparable to that of normal fetal brain development. When applied on iPSCs with T21, transcriptome and proteome signatures at two stages of differentiation revealed strong temporal dynamics of dysregulated genes, proteins and pathways belonging to 11 major functional clusters. DNA replication, synaptic maturation and neuroactive clusters were disturbed at the early differentiation time point accompanied by a skewed transition from the neural progenitor cell stage and reduced cellular growth. With differentiation, growth factor and extracellular matrix, oxidative phosphorylation and glycolysis emerged as major perturbed clusters. Furthermore, we identified a marked dysregulation of a set of genes encoded by chromosome 21 including an early upregulation of the hub gene APP, supporting its role for disturbed neurogenesis, and the transcription factors OLIG1, OLIG2 and RUNX1, consistent with deficient myelination and neuronal differentiation. Taken together, our findings highlight novel sequential and differentiation-dependent dynamics of disturbed functions, pathways and elements in T21 neurogenesis, providing further insights into developmental abnormalities of the DS brain.", "doi": "10.1007/s12035-019-1585-3", "pmid": "30989628", "labels": {"National Genomics Infrastructure": "Collaborative", "NGI Uppsala (SNP&SEQ Technology Platform)": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1007/s12035-019-1585-3"}, {"db": "pmc", "key": "PMC6728280"}], "notes": [], "created": "2019-05-03T06:15:57.377Z", "modified": "2024-01-16T13:48:43.744Z"}, {"entity": "publication", "iuid": "378b63c4286e4e488c86354c390f0ad9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/378b63c4286e4e488c86354c390f0ad9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/378b63c4286e4e488c86354c390f0ad9"}}, "title": "Genetic variations in A20 DUB domain provide a genetic link to citrullination and neutrophil extracellular traps in systemic lupus erythematosus.", "authors": [{"family": "Odqvist", "given": "Lina", "initials": "L", "orcid": "0000-0001-6002-0968", "researcher": {"href": "https://publications.scilifelab.se/researcher/3e1f6b2d0a50437fa42f41b237a2b111.json"}}, {"family": "Jevnikar", "given": "Zala", "initials": "Z"}, {"family": "Riise", "given": "Rebecca", "initials": "R"}, {"family": "\u00d6berg", "given": "Lisa", "initials": "L"}, {"family": "Rhedin", "given": "Magdalena", "initials": "M"}, {"family": "Leonard", "given": "Dag", "initials": "D"}, {"family": "Yrlid", "given": "Linda", "initials": "L"}, {"family": "Jackson", "given": "Sonya", "initials": "S"}, {"family": "Mattsson", "given": "Johan", "initials": "J"}, {"family": "Nanda", "given": "Sambit", "initials": "S"}, {"family": "Cohen", "given": "Philip", "initials": "P"}, {"family": "Knebel", "given": "Axel", "initials": "A"}, {"family": "Arthur", "given": "Simon", "initials": "S"}, {"family": "Th\u00f6rn", "given": "Kristofer", "initials": "K"}, {"family": "Svenungsson", "given": "Elisabet", "initials": "E"}, {"family": "J\u00f6nsen", "given": "Andreas", "initials": "A"}, {"family": "Gunnarsson", "given": "Iva", "initials": "I"}, {"family": "Tandre", "given": "Karolina", "initials": "K"}, {"family": "Alexsson", "given": "Andrei", "initials": "A"}, {"family": "Kastbom", "given": "Alf", "initials": "A"}, {"family": "Rantap\u00e4\u00e4-Dahlqvist", "given": "Solbritt", "initials": "S"}, {"family": "Eloranta", "given": "Maija-Leena", "initials": "ML"}, {"family": "Syv\u00e4nen", "given": "Ann-Christine", "initials": "AC", "orcid": "0000-0002-9681-9146", "researcher": {"href": "https://publications.scilifelab.se/researcher/f7012e35025543379380cb90efd71243.json"}}, {"family": "Bengtsson", "given": "Anders", "initials": "A"}, {"family": "Johansson", "given": "Patrik", "initials": "P"}, {"family": "Sandling", "given": "Johanna K", "initials": "JK"}, {"family": "Sj\u00f6wall", "given": "Christopher", "initials": "C", "orcid": "0000-0003-0900-2048", "researcher": {"href": "https://publications.scilifelab.se/researcher/fe4dd47b8ca1436e8a26fdea33f5e7f6.json"}}, {"family": "R\u00f6nnblom", "given": "Lars", "initials": "L"}, {"family": "Collins", "given": "Barry", "initials": "B"}, {"family": "Vaarala", "given": "Outi", "initials": "O"}], "type": "journal article", "published": "2019-10-00", "journal": {"volume": "78", "issn": "1468-2060", "issue": "10", "pages": "1363-1370", "title": "Ann. Rheum. Dis.", "issn-l": "0003-4967"}, "abstract": "Genetic variations in TNFAIP3 (A20) de-ubiquitinase (DUB) domain increase the risk of systemic lupus erythematosus (SLE) and rheumatoid arthritis. A20 is a negative regulator of NF-\u03baB but the role of its DUB domain and related genetic variants remain unclear. We aimed to study the functional effects of A20 DUB-domain alterations in immune cells and understand its link to SLE pathogenesis.\n\nCRISPR/Cas9 was used to generate human U937 monocytes with A20 DUB-inactivating C103A knock-in (KI) mutation. Whole genome RNA-sequencing was used to identify differentially expressed genes between WT and C103A KI cells. Functional studies were performed in A20 C103A U937 cells and in immune cells from A20 C103A mice and genotyped healthy individuals with A20 DUB polymorphism rs2230926. Neutrophil extracellular trap (NET) formation was addressed ex vivo in neutrophils from A20 C103A mice and SLE-patients with rs2230926.\n\nGenetic disruption of A20 DUB domain in human and murine myeloid cells did not give rise to enhanced NF-\u03baB signalling. Instead, cells with C103A mutation or rs2230926 polymorphism presented an upregulated expression of PADI4, an enzyme regulating protein citrullination and NET formation, two key mechanisms in autoimmune pathology. A20 C103A cells exhibited enhanced protein citrullination and extracellular trap formation, which could be suppressed by selective PAD4 inhibition. Moreover, SLE-patients with rs2230926 showed increased NETs and increased frequency of autoantibodies to citrullinated epitopes.\n\nWe propose that genetic alterations disrupting the A20 DUB domain mediate increased susceptibility to SLE through the upregulation of PADI4 with resultant protein citrullination and extracellular trap formation.", "doi": "10.1136/annrheumdis-2019-215434", "pmid": "31300459", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "annrheumdis-2019-215434"}, {"db": "pmc", "key": "PMC6788882"}], "notes": [], "created": "2019-12-03T12:19:34.048Z", "modified": "2021-07-07T14:57:19.927Z"}, {"entity": "publication", "iuid": "e0e653f6b4f54d8584da0f7e3225d6ab", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e0e653f6b4f54d8584da0f7e3225d6ab.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e0e653f6b4f54d8584da0f7e3225d6ab"}}, "title": "Genetic basis and timing of a major mating system shift in Capsella.", "authors": [{"family": "Bachmann", "given": "J\u00f6rg A", "initials": "JA"}, {"family": "Tedder", "given": "Andrew", "initials": "A", "orcid": "0000-0002-7378-4673", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a29b3c1160f46bf8b21e331268eb4b1.json"}}, {"family": "Laenen", "given": "Benjamin", "initials": "B"}, {"family": "Fracassetti", "given": "Marco", "initials": "M", "orcid": "0000-0002-2962-2669", "researcher": {"href": "https://publications.scilifelab.se/researcher/695213cdd1a645cbbf10d44122237b18.json"}}, {"family": "D\u00e9samor\u00e9", "given": "Aur\u00e9lie", "initials": "A", "orcid": "0000-0003-1922-3557", "researcher": {"href": "https://publications.scilifelab.se/researcher/e117d822871c4a38960b526e3d0dcd0a.json"}}, {"family": "Lafon-Placette", "given": "Cl\u00e9ment", "initials": "C", "orcid": "0000-0001-6634-8104", "researcher": {"href": "https://publications.scilifelab.se/researcher/63262f71f9c54f438d6f08380d799d96.json"}}, {"family": "Steige", "given": "Kim A", "initials": "KA"}, {"family": "Callot", "given": "Caroline", "initials": "C"}, {"family": "Marande", "given": "William", "initials": "W"}, {"family": "Neuffer", "given": "Barbara", "initials": "B"}, {"family": "Berg\u00e8s", "given": "H\u00e9l\u00e8ne", "initials": "H", "orcid": "0000-0002-5492-1062", "researcher": {"href": "https://publications.scilifelab.se/researcher/728be2338bd2407980d11b8850d85d9c.json"}}, {"family": "K\u00f6hler", "given": "Claudia", "initials": "C", "orcid": "0000-0002-2619-4857", "researcher": {"href": "https://publications.scilifelab.se/researcher/accd3f9307614c8ab67154dd5e50cdac.json"}}, {"family": "Castric", "given": "Vincent", "initials": "V", "orcid": "0000-0002-4461-4915", "researcher": {"href": "https://publications.scilifelab.se/researcher/f891128567d64aaba03bdd9f4bc5d458.json"}}, {"family": "Slotte", "given": "Tanja", "initials": "T", "orcid": "0000-0001-6020-5102", "researcher": {"href": "https://publications.scilifelab.se/researcher/67c69ee78bae41478465a7e5fa63b946.json"}}], "type": "journal article", "published": "2019-10-00", "journal": {"volume": "224", "issn": "1469-8137", "issue": "1", "pages": "505-517", "title": "New Phytol.", "issn-l": "0028-646X"}, "abstract": "A crucial step in the transition from outcrossing to self-fertilization is the loss of genetic self-incompatibility (SI). In the Brassicaceae, SI involves the interaction of female and male specificity components, encoded by the genes SRK and SCR at the self-incompatibility locus (S-locus). Theory predicts that S-linked mutations, and especially dominant mutations in SCR, are likely to contribute to loss of SI. However, few studies have investigated the contribution of dominant mutations to loss of SI in wild plant species. Here, we investigate the genetic basis of loss of SI in the self-fertilizing crucifer species Capsella orientalis, by combining genetic mapping, long-read sequencing of complete S-haplotypes, gene expression analyses and controlled crosses. We show that loss of SI in C. orientalis occurred < 2.6 Mya and maps as a dominant trait to the S-locus. We identify a fixed frameshift deletion in the male specificity gene SCR and confirm loss of male SI specificity. We further identify an S-linked small RNA that is predicted to cause dominance of self-compatibility. Our results agree with predictions on the contribution of dominant S-linked mutations to loss of SI, and thus provide new insights into the molecular basis of mating system transitions.", "doi": "10.1111/nph.16035", "pmid": "31254395", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "GENBANK", "key": "PRJEB32122"}, {"db": "GENBANK", "key": "KJ772374.1"}], "notes": [], "created": "2019-12-03T10:47:11.816Z", "modified": "2024-01-16T13:48:43.769Z"}, {"entity": "publication", "iuid": "885ef893417d418db138a1903108bcd8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/885ef893417d418db138a1903108bcd8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/885ef893417d418db138a1903108bcd8"}}, "title": "Exploring a Pool-seq-only approach for gaining population genomic insights in nonmodel species.", "authors": [{"family": "Kurland", "given": "Sara", "initials": "S", "orcid": "0000-0002-5370-1236", "researcher": {"href": "https://publications.scilifelab.se/researcher/fdfc16fe9c7c4065b3e3d3f6877424f7.json"}}, {"family": "Wheat", "given": "Christopher W", "initials": "CW"}, {"family": "de la Paz Celorio Mancera", "given": "Maria", "initials": "M", "orcid": "0000-0003-0296-0577", "researcher": {"href": "https://publications.scilifelab.se/researcher/2abfa65f99b44f1ba6f8f0e6f3d7d8a4.json"}}, {"family": "Kutschera", "given": "Verena E", "initials": "VE", "orcid": "0000-0002-8930-534X", "researcher": {"href": "https://publications.scilifelab.se/researcher/4f80fb4d234c4f2fa2179ad1e7c6a6db.json"}}, {"family": "Hill", "given": "Jason", "initials": "J"}, {"family": "Andersson", "given": "Anastasia", "initials": "A"}, {"family": "Rubin", "given": "Carl-Johan", "initials": "CJ"}, {"family": "Andersson", "given": "Leif", "initials": "L", "orcid": "0000-0002-4085-6968", "researcher": {"href": "https://publications.scilifelab.se/researcher/bd3343c12f994b1fabcae23027d3a76d.json"}}, {"family": "Ryman", "given": "Nils", "initials": "N", "orcid": "0000-0003-3342-8479", "researcher": {"href": "https://publications.scilifelab.se/researcher/97201873ea354e959e294d8d2d69be13.json"}}, {"family": "Laikre", "given": "Linda", "initials": "L", "orcid": "0000-0001-9286-3361", "researcher": {"href": "https://publications.scilifelab.se/researcher/b7c7ebbb5d7a4af582746b6ab2c2d132.json"}}], "type": "journal article", "published": "2019-10-00", "journal": {"title": "Ecol Evol", "issn": "2045-7758", "issn-l": "2045-7758", "volume": "9", "issue": "19", "pages": "11448-11463"}, "abstract": "Developing genomic insights is challenging in nonmodel species for which resources are often scarce and prohibitively costly. Here, we explore the potential of a recently established approach using Pool-seq data to generate a de novo genome assembly for mining exons, upon which Pool-seq data are used to estimate population divergence and diversity. We do this for two pairs of sympatric populations of brown trout (Salmo trutta): one naturally sympatric set of populations and another pair of populations introduced to a common environment. We validate our approach by comparing the results to those from markers previously used to describe the populations (allozymes and individual-based single nucleotide polymorphisms [SNPs]) and from mapping the Pool-seq data to a reference genome of the closely related Atlantic salmon (Salmo salar). We find that genomic differentiation (F ST) between the two introduced populations exceeds that of the naturally sympatric populations (F ST = 0.13 and 0.03 between the introduced and the naturally sympatric populations, respectively), in concordance with estimates from the previously used SNPs. The same level of population divergence is found for the two genome assemblies, but estimates of average nucleotide diversity differ ( \u2248 0.002 and \u03c0 \u00af \u2248 0.001 when mapping to \u03c0 \u00afS. trutta and S. salar, respectively), although the relationships between population values are largely consistent. This discrepancy might be attributed to biases when mapping to a haploid condensed assembly made of highly fragmented read data compared to using a high-quality reference assembly from a divergent species. We conclude that the Pool-seq-only approach can be suitable for detecting and quantifying genome-wide population differentiation, and for comparing genomic diversity in populations of nonmodel species where reference genomes are lacking.", "doi": "10.1002/ece3.5646", "pmid": "31641485", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC6802065"}, {"db": "pii", "key": "ECE35646"}, {"db": "Dryad", "key": "10.5061/dryad.q1h4k0n"}], "notes": [], "created": "2019-11-20T09:43:21.469Z", "modified": "2024-01-16T13:48:43.776Z"}, {"entity": "publication", "iuid": "2407f47a927f481cbb3dbe14fd13b174", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2407f47a927f481cbb3dbe14fd13b174.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2407f47a927f481cbb3dbe14fd13b174"}}, "title": "Distribution of bacteria between different milk fractions, investigated using culture-dependent methods and molecular-based and fluorescent microscopy approaches.", "authors": [{"family": "Sun", "given": "L", "initials": "L", "orcid": "0000-0002-7027-1135", "researcher": {"href": "https://publications.scilifelab.se/researcher/fa23b6866dfb4cb79ee0ce173180cb7c.json"}}, {"family": "Dicksved", "given": "J", "initials": "J"}, {"family": "Priyashantha", "given": "H", "initials": "H", "orcid": "0000-0003-0190-9075", "researcher": {"href": "https://publications.scilifelab.se/researcher/c82583532c204444b2a35ca4541b8d9d.json"}}, {"family": "Lundh", "given": "\u00c5", "initials": "\u00c5", "orcid": "0000-0002-1626-7063", "researcher": {"href": "https://publications.scilifelab.se/researcher/a224c2dba7b64eb6926b1ae3b2a8f276.json"}}, {"family": "Johansson", "given": "M", "initials": "M"}], "type": "journal article", "published": "2019-10-00", "journal": {"volume": "127", "issn": "1365-2672", "issue": "4", "pages": "1028-1037", "title": "J Appl Microbiol", "issn-l": "1364-5072"}, "abstract": "To develop a protocol for DNA extraction using whole milk and further, to investigate how the use of whole instead of skimmed milk during DNA extraction affected the resulting microbial composition.\n\nIn a model study, three selected bacterial species (Staphylococcus aureus ATCC 25923, Escherichia coli ATCC 11775 and Lactobacillus reuteri PTA 4659) were added to raw milk and their distribution between different milk fractions was examined by cultivation on selective agar plates. Quantitative real-time PCR (qPCR) assays and Illumina amplicon sequencing were conducted after DNA extraction of whole milk and skimmed milk. In addition, fluorescent microscopy was used to visualize the distribution of Lactobacillus reuteri R2LC mCherry in milk samples with different fat contents. Depending on spike-in bacterial species, recovery rates of 7\u00b74-26\u00b75% of added bacteria were obtained in the fat fraction in culture-based enumeration. qPCR showed a 7-9 fold increase in recovery of spike-in bacteria when the milk fat fraction was combined with the pellet during the DNA extraction step. In the Illumina 16S amplicon approach, relative abundance of six of the top 11 operational taxonomic units identified differed significantly when comparing skimmed milk and whole milk as starting material. Fluorescent microscopy images demonstrated that L. reuteri R2LC mCherry was associated with fat globules in whole milk samples.\n\nThis study demonstrates that milk fat harbours bacterial species that might be underestimated when skimmed milk, rather than whole milk, is used for DNA extraction.\n\nThis study emphasizes the importance of using whole instead of skimmed milk for DNA extraction. A protocol for extracting DNA from whole milk is suggested.", "doi": "10.1111/jam.14377", "pmid": "31287608", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2019-12-03T10:46:57.253Z", "modified": "2024-01-16T13:48:43.783Z"}, {"entity": "publication", "iuid": "9cf391ad464e47f79d7b9e7f0c5c446b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9cf391ad464e47f79d7b9e7f0c5c446b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9cf391ad464e47f79d7b9e7f0c5c446b"}}, "title": "Predisposition to childhood acute lymphoblastic leukemia caused by a constitutional translocation disrupting ETV6.", "authors": [{"family": "J\u00e4rviaho", "given": "Tekla", "initials": "T"}, {"family": "Bang", "given": "Benedicte", "initials": "B"}, {"family": "Zachariadis", "given": "Vasilios", "initials": "V"}, {"family": "Taylan", "given": "Fulya", "initials": "F"}, {"family": "Moilanen", "given": "Jukka", "initials": "J"}, {"family": "M\u00f6tt\u00f6nen", "given": "Merja", "initials": "M"}, {"family": "Smith", "given": "C I Edvard", "initials": "CIE"}, {"family": "Harila-Saari", "given": "Arja", "initials": "A"}, {"family": "Niinim\u00e4ki", "given": "Riitta", "initials": "R"}, {"family": "Nordgren", "given": "Ann", "initials": "A"}], "type": "journal article", "published": "2019-09-24", "journal": {"volume": "3", "issn": "2473-9537", "issue": "18", "pages": "2722-2731", "title": "Blood Adv", "issn-l": "2473-9529"}, "abstract": "Pathogenic germline variants in \r\n                ETV6 have been associated with familial predisposition to thrombocytopenia and hematological malignancies, predominantly childhood B-cell precursor acute lymphoblastic leukemia (BCP-ALL). In addition, overrepresentation of a high hyperdiploid subtype and older age at diagnosis have been reported among sporadic BCP-ALL cases with germline variants in ETV6 We studied a family with 2 second-degree relatives who developed childhood high hyperdiploid BCP-ALL at ages 8 and 12 years, respectively. A constitutional balanced reciprocal translocation t(12;14)(p13.2;q23.1) was discovered in both patients by routine karyotyping at diagnosis and, subsequently, in 7 healthy family members who had not experienced hematological malignancies. No carriers had thrombocytopenia. Whole-genome sequencing confirmed the translocation, resulting in 2 actively transcribed but nonfunctional fusion genes, causing heterozygous loss and consequently monoallelic expression of ETV6 Whole-genome sequencing analysis of the affected female subjects' leukemia excluded additional somatic aberrations in ETV6 and RTN1 as well as shared somatic variants in other genes. Expression studies, performed to confirm decreased expression of ETV6, were not conclusive. We suggest that germline aberrations resulting in monoallelic expression of ETV6 contribute to leukemia susceptibility, whereas more severe functional deficiency of ETV6 is required for developing THC5. To our knowledge, this report is the first of a constitutional translocation disrupting ETV6 causing predisposition to childhood ALL.", "doi": "10.1182/bloodadvances.2018028795", "pmid": "31519648", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "bloodadvances.2018028795"}], "notes": [], "created": "2019-09-16T11:35:19.734Z", "modified": "2024-01-16T13:48:43.828Z"}, {"entity": "publication", "iuid": "67dee8a179784e9e8426f44dfcab95be", "links": {"self": {"href": "https://publications.scilifelab.se/publication/67dee8a179784e9e8426f44dfcab95be.json"}, "display": {"href": "https://publications.scilifelab.se/publication/67dee8a179784e9e8426f44dfcab95be"}}, "title": "IGEMS: The Consortium on Interplay of Genes and Environment Across Multiple Studies - An Update.", "authors": [{"family": "Pedersen", "given": "Nancy L", "initials": "NL"}, {"family": "Gatz", "given": "Margaret", "initials": "M"}, {"family": "Finch", "given": "Brian K", "initials": "BK"}, {"family": "Finkel", "given": "Deborah", "initials": "D"}, {"family": "Butler", "given": "David A", "initials": "DA"}, {"family": "Dahl Aslan", "given": "Anna", "initials": "A"}, {"family": "Franz", "given": "Carol E", "initials": "CE"}, {"family": "Kaprio", "given": "Jaakko", "initials": "J"}, {"family": "Lapham", "given": "Susan", "initials": "S"}, {"family": "McGue", "given": "Matt", "initials": "M"}, {"family": "Mosing", "given": "Miriam A", "initials": "MA"}, {"family": "Neiderhiser", "given": "Jenae", "initials": "J"}, {"family": "Nygaard", "given": "Marianne", "initials": "M"}, {"family": "Panizzon", "given": "Matthew", "initials": "M"}, {"family": "Prescott", "given": "Carol A", "initials": "CA"}, {"family": "Reynolds", "given": "Chandra A", "initials": "CA"}, {"family": "Sachdev", "given": "Perminder", "initials": "P"}, {"family": "Whitfield", "given": "Keith E", "initials": "KE"}], "type": "journal article", "published": "2019-09-23", "journal": {"volume": null, "issn": "1832-4274", "issue": null, "pages": "1-8", "title": "Twin Res Hum Genet", "issn-l": null}, "abstract": "The Interplay of Genes and Environment across Multiple Studies (IGEMS) is a consortium of 18 twin studies from 5 different countries (Sweden, Denmark, Finland, United States, and Australia) established to explore the nature of gene-environment (GE) interplay in functioning across the adult lifespan. Fifteen of the studies are longitudinal, with follow-up as long as 59 years after baseline. The combined data from over 76,000 participants aged 14-103 at intake (including over 10,000 monozygotic and over 17,000 dizygotic twin pairs) support two primary research emphases: (1) investigation of models of GE interplay of early life adversity, and social factors at micro and macro environmental levels and with diverse outcomes, including mortality, physical functioning and psychological functioning; and (2) improved understanding of risk and protective factors for dementia by incorporating unmeasured and measured genetic factors with a wide range of exposures measured in young adulthood, midlife and later life.", "doi": "10.1017/thg.2019.76", "pmid": "31544729", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "S1832427419000768"}], "notes": [], "created": "2019-09-26T06:48:23.532Z", "modified": "2020-01-21T13:56:14.597Z"}, {"entity": "publication", "iuid": "d5672f9c78a34140873fcaa57aaafb89", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d5672f9c78a34140873fcaa57aaafb89.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d5672f9c78a34140873fcaa57aaafb89"}}, "title": "Hypermethylation-associated downregulation of microRNA-4456 in hypersexual disorder with putative influence on oxytocin signalling: A DNA methylation analysis of miRNA genes.", "authors": [{"family": "Bostr\u00f6m", "given": "Adrian E", "initials": "AE"}, {"family": "Chatzittofis", "given": "Andreas", "initials": "A"}, {"family": "Ciuculete", "given": "Diana-Maria", "initials": "DM"}, {"family": "Flanagan", "given": "John N", "initials": "JN"}, {"family": "Krattinger", "given": "Regina", "initials": "R"}, {"family": "Bandstein", "given": "Marcus", "initials": "M"}, {"family": "Mwinyi", "given": "Jessica", "initials": "J"}, {"family": "Kullak-Ublick", "given": "Gerd A", "initials": "GA"}, {"family": "\u00d6berg", "given": "Katarina G\u00f6rts", "initials": "KG"}, {"family": "Arver", "given": "Stefan", "initials": "S"}, {"family": "Schi\u00f6th", "given": "Helgi B", "initials": "HB"}, {"family": "Jokinen", "given": "Jussi", "initials": "J"}], "type": "journal article", "published": "2019-09-22", "journal": {"volume": null, "issn": "1559-2308", "issue": null, "pages": "1-16", "title": "Epigenetics", "issn-l": "1559-2294"}, "abstract": "Hypersexual disorder (HD) was proposed as a diagnosis in the DSM-5 and the classification 'Compulsive Sexual Behavior Disorder' is now presented as an impulse-control disorder in ICD-11. HD incorporates several pathophysiological mechanisms; including impulsivity, compulsivity, sexual desire dysregulation and sexual addiction. No previous study investigated HD in a methylation analysis limited to microRNA (miRNA) associated CpG-sites. The genome wide methylation pattern was measured in whole blood from 60 subjects with HD and 33 healthy volunteers using the Illumina EPIC BeadChip. 8,852 miRNA associated CpG-sites were investigated in multiple linear regression analyses of methylation M-values to a binary independent variable of disease state (HD or healthy volunteer), adjusting for optimally determined covariates. Expression levels of candidate miRNAs were investigated in the same individuals for differential expression analysis. Candidate methylation loci were further studied for an association with alcohol dependence in an independent cohort of 107 subjects. Two CpG-sites were borderline significant in HD - cg18222192 (MIR708)(\n            p < 10E-05,pFDR = 5.81E-02) and cg01299774 (MIR4456)(p < 10E-06, pFDR = 5.81E-02). MIR4456 was significantly lower expressed in HD in both univariate (p < 0.0001) and multivariate (p < 0.05) analyses. Cg01299774 methylation levels were inversely correlated with expression levels of MIR4456 (p < 0.01) and were also differentially methylated in alcohol dependence (p = 0.026). Gene target prediction and pathway analysis revealed that MIR4456 putatively targets genes preferentially expressed in brain and that are involved in major neuronal molecular mechanisms thought to be relevant for HD, e.g., the oxytocin signalling pathway. In summary, our study implicates a potential contribution of MIR4456 in the pathophysiology of HD by putatively influencing oxytocin signalling.", "doi": "10.1080/15592294.2019.1656157", "pmid": "31542994", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2019-09-26T06:48:24.191Z", "modified": "2024-01-16T13:48:43.861Z"}, {"entity": "publication", "iuid": "066cfae0c81d420a8e8a1191c72d3ace", "links": {"self": {"href": "https://publications.scilifelab.se/publication/066cfae0c81d420a8e8a1191c72d3ace.json"}, "display": {"href": "https://publications.scilifelab.se/publication/066cfae0c81d420a8e8a1191c72d3ace"}}, "title": "Phylogenetic microbiota profiling in fecal samples depends on combination of sequencing depth and choice of NGS analysis method.", "authors": [{"family": "Rajan", "given": "Sukithar K", "initials": "SK"}, {"family": "Lindqvist", "given": "M\u00e5rten", "initials": "M"}, {"family": "Brummer", "given": "Robert Jan", "initials": "RJ"}, {"family": "Schoultz", "given": "Ida", "initials": "I"}, {"family": "Repsilber", "given": "Dirk", "initials": "D", "orcid": "0000-0002-7173-5579", "researcher": {"href": "https://publications.scilifelab.se/researcher/86ad21e955ed4524b24822ba4c0de43e.json"}}], "type": "journal article", "published": "2019-09-17", "journal": {"volume": "14", "issn": "1932-6203", "issue": "9", "pages": "e0222171", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "The human gut microbiota is well established as an important factor in health and disease. Fecal sample microbiota are often analyzed as a proxy for gut microbiota, and characterized with respect to their composition profiles. Modern approaches employ whole genome shotgun next-generation sequencing as the basis for these analyses. Sequencing depth as well as choice of next-generation sequencing data analysis method constitute two main interacting methodological factors for such an approach. In this study, we used 200 million sequence read pairs from one fecal sample for comparing different taxonomy classification methods, using default and custom-made reference databases, at different sequencing depths. A mock community data set with known composition was used for validating the classification methods. Results suggest that sequencing beyond 60 million read pairs does not seem to improve classification. The phylogeny prediction pattern, when using the default databases and the consensus database, appeared to be similar for all three methods. Moreover, these methods predicted rather different species. We conclude that the choice of sequencing depth and classification method has important implications for taxonomy composition prediction. A multi-method-consensus approach for robust gut microbiota NGS analysis is recommended.", "doi": "10.1371/journal.pone.0222171", "pmid": "31527871", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "PONE-D-19-08745"}, {"db": "pmc", "key": "PMC6748435"}], "notes": [], "created": "2019-12-03T10:46:32.234Z", "modified": "2021-06-18T14:06:50.523Z"}, {"entity": "publication", "iuid": "177f8de8154a4af7973a67c59e5500d0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/177f8de8154a4af7973a67c59e5500d0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/177f8de8154a4af7973a67c59e5500d0"}}, "title": "Genome-wide association meta-analyses and fine-mapping elucidate pathways influencing albuminuria.", "authors": [{"family": "Teumer", "given": "Alexander", "initials": "A"}, {"family": "Li", "given": "Yong", "initials": "Y"}, {"family": "Ghasemi", "given": "Sahar", "initials": "S"}, {"family": "Prins", "given": "Bram P", "initials": "BP"}, {"family": "Wuttke", "given": "Matthias", "initials": "M"}, {"family": "Hermle", "given": "Tobias", "initials": "T"}, {"family": "Giri", "given": "Ayush", "initials": "A"}, {"family": "Sieber", "given": "Karsten B", "initials": "KB"}, {"family": "Qiu", "given": "Chengxiang", "initials": "C"}, {"family": "Kirsten", "given": "Holger", "initials": "H"}, {"family": "Tin", "given": "Adrienne", "initials": "A"}, {"family": "Chu", "given": "Audrey Y", "initials": "AY"}, {"family": "Bansal", "given": "Nisha", "initials": "N"}, {"family": "Feitosa", "given": "Mary F", "initials": "MF"}, {"family": "Wang", "given": "Lihua", "initials": "L"}, {"family": "Chai", "given": "Jin-Fang", "initials": "JF"}, {"family": "Cocca", "given": "Massimiliano", "initials": "M"}, {"family": "Fuchsberger", "given": "Christian", "initials": "C"}, {"family": "Gorski", "given": "Mathias", "initials": "M"}, {"family": "Hoppmann", "given": "Anselm", "initials": "A"}, {"family": "Horn", "given": "Katrin", "initials": "K"}, {"family": "Li", "given": "Man", "initials": "M"}, {"family": "Marten", "given": "Jonathan", "initials": "J"}, {"family": "Noce", "given": "Damia", "initials": "D"}, {"family": "Nutile", "given": "Teresa", "initials": "T"}, {"family": "Sedaghat", "given": "Sanaz", "initials": "S"}, {"family": "Sveinbjornsson", "given": "Gardar", "initials": "G"}, {"family": "Tayo", "given": "Bamidele O", "initials": "BO"}, {"family": "van der Most", "given": "Peter J", "initials": "PJ"}, {"family": "Xu", "given": "Yizhe", "initials": "Y"}, {"family": "Yu", "given": "Zhi", "initials": "Z"}, {"family": "Gerstner", "given": "Lea", "initials": "L"}, {"family": "\u00c4rnl\u00f6v", "given": "Johan", "initials": "J"}, {"family": "Bakker", "given": "Stephan J L", "initials": "SJL"}, {"family": "Baptista", "given": "Daniela", "initials": "D"}, {"family": "Biggs", "given": "Mary L", "initials": "ML"}, {"family": "Boerwinkle", "given": "Eric", "initials": "E"}, {"family": "Brenner", "given": "Hermann", "initials": "H"}, {"family": "Burkhardt", "given": "Ralph", "initials": "R"}, {"family": "Carroll", "given": "Robert J", "initials": "RJ"}, {"family": "Chee", "given": "Miao-Li", "initials": "ML"}, {"family": "Chee", "given": "Miao-Ling", "initials": "ML"}, {"family": "Chen", "given": "Mengmeng", "initials": "M"}, {"family": "Cheng", "given": "Ching-Yu", "initials": "CY"}, {"family": "Cook", "given": "James P", "initials": "JP"}, {"family": "Coresh", "given": "Josef", "initials": "J"}, {"family": "Corre", "given": "Tanguy", "initials": "T"}, {"family": "Danesh", "given": "John", "initials": "J"}, {"family": "de Borst", "given": "Martin H", "initials": "MH"}, {"family": "De Grandi", "given": "Alessandro", "initials": "A"}, {"family": "de Mutsert", "given": "Ren\u00e9e", "initials": "R"}, {"family": "de Vries", "given": "Aiko P J", "initials": "APJ"}, {"family": "Degenhardt", "given": "Frauke", "initials": "F"}, {"family": "Dittrich", "given": "Katalin", "initials": "K"}, {"family": "Divers", "given": "Jasmin", "initials": "J"}, {"family": "Eckardt", "given": "Kai-Uwe", "initials": "KU"}, {"family": "Ehret", "given": "Georg", "initials": "G"}, {"family": "Endlich", "given": "Karlhans", "initials": "K"}, {"family": "Felix", "given": "Janine F", "initials": "JF"}, {"family": "Franco", "given": "Oscar H", "initials": "OH"}, {"family": "Franke", "given": "Andre", "initials": "A"}, {"family": "Freedman", "given": "Barry I", "initials": "BI"}, {"family": "Freitag-Wolf", "given": "Sandra", "initials": "S"}, {"family": "Gansevoort", "given": "Ron T", "initials": "RT"}, {"family": "Giedraitis", "given": "Vilmantas", "initials": "V"}, {"family": "G\u00f6gele", "given": "Martin", "initials": "M"}, {"family": "Grundner-Culemann", "given": "Franziska", "initials": "F"}, {"family": "Gudbjartsson", "given": "Daniel F", "initials": "DF"}, {"family": "Gudnason", "given": "Vilmundur", "initials": "V"}, {"family": "Hamet", "given": "Pavel", "initials": "P"}, {"family": "Harris", "given": "Tamara B", "initials": "TB"}, {"family": "Hicks", "given": "Andrew A", "initials": "AA"}, {"family": "Holm", "given": "Hilma", "initials": "H"}, {"family": "Foo", "given": "Valencia Hui Xian", "initials": "VHX"}, {"family": "Hwang", "given": "Shih-Jen", "initials": "SJ"}, {"family": "Ikram", "given": "M Arfan", "initials": "MA"}, {"family": "Ingelsson", "given": "Erik", "initials": "E"}, {"family": "Jaddoe", "given": "Vincent W V", "initials": "VWV"}, {"family": "Jakobsdottir", "given": "Johanna", "initials": "J"}, {"family": "Josyula", "given": "Navya Shilpa", "initials": "NS"}, {"family": "Jung", "given": "Bettina", "initials": "B"}, {"family": "K\u00e4h\u00f6nen", "given": "Mika", "initials": "M"}, {"family": "Khor", "given": "Chiea-Chuen", "initials": "CC"}, {"family": "Kiess", "given": "Wieland", "initials": "W"}, {"family": "Koenig", "given": "Wolfgang", "initials": "W"}, {"family": "K\u00f6rner", "given": "Antje", "initials": "A"}, {"family": "Kovacs", "given": "Peter", "initials": "P"}, {"family": "Kramer", "given": "Holly", "initials": "H"}, {"family": "Kr\u00e4mer", "given": "Bernhard K", "initials": "BK"}, {"family": "Kronenberg", "given": "Florian", "initials": "F"}, {"family": "Lange", "given": "Leslie A", "initials": "LA"}, {"family": "Langefeld", "given": "Carl D", "initials": "CD"}, {"family": "Lee", "given": "Jeannette Jen-Mai", "initials": "JJ"}, {"family": "Lehtim\u00e4ki", "given": "Terho", "initials": "T"}, {"family": "Lieb", "given": "Wolfgang", "initials": "W"}, {"family": "Lim", "given": "Su-Chi", "initials": "SC"}, {"family": "Lind", "given": "Lars", "initials": "L"}, {"family": "Lindgren", "given": "Cecilia M", "initials": "CM"}, {"family": "Liu", "given": "Jianjun", "initials": "J"}, {"family": "Loeffler", "given": "Markus", "initials": "M"}, {"family": "Lyytik\u00e4inen", "given": "Leo-Pekka", "initials": "LP"}, {"family": "Mahajan", "given": "Anubha", "initials": "A"}, {"family": "Maranville", "given": "Joseph C", "initials": "JC"}, {"family": "Mascalzoni", "given": "Deborah", "initials": "D"}, {"family": "McMullen", "given": "Barbara", "initials": "B"}, {"family": "Meisinger", "given": "Christa", "initials": "C"}, {"family": "Meitinger", "given": "Thomas", "initials": "T"}, {"family": "Miliku", "given": "Kozeta", "initials": "K"}, {"family": "Mook-Kanamori", "given": "Dennis O", "initials": "DO"}, {"family": "M\u00fcller-Nurasyid", "given": "Martina", "initials": "M"}, {"family": "Mychaleckyj", "given": "Josyf C", "initials": "JC"}, {"family": "Nauck", "given": "Matthias", "initials": "M"}, {"family": "Nikus", "given": "Kjell", "initials": "K"}, {"family": "Ning", "given": "Boting", "initials": "B"}, {"family": "Noordam", "given": "Raymond", "initials": "R"}, {"family": "Connell", "given": "Jeffrey O'", "initials": "JO"}, {"family": "Olafsson", "given": "Isleifur", "initials": "I"}, {"family": "Palmer", "given": "Nicholette D", "initials": "ND"}, {"family": "Peters", "given": "Annette", "initials": "A"}, {"family": "Podgornaia", "given": "Anna I", "initials": "AI"}, {"family": "Ponte", "given": "Belen", "initials": "B"}, {"family": "Poulain", "given": "Tanja", "initials": "T"}, {"family": "Pramstaller", "given": "Peter P", "initials": "PP"}, {"family": "Rabelink", "given": "Ton J", "initials": "TJ"}, {"family": "Raffield", "given": "Laura M", "initials": "LM"}, {"family": "Reilly", "given": "Dermot F", "initials": "DF"}, {"family": "Rettig", "given": "Rainer", "initials": "R"}, {"family": "Rheinberger", "given": "Myriam", "initials": "M"}, {"family": "Rice", "given": "Kenneth M", "initials": "KM"}, {"family": "Rivadeneira", "given": "Fernando", "initials": "F"}, {"family": "Runz", "given": "Heiko", "initials": "H"}, {"family": "Ryan", "given": "Kathleen A", "initials": "KA"}, {"family": "Sabanayagam", "given": "Charumathi", "initials": "C"}, {"family": "Saum", "given": "Kai-Uwe", "initials": "KU"}, {"family": "Sch\u00f6ttker", "given": "Ben", "initials": "B"}, {"family": "Shaffer", "given": "Christian M", "initials": "CM"}, {"family": "Shi", "given": "Yuan", "initials": "Y"}, {"family": "Smith", "given": "Albert V", "initials": "AV"}, {"family": "Strauch", "given": "Konstantin", "initials": "K"}, {"family": "Stumvoll", "given": "Michael", "initials": "M"}, {"family": "Sun", "given": "Benjamin B", "initials": "BB"}, {"family": "Szymczak", "given": "Silke", "initials": "S"}, {"family": "Tai", "given": "E-Shyong", "initials": "ES"}, {"family": "Tan", "given": "Nicholas Y Q", "initials": "NYQ"}, {"family": "Taylor", "given": "Kent D", "initials": "KD"}, {"family": "Teren", "given": "Andrej", "initials": "A"}, {"family": "Tham", "given": "Yih-Chung", "initials": "YC"}, {"family": "Thiery", "given": "Joachim", "initials": "J"}, {"family": "Thio", "given": "Chris H L", "initials": "CHL"}, {"family": "Thomsen", "given": "Hauke", "initials": "H"}, {"family": "Thorsteinsdottir", "given": "Unnur", "initials": "U"}, {"family": "T\u00f6njes", "given": "Anke", "initials": "A"}, {"family": "Tremblay", "given": "Johanne", "initials": "J"}, {"family": "Uitterlinden", "given": "Andr\u00e9 G", "initials": "AG"}, {"family": "van der Harst", "given": "Pim", "initials": "P"}, {"family": "Verweij", "given": "Niek", "initials": "N"}, {"family": "Vogelezang", "given": "Suzanne", "initials": "S"}, {"family": "V\u00f6lker", "given": "Uwe", "initials": "U"}, {"family": "Waldenberger", "given": "Melanie", "initials": "M"}, {"family": "Wang", "given": "Chaolong", "initials": "C"}, {"family": "Wilson", "given": "Otis D", "initials": "OD"}, {"family": "Wong", "given": "Charlene", "initials": "C"}, {"family": "Wong", "given": "Tien-Yin", "initials": "TY"}, {"family": "Yang", "given": "Qiong", "initials": "Q"}, {"family": "Yasuda", "given": "Masayuki", "initials": "M"}, {"family": "Akilesh", "given": "Shreeram", "initials": "S"}, {"family": "Bochud", "given": "Murielle", "initials": "M"}, {"family": "B\u00f6ger", "given": "Carsten A", "initials": "CA"}, {"family": "Devuyst", "given": "Olivier", "initials": "O"}, {"family": "Edwards", "given": "Todd L", "initials": "TL"}, {"family": "Ho", "given": "Kevin", "initials": "K"}, {"family": "Morris", "given": "Andrew P", "initials": "AP"}, {"family": "Parsa", "given": "Afshin", "initials": "A"}, {"family": "Pendergrass", "given": "Sarah A", "initials": "SA"}, {"family": "Psaty", "given": "Bruce M", "initials": "BM"}, {"family": "Rotter", "given": "Jerome I", "initials": "JI"}, {"family": "Stefansson", "given": "Kari", "initials": "K"}, {"family": "Wilson", "given": "James G", "initials": "JG"}, {"family": "Susztak", "given": "Katalin", "initials": "K"}, {"family": "Snieder", "given": "Harold", "initials": "H"}, {"family": "Heid", "given": "Iris M", "initials": "IM"}, {"family": "Scholz", "given": "Markus", "initials": "M"}, {"family": "Butterworth", "given": "Adam S", "initials": "AS"}, {"family": "Hung", "given": "Adriana M", "initials": "AM"}, {"family": "Pattaro", "given": "Cristian", "initials": "C"}, {"family": "K\u00f6ttgen", "given": "Anna", "initials": "A"}], "type": "journal article", "published": "2019-09-11", "journal": {"volume": "10", "issn": "2041-1723", "issue": "1", "pages": "4130", "title": "Nat Commun", "issn-l": "2041-1723"}, "abstract": "Increased levels of the urinary albumin-to-creatinine ratio (UACR) are associated with higher risk of kidney disease progression and cardiovascular events, but underlying mechanisms are incompletely understood. Here, we conduct trans-ethnic (n\u2009=\u2009564,257) and European-ancestry specific meta-analyses of genome-wide association studies of UACR, including ancestry- and diabetes-specific analyses, and identify 68 UACR-associated loci. Genetic correlation analyses and risk score associations in an independent electronic medical records database (n\u2009=\u2009192,868) reveal connections with proteinuria, hyperlipidemia, gout, and hypertension. Fine-mapping and trans-Omics analyses with gene expression in 47 tissues and plasma protein levels implicate genes potentially operating through differential expression in kidney (including TGFB1, MUC1, PRKCI, and OAF), and allow coupling of UACR associations to altered plasma OAF concentrations. Knockdown of OAF and PRKCI orthologs in Drosophila nephrocytes reduces albumin endocytosis. Silencing fly PRKCI further impairs slit diaphragm formation. These results generate a priority list of genes and pathways for translational research to reduce albuminuria.", "doi": "10.1038/s41467-019-11576-0", "pmid": "31511532", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-019-11576-0"}, {"db": "pmc", "key": "PMC6739370"}], "notes": [], "created": "2019-09-16T11:35:17.679Z", "modified": "2020-01-21T13:56:14.381Z"}, {"entity": "publication", "iuid": "c99b8ca4a3ec485baadfc7ac77ad0ee5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c99b8ca4a3ec485baadfc7ac77ad0ee5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c99b8ca4a3ec485baadfc7ac77ad0ee5"}}, "title": "Recurrent convergent evolution at amino acid residue 261 in fish rhodopsin.", "authors": [{"family": "Hill", "given": "Jason", "initials": "J"}, {"family": "Enbody", "given": "Erik D", "initials": "ED"}, {"family": "Pettersson", "given": "Mats E", "initials": "ME"}, {"family": "Sprehn", "given": "C Grace", "initials": "CG"}, {"family": "Bekkevold", "given": "Dorte", "initials": "D", "orcid": "0000-0002-5297-032X", "researcher": {"href": "https://publications.scilifelab.se/researcher/38c62afa02e94554ba1c3afcfc622555.json"}}, {"family": "Folkvord", "given": "Arild", "initials": "A", "orcid": "0000-0002-4763-0590", "researcher": {"href": "https://publications.scilifelab.se/researcher/18e48870c7654bf0898cb9ff2a064b99.json"}}, {"family": "Laikre", "given": "Linda", "initials": "L"}, {"family": "Kleinau", "given": "Gunnar", "initials": "G"}, {"family": "Scheerer", "given": "Patrick", "initials": "P"}, {"family": "Andersson", "given": "Leif", "initials": "L", "orcid": "0000-0002-4085-6968", "researcher": {"href": "https://publications.scilifelab.se/researcher/bd3343c12f994b1fabcae23027d3a76d.json"}}], "type": "journal article", "published": "2019-09-10", "journal": {"volume": "116", "issn": "1091-6490", "issue": "37", "pages": "18473-18478", "title": "Proc. Natl. Acad. Sci. U.S.A.", "issn-l": "0027-8424"}, "abstract": "The evolutionary process that occurs when a species colonizes a new environment provides an opportunity to explore the mechanisms underlying genetic adaptation, which is essential knowledge for understanding evolution and the maintenance of biodiversity. Atlantic herring has an estimated total breeding stock of about 1 trillion (10 12) and has colonized the brackish Baltic Sea within the last 10,000 y. Minute genetic differentiation between Atlantic and Baltic herring populations at selectively neutral loci combined with this rapid adaptation to a new environment facilitated the identification of hundreds of loci underlying ecological adaptation. A major question in the field of evolutionary biology is to what extent such an adaptive process involves selection of novel mutations with large effects or genetic changes at many loci, each with a small effect on phenotype (i.e., selection on standing genetic variation). Here we show that a missense mutation in rhodopsin (Phe261Tyr) is an adaptation to the red-shifted Baltic Sea light environment. The transition from phenylalanine to tyrosine differs only by the presence of a hydroxyl moiety in the latter, but this results in an up to 10-nm red-shifted light absorbance of the receptor. Remarkably, an examination of the rhodopsin sequences from 2,056 species of fish revealed that the same missense mutation has occurred independently and been selected for during at least 20 transitions between light environments across all fish. Our results provide a spectacular example of convergent evolution and how a single amino acid change can have a major effect on ecological adaptation.", "doi": "10.1073/pnas.1908332116", "pmid": "31451650", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "1908332116"}, {"db": "pmc", "key": "PMC6744887"}], "notes": [], "created": "2019-11-25T14:59:20.457Z", "modified": "2024-01-16T13:48:43.886Z"}, {"entity": "publication", "iuid": "91f35a34439e4e7d88cafce065a3d24d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/91f35a34439e4e7d88cafce065a3d24d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/91f35a34439e4e7d88cafce065a3d24d"}}, "title": "Evaluation of the Genetic Association Between Adult Obesity and Neuropsychiatric Disease.", "authors": [{"family": "Stahel", "given": "Priska", "initials": "P"}, {"family": "Nahmias", "given": "Avital", "initials": "A"}, {"family": "Sud", "given": "Shawn K", "initials": "SK"}, {"family": "Lee", "given": "So Jeong", "initials": "SJ"}, {"family": "Pucci", "given": "Andrea", "initials": "A"}, {"family": "Yousseif", "given": "Ahmed", "initials": "A"}, {"family": "Yosseff", "given": "Alaa", "initials": "A"}, {"family": "Jackson", "given": "Timothy", "initials": "T"}, {"family": "Urbach", "given": "David R", "initials": "DR"}, {"family": "Okrainec", "given": "Allan", "initials": "A"}, {"family": "Allard", "given": "Johane P", "initials": "JP"}, {"family": "Sockalingam", "given": "Sanjeev", "initials": "S"}, {"family": "Yao", "given": "Jing", "initials": "J"}, {"family": "Barua", "given": "Moumita", "initials": "M"}, {"family": "Jiao", "given": "Hong", "initials": "H"}, {"family": "Magi", "given": "Reedik", "initials": "R"}, {"family": "Bassett", "given": "Anne S", "initials": "AS"}, {"family": "Paterson", "given": "Andrew D", "initials": "AD"}, {"family": "Dahlman", "given": "Ingrid", "initials": "I"}, {"family": "Batterham", "given": "Rachel L", "initials": "RL"}, {"family": "Dash", "given": "Satya", "initials": "S"}], "type": "journal article", "published": "2019-09-10", "journal": {"volume": null, "issn": "1939-327X", "issue": null, "title": "Diabetes", "issn-l": "0012-1797"}, "abstract": "Extreme obesity (EO, BMI>50) is frequently associated with neuropsychiatric disease (NPD). As both EO and NPD are heritable central nervous system disorders, we assessed the prevalence of protein truncating (PTV) and copy number variants (CNV) in genes/regions previously implicated in NPD, in adults with EO (n=149) referred for weight loss/bariatric surgery. We also assessed the prevalence of CNVs in patients referred to University College London Hospital (UCLH) with EO (n=218) and obesity (O, BMI 35-50, n=374) and a Swedish cohort of participants from the community with predominantly O (n=161). The prevalence of variants was compared to controls in ExAC/gnomAd database.In the discovery cohort (high NPD prevalence: 77%), the cumulative PTV/CNV allele frequency (AF) was 7.7 % vs 2.6% in controls (Odds Ratio (OR) 3.1, (95% CI 2-4.1, p<0.0001). In the UCLH EO cohort (intermediate NPD prevalence: 47%), CNV AF (1.8% vs 0.9% in controls, OR 1.95, 95% CI 0.96-3.93, p=0.06) was lower than the discovery cohort. CNV AF was not increased in the UCLH O cohort (0.8%). No CNVs were identified in the Swedish cohort with no NPD.These findings suggest PTV/CNVs, in genes/regions previously associated with NPD, may contribute to NPD in patients with EO.", "doi": "10.2337/db18-1254", "pmid": "31506345", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "db18-1254"}], "notes": [], "created": "2019-09-16T11:35:18.540Z", "modified": "2020-01-21T13:56:14.401Z"}, {"entity": "publication", "iuid": "55e97ce1989c4bb184fae3027bb2bf9c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/55e97ce1989c4bb184fae3027bb2bf9c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/55e97ce1989c4bb184fae3027bb2bf9c"}}, "title": "Differential gene expression in bovine endometrial epithelial cells after challenge with LPS; specific implications for genes involved in embryo maternal interactions.", "authors": [{"family": "Guo", "given": "Yongzhi", "initials": "Y", "orcid": "0000-0002-5057-9095", "researcher": {"href": "https://publications.scilifelab.se/researcher/8040d6c76eb6467585d054d55a1965fe.json"}}, {"family": "van Schaik", "given": "Tom", "initials": "T", "orcid": "0000-0001-7850-5074", "researcher": {"href": "https://publications.scilifelab.se/researcher/79ccfcbccc214a7591e33d611edf0e8a.json"}}, {"family": "Jhamat", "given": "Naveed", "initials": "N"}, {"family": "Niazi", "given": "Adnan", "initials": "A", "orcid": "0000-0003-0311-5279", "researcher": {"href": "https://publications.scilifelab.se/researcher/c9e07c9891804a60980eb07956a7cd0d.json"}}, {"family": "Chanrot", "given": "Metasu", "initials": "M"}, {"family": "Charpigny", "given": "Gilles", "initials": "G"}, {"family": "Valarcher", "given": "Jean Francois", "initials": "JF"}, {"family": "Bongcam-Rudloff", "given": "Erik", "initials": "E"}, {"family": "Andersson", "given": "G\u00f6ran", "initials": "G"}, {"family": "Humblot", "given": "Patrice", "initials": "P"}], "type": "journal article", "published": "2019-09-05", "journal": {"title": "PLoS ONE", "issn": "1932-6203", "volume": "14", "issue": "9", "pages": "e0222081", "issn-l": "1932-6203"}, "abstract": "Lipopolysaccharide (LPS) expressed on the surface of Gram-negative bacteria activates pro-inflammatory pathways, dys-regulates the function of endometrial cells and is a key player in the mechanisms involved in endometritis. This study aimed to investigate the effects of LPS on bovine endometrial epithelial cells (bEEC) from whole transcriptome with a special focus on genes involved in embryo-maternal interactions. Following in vitro culture, bEEC from three cows were exposed to 0, 2, and 8 \u03bcg/mL LPS for 24h. RNA samples extracted at 0 and 24 hours were analyzed by RNA sequencing (RNA-seq). At 24h, 2035 differentially expressed genes (DEGs) were identified between controls and samples treated with 2 \u03bcg/mL LPS. Gene ontology analysis showed that over-expressed DEGs were associated to immune response, response to stress and external stimuli, catalytic activity, and cell cycle. Genes associated with cell membrane and cell adhesion pathways were under-expressed. LPS induced changes in expression of specific genes related to embryo-maternal interactions including under-expression of eight members of the cadherin superfamily, over-expression of six members of the mucin family, and differential expression of a large set of genes binding the above molecules and of more than 20 transcripts coding for cytokines and their receptors. Type I interferon-\u03c4 dependent genes were also over-expressed. From a sub-set of 19 genes, (biological replicates of bEEC from cows taken at time 6 (n = 3), 24 (n = 6) and 48 hours (n = 3), and 2 technical replicates per sample) differential gene expression was confirmed by RT2-qPCR (r2 between fold changes at 24 hours by RT2-qPCR and RNA-seq = 0.97). These results indicate that LPS affects the function of bEEC in many ways by differential transcription, glycolytic metabolism and oxidative stress. Many transcriptomic signatures related to implantation and embryo maternal interactions were strongly affected by LPS. These results pave the way for further studies to investigate the duration of these changes and their possible impact on endometrial function and fertility.", "doi": "10.1371/journal.pone.0222081", "pmid": "31487323", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC6728075"}, {"db": "pii", "key": "PONE-D-19-15238"}], "notes": [], "created": "2024-09-30T06:07:45.782Z", "modified": "2024-09-30T06:07:46.035Z"}, {"entity": "publication", "iuid": "ab8cc4b513fa415a86818db9642fdae6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ab8cc4b513fa415a86818db9642fdae6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ab8cc4b513fa415a86818db9642fdae6"}}, "title": "Associations of Smoking and Alcohol and Coffee Intake with Fracture and Bone Mineral Density: A Mendelian Randomization Study.", "authors": [{"family": "Yuan", "given": "Shuai", "initials": "S"}, {"family": "Micha\u00eblsson", "given": "Karl", "initials": "K"}, {"family": "Wan", "given": "Zihao", "initials": "Z"}, {"family": "Larsson", "given": "Susanna C", "initials": "SC"}], "type": "journal article", "published": "2019-09-04", "journal": {"volume": null, "issn": "1432-0827", "issue": null, "title": "Calcif. Tissue Int.", "issn-l": "0171-967X"}, "abstract": "The causal associations of smoking and alcohol and coffee intake with fracture and bone mineral density are unknown. We investigated the associations using Mendelian randomization (MR). Summary-level data from UK Biobank for bone fractures (main outcome) (53,184 cases; 373,611 non-cases) and estimated bone mineral density (eBMD) (n\u2009=\u2009426,824 individuals) were used. Single-nucleotide polymorphisms associated with smoking initiation (n\u2009=\u2009378) and alcohol (n\u2009=\u200999) and coffee (n\u2009=\u200915) intake at the genome-wide significance threshold (P\u2009=\u20095\u2009\u00d7\u200910\n            -8) were identified from published genome-wide association studies. Univariable and multivariable inverse-variance weighted, weighted median, MR-Egger, and MR-PRESSO methods were used for statistical analyses. Genetic predisposition to smoking initiation was associated with fracture but not eBMD. The odds ratio of fracture per one-unit increase in log odds of smoking was 1.09 (95% confidence interval 1.04, 1.15; P\u2009=\u20098.58\u2009\u00d7\u200910-4) after adjustment for alcohol intake in the multivariable MR analysis. The association remained in complementary analyses. Genetically predicted alcohol and coffee intake was not associated with fracture or eBMD. Nevertheless, genetic liability to alcohol dependence, based on variants in the ALD1B gene, was associated with fracture and lower eBMD. The odds ratio was 1.06 (95% confidence interval 1.01, 1.12; P\u2009=\u20090.018) per genetically predicted one-unit higher log odds of liability to alcohol dependence. This MR study strengthens the causal inference on an association between smoking and higher fracture risk but found no linear association of modestly higher alcohol and coffee intake with fracture or BMD. However, alcohol dependence may increase fracture risk.", "doi": "10.1007/s00223-019-00606-0", "pmid": "31482193", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1007/s00223-019-00606-0"}], "notes": [], "created": "2019-09-05T12:01:52.118Z", "modified": "2024-01-16T13:48:43.910Z"}, {"entity": "publication", "iuid": "f5da15486d854d6eb5e8a778882e7721", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f5da15486d854d6eb5e8a778882e7721.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f5da15486d854d6eb5e8a778882e7721"}}, "title": "Genetic Affinities among Southern Africa Hunter-Gatherers and the Impact of Admixing Farmer and Herder Populations.", "authors": [{"family": "Vicente", "given": "M\u00e1rio", "initials": "M"}, {"family": "Jakobsson", "given": "Mattias", "initials": "M", "orcid": "0000-0001-7840-7853", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a4abe0fcb20492d9ec849c9fbf58a71.json"}}, {"family": "Ebbesen", "given": "Peter", "initials": "P"}, {"family": "Schlebusch", "given": "Carina M", "initials": "CM"}], "type": "journal article", "published": "2019-09-01", "journal": {"volume": "36", "issn": "1537-1719", "issue": "9", "title": "Mol. Biol. Evol.", "pages": "1849-1861", "issn-l": "0737-4038"}, "abstract": "Southern African indigenous groups, traditionally hunter-gatherers (San) and herders (Khoekhoe), are commonly referred to as \"Khoe-San\" populations and have a long history in southern Africa. Their ancestors were largely isolated up until \u223c2,000 years ago before the arrival of pastoralists and farmers in southern Africa. Assessing relationships among regional Khoe-San groups has been challenging due to admixture with immigrant populations that obscure past population affinities and gene flow among these autochthonous communities. We re-evaluate a combined genome-wide data set of previously published southern Africa Khoe-San populations in conjunction with novel data from Khoe-San individuals collected in Xade (Central Kalahari Game Reserve, Botswana) prior to their resettlement outside the reserve. After excluding regions in the genome that trace their ancestry to recent migrant groups, the genetic diversity of 20 Khoe-San groups fitted an isolation-by-distance model. Even though isolation-by-distance explained most genetic affinities between the different autochthonous groups, additional signals of contact between Khoe-San groups could be detected. For instance, we found stronger genetic affinities, than what would be explained by isolation-by-distance gene flow, between the two geographically separated Khoe-San groups, who speak branches of the Kx'a-language family (\u01c2Hoan and Ju). We also scanned the genome-wide data for signals of adaptive gene flow from farmers/herders into Khoe-San groups and identified a number of genomic regions potentially introduced by the arrival of the new groups. This study provides a comprehensive picture of affinities among Khoe-San groups, prior to the arrival of recent migrants, and found that these affinities are primarily determined by the geographic landscape.", "doi": "10.1093/molbev/msz089", "pmid": "31288264", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "5475268"}, {"db": "pmc", "key": "PMC6735883"}], "notes": [], "created": "2019-08-13T12:15:29.091Z", "modified": "2024-01-16T13:48:43.925Z"}, {"entity": "publication", "iuid": "07b94576da744a20b022d0f0bb243c4f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/07b94576da744a20b022d0f0bb243c4f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/07b94576da744a20b022d0f0bb243c4f"}}, "title": "Ancestral Admixture Is the Main Determinant of Global Biodiversity in Fission Yeast.", "authors": [{"family": "Tusso", "given": "Sergio", "initials": "S"}, {"family": "Nieuwenhuis", "given": "Bart P S", "initials": "BPS"}, {"family": "Sedlazeck", "given": "Fritz J", "initials": "FJ"}, {"family": "Davey", "given": "John W", "initials": "JW"}, {"family": "Jeffares", "given": "Daniel C", "initials": "DC"}, {"family": "Wolf", "given": "Jochen B W", "initials": "JBW"}], "type": "journal article", "published": "2019-09-01", "journal": {"volume": "36", "issn": "1537-1719", "issue": "9", "pages": "1975-1989", "title": "Mol. Biol. Evol.", "issn-l": "0737-4038"}, "abstract": "Mutation and recombination are key evolutionary processes governing phenotypic variation and reproductive isolation. We here demonstrate that biodiversity within all globally known strains of Schizosaccharomyces pombe arose through admixture between two divergent ancestral lineages. Initial hybridization was inferred to have occurred \u223c20-60 sexual outcrossing generations ago consistent with recent, human-induced migration at the onset of intensified transcontinental trade. Species-wide heritable phenotypic variation was explained near-exclusively by strain-specific arrangements of alternating ancestry components with evidence for transgressive segregation. Reproductive compatibility between strains was likewise predicted by the degree of shared ancestry. To assess the genetic determinants of ancestry block distribution across the genome, we characterized the type, frequency, and position of structural genomic variation using nanopore and single-molecule real-time sequencing. Despite being associated with double-strand break initiation points, over 800 segregating structural variants exerted overall little influence on the introgression landscape or on reproductive compatibility between strains. In contrast, we found strong ancestry disequilibrium consistent with negative epistatic selection shaping genomic ancestry combinations during the course of hybridization. This study provides a detailed, experimentally tractable example that genomes of natural populations are mosaics reflecting different evolutionary histories. Exploiting genome-wide heterogeneity in the history of ancestral recombination and lineage-specific mutations sheds new light on the population history of S. pombe and highlights the importance of hybridization as a creative force in generating biodiversity.", "doi": "10.1093/molbev/msz126", "pmid": "31225876", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "5492083"}, {"db": "pmc", "key": "PMC6736153"}], "notes": [], "created": "2019-11-25T14:56:12.690Z", "modified": "2024-01-16T13:48:43.947Z"}, {"entity": "publication", "iuid": "7e4ab87cd1154a83990d12f76cad4ee8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7e4ab87cd1154a83990d12f76cad4ee8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7e4ab87cd1154a83990d12f76cad4ee8"}}, "title": "Impact of demography on linked selection in two outcrossing Brassicaceae species.", "authors": [{"family": "Mattila", "given": "Tiina M", "initials": "TM", "orcid": "0000-0002-1298-7370", "researcher": {"href": "https://publications.scilifelab.se/researcher/0dbb4f417ab0440fb02a305aaf81b3d5.json"}}, {"family": "Laenen", "given": "Benjamin", "initials": "B"}, {"family": "Horvath", "given": "Robert", "initials": "R"}, {"family": "H\u00e4m\u00e4l\u00e4", "given": "Tuomas", "initials": "T", "orcid": "0000-0001-8306-3397", "researcher": {"href": "https://publications.scilifelab.se/researcher/ac9fe6733a03417fbd5f6ca780c5589f.json"}}, {"family": "Savolainen", "given": "Outi", "initials": "O"}, {"family": "Slotte", "given": "Tanja", "initials": "T", "orcid": "0000-0001-6020-5102", "researcher": {"href": "https://publications.scilifelab.se/researcher/67c69ee78bae41478465a7e5fa63b946.json"}}], "type": "journal article", "published": "2019-09-00", "journal": {"volume": "9", "issn": "2045-7758", "issue": "17", "pages": "9532-9545", "title": "Ecol Evol", "issn-l": "2045-7758"}, "abstract": "Genetic diversity is shaped by mutation, genetic drift, gene flow, recombination, and selection. The dynamics and interactions of these forces shape genetic diversity across different parts of the genome, between populations and species. Here, we have studied the effects of linked selection on nucleotide diversity in outcrossing populations of two Brassicaceae species, Arabidopsis lyrata and Capsella grandiflora, with contrasting demographic history. In agreement with previous estimates, we found evidence for a modest population size expansion thousands of generations ago, as well as efficient purifying selection in C. grandiflora. In contrast, the A. lyrata population exhibited evidence for very recent strong population size decline and weaker efficacy of purifying selection. Using multiple regression analyses with recombination rate and other genomic covariates as explanatory variables, we can explain 47% of the variance in neutral diversity in the C. grandiflora population, while in the A. lyrata population, only 11% of the variance was explained by the model. Recombination rate had a significant positive effect on neutral diversity in both species, suggesting that selection at linked sites has an effect on patterns of neutral variation. In line with this finding, we also found reduced neutral diversity in the vicinity of genes in the C. grandiflora population. However, in A. lyrata no such reduction in diversity was evident, a finding that is consistent with expectations of the impact of a recent bottleneck on patterns of neutral diversity near genes. This study thus empirically demonstrates how differences in demographic history modulate the impact of selection at linked sites in natural populations.", "doi": "10.1002/ece3.5463", "pmid": "31534673", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "ECE35463"}, {"db": "pmc", "key": "PMC6745670"}], "notes": [], "created": "2019-12-03T13:10:35.648Z", "modified": "2024-01-16T13:48:43.958Z"}, {"entity": "publication", "iuid": "4742c0db10134b1d8446038f214e134f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4742c0db10134b1d8446038f214e134f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4742c0db10134b1d8446038f214e134f"}}, "title": "Copy number variation and neuropsychiatric problems in females and males in the general population.", "authors": [{"family": "Martin", "given": "Joanna", "initials": "J"}, {"family": "Tammimies", "given": "Kristiina", "initials": "K"}, {"family": "Karlsson", "given": "Robert", "initials": "R"}, {"family": "Lu", "given": "Yi", "initials": "Y"}, {"family": "Larsson", "given": "Henrik", "initials": "H"}, {"family": "Lichtenstein", "given": "Paul", "initials": "P"}, {"family": "Magnusson", "given": "Patrik K E", "initials": "PKE"}], "type": "journal article", "published": "2019-09-00", "journal": {"volume": "180", "issn": "1552-485X", "issue": "6", "pages": "341-350", "title": "Am. J. Med. Genet. B Neuropsychiatr. Genet.", "issn-l": "1552-4841"}, "abstract": "Neurodevelopmental problems (NPs) are more common in males, whereas anxiety and depression are more common in females. Rare copy number variants (CNVs) have been implicated in neurodevelopmental disorders. The aim of this study was to characterize the relationship between rare CNVs with NPs, anxiety, and depression in a childhood population sample, as well as to examine sex-specific effects. We analyzed a sample of N\u2009=\u200912,982 children, of whom 5.3% had narrowly defined NPs (clinically diagnosed), 20.9% had broadly defined NPs (based on validated screening measures, but no diagnosis), and 3.0% had clinically diagnosed anxiety or depression. Rare (<1% frequency) CNVs were categorized by size (100-500\u2009kb or\u2009>\u2009500\u2009kb), type, and putative relevance to NPs. We tested for association of CNV categories with outcomes and examined sex-specific effects. Medium deletions (OR[CI]\u2009=\u20091.18[1.05-1.33], p\u2009=\u2009.0053) and large duplications (OR[CI]\u2009=\u20091.45[1.19-1.75], p\u2009=\u2009.00017) were associated with broadly defined NPs. Large deletions (OR[CI]\u2009=\u20091.85[1.14-3.01], p\u2009=\u2009.013) were associated with narrowly defined NPs. There were no significant sex differences in CNV burden in individuals with NPs. Although CNVs were not associated with anxiety/depression in the whole sample, in individuals diagnosed with these disorders, females were more likely to have large CNVs (OR[CI]\u2009=\u20093.75[1.45-9.68], p\u2009=\u2009.0064). Rare CNVs are associated with both narrowly and broadly defined NPs in a general population sample of children. Our results also suggest that large, rare CNVs may show sex-specific phenotypic effects.", "doi": "10.1002/ajmg.b.32685", "pmid": "30307693", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2019-09-17T16:24:46.316Z", "modified": "2024-01-16T13:48:43.973Z"}, {"entity": "publication", "iuid": "f9a66158f46247acaa65eb2554967b12", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f9a66158f46247acaa65eb2554967b12.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f9a66158f46247acaa65eb2554967b12"}}, "title": "Large-scale GWAS reveals insights into the genetic architecture of same-sex sexual behavior.", "authors": [{"family": "Ganna", "given": "Andrea", "initials": "A"}, {"family": "Verweij", "given": "Karin J H", "initials": "KJH"}, {"family": "Nivard", "given": "Michel G", "initials": "MG"}, {"family": "Maier", "given": "Robert", "initials": "R"}, {"family": "Wedow", "given": "Robbee", "initials": "R"}, {"family": "Busch", "given": "Alexander S", "initials": "AS"}, {"family": "Abdellaoui", "given": "Abdel", "initials": "A"}, {"family": "Guo", "given": "Shengru", "initials": "S"}, {"family": "Sathirapongsasuti", "given": "J Fah", "initials": "JF"}, {"family": "23andMe Research Team", "given": "", "initials": ""}, {"family": "Lichtenstein", "given": "Paul", "initials": "P"}, {"family": "Lundstr\u00f6m", "given": "Sebastian", "initials": "S"}, {"family": "L\u00e5ngstr\u00f6m", "given": "Niklas", "initials": "N"}, {"family": "Auton", "given": "Adam", "initials": "A"}, {"family": "Harris", "given": "Kathleen Mullan", "initials": "KM"}, {"family": "Beecham", "given": "Gary W", "initials": "GW"}, {"family": "Martin", "given": "Eden R", "initials": "ER"}, {"family": "Sanders", "given": "Alan R", "initials": "AR"}, {"family": "Perry", "given": "John R B", "initials": "JRB"}, {"family": "Neale", "given": "Benjamin M", "initials": "BM"}, {"family": "Zietsch", "given": "Brendan P", "initials": "BP"}], "type": "journal article", "published": "2019-08-30", "journal": {"volume": "365", "issn": "1095-9203", "issue": "6456", "title": "Science", "issn-l": "0036-8075"}, "abstract": "Twin and family studies have shown that same-sex sexual behavior is partly genetically influenced, but previous searches for specific genes involved have been underpowered. We performed a genome-wide association study (GWAS) on 477,522 individuals, revealing five loci significantly associated with same-sex sexual behavior. In aggregate, all tested genetic variants accounted for 8 to 25% of variation in same-sex sexual behavior, only partially overlapped between males and females, and do not allow meaningful prediction of an individual's sexual behavior. Comparing these GWAS results with those for the proportion of same-sex to total number of sexual partners among nonheterosexuals suggests that there is no single continuum from opposite-sex to same-sex sexual behavior. Overall, our findings provide insights into the genetics underlying same-sex sexual behavior and underscore the complexity of sexuality.", "doi": "10.1126/science.aat7693", "pmid": "31467194", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "365/6456/eaat7693"}], "notes": [], "created": "2019-09-05T12:01:53.760Z", "modified": "2024-01-16T13:48:43.981Z"}, {"entity": "publication", "iuid": "e22e85d97f2f4687bc03de814e345859", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e22e85d97f2f4687bc03de814e345859.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e22e85d97f2f4687bc03de814e345859"}}, "title": "Neuroticism as a predictor of frailty in old age: a genetically informative approach.", "authors": [{"family": "Danielsdottir", "given": "Hilda Bjork", "initials": "HB"}, {"family": "Jylh\u00e4v\u00e4", "given": "Juulia", "initials": "J"}, {"family": "H\u00e4gg", "given": "Sara", "initials": "S"}, {"family": "Lu", "given": "Yi", "initials": "Y"}, {"family": "Colodro-Conde", "given": "Luc\u00eda", "initials": "L"}, {"family": "Martin", "given": "Nicholas G", "initials": "NG"}, {"family": "Pedersen", "given": "Nancy L", "initials": "NL"}, {"family": "Mosing", "given": "Miriam A", "initials": "MA"}, {"family": "Lehto", "given": "Kelli", "initials": "K"}], "type": "journal article", "published": "2019-08-28", "journal": {"volume": null, "issn": "1534-7796", "issue": null, "title": "Psychosom Med", "issn-l": "0033-3174"}, "abstract": "Neuroticism is associated with poor health outcomes, but its contribution to the accumulation of health deficits in old age, i.e. the frailty index, is largely unknown. We aimed to explore associations between neuroticism and frailty cross-sectionally and longitudinally, and to investigate the contribution of shared genetic influences.\n\nData were derived from the UK Biobank (UKB, n=274,951), the Australian Over 50's Study (AO50, n=2,849) and the Swedish Twin Registry (SALT n=18,960, SATSA n=1,365). Associations between neuroticism and the frailty index were investigated using regression analysis cross-sectionally in UKB, AO50 and SATSA, and longitudinally in SALT (25-29y follow-up) and SATSA (6 and 23y follow-up). The co-twin control method was applied to explore the contribution of underlying shared familial factors (SALT, SATSA, AO50). Genome-wide polygenic risk scores for neuroticism were used in all samples to further assess whether common genetic variants associated with neuroticism predict frailty.\n\nHigh neuroticism was consistently associated with greater frailty cross-sectionally (adjusted \u03b2 [95% confidence intervals] in UKB=0.32[0.32-0.33]; AO50=0.35[0.31-0.39]; SATSA=0.33[0.27-0.39]) and longitudinally up to 29 years (SALT=0.24[0.22-0.25]; SATSA 6y=0.31[0.24-0.38]; SATSA 23y=0.16[0.07-0.25]). When adjusting for underlying shared genetic and environmental factors the neuroticism-frailty association remained significant, although decreased. Polygenic risk scores for neuroticism significantly predicted frailty in the two larger samples (meta-analyzed total \u03b2=0.059[0.055-0.062]).\n\nNeuroticism in mid-life predicts frailty in late-life. Neuroticism may have a causal influence on frailty, whereas both environmental and genetic influences, including neuroticism-associated common genetic variants, contribute to this relationship.", "doi": "10.1097/PSY.0000000000000742", "pmid": "31469771", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2019-09-05T12:01:52.859Z", "modified": "2024-01-16T13:48:43.988Z"}, {"entity": "publication", "iuid": "1c98fce597774e6dab18b9be87b735a2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1c98fce597774e6dab18b9be87b735a2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1c98fce597774e6dab18b9be87b735a2"}}, "title": "Genotyping by low-coverage whole-genome sequencing in intercross pedigrees from outbred founders: a cost-efficient approach.", "authors": [{"family": "Zan", "given": "Yanjun", "initials": "Y"}, {"family": "Payen", "given": "Thibaut", "initials": "T"}, {"family": "Lillie", "given": "Mette", "initials": "M"}, {"family": "Honaker", "given": "Christa F", "initials": "CF"}, {"family": "Siegel", "given": "Paul B", "initials": "PB"}, {"family": "Carlborg", "given": "\u00d6rjan", "initials": "\u00d6", "orcid": "0000-0002-2722-5264", "researcher": {"href": "https://publications.scilifelab.se/researcher/4efb0861e6144f00b8b4f5dd8a83c75b.json"}}], "type": "journal article", "published": "2019-08-14", "journal": {"volume": "51", "issn": "1297-9686", "issue": "1", "pages": "44", "title": "Genet. Sel. Evol.", "issn-l": "0999-193X"}, "abstract": "Experimental intercrosses between outbred founder populations are powerful resources for mapping loci that contribute to complex traits i.e. quantitative trait loci (QTL). Here, we present an approach and its accompanying software for high-resolution reconstruction of founder mosaic genotypes in the intercross offspring from such populations using whole-genome high-coverage sequence data on founder individuals (~ 30\u00d7) and very low-coverage sequence data on intercross individuals (< 0.5\u00d7). Sets of founder-line informative markers were selected for each full-sib family and used to infer the founder mosaic genotypes of the intercross individuals. The application of this approach and the quality of the estimated genome-wide genotypes are illustrated in a large F2 pedigree between two divergently selected lines of chickens.\n\nWe describe how we obtained whole-genome genotype data for hundreds of individuals in a cost- and time-efficient manner by using a Tn5-based library preparation protocol and an imputation algorithm that was optimized for this application. In total, 7.6 million markers segregated in this pedigree and, within each full-sib family, between 10.0 and 13.7% of these were fully informative, i.e. fixed for alternative alleles in the founders from the divergent lines, and were used for reconstruction of the offspring mosaic genotypes. The genotypes that were estimated based on the low-coverage sequence data were highly consistent (> 95% agreement) with those obtained using individual single nucleotide polymorphism (SNP) genotyping. The estimated resolution of the inferred recombination breakpoints was relatively high, with 50% of them being defined on regions shorter than 10 kb.\n\nA method and software for inferring founder mosaic genotypes in intercross offspring from low-coverage whole-genome sequencing in pedigrees from heterozygous founders are described. They provide high-quality, high-resolution genotypes in a time- and cost-efficient manner. The software is freely available at https://github.com/CarlborgGenomics/Stripes .", "doi": "10.1186/s12711-019-0487-1", "pmid": "31412777", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Protein Science Facility (PSF)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC6694510"}, {"db": "pii", "key": "10.1186/s12711-019-0487-1"}], "notes": [], "created": "2020-01-08T12:42:05.530Z", "modified": "2024-04-03T14:29:27.841Z"}, {"entity": "publication", "iuid": "e63038cec18447a5b11525315a03bc11", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e63038cec18447a5b11525315a03bc11.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e63038cec18447a5b11525315a03bc11"}}, "title": "Lack of gene flow: Narrow and dispersed differentiation islands in a triplet of Leptidea butterfly species", "authors": [{"family": "Talla", "given": "Venkat", "initials": "V"}, {"family": "Johansson", "given": "Anna", "initials": "A"}, {"family": "Dinc\u0103", "given": "Vlad", "initials": "V"}, {"family": "Vila", "given": "Roger", "initials": "R"}, {"family": "Friberg", "given": "Magne", "initials": "M"}, {"family": "Wiklund", "given": "Christer", "initials": "C"}, {"family": "Backstr\u00f6m", "given": "Niclas", "initials": "N"}], "type": "journal-article", "published": "2019-08-08", "journal": {"volume": "28", "issn": "0962-1083", "issue": "6", "pages": "3756-3770", "title": "Mol Ecol", "issn-l": "0962-1083"}, "abstract": "Genome scans in recently separated species can inform on molecular mechanisms and evolutionary processes driving divergence. Large-scale polymorphism data from multiple species pairs are also key to investigate the repeatability of divergence-whether radiations tend to show parallel responses to similar selection pressures and/or underlying molecular forces. Here, we used whole-genome resequencing data from six wood white (Leptidea sp.) butterfly populations, representing three closely related species with karyomorph variation, to infer the species' demographic history and characterize patterns of genomic diversity and differentiation. The analyses supported previously established species relationships, and there was no evidence for postdivergence gene flow. We identified significant intraspecific genetic structure, in particular between karyomorph extremes in the wood white (L. sinapis)-a species with a remarkable chromosome number cline across the distribution range. The genomic landscapes of differentiation were erratic, and outlier regions were narrow and dispersed. Highly differentiated (F ST ) regions generally had low genetic diversity (\u03b8\u03c0 ), but increased absolute divergence (DXY ) and excess of rare frequency variants (low Tajima's D). A minority of differentiation peaks were shared across species and population comparisons. However, highly differentiated regions contained genes with overrepresented functions related to metabolism, response to stimulus and cellular processes, indicating recurrent directional selection on a specific set of traits in all comparisons. In contrast to the majority of genome scans in recently diverged lineages, our data suggest that divergence landscapes in Leptidea have been shaped by directional selection and genetic drift rather than stable recombination landscapes and/or introgression.", "doi": "10.1111/mec.15188", "pmid": "31325366", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "ENA", "description": "Leptidea DNA sequence reads, genome assembly and genotype calls", "key": "PRJEB21838"}], "notes": [], "created": "2019-08-14T08:50:31.009Z", "modified": "2024-01-16T13:48:44.002Z"}, {"entity": "publication", "iuid": "7de54f7a41584846bda2b59d9e34b17a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7de54f7a41584846bda2b59d9e34b17a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7de54f7a41584846bda2b59d9e34b17a"}}, "title": "Classical Human Leukocyte Antigen Alleles and C4 Haplotypes Are Not Significantly Associated With Depression.", "authors": [{"family": "Glanville", "given": "Kylie P", "initials": "KP"}, {"family": "Coleman", "given": "Jonathan R I", "initials": "JRI"}, {"family": "Hanscombe", "given": "Ken B", "initials": "KB"}, {"family": "Euesden", "given": "Jack", "initials": "J"}, {"family": "Choi", "given": "Shing Wan", "initials": "SW"}, {"family": "Purves", "given": "Kirstin L", "initials": "KL"}, {"family": "Breen", "given": "Gerome", "initials": "G"}, {"family": "Air", "given": "Tracy M", "initials": "TM"}, {"family": "Andlauer", "given": "Till F M", "initials": "TFM"}, {"family": "Baune", "given": "Bernhard T", "initials": "BT"}, {"family": "Binder", "given": "Elisabeth B", "initials": "EB"}, {"family": "Blackwood", "given": "Douglas H R", "initials": "DHR"}, {"family": "Boomsma", "given": "Dorret I", "initials": "DI"}, {"family": "Buttensch\u00f8n", "given": "Henriette N", "initials": "HN"}, {"family": "Colodro-Conde", "given": "Luc\u00eda", "initials": "L"}, {"family": "Dannlowski", "given": "Udo", "initials": "U"}, {"family": "Direk", "given": "Nese", "initials": "N"}, {"family": "Dunn", "given": "Erin C", "initials": "EC"}, {"family": "Forstner", "given": "Andreas J", "initials": "AJ"}, {"family": "de Geus", "given": "Eco J C", "initials": "EJC"}, {"family": "Grabe", "given": "Hans J", "initials": "HJ"}, {"family": "Hamilton", "given": "Steven P", "initials": "SP"}, {"family": "Jones", "given": "Ian", "initials": "I"}, {"family": "Jones", "given": "Lisa A", "initials": "LA"}, {"family": "Knowles", "given": "James A", "initials": "JA"}, {"family": "Kutalik", "given": "Zolt\u00e1n", "initials": "Z"}, {"family": "Levinson", "given": "Douglas F", "initials": "DF"}, {"family": "Lewis", "given": "Glyn", "initials": "G"}, {"family": "Lind", "given": "Penelope A", "initials": "PA"}, {"family": "Lucae", "given": "Susanne", "initials": "S"}, {"family": "Magnusson", "given": "Patrik K", "initials": "PK"}, {"family": "McGuffin", "given": "Peter", "initials": "P"}, {"family": "McIntosh", "given": "Andrew M", "initials": "AM"}, {"family": "Milaneschi", "given": "Yuri", "initials": "Y"}, {"family": "Mors", "given": "Ole", "initials": "O"}, {"family": "Mostafavi", "given": "Sara", "initials": "S"}, {"family": "M\u00fcller-Myhsok", "given": "Bertram", "initials": "B"}, {"family": "Pedersen", "given": "Nancy L", "initials": "NL"}, {"family": "Penninx", "given": "Brenda W J H", "initials": "BWJH"}, {"family": "Potash", "given": "James B", "initials": "JB"}, {"family": "Preisig", "given": "Martin", "initials": "M"}, {"family": "Ripke", "given": "Stephan", "initials": "S"}, {"family": "Shi", "given": "Jianxin", "initials": "J"}, {"family": "Shyn", "given": "Stanley I", "initials": "SI"}, {"family": "Smoller", "given": "Jordan W", "initials": "JW"}, {"family": "Streit", "given": "Fabian", "initials": "F"}, {"family": "Sullivan", "given": "Patrick F", "initials": "PF"}, {"family": "Tiemeier", "given": "Henning", "initials": "H"}, {"family": "Uher", "given": "Rudolf", "initials": "R"}, {"family": "Van der Auwera", "given": "Sandra", "initials": "S"}, {"family": "Weissman", "given": "Myrna M", "initials": "MM"}, {"family": "Major Depressive Disorder Working Group of the Psychiatric Genomics Consortium", "given": "", "initials": ""}, {"family": "O'Reilly", "given": "Paul F", "initials": "PF"}, {"family": "Lewis", "given": "Cathryn M", "initials": "CM"}], "type": "journal article", "published": "2019-08-05", "journal": {"volume": null, "issn": "1873-2402", "issue": null, "title": "Biol. Psychiatry", "issn-l": "0006-3223"}, "abstract": "The prevalence of depression is higher in individuals with autoimmune diseases, but the mechanisms underlying the observed comorbidities are unknown. Shared genetic etiology is a plausible explanation for the overlap, and in this study we tested whether genetic variation in the major histocompatibility complex (MHC), which is associated with risk for autoimmune diseases, is also associated with risk for depression.\n\nWe fine-mapped the classical MHC (chr6: 29.6-33.1 Mb), imputing 216 human leukocyte antigen (HLA) alleles and 4 complement component 4 (C4) haplotypes in studies from the Psychiatric Genomics Consortium Major Depressive Disorder Working Group and the UK Biobank. The total sample size was 45,149 depression cases and 86,698 controls. We tested for association between depression status and imputed MHC variants, applying both a region-wide significance threshold (3.9\u00a0\u00d7 10\n                -6) and a candidate threshold (1.6\u00a0\u00d7 10-4).\n\nNo HLA alleles or C4 haplotypes were associated with depression at the region-wide threshold. HLA-B*08:01 was associated with modest protection for depression at the candidate threshold for testing in HLA genes in the meta-analysis (odds ratio\u00a0= 0.98, 95% confidence interval\u00a0= 0.97-0.99).\n\nWe found no evidence that an increased risk for depression was conferred by HLA alleles, which play a major role in the genetic susceptibility to autoimmune diseases, or C4 haplotypes, which are strongly associated with schizophrenia. These results suggest that any HLA or C4 variants associated with depression either are rare or have very modest effect sizes.", "doi": "10.1016/j.biopsych.2019.06.031", "pmid": "31570195", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "S0006-3223(19)31558-6"}], "notes": [], "created": "2019-10-16T15:10:17.824Z", "modified": "2020-02-20T11:30:29.890Z"}, {"entity": "publication", "iuid": "ff45e6aec7a34cc583c6229238538107", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ff45e6aec7a34cc583c6229238538107.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ff45e6aec7a34cc583c6229238538107"}}, "title": "Tobacco smoking induces changes in true DNA methylation, hydroxymethylation and gene expression in bronchoalveolar lavage cells.", "authors": [{"family": "Ringh", "given": "Mikael V", "initials": "MV"}, {"family": "Hagemann-Jensen", "given": "Michael", "initials": "M"}, {"family": "Needhamsen", "given": "Maria", "initials": "M"}, {"family": "Kular", "given": "Lara", "initials": "L"}, {"family": "Breeze", "given": "Charles E", "initials": "CE"}, {"family": "Sj\u00f6holm", "given": "Louise K", "initials": "LK"}, {"family": "Slavec", "given": "Lara", "initials": "L"}, {"family": "Kullberg", "given": "Susanna", "initials": "S"}, {"family": "Wahlstr\u00f6m", "given": "Jan", "initials": "J"}, {"family": "Grunewald", "given": "Johan", "initials": "J"}, {"family": "Brynedal", "given": "Boel", "initials": "B"}, {"family": "Liu", "given": "Yun", "initials": "Y"}, {"family": "Almgren", "given": "Malin", "initials": "M"}, {"family": "Jagodic", "given": "Maja", "initials": "M"}, {"family": "\u00d6ckinger", "given": "Johan", "initials": "J"}, {"family": "Ekstr\u00f6m", "given": "Tomas J", "initials": "TJ"}], "type": "journal article", "published": "2019-08-00", "journal": {"volume": "46", "issn": "2352-3964", "issue": null, "pages": "290-304", "title": "EBioMedicine", "issn-l": "2352-3964"}, "abstract": "While smoking is known to associate with development of multiple diseases, the underlying mechanisms are still poorly understood. Tobacco smoking can modify the chemical integrity of DNA leading to changes in transcriptional activity, partly through an altered epigenetic state. We aimed to investigate the impact of smoking on lung cells collected from bronchoalveolar lavage (BAL).\n\nWe profiled changes in DNA methylation (5mC) and its oxidised form hydroxymethylation (5hmC) using conventional bisulphite (BS) treatment and oxidative bisulphite treatment with Illumina Infinium MethylationEPIC BeadChip, and examined gene expression by RNA-seq in healthy smokers.\n\nWe identified 1667 total 5mC\u202f+\u202f5hmC, 1756 5mC and 67 5hmC differentially methylated positions (DMPs) between smokers and non-smokers (FDR-adjusted P <.05, absolute \u0394\u03b2 >0.15). Both 5mC DMPs and to a lesser extent 5mC\u202f+\u202f5hmC were predominantly hypomethylated. In contrast, almost all 5hmC DMPs were hypermethylated, supporting the hypothesis that smoking-associated oxidative stress can lead to DNA demethylation, via the established sequential oxidation of which 5hmC is the first step. While we confirmed differential methylation of previously reported smoking-associated 5mC\u202f+\u202f5hmC CpGs using former generations of BeadChips in alveolar macrophages, the large majority of identified DMPs, 5mC\u202f+\u202f5hmC (1639/1667), 5mC (1738/1756), and 5hmC (67/67), have not been previously reported. Most of these novel smoking-associating sites are specific to the EPIC BeadChip and, interestingly, many of them are associated to FANTOM5 enhancers. Transcriptional changes affecting 633 transcripts were consistent with DNA methylation profiles and converged to alteration of genes involved in migration, signalling and inflammatory response of immune cells.\n\nCollectively, these findings suggest that tobacco smoke exposure epigenetically modifies BAL cells, possibly involving a continuous active demethylation and subsequent increased activity of inflammatory processes in the lungs. FUND: The study was supported by the Swedish Research Council, the Swedish Heart-Lung Foundation, the Stockholm County Council (ALF), the King Gustav's and Queen Victoria's Freemasons' Foundation, Knut and Alice Wallenberg Foundation, Neuro Sweden, and the Swedish MS foundation.", "doi": "10.1016/j.ebiom.2019.07.006", "pmid": "31303497", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "S2352-3964(19)30441-4"}, {"db": "pmc", "key": "PMC6710853"}], "notes": [], "created": "2019-09-17T16:24:25.920Z", "modified": "2024-01-16T13:48:44.009Z"}, {"entity": "publication", "iuid": "983ea2c3052b425c903696a9faff59e9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/983ea2c3052b425c903696a9faff59e9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/983ea2c3052b425c903696a9faff59e9"}}, "title": "Maintenance of High Genome Integrity over Vegetative Growth in the Fairy-Ring Mushroom Marasmius oreades", "authors": [{"family": "Hiltunen", "given": "Markus", "initials": "M"}, {"family": "Grudzinska-Sterno", "given": "Magdalena", "initials": "M"}, {"family": "Wallerman", "given": "Ola", "initials": "O"}, {"family": "Ryberg", "given": "Martin", "initials": "M"}, {"family": "Johannesson", "given": "Hanna", "initials": "H"}], "type": "journal-article", "published": "2019-08-00", "journal": {"volume": "29", "issn": "0960-9822", "issue": "16", "pages": "2758-2765.e6", "title": "Current Biology", "issn-l": "0960-9822"}, "abstract": "Most mutations in coding regions of the genome are deleterious, causing selection to favor mechanisms that minimize the mutational load over time [1-5]. DNA replication during cell division is a major source of new mutations. It is therefore important to limit the number of cell divisions between generations, particularly for large and long-lived organisms [6-9]. The germline cells of animals and the slowly dividing cells in plant meristems are adaptations to control the number of mutations that accumulate over generations [9-11]. Fungi lack a separated germline while harboring species with very large and long-lived individuals that appear to maintain highly stable genomes within their mycelia [8, 12, 13]. Here, we studied genomic mutation accumulation in the fairy-ring mushroom Marasmius oreades. We generated a chromosome-level genome assembly using a combination of cutting-edge DNA sequencing technologies and re-sequenced 40 samples originating from six individuals of this fungus. The low number of mutations recovered in the sequencing data suggests the presence of an unknown mechanism that works to maintain extraordinary genome integrity over vegetative growth in M. oreades. The highly structured growth pattern of M. oreades allowed us to estimate the number of cell divisions leading up to each sample [14, 15], and from this data, we infer an incredibly low per mitosis mutation rate (3.8 \u00d7 10 -12 mutations per site and cell division) as one of several possible explanations for the low number of identified mutations.", "doi": "10.1016/j.cub.2019.07.025", "pmid": "31402298", "labels": {"NGI Stockholm (Genomics Production)": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2019-11-25T14:43:11.225Z", "modified": "2024-01-16T13:48:44.031Z"}, {"entity": "publication", "iuid": "f0b61c7f79764e5b80784ea748d8ef40", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f0b61c7f79764e5b80784ea748d8ef40.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f0b61c7f79764e5b80784ea748d8ef40"}}, "title": "Linkage analysis revealed risk loci on 6p21 and 18p11.2-q11.2 in familial colon and rectal cancer, respectively.", "authors": [{"family": "von Holst", "given": "Susanna", "initials": "S"}, {"family": "Jiao", "given": "Xiang", "initials": "X"}, {"family": "Liu", "given": "Wen", "initials": "W"}, {"family": "Kontham", "given": "Vinaykumar", "initials": "V"}, {"family": "Thutkawkorapin", "given": "Jessada", "initials": "J"}, {"family": "Ringdahl", "given": "Jenny", "initials": "J"}, {"family": "Bryant", "given": "Patrick", "initials": "P"}, {"family": "Lindblom", "given": "Annika", "initials": "A"}], "type": "journal article", "published": "2019-08-00", "journal": {"volume": "27", "issn": "1476-5438", "issue": "8", "pages": "1286-1295", "title": "Eur. J. Hum. Genet.", "issn-l": "1018-4813"}, "abstract": "Colorectal cancer (CRC) is one of the major cancer types in the western world including Sweden. However, known genetic risk factors could only explain a limited part of heritability of the disease. Moreover, colon and rectal cancers are habitually discussed as one entity, colorectal cancer, although different carcinogenesis has been recognized. A genome-wide linkage scan in 32 colon- and 56 rectal cancer families from Sweden was performed based on 475 non-FAP/HNPCC patients genotyped using SNP arrays. A maximum HLOD of 2.50 at locus 6p21.1-p12.1 and a HLOD of 2.56 at 18p11.2 was obtained for colon and rectal cancer families, respectively. Exome sequencing over the regions of interest in 12 patients from six families identified 22 and 25 candidate risk variants for colon and rectal cancer, respectively. Haplotype association analysis in the two regions was carried out between additional 477 familial CRC cases and 4780 controls and suggested candidate haplotypes possibly associated with CRC risk. This study suggested two new linkage regions for colon cancer and rectal cancer with candidate predisposing variants. Further studies are required to elucidate the pathogenic mechanism of these regions and to pinpoint the causative genes.", "doi": "10.1038/s41431-019-0388-3", "pmid": "30952955", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41431-019-0388-3"}], "notes": [], "created": "2019-08-13T12:15:30.342Z", "modified": "2024-01-16T13:48:44.038Z"}, {"entity": "publication", "iuid": "0bbce1af6ae44c98baf2d3b84ce452ef", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0bbce1af6ae44c98baf2d3b84ce452ef.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0bbce1af6ae44c98baf2d3b84ce452ef"}}, "title": "Shared and Unique Patterns of DNA Methylation in Systemic Lupus Erythematosus and Primary Sj\u00f6gren's Syndrome.", "authors": [{"family": "Imgenberg-Kreuz", "given": "Juliana", "initials": "J"}, {"family": "Alml\u00f6f", "given": "Jonas Carlsson", "initials": "JC"}, {"family": "Leonard", "given": "Dag", "initials": "D"}, {"family": "Sj\u00f6wall", "given": "Christopher", "initials": "C"}, {"family": "Syv\u00e4nen", "given": "Ann-Christine", "initials": "AC", "orcid": "0000-0002-9681-9146", "researcher": {"href": "https://publications.scilifelab.se/researcher/f7012e35025543379380cb90efd71243.json"}}, {"family": "R\u00f6nnblom", "given": "Lars", "initials": "L"}, {"family": "Sandling", "given": "Johanna K", "initials": "JK"}, {"family": "Nordmark", "given": "Gunnel", "initials": "G"}], "type": "journal article", "published": "2019-07-30", "journal": {"volume": "10", "issn": "1664-3224", "issue": null, "pages": "1686", "title": "Front Immunol", "issn-l": "1664-3224"}, "abstract": "Objectives: To perform a cross-comparative analysis of DNA methylation in patients with systemic lupus erythematosus (SLE), patients with primary Sj\u00f6gren's syndrome (pSS), and healthy controls addressing the question of epigenetic sharing and aiming to detect disease-specific alterations. Methods: DNA extracted from peripheral blood from 347 cases with SLE, 100 cases with pSS, and 400 healthy controls were analyzed on the Human Methylation 450k array, targeting 485,000 CpG sites across the genome. A linear regression model including age, sex, and blood cell type distribution as covariates was fitted, and association p-values were Bonferroni corrected. A random forest machine learning classifier was designed for prediction of disease status based on DNA methylation data. Results: We established a combined set of 4,945 shared differentially methylated CpG sites (DMCs) in SLE and pSS compared to controls. In pSS, hypomethylation at type I interferon induced genes was mainly driven by patients who were positive for Ro/SSA and/or La/SSB autoantibodies. Analysis of differential methylation between SLE and pSS identified 2,244 DMCs with a majority of sites showing decreased methylation in SLE compared to pSS. The random forest classifier demonstrated good performance in discerning between disease status with an area under the curve (AUC) between 0.83 and 0.96. Conclusions: The majority of differential DNA methylation is shared between SLE and pSS, however, important quantitative differences exist. Our data highlight neutrophil dysregulation as a shared mechanism, emphasizing the role of neutrophils in the pathogenesis of systemic autoimmune diseases. The current study provides evidence for genes and molecular pathways driving common and disease-specific pathogenic mechanisms.", "doi": "10.3389/fimmu.2019.01686", "pmid": "31428085", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC6688520"}], "notes": [], "created": "2019-09-17T16:24:25.212Z", "modified": "2024-01-16T13:48:44.069Z"}, {"entity": "publication", "iuid": "5d4e13be48654809967601ba6e83e16e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5d4e13be48654809967601ba6e83e16e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5d4e13be48654809967601ba6e83e16e"}}, "title": "Combinations of Spok genes create multiple meiotic drivers in Podospora.", "authors": [{"family": "Vogan", "given": "Aaron A", "initials": "AA"}, {"family": "Ament-Vel\u00e1squez", "given": "S Lorena", "initials": "SL"}, {"family": "Granger-Farbos", "given": "Alexandra", "initials": "A"}, {"family": "Svedberg", "given": "Jesper", "initials": "J"}, {"family": "Bastiaans", "given": "Eric", "initials": "E"}, {"family": "Debets", "given": "Alfons Jm", "initials": "AJ"}, {"family": "Coustou", "given": "Virginie", "initials": "V"}, {"family": "Yvanne", "given": "H\u00e9l\u00e8ne", "initials": "H"}, {"family": "Clav\u00e9", "given": "Corinne", "initials": "C"}, {"family": "Saupe", "given": "Sven J", "initials": "SJ"}, {"family": "Johannesson", "given": "Hanna", "initials": "H"}], "type": "journal article", "published": "2019-07-26", "journal": {"volume": "8", "issn": "2050-084X", "issue": null, "pages": null, "title": "Elife", "issn-l": "2050-084X"}, "abstract": "Meiotic drive is the preferential transmission of a particular allele during sexual reproduction. The phenomenon is observed as spore killing in multiple fungi. In natural populations of \r\n                Podospora anserina, seven spore killer types (Psks) have been identified through classical genetic analyses. Here we show that the Spok gene family underlies the Psks. The combination of Spok genes at different chromosomal locations defines the spore killer types and creates a killing hierarchy within a population. We identify two novel Spok homologs located within a large (74-167 kbp) region (the Spok block) that resides in different chromosomal locations in different strains. We confirm that the SPOK protein performs both killing and resistance functions and show that these activities are dependent on distinct domains, a predicted nuclease and kinase domain. Genomic and phylogenetic analyses across ascomycetes suggest that the Spok genes disperse through cross-species transfer, and evolve by duplication and diversification within lineages.", "doi": "10.7554/eLife.46454", "pmid": "31347500", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "46454"}, {"db": "pmc", "key": "PMC6660238"}, {"db": "Dryad", "key": "10.5061/dryad.vm1192g"}], "notes": [], "created": "2019-08-26T19:26:49.323Z", "modified": "2024-01-16T13:48:44.095Z"}, {"entity": "publication", "iuid": "46cd7cf01fbc4ddf87f7503100fbaaab", "links": {"self": {"href": "https://publications.scilifelab.se/publication/46cd7cf01fbc4ddf87f7503100fbaaab.json"}, "display": {"href": "https://publications.scilifelab.se/publication/46cd7cf01fbc4ddf87f7503100fbaaab"}}, "title": "TAF1, associated with intellectual disability in humans, is essential for embryogenesis and regulates neurodevelopmental processes in zebrafish.", "authors": [{"family": "Gudmundsson", "given": "Sanna", "initials": "S", "orcid": "0000-0002-2332-074X", "researcher": {"href": "https://publications.scilifelab.se/researcher/adb097c987504b2ca309e5f4e1cea5d2.json"}}, {"family": "Wilbe", "given": "Maria", "initials": "M"}, {"family": "Filipek-G\u00f3rniok", "given": "Beata", "initials": "B", "orcid": "0000-0002-6757-5410", "researcher": {"href": "https://publications.scilifelab.se/researcher/11f0b7b3e0b045f082d2aff1dd23ec0e.json"}}, {"family": "Molin", "given": "Anna-Maja", "initials": "A"}, {"family": "Ekvall", "given": "Sara", "initials": "S"}, {"family": "Johansson", "given": "Josefin", "initials": "J", "orcid": "0000-0002-5152-4096", "researcher": {"href": "https://publications.scilifelab.se/researcher/e568827124304b769a3f336d76b6954e.json"}}, {"family": "Allalou", "given": "Amin", "initials": "A"}, {"family": "Gylje", "given": "Hans", "initials": "H"}, {"family": "Kalscheuer", "given": "Vera M", "initials": "VM", "orcid": "0000-0001-6898-3259", "researcher": {"href": "https://publications.scilifelab.se/researcher/fb8107a11ed144bc8f4c236042f9bc8c.json"}}, {"family": "Ledin", "given": "Johan", "initials": "J", "orcid": "0000-0002-7319-7735", "researcher": {"href": "https://publications.scilifelab.se/researcher/92e482abc18c49d881d3bf0132b3fbcd.json"}}, {"family": "Anner\u00e9n", "given": "G\u00f6ran", "initials": "G"}, {"family": "Bondeson", "given": "Marie-Louise", "initials": "M"}], "type": "journal article", "published": "2019-07-24", "journal": {"title": "Sci Rep", "issn": "2045-2322", "issn-l": "2045-2322", "volume": "9", "issue": "1", "pages": "10730"}, "abstract": "The TATA-box binding protein associated factor 1 (TAF1) protein is a key unit of the transcription factor II D complex that serves a vital function during transcription initiation. Variants of TAF1 have been associated with neurodevelopmental disorders, but TAF1's molecular functions remain elusive. In this study, we present a five-generation family affected with X-linked intellectual disability that co-segregated with a TAF1 c.3568C>T, p.(Arg1190Cys) variant. All affected males presented with intellectual disability and dysmorphic features, while heterozygous females were asymptomatic and had completely skewed X-chromosome inactivation. We investigated the role of TAF1 and its association to neurodevelopment by creating the first complete knockout model of the TAF1 orthologue in zebrafish. A crucial function of human TAF1 during embryogenesis can be inferred from the model, demonstrating that intact taf1 is essential for embryonic development. Transcriptome analysis of taf1 zebrafish knockout revealed enrichment for genes associated with neurodevelopmental processes. In conclusion, we propose that functional TAF1 is essential for embryonic development and specifically neurodevelopmental processes.", "doi": "10.1038/s41598-019-46632-8", "pmid": "31341187", "labels": {"Clinical Genomics Uppsala": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Service", "Genome Engineering Zebrafish": "Collaborative", "Bioinformatics Support and Infrastructure": "Service", "BioImage Informatics": "Collaborative", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative", "Clinical Genomics": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-019-46632-8"}, {"db": "pmc", "key": "PMC6656882"}], "notes": [], "created": "2019-11-29T13:27:12.056Z", "modified": "2024-01-16T13:48:44.102Z"}, {"entity": "publication", "iuid": "944a0db828b548448d06f8a67b9c9c2a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/944a0db828b548448d06f8a67b9c9c2a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/944a0db828b548448d06f8a67b9c9c2a"}}, "title": "Genetic analyses supporting colorectal, gastric, and prostate cancer syndromes.", "authors": [{"family": "Wallander", "given": "Karin", "initials": "K"}, {"family": "Liu", "given": "Wen", "initials": "W"}, {"family": "von Holst", "given": "Susanna", "initials": "S"}, {"family": "Thutkawkorapin", "given": "Jessada", "initials": "J"}, {"family": "Kontham", "given": "Vinaykumar", "initials": "V"}, {"family": "Forsberg", "given": "Anna", "initials": "A"}, {"family": "Lindblom", "given": "Annika", "initials": "A"}, {"family": "Lagerstedt-Robinson", "given": "Kristina", "initials": "K"}], "type": "journal article", "published": "2019-07-23", "journal": {"volume": null, "issn": "1098-2264", "issue": null, "title": "Genes Chromosomes Cancer", "issn-l": "1045-2257"}, "abstract": "Colorectal cancer (CRC), prostate cancer (PrC), and gastric cancer (GC) are common worldwide, and the incidence is to a certain extent dependent on genetics. We have recently shown that in families with more than one case of CRC, the risk of other malignancies is increased. We therefore suggested the presence of not yet described CRC syndromes. In this study, we have searched for genetic susceptibility loci for potential cancer syndromes involving CRC combined with PrC and/or GC. We have performed SNP (single-nucleotide polymorphism)-based linkage analyses in 45 families with CRC, PrC, and GC. In the regions with suggested linkage, we performed exome and association haplotype analyses. Five loci generated a high logarithm of odds (HLOD) score >2, suggestive of linkage, in chromosome bands 1q31-32, 1q24-25, 6q25-26, 18p11-q11, and Xp11. Exome analysis detected no potential pathogenic sequence variants. The haplotype association study showed that one of the top five haplotypes with the lowest P value in the chromosome band 6q25 interestingly was found in the family which contributed the most to the increased HLOD at that locus. This study supports a suggested hereditary cancer syndrome involving CRC and PrC and indicates a location at 6q25. The impact of this locus needs to be confirmed in additional studies.", "doi": "10.1002/gcc.22786", "pmid": "31334572", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2019-08-13T12:15:28.354Z", "modified": "2024-01-16T13:48:44.111Z"}, {"entity": "publication", "iuid": "93379f5a15c7458fac70fdb76edbaee8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/93379f5a15c7458fac70fdb76edbaee8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/93379f5a15c7458fac70fdb76edbaee8"}}, "title": "Mutation dynamics of CpG dinucleotides during a recent event of vertebrate diversification.", "authors": [{"family": "P\u00e9rtille", "given": "F\u00e1bio", "initials": "F", "orcid": "0000-0002-7214-9184", "researcher": {"href": "https://publications.scilifelab.se/researcher/2279c5ebf16f419bab7c3af87bac81d3.json"}}, {"family": "Da Silva", "given": "Vinicius H", "initials": "VH"}, {"family": "Johansson", "given": "Anna M", "initials": "AM", "orcid": "0000-0002-9762-0497", "researcher": {"href": "https://publications.scilifelab.se/researcher/dbd1ea80ec964bc3ab675e84b27d17e6.json"}}, {"family": "Lindstr\u00f6m", "given": "Tom", "initials": "T", "orcid": "0000-0001-7856-2925", "researcher": {"href": "https://publications.scilifelab.se/researcher/1a619b495eed4a41a65f2bc7a3c7c5dc.json"}}, {"family": "Wright", "given": "Dominic", "initials": "D"}, {"family": "Coutinho", "given": "Luiz L", "initials": "LL"}, {"family": "Jensen", "given": "Per", "initials": "P"}, {"family": "Guerrero-Bosagna", "given": "Carlos", "initials": "C", "orcid": "0000-0003-1935-5875", "researcher": {"href": "https://publications.scilifelab.se/researcher/0175a0da7ca147d4a0430b085ed23669.json"}}], "type": "journal article", "published": "2019-07-00", "journal": {"volume": "14", "issn": "1559-2308", "issue": "7", "pages": "685-707", "title": "Epigenetics", "issn-l": "1559-2294"}, "abstract": "DNA methylation in CpGs dinucleotides is associated with high mutability and disappearance of CpG sites during evolution. Although the high mutability of CpGs is thought to be relevant for vertebrate evolution, very little is known on the role of CpG-related mutations in the genomic diversification of vertebrates. Our study analysed genetic differences in chickens, between Red Junglefowl (RJF; the living closest relative to the ancestor of domesticated chickens) and domesticated breeds, to identify genomic dynamics that have occurred during the process of their domestication, focusing particularly on CpG-related mutations. Single nucleotide polymorphisms (SNPs) and copy number variations (CNVs) between RJF and these domesticated breeds were assessed in a reduced fraction of their genome. Additionally, DNA methylation in the same fraction of the genome was measured in the sperm of RJF individuals to identify possible correlations with the mutations found between RJF and the domesticated breeds. Our study shows that although the vast majority of CpG-related mutations found relate to CNVs, CpGs disproportionally associate to SNPs in comparison to CNVs, where they are indeed substantially under-represented. Moreover, CpGs seem to be hotspots of mutations related to speciation. We suggest that, on the one hand, CpG-related mutations in CNV regions would promote genomic 'flexibility' in evolution, i.e., the ability of the genome to expand its functional possibilities; on the other hand, CpG-related mutations in SNPs would relate to genomic 'specificity' in evolution, thus, representing mutations that would associate with phenotypic traits relevant for speciation.", "doi": "10.1080/15592294.2019.1609868", "pmid": "31070073", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC6557589"}], "notes": [], "created": "2020-01-08T12:39:10.372Z", "modified": "2021-06-18T14:18:18.038Z"}, {"entity": "publication", "iuid": "d7126a538cb7490bbda8262de3cd421e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d7126a538cb7490bbda8262de3cd421e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d7126a538cb7490bbda8262de3cd421e"}}, "title": "Epigenome-wide association study of lung function level and its change.", "authors": [{"family": "Imboden", "given": "Medea", "initials": "M"}, {"family": "Wielscher", "given": "Matthias", "initials": "M"}, {"family": "Rezwan", "given": "Faisal I", "initials": "FI"}, {"family": "Amaral", "given": "Andr\u00e9 F S", "initials": "AFS"}, {"family": "Schaffner", "given": "Emmanuel", "initials": "E"}, {"family": "Jeong", "given": "Ayoung", "initials": "A"}, {"family": "Beckmeyer-Borowko", "given": "Anna", "initials": "A"}, {"family": "Harris", "given": "Sarah E", "initials": "SE"}, {"family": "Starr", "given": "John M", "initials": "JM"}, {"family": "Deary", "given": "Ian J", "initials": "IJ"}, {"family": "Flexeder", "given": "Claudia", "initials": "C"}, {"family": "Waldenberger", "given": "Melanie", "initials": "M"}, {"family": "Peters", "given": "Annette", "initials": "A"}, {"family": "Schulz", "given": "Holger", "initials": "H"}, {"family": "Chen", "given": "Su", "initials": "S"}, {"family": "Sunny", "given": "Shadia Khan", "initials": "SK"}, {"family": "Karmaus", "given": "Wilfried J J", "initials": "WJJ"}, {"family": "Jiang", "given": "Yu", "initials": "Y"}, {"family": "Erhart", "given": "Gertraud", "initials": "G"}, {"family": "Kronenberg", "given": "Florian", "initials": "F"}, {"family": "Arathimos", "given": "Ryan", "initials": "R"}, {"family": "Sharp", "given": "Gemma C", "initials": "GC"}, {"family": "Henderson", "given": "Alexander John", "initials": "AJ"}, {"family": "Fu", "given": "Yu", "initials": "Y"}, {"family": "Piiril\u00e4", "given": "P\u00e4ivi", "initials": "P"}, {"family": "Pietil\u00e4inen", "given": "Kirsi H", "initials": "KH"}, {"family": "Ollikainen", "given": "Miina", "initials": "M"}, {"family": "Johansson", "given": "Asa", "initials": "A"}, {"family": "Gyllensten", "given": "Ulf", "initials": "U"}, {"family": "de Vries", "given": "Maaike", "initials": "M"}, {"family": "van der Plaat", "given": "Diana A", "initials": "DA"}, {"family": "de Jong", "given": "Kim", "initials": "K"}, {"family": "Boezen", "given": "H Marike", "initials": "HM"}, {"family": "Hall", "given": "Ian P", "initials": "IP"}, {"family": "Tobin", "given": "Martin D", "initials": "MD"}, {"family": "Jarvelin", "given": "Marjo-Riitta", "initials": "MR"}, {"family": "Holloway", "given": "John W", "initials": "JW"}, {"family": "Jarvis", "given": "Deborah", "initials": "D"}, {"family": "Probst-Hensch", "given": "Nicole M", "initials": "NM"}], "type": "journal article", "published": "2019-07-00", "journal": {"volume": "54", "issn": "1399-3003", "issue": "1", "title": "Eur. Respir. J.", "issn-l": "0903-1936"}, "abstract": "Previous reports link differential DNA methylation (DNAme) to environmental exposures that are associated with lung function. Direct evidence on lung function DNAme is, however, limited. We undertook an agnostic epigenome-wide association study (EWAS) on pre-bronchodilation lung function and its change in adults.In a discovery-replication EWAS design, DNAme in blood and spirometry were measured twice, 6-15\u2005years apart, in the same participants of three adult population-based discovery cohorts (n=2043). Associated DNAme markers (p<5\u00d710\n                -7) were tested in seven replication cohorts (adult: n=3327; childhood: n=420). Technical bias-adjusted residuals of a regression of the normalised absolute \u03b2-values on control probe-derived principle components were regressed on level and change of forced expiratory volume in 1\u2005s (FEV1), forced vital capacity (FVC) and their ratio (FEV1/FVC) in the covariate-adjusted discovery EWAS. Inverse-variance-weighted meta-analyses were performed on results from discovery and replication samples in all participants and never-smokers.EWAS signals were enriched for smoking-related DNAme. We replicated 57 lung function DNAme markers in adult, but not childhood samples, all previously associated with smoking. Markers not previously associated with smoking failed replication. cg05575921 (AHRR (aryl hydrocarbon receptor repressor)) showed the statistically most significant association with cross-sectional lung function (FEV1/FVC: pdiscovery=3.96\u00d710-21 and pcombined=7.22\u00d710-50). A score combining 10 DNAme markers previously reported to mediate the effect of smoking on lung function was associated with lung function (FEV1/FVC: p=2.65\u00d710-20).Our results reveal that lung function-associated methylation signals in adults are predominantly smoking related, and possibly of clinical utility in identifying poor lung function and accelerated decline. Larger studies with more repeat time-points are needed to identify lung function DNAme in never-smokers and in children.", "doi": "10.1183/13993003.00457-2019", "pmid": "31073081", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "13993003.00457-2019"}, {"db": "pmc", "key": "PMC6610463"}], "notes": [], "created": "2019-09-17T16:24:26.756Z", "modified": "2020-01-21T13:56:14.486Z"}, {"entity": "publication", "iuid": "730cccddf3cc4f76980613b9d5a7f984", "links": {"self": {"href": "https://publications.scilifelab.se/publication/730cccddf3cc4f76980613b9d5a7f984.json"}, "display": {"href": "https://publications.scilifelab.se/publication/730cccddf3cc4f76980613b9d5a7f984"}}, "title": "Analyzing DNA methylation patterns in subjects diagnosed with schizophrenia using machine learning methods.", "authors": [{"family": "Torabi Moghadam", "given": "Behrooz", "initials": "B"}, {"family": "Etemadikhah", "given": "Mitra", "initials": "M"}, {"family": "Rajkowska", "given": "Grazyna", "initials": "G"}, {"family": "Stockmeier", "given": "Craig", "initials": "C"}, {"family": "Grabherr", "given": "Manfred", "initials": "M"}, {"family": "Komorowski", "given": "Jan", "initials": "J"}, {"family": "Feuk", "given": "Lars", "initials": "L"}, {"family": "Carlstr\u00f6m", "given": "Eva Lindholm", "initials": "EL"}], "type": "journal article", "published": "2019-07-00", "journal": {"volume": "114", "issn": "1879-1379", "issue": null, "pages": "41-47", "title": "J Psychiatr Res", "issn-l": "0022-3956"}, "abstract": "Schizophrenia is a common mental disorder with high heritability. It is genetically complex and to date more than a hundred risk loci have been identified. Association of environmental factors and schizophrenia has also been reported, while epigenetic analyses have yielded ambiguous and sometimes conflicting results. Here, we analyzed fresh frozen post-mortem brain tissue from a cohort of 73 subjects diagnosed with schizophrenia and 52 control samples, using the Illumina Infinium HumanMethylation450 Bead Chip, to investigate genome-wide DNA methylation patterns in the two groups. Analysis of differential methylation was performed with the Bioconductor Minfi package and modern machine-learning and visualization techniques, which were shown previously to be successful in detecting and highlighting differentially methylated patterns in case-control studies. In this dataset, however, these methods did not uncover any significant signals discerning the patient group and healthy controls, suggesting that if there are methylation changes associated with schizophrenia, they are heterogeneous and complex with small effect.", "doi": "10.1016/j.jpsychires.2019.04.001", "pmid": "31022588", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "S0022-3956(18)31394-3"}], "notes": [], "created": "2019-10-30T08:39:03.432Z", "modified": "2024-01-16T13:48:44.199Z"}, {"entity": "publication", "iuid": "b11534132a8b41c1bab76ccf6bf76275", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b11534132a8b41c1bab76ccf6bf76275.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b11534132a8b41c1bab76ccf6bf76275"}}, "title": "Influence of ABO Locus on PFA-100 Collagen-ADP Closure Time Is Not Totally Dependent on the Von Willebrand Factor. Results of a GWAS on GAIT-2 Project Phenotypes.", "authors": [{"family": "Pujol-Moix", "given": "N\u00faria", "initials": "N"}, {"family": "Martinez-Perez", "given": "Angel", "initials": "A"}, {"family": "Sabater-Lleal", "given": "Maria", "initials": "M"}, {"family": "Llobet", "given": "Dolors", "initials": "D"}, {"family": "Vilalta", "given": "No\u00e8lia", "initials": "N"}, {"family": "Hamsten", "given": "Anders", "initials": "A"}, {"family": "Souto", "given": "Joan Carles", "initials": "JC"}, {"family": "Soria", "given": "Jos\u00e9 Manuel", "initials": "JM"}], "type": "journal article", "published": "2019-06-30", "journal": {"volume": "20", "issn": "1422-0067", "issue": "13", "pages": null, "title": "Int J Mol Sci", "issn-l": null}, "abstract": "(1) Background: In a previous study, we found that two phenotypes related to platelet reactivity, measured with the PFA-100 system, were highly heritable. The aim of the present study was to identify genetic determinants that influence the variability of these phenotypes: closure time of collagen-ADP (Col-ADP) and of collagen-epinephrine (Col-Epi). (2) Methods: As part of the GAIT-2 (Genetic Analysis of Idiopathic Thrombophilia (2) Project, 935 individuals from 35 large Spanish families were studied. A genome-wide association study (GWAS) with \u2248 10 M single nucleotide polymorphisms (SNPs) was carried out with Col-ADP and Col-Epi phenotypes. (3) Results: The study yielded significant genetic signals that mapped to the \r\n            ABO locus. After adjusting both phenotypes for the ABO genotype, these signals disappeared. After adjusting for von Willebrand factor (VWF) or for coagulation factor VIII (FVIII), the significant signals disappeared totally for Col-Epi phenotype but only partially for Col-ADP phenotype. (4) Conclusion: Our results suggest that the ABO locus exerts the main genetic influence on PFA-100 phenotypes. However, while the effect of the ABO locus on Col-Epi phenotype is mediated through VWF and/or FVIII, the effect of the ABO locus on Col-ADP phenotype is partly produced through VWF and/or FVIII, and partly through other mechanisms.", "doi": "10.3390/ijms20133221", "pmid": "31262040", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "ijms20133221"}], "notes": [], "created": "2019-07-05T12:56:37.940Z", "modified": "2020-01-21T13:56:14.754Z"}, {"entity": "publication", "iuid": "502166a5168b4ccaa7046e496d8133e1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/502166a5168b4ccaa7046e496d8133e1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/502166a5168b4ccaa7046e496d8133e1"}}, "title": "Allelic Variation in Taste Genes Is Associated with Taste and Diet Preferences and Dental Caries.", "authors": [{"family": "Eriksson", "given": "Linda", "initials": "L"}, {"family": "Esberg", "given": "Anders", "initials": "A"}, {"family": "Haworth", "given": "Simon", "initials": "S"}, {"family": "Holgerson", "given": "Pernilla Lif", "initials": "PL"}, {"family": "Johansson", "given": "Ingegerd", "initials": "I"}], "type": "journal article", "published": "2019-06-29", "journal": {"title": "Nutrients", "issn": "2072-6643", "volume": "11", "issue": "7", "issn-l": "2072-6643"}, "abstract": "Taste and diet preferences are complex and influenced by both environmental and host traits while affecting both food selection and associated health outcomes. The present study genotyped 94 single nucleotide polymorphisms (SNPs) in previously reported taste and food intake related genes and assessed associations with taste threshold (TT) and preferred intensity (PT) of sweet, sour and bitter, food preferences, habitual diet intake, and caries status in healthy young Swedish men and women ( n = 127). Polymorphisms in the GNAT3, SLC2A4, TAS1R1 and TAS1R2 genes were associated with variation in TT and PT for sweet taste as well as sweet food intake. Increasing PT for sweet was associated with increasing preference and intake of sugary foods. Similarly, increasing TT for sour was associated with increasing intake of sour foods, whereas the associations between food preference/intake and TT/PT for bitter was weak in this study group. Finally, allelic variation in the GNAT3, SLC2A2, SLC2A4, TAS1R1 and TAS1R2 genes was associated with caries status, whereas TT, PT and food preferences were not. It was concluded that variations in taste receptor, glucose transporter and gustducin encoding genes are related to taste perception, food preference and intake as well as the sugar-dependent caries disease.", "doi": "10.3390/nu11071491", "pmid": "31261961", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "nu11071491"}, {"db": "pmc", "key": "PMC6682888"}], "notes": [], "created": "2020-03-16T09:47:52.642Z", "modified": "2020-03-16T09:47:52.652Z"}, {"entity": "publication", "iuid": "6d5825bc3f97412e8dd890b55cb40b8e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6d5825bc3f97412e8dd890b55cb40b8e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6d5825bc3f97412e8dd890b55cb40b8e"}}, "title": "Pharmacogenomics of statin-related myopathy: Meta-analysis of rare variants from whole-exome sequencing.", "authors": [{"family": "Floyd", "given": "James S", "initials": "JS"}, {"family": "Bloch", "given": "Katarzyna M", "initials": "KM"}, {"family": "Brody", "given": "Jennifer A", "initials": "JA"}, {"family": "Maroteau", "given": "Cyrielle", "initials": "C"}, {"family": "Siddiqui", "given": "Moneeza K", "initials": "MK"}, {"family": "Gregory", "given": "Richard", "initials": "R"}, {"family": "Carr", "given": "Daniel F", "initials": "DF"}, {"family": "Molokhia", "given": "Mariam", "initials": "M"}, {"family": "Liu", "given": "Xiaoming", "initials": "X"}, {"family": "Bis", "given": "Joshua C", "initials": "JC"}, {"family": "Ahmed", "given": "Ammar", "initials": "A"}, {"family": "Liu", "given": "Xuan", "initials": "X"}, {"family": "Hallberg", "given": "P\u00e4r", "initials": "P"}, {"family": "Yue", "given": "Qun-Ying", "initials": "QY"}, {"family": "Magnusson", "given": "Patrik K E", "initials": "PKE"}, {"family": "Brisson", "given": "Diane", "initials": "D"}, {"family": "Wiggins", "given": "Kerri L", "initials": "KL"}, {"family": "Morrison", "given": "Alanna C", "initials": "AC"}, {"family": "Khoury", "given": "Etienne", "initials": "E"}, {"family": "McKeigue", "given": "Paul", "initials": "P"}, {"family": "Stricker", "given": "Bruno H", "initials": "BH"}, {"family": "Lapeyre-Mestre", "given": "Maryse", "initials": "M"}, {"family": "Heckbert", "given": "Susan R", "initials": "SR"}, {"family": "Gallagher", "given": "Arlene M", "initials": "AM"}, {"family": "Chinoy", "given": "Hector", "initials": "H"}, {"family": "Gibbs", "given": "Richard A", "initials": "RA"}, {"family": "Bondon-Guitton", "given": "Emmanuelle", "initials": "E"}, {"family": "Tracy", "given": "Russell", "initials": "R"}, {"family": "Boerwinkle", "given": "Eric", "initials": "E"}, {"family": "Gaudet", "given": "Daniel", "initials": "D"}, {"family": "Conforti", "given": "Anita", "initials": "A"}, {"family": "van Staa", "given": "Tjeerd", "initials": "T"}, {"family": "Sitlani", "given": "Colleen M", "initials": "CM"}, {"family": "Rice", "given": "Kenneth M", "initials": "KM"}, {"family": "Maitland-van der Zee", "given": "Anke-Hilse", "initials": "AH"}, {"family": "Wadelius", "given": "Mia", "initials": "M"}, {"family": "Morris", "given": "Andrew P", "initials": "AP"}, {"family": "Pirmohamed", "given": "Munir", "initials": "M"}, {"family": "Palmer", "given": "Colin A N", "initials": "CAN"}, {"family": "Psaty", "given": "Bruce M", "initials": "BM"}, {"family": "Alfirevic", "given": "Ana", "initials": "A"}, {"family": "PREDICTION-ADR Consortium and EUDRAGENE", "given": "", "initials": ""}], "type": "journal article", "published": "2019-06-26", "journal": {"volume": "14", "issn": "1932-6203", "issue": "6", "pages": "e0218115", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "Statin-related myopathy (SRM), which includes rhabdomyolysis, is an uncommon but important adverse drug reaction because the number of people prescribed statins world-wide is large. Previous association studies of common genetic variants have had limited success in identifying a genetic basis for this adverse drug reaction. We conducted a multi-site whole-exome sequencing study to investigate whether rare coding variants confer an increased risk of SRM.\n\nSRM 3-5 cases (N = 505) and statin treatment-tolerant controls (N = 2047) were recruited from multiple sites in North America and Europe. SRM 3-5 was defined as symptoms consistent with muscle injury and an elevated creatine phosphokinase level >4 times upper limit of normal without another likely cause of muscle injury. Whole-exome sequencing and variant calling was coordinated from two analysis centres, and results of single-variant and gene-based burden tests were meta-analysed. No genome-wide significant associations were identified. Given the large number of cases, we had 80% power to identify a variant with minor allele frequency of 0.01 that increases the risk of SRM 6-fold at genome-wide significance.\n\nIn this large whole-exome sequencing study of severe statin-related muscle injury conducted to date, we did not find evidence that rare coding variants are responsible for this adverse drug reaction. Larger sample sizes would be required to identify rare variants with small effects, but it is unclear whether such findings would be clinically actionable.", "doi": "10.1371/journal.pone.0218115", "pmid": "31242253", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "PONE-D-19-00673"}], "notes": [], "created": "2019-07-05T12:56:38.756Z", "modified": "2020-01-21T13:56:14.287Z"}, {"entity": "publication", "iuid": "cb37677921194ab3a4e0306fa262a79c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/cb37677921194ab3a4e0306fa262a79c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/cb37677921194ab3a4e0306fa262a79c"}}, "title": "Genome-wide analysis of dental caries and periodontitis combining clinical and self-reported data.", "authors": [{"family": "Shungin", "given": "Dmitry", "initials": "D"}, {"family": "Haworth", "given": "Simon", "initials": "S", "orcid": "0000-0001-7793-7326", "researcher": {"href": "https://publications.scilifelab.se/researcher/43fa9fb331c849b58d4ac4b14f04fbda.json"}}, {"family": "Divaris", "given": "Kimon", "initials": "K", "orcid": "0000-0003-1290-7251", "researcher": {"href": "https://publications.scilifelab.se/researcher/faf6f5fd1c224f8e8733c944a62c6821.json"}}, {"family": "Agler", "given": "Cary S", "initials": "CS"}, {"family": "Kamatani", "given": "Yoichiro", "initials": "Y", "orcid": "0000-0001-8748-5597", "researcher": {"href": "https://publications.scilifelab.se/researcher/6cf00b09991c4b40bd77a4f2c5bfad97.json"}}, {"family": "Keun Lee", "given": "Myoung", "initials": "M"}, {"family": "Grinde", "given": "Kelsey", "initials": "K"}, {"family": "Hindy", "given": "George", "initials": "G"}, {"family": "Alaraudanjoki", "given": "Viivi", "initials": "V"}, {"family": "Pesonen", "given": "Paula", "initials": "P"}, {"family": "Teumer", "given": "Alexander", "initials": "A", "orcid": "0000-0002-8309-094X", "researcher": {"href": "https://publications.scilifelab.se/researcher/dc9c2667a55b47a6a08aea764fab0946.json"}}, {"family": "Holtfreter", "given": "Birte", "initials": "B"}, {"family": "Sakaue", "given": "Saori", "initials": "S", "orcid": "0000-0003-3618-9717", "researcher": {"href": "https://publications.scilifelab.se/researcher/4b766fd8b9f54da4aee3275bc5864bc5.json"}}, {"family": "Hirata", "given": "Jun", "initials": "J"}, {"family": "Yu", "given": "Yau-Hua", "initials": "YH", "orcid": "0000-0002-4723-5064", "researcher": {"href": "https://publications.scilifelab.se/researcher/1721a03cdef84fbc848c40757d4d33cf.json"}}, {"family": "Ridker", "given": "Paul M", "initials": "PM"}, {"family": "Giulianini", "given": "Franco", "initials": "F"}, {"family": "Chasman", "given": "Daniel I", "initials": "DI"}, {"family": "Magnusson", "given": "Patrik K E", "initials": "PKE", "orcid": "0000-0002-7315-7899", "researcher": {"href": "https://publications.scilifelab.se/researcher/b277b6387de142bbab91fad82d9eff09.json"}}, {"family": "Sudo", "given": "Takeaki", "initials": "T"}, {"family": "Okada", "given": "Yukinori", "initials": "Y", "orcid": "0000-0002-0311-8472", "researcher": {"href": "https://publications.scilifelab.se/researcher/40b13860bfef41959c29be2de853b456.json"}}, {"family": "V\u00f6lker", "given": "Uwe", "initials": "U", "orcid": "0000-0002-5689-3448", "researcher": {"href": "https://publications.scilifelab.se/researcher/e529a40052644d83bdef588a3e4f4e99.json"}}, {"family": "Kocher", "given": "Thomas", "initials": "T", "orcid": "0000-0001-9605-2822", "researcher": {"href": "https://publications.scilifelab.se/researcher/eda3d0e849684448992e43011860b1ed.json"}}, {"family": "Anttonen", "given": "Vuokko", "initials": "V"}, {"family": "Laitala", "given": "Marja-Liisa", "initials": "ML", "orcid": "0000-0001-7323-9862", "researcher": {"href": "https://publications.scilifelab.se/researcher/a5a4749f0323465faa3ac823fc057f22.json"}}, {"family": "Orho-Melander", "given": "Marju", "initials": "M"}, {"family": "Sofer", "given": "Tamar", "initials": "T", "orcid": "0000-0001-8520-8860", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a07473be2d0489a83ba0180d19eef95.json"}}, {"family": "Shaffer", "given": "John R", "initials": "JR", "orcid": "0000-0003-1897-1131", "researcher": {"href": "https://publications.scilifelab.se/researcher/8bcd086471fe49d49534518327f66a50.json"}}, {"family": "Vieira", "given": "Alexandre", "initials": "A"}, {"family": "Marazita", "given": "Mary L", "initials": "ML"}, {"family": "Kubo", "given": "Michiaki", "initials": "M"}, {"family": "Furuichi", "given": "Yasushi", "initials": "Y"}, {"family": "North", "given": "Kari E", "initials": "KE"}, {"family": "Offenbacher", "given": "Steve", "initials": "S"}, {"family": "Ingelsson", "given": "Erik", "initials": "E"}, {"family": "Franks", "given": "Paul W", "initials": "PW"}, {"family": "Timpson", "given": "Nicholas J", "initials": "NJ", "orcid": "0000-0002-7141-9189", "researcher": {"href": "https://publications.scilifelab.se/researcher/764ab7a82db24557a5de0fad97bf53f3.json"}}, {"family": "Johansson", "given": "Ingegerd", "initials": "I"}], "type": "journal article", "published": "2019-06-24", "journal": {"volume": "10", "issn": "2041-1723", "issue": "1", "pages": "2773", "title": "Nat Commun", "issn-l": "2041-1723"}, "abstract": "Dental caries and periodontitis account for a vast burden of morbidity and healthcare spending, yet their genetic basis remains largely uncharacterized. Here, we identify self-reported dental disease proxies which have similar underlying genetic contributions to clinical disease measures and then combine these in a genome-wide association study meta-analysis, identifying 47 novel and conditionally-independent risk loci for dental caries. We show that the heritability of dental caries is enriched for conserved genomic regions and partially overlapping with a range of complex traits including smoking, education, personality traits and metabolic measures. Using cardio-metabolic traits as an example in Mendelian randomization analysis, we estimate causal relationships and provide evidence suggesting that the processes contributing to dental caries may have undesirable downstream effects on health.", "doi": "10.1038/s41467-019-10630-1", "pmid": "31235808", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC6591304"}, {"db": "pii", "key": "10.1038/s41467-019-10630-1"}], "notes": [], "created": "2019-07-05T12:56:39.673Z", "modified": "2023-06-19T13:23:39.048Z"}, {"entity": "publication", "iuid": "6b812784022e4f1e8c0e5f4d03e6ab5a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6b812784022e4f1e8c0e5f4d03e6ab5a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6b812784022e4f1e8c0e5f4d03e6ab5a"}}, "title": "Comparative genomics of Mycobacterium mucogenicum and Mycobacterium neoaurum clade members emphasizing tRNA and non-coding RNA.", "authors": [{"family": "Behra", "given": "Phani Rama Krishna", "initials": "PRK"}, {"family": "Pettersson", "given": "B M Fredrik", "initials": "BMF"}, {"family": "Das", "given": "Sarbashis", "initials": "S"}, {"family": "Dasgupta", "given": "Santanu", "initials": "S"}, {"family": "Kirsebom", "given": "Leif A", "initials": "LA", "orcid": "0000-0002-5092-512X", "researcher": {"href": "https://publications.scilifelab.se/researcher/e80849a89d0043b0b4daff9804c67332.json"}}], "type": "journal article", "published": "2019-06-18", "journal": {"volume": "19", "issn": "1471-2148", "issue": "1", "pages": "124", "title": "BMC Evol. Biol.", "issn-l": "1471-2148"}, "abstract": "Mycobacteria occupy various ecological niches and can be isolated from soil, tap water and ground water. Several cause diseases in humans and animals. To get deeper insight into our understanding of mycobacterial evolution focusing on tRNA and non-coding (nc)RNA, we conducted a comparative genome analysis of Mycobacterium mucogenicum (Mmuc) and Mycobacterium neoaurum (Mneo) clade members.\n\nGenome sizes for Mmuc- and Mneo-clade members vary between 5.4 and 6.5 Mbps with the complete Mmuc T (type strain) genome encompassing 6.1 Mbp. The number of tRNA genes range between 46 and 79 (including one pseudo tRNA gene) with 39 tRNA genes common among the members of these clades, while additional tRNA genes were probably acquired through horizontal gene transfer. Selected tRNAs and ncRNAs (RNase P RNA, tmRNA, 4.5S RNA, Ms1 RNA and 6C RNA) are expressed, and the levels for several of these are higher in stationary phase compared to exponentially growing cells. The rare tRNAIleTAT isoacceptor and two for mycobacteria novel ncRNAs: the Lactobacillales-derived GOLLD RNA and a homolog to the antisense Salmonella typhimurium phage Sar RNA, were shown to be present and expressed in certain Mmuc-clade members.\n\nPhages, IS elements, horizontally transferred tRNA gene clusters, and phage-derived ncRNAs appears to have influenced the evolution of the Mmuc- and Mneo-clades. While the number of predicted coding sequences correlates with genome size, the number of tRNA coding genes does not. The majority of the tRNA genes in mycobacteria are transcribed mainly from single genes and the levels of certain ncRNAs, including RNase P RNA (essential for the processing of tRNAs), are higher at stationary phase compared to exponentially growing cells. We provide supporting evidence that Ms1 RNA represents a mycobacterial 6S RNA variant. The evolutionary routes for the ncRNAs RNase P RNA, tmRNA and Ms1 RNA are different from that of the core genes.", "doi": "10.1186/s12862-019-1447-7", "pmid": "31215393", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1186/s12862-019-1447-7"}, {"db": "pmc", "key": "PMC6582537"}], "notes": [], "created": "2019-11-25T14:08:36.735Z", "modified": "2024-01-16T13:48:44.244Z"}, {"entity": "publication", "iuid": "fffa2a55e4ee4e7792be485b71063ffa", "links": {"self": {"href": "https://publications.scilifelab.se/publication/fffa2a55e4ee4e7792be485b71063ffa.json"}, "display": {"href": "https://publications.scilifelab.se/publication/fffa2a55e4ee4e7792be485b71063ffa"}}, "title": "Microbiota data from low biomass milk samples is markedly affected by laboratory and reagent contamination.", "authors": [{"family": "Dahlberg", "given": "Josef", "initials": "J", "orcid": "0000-0001-8131-6725", "researcher": {"href": "https://publications.scilifelab.se/researcher/090cf8219ee047be97d9b75b104d8b7c.json"}}, {"family": "Sun", "given": "Li", "initials": "L"}, {"family": "Persson Waller", "given": "Karin", "initials": "K"}, {"family": "\u00d6stensson", "given": "Karin", "initials": "K"}, {"family": "McGuire", "given": "Mark", "initials": "M"}, {"family": "Agen\u00e4s", "given": "Sigrid", "initials": "S"}, {"family": "Dicksved", "given": "Johan", "initials": "J"}], "type": "journal article", "published": "2019-06-13", "journal": {"volume": "14", "issn": "1932-6203", "issue": "6", "pages": "e0218257", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "Discoveries of bacterial communities in environments that previously have been described as sterile have in recent years radically challenged the view of these environments. In this study we aimed to use 16S rRNA sequencing to describe the composition and temporal stability of the bacterial microbiota in bovine milk from healthy udder quarters, an environment previously believed to be sterile. Sequencing of the 16S rRNA gene is a technique commonly used to describe bacterial composition and diversity in various environments. With the increased use of 16S rRNA gene sequencing, awareness of methodological pitfalls such as biases and contamination has increased although not in equal amount. Evaluation of the composition and temporal stability of the microbiota in 288 milk samples was largely hampered by background contamination, despite careful and aseptic sample processing. Sequencing of no template control samples, positive control samples, with defined levels of bacteria, and 288 milk samples with various levels of bacterial growth, revealed that the data was influenced by contaminating taxa, primarily Methylobacterium. We observed an increasing impact of contamination with decreasing microbial biomass where the contaminating taxa became dominant in samples with less than 104 bacterial cells per mL. By applying a contamination filtration on the sequence data, the amount of sequences was substantially reduced but only a minor impact on number of identified taxa and by culture known endogenous taxa was observed. This suggests that data filtration can be useful for identifying biologically relevant associations in milk microbiota data.", "doi": "10.1371/journal.pone.0218257", "pmid": "31194836", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support and Infrastructure": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pii", "key": "PONE-D-18-29659"}, {"db": "pmc", "key": "PMC6564671"}], "notes": [], "created": "2019-12-03T10:48:01.523Z", "modified": "2021-06-21T10:00:19.458Z"}, {"entity": "publication", "iuid": "9a6efccfa136436c90bdc26ecf092c06", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9a6efccfa136436c90bdc26ecf092c06.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9a6efccfa136436c90bdc26ecf092c06"}}, "title": "The effect of Wolbachia on gene expression in Drosophila paulistorum and its implications for symbiont-induced host speciation.", "authors": [{"family": "Bai\u00e3o", "given": "Guilherme C", "initials": "GC"}, {"family": "Schneider", "given": "Daniela I", "initials": "DI"}, {"family": "Miller", "given": "Wolfgang J", "initials": "WJ"}, {"family": "Klasson", "given": "Lisa", "initials": "L", "orcid": "0000-0002-5874-7153", "researcher": {"href": "https://publications.scilifelab.se/researcher/409de77af489419db6d2b599b590d02f.json"}}], "type": "journal article", "published": "2019-06-07", "journal": {"volume": "20", "issn": "1471-2164", "issue": "1", "pages": "465", "title": "BMC Genomics", "issn-l": "1471-2164"}, "abstract": "The Neotropical fruit fly Drosophila paulistorum (Diptera: Drosophilidae) is a species complex in statu nascendi comprising six reproductively isolated semispecies, each harboring mutualistic Wolbachia strains. Although wild type flies of each semispecies are isolated from the others by both pre- and postmating incompatibilities, mating between semispecies and successful offspring development can be achieved once flies are treated with antibiotics to reduce Wolbachia titer. Here we use RNA-seq to study the impact of Wolbachia on D. paulistorum and investigate the hypothesis that the symbiont may play a role in host speciation. For that goal, we analyze samples of heads and abdomens of both sexes of the Amazonian, Centro American and Orinocan semispecies of D. paulistorum.\n\nWe identify between 175 and 1192 differentially expressed genes associated with a variety of biological processes that respond either globally or according to tissue, sex or condition in the three semispecies. Some of the functions associated with differentially expressed genes are known to be affected by Wolbachia in other species, such as metabolism and immunity, whereas others represent putative novel phenotypes involving muscular functions, pheromone signaling, and visual perception.\n\nOur results show that Wolbachia affect a large number of biological functions in D. paulistorum, particularly when present in high titer. We suggest that the significant metabolic impact of the infection on the host may cause several of the other putative and observed phenotypes. We also speculate that the observed differential expression of genes associated with chemical communication and reproduction may be associated with the emergence of pre- and postmating barriers between semispecies, which supports a role for Wolbachia in the speciation of D. paulistorum.", "doi": "10.1186/s12864-019-5816-9", "pmid": "31174466", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1186/s12864-019-5816-9"}, {"db": "pmc", "key": "PMC6555960"}], "notes": [], "created": "2020-01-08T12:42:20.556Z", "modified": "2021-06-16T14:45:31.213Z"}, {"entity": "publication", "iuid": "21965e21cdab4364bb6878e4fb8cd2dc", "links": {"self": {"href": "https://publications.scilifelab.se/publication/21965e21cdab4364bb6878e4fb8cd2dc.json"}, "display": {"href": "https://publications.scilifelab.se/publication/21965e21cdab4364bb6878e4fb8cd2dc"}}, "title": "Multiancestry Genome-Wide Association Study of Lipid Levels Incorporating Gene-Alcohol Interactions.", "authors": [{"family": "de Vries", "given": "Paul S", "initials": "PS"}, {"family": "Brown", "given": "Michael R", "initials": "MR"}, {"family": "Bentley", "given": "Amy R", "initials": "AR"}, {"family": "Sung", "given": "Yun J", "initials": "YJ"}, {"family": "Winkler", "given": "Thomas W", "initials": "TW"}, {"family": "Ntalla", "given": "Ioanna", "initials": "I"}, {"family": "Schwander", "given": "Karen", "initials": "K"}, {"family": "Kraja", "given": "Aldi T", "initials": "AT"}, {"family": "Guo", "given": "Xiuqing", "initials": "X"}, {"family": "Franceschini", "given": "Nora", "initials": "N"}, {"family": "Cheng", "given": "Ching-Yu", "initials": "CY"}, {"family": "Sim", "given": "Xueling", "initials": "X"}, {"family": "Vojinovic", "given": "Dina", "initials": "D"}, {"family": "Huffman", "given": "Jennifer E", "initials": "JE"}, {"family": "Musani", "given": "Solomon K", "initials": "SK"}, {"family": "Li", "given": "Changwei", "initials": "C"}, {"family": "Feitosa", "given": "Mary F", "initials": "MF"}, {"family": "Richard", "given": "Melissa A", "initials": "MA"}, {"family": "Noordam", "given": "Raymond", "initials": "R"}, {"family": "Aschard", "given": "Hugues", "initials": "H"}, {"family": "Bartz", "given": "Traci M", "initials": "TM"}, {"family": "Bielak", "given": "Lawrence F", "initials": "LF"}, {"family": "Deng", "given": "Xuan", "initials": "X"}, {"family": "Dorajoo", "given": "Rajkumar", "initials": "R"}, {"family": "Lohman", "given": "Kurt K", "initials": "KK"}, {"family": "Manning", "given": "Alisa K", "initials": "AK"}, {"family": "Rankinen", "given": "Tuomo", "initials": "T"}, {"family": "Smith", "given": "Albert V", "initials": "AV"}, {"family": "Tajuddin", "given": "Salman M", "initials": "SM"}, {"family": "Evangelou", "given": "Evangelos", "initials": "E"}, {"family": "Graff", "given": "Mariaelisa", "initials": "M"}, {"family": "Alver", "given": "Maris", "initials": "M"}, {"family": "Boissel", "given": "Mathilde", "initials": "M"}, {"family": "Chai", "given": "Jin Fang", "initials": "JF"}, {"family": "Chen", "given": "Xu", "initials": "X"}, {"family": "Divers", "given": "Jasmin", "initials": "J"}, {"family": "Gandin", "given": "Ilaria", "initials": "I"}, {"family": "Gao", "given": "Chuan", "initials": "C"}, {"family": "Goel", "given": "Anuj", "initials": "A"}, {"family": "Hagemeijer", "given": "Yanick", "initials": "Y"}, {"family": "Harris", "given": "Sarah E", "initials": "SE"}, {"family": "Hartwig", "given": "Fernando P", "initials": "FP"}, {"family": "He", "given": "Meian", "initials": "M"}, {"family": "Horimoto", "given": "Andrea R V R", "initials": "ARVR"}, {"family": "Hsu", "given": "Fang-Chi", "initials": "FC"}, {"family": "Jackson", "given": "Anne U", "initials": "AU"}, {"family": "Kasturiratne", "given": "Anuradhani", "initials": "A"}, {"family": "Komulainen", "given": "Pirjo", "initials": "P"}, {"family": "K\u00fchnel", "given": "Brigitte", "initials": "B"}, {"family": "Laguzzi", "given": "Federica", "initials": "F"}, {"family": "Lee", "given": "Joseph H", "initials": "JH"}, {"family": "Luan", "given": "Jian'an", "initials": "J"}, {"family": "Lyytik\u00e4inen", "given": "Leo-Pekka", "initials": "LP"}, {"family": "Matoba", "given": "Nana", "initials": "N"}, {"family": "Nolte", "given": "Ilja M", "initials": "IM"}, {"family": "Pietzner", "given": "Maik", "initials": "M"}, {"family": "Riaz", "given": "Muhammad", "initials": "M"}, {"family": "Said", "given": "M Abdullah", "initials": "MA"}, {"family": "Scott", "given": "Robert A", "initials": "RA"}, {"family": "Sofer", "given": "Tamar", "initials": "T"}, {"family": "Stan\u010d\u00e1kov\u00e1", "given": "Alena", "initials": "A"}, {"family": "Takeuchi", "given": "Fumihiko", "initials": "F"}, {"family": "Tayo", "given": "Bamidele O", "initials": "BO"}, {"family": "van der Most", "given": "Peter J", "initials": "PJ"}, {"family": "Varga", "given": "Tibor V", "initials": "TV"}, {"family": "Wang", "given": "Yajuan", "initials": "Y"}, {"family": "Ware", "given": "Erin B", "initials": "EB"}, {"family": "Wen", "given": "Wanqing", "initials": "W"}, {"family": "Yanek", "given": "Lisa R", "initials": "LR"}, {"family": "Zhang", "given": "Weihua", "initials": "W"}, {"family": "Zhao", "given": "Jing Hua", "initials": "JH"}, {"family": "Afaq", "given": "Saima", "initials": "S"}, {"family": "Amin", "given": "Najaf", "initials": "N"}, {"family": "Amini", "given": "Marzyeh", "initials": "M"}, {"family": "Arking", "given": "Dan E", "initials": "DE"}, {"family": "Aung", "given": "Tin", "initials": "T"}, {"family": "Ballantyne", "given": "Christie", "initials": "C"}, {"family": "Boerwinkle", "given": "Eric", "initials": "E"}, {"family": "Broeckel", "given": "Ulrich", "initials": "U"}, {"family": "Campbell", "given": "Archie", "initials": "A"}, {"family": "Canouil", "given": "Micka\u00ebl", "initials": "M"}, {"family": "Charumathi", "given": "Sabanayagam", "initials": "S"}, {"family": "Chen", "given": "Yii-Der Ida", "initials": "YI"}, {"family": "Connell", "given": "John M", "initials": "JM"}, {"family": "de Faire", "given": "Ulf", "initials": "U"}, {"family": "de Las Fuentes", "given": "Lisa", "initials": "L"}, {"family": "de Mutsert", "given": "Ren\u00e9e", "initials": "R"}, {"family": "de Silva", "given": "H Janaka", "initials": "HJ"}, {"family": "Ding", "given": "Jingzhong", "initials": "J"}, {"family": "Dominiczak", "given": "Anna F", "initials": "AF"}, {"family": "Duan", "given": "Qing", "initials": "Q"}, {"family": "Eaton", "given": "Charles B", "initials": "CB"}, {"family": "Eppinga", "given": "Ruben N", "initials": "RN"}, {"family": "Faul", "given": "Jessica D", "initials": "JD"}, {"family": "Fisher", "given": "Virginia", "initials": "V"}, {"family": "Forrester", "given": "Terrence", "initials": "T"}, {"family": "Franco", "given": "Oscar H", "initials": "OH"}, {"family": "Friedlander", "given": "Yechiel", "initials": "Y"}, {"family": "Ghanbari", "given": "Mohsen", "initials": "M"}, {"family": "Giulianini", "given": "Franco", "initials": "F"}, {"family": "Grabe", "given": "Hans J", "initials": "HJ"}, {"family": "Grove", "given": "Megan L", "initials": "ML"}, {"family": "Gu", "given": "C Charles", "initials": "CC"}, {"family": "Harris", "given": "Tamara B", "initials": "TB"}, {"family": "Heikkinen", "given": "Sami", "initials": "S"}, {"family": "Heng", "given": "Chew-Kiat", "initials": "CK"}, {"family": "Hirata", "given": "Makoto", "initials": "M"}, {"family": "Hixson", "given": "James E", "initials": "JE"}, {"family": "Howard", "given": "Barbara V", "initials": "BV"}, {"family": "Ikram", "given": "M Arfan", "initials": "MA"}, {"family": "InterAct Consortium", "given": "", "initials": ""}, {"family": "Jacobs", "given": "David R", "initials": "DR"}, {"family": "Johnson", "given": "Craig", "initials": "C"}, {"family": "Jonas", "given": "Jost Bruno", "initials": "JB"}, {"family": "Kammerer", "given": "Candace M", "initials": "CM"}, {"family": "Katsuya", "given": "Tomohiro", "initials": "T"}, {"family": "Khor", "given": "Chiea Chuen", "initials": "CC"}, {"family": "Kilpel\u00e4inen", "given": "Tuomas O", "initials": "TO"}, {"family": "Koh", "given": "Woon-Puay", "initials": "WP"}, {"family": "Koistinen", "given": "Heikki A", "initials": "HA"}, {"family": "Kolcic", "given": "Ivana", "initials": "I"}, {"family": "Kooperberg", "given": "Charles", "initials": "C"}, {"family": "Krieger", "given": "Jose E", "initials": "JE"}, {"family": "Kritchevsky", "given": "Steve B", "initials": "SB"}, {"family": "Kubo", "given": "Michiaki", "initials": "M"}, {"family": "Kuusisto", "given": "Johanna", "initials": "J"}, {"family": "Lakka", "given": "Timo A", "initials": "TA"}, {"family": "Langefeld", "given": "Carl D", "initials": "CD"}, {"family": "Langenberg", "given": "Claudia", "initials": "C"}, {"family": "Launer", "given": "Lenore J", "initials": "LJ"}, {"family": "Lehne", "given": "Benjamin", "initials": "B"}, {"family": "Lemaitre", "given": "Rozenn N", "initials": "RN"}, {"family": "Li", "given": "Yize", "initials": "Y"}, {"family": "Liang", "given": "Jingjing", "initials": "J"}, {"family": "Liu", "given": "Jianjun", "initials": "J"}, {"family": "Liu", "given": "Kiang", "initials": "K"}, {"family": "Loh", "given": "Marie", "initials": "M"}, {"family": "Louie", "given": "Tin", "initials": "T"}, {"family": "M\u00e4gi", "given": "Reedik", "initials": "R"}, {"family": "Manichaikul", "given": "Ani W", "initials": "AW"}, {"family": "McKenzie", "given": "Colin A", "initials": "CA"}, {"family": "Meitinger", "given": "Thomas", "initials": "T"}, {"family": "Metspalu", "given": "Andres", "initials": "A"}, {"family": "Milaneschi", "given": "Yuri", "initials": "Y"}, {"family": "Milani", "given": "Lili", "initials": "L"}, {"family": "Mohlke", "given": "Karen L", "initials": "KL"}, {"family": "Mosley", "given": "Thomas H", "initials": "TH"}, {"family": "Mukamal", "given": "Kenneth J", "initials": "KJ"}, {"family": "Nalls", "given": "Mike A", "initials": "MA"}, {"family": "Nauck", "given": "Matthias", "initials": "M"}, {"family": "Nelson", "given": "Christopher P", "initials": "CP"}, {"family": "Sotoodehnia", "given": "Nona", "initials": "N"}, {"family": "O'Connell", "given": "Jeff R", "initials": "JR"}, {"family": "Palmer", "given": "Nicholette D", "initials": "ND"}, {"family": "Pazoki", "given": "Raha", "initials": "R"}, {"family": "Pedersen", "given": "Nancy L", "initials": "NL"}, {"family": "Peters", "given": "Annette", "initials": "A"}, {"family": "Peyser", "given": "Patricia A", "initials": "PA"}, {"family": "Polasek", "given": "Ozren", "initials": "O"}, {"family": "Poulter", "given": "Neil", "initials": "N"}, {"family": "Raffel", "given": "Leslie J", "initials": "LJ"}, {"family": "Raitakari", "given": "Olli T", "initials": "OT"}, {"family": "Reiner", "given": "Alex P", "initials": "AP"}, {"family": "Rice", "given": "Treva K", "initials": "TK"}, {"family": "Rich", "given": "Stephen S", "initials": "SS"}, {"family": "Robino", "given": "Antonietta", "initials": "A"}, {"family": "Robinson", "given": "Jennifer G", "initials": "JG"}, {"family": "Rose", "given": "Lynda M", "initials": "LM"}, {"family": "Rudan", "given": "Igor", "initials": "I"}, {"family": "Schmidt", "given": "Carsten O", "initials": "CO"}, {"family": "Schreiner", "given": "Pamela J", "initials": "PJ"}, {"family": "Scott", "given": "William R", "initials": "WR"}, {"family": "Sever", "given": "Peter", "initials": "P"}, {"family": "Shi", "given": "Yuan", "initials": "Y"}, {"family": "Sidney", "given": "Stephen", "initials": "S"}, {"family": "Sims", "given": "Mario", "initials": "M"}, {"family": "Smith", "given": "Blair H", "initials": "BH"}, {"family": "Smith", "given": "Jennifer A", "initials": "JA"}, {"family": "Snieder", "given": "Harold", "initials": "H"}, {"family": "Starr", "given": "John M", "initials": "JM"}, {"family": "Strauch", "given": "Konstantin", "initials": "K"}, {"family": "Tan", "given": "Nicholas", "initials": "N"}, {"family": "Taylor", "given": "Kent D", "initials": "KD"}, {"family": "Teo", "given": "Yik Ying", "initials": "YY"}, {"family": "Tham", "given": "Yih Chung", "initials": "YC"}, {"family": "Uitterlinden", "given": "Andr\u00e9 G", "initials": "AG"}, {"family": "van Heemst", "given": "Diana", "initials": "D"}, {"family": "Vuckovic", "given": "Dragana", "initials": "D"}, {"family": "Waldenberger", "given": "Melanie", "initials": "M"}, {"family": "Wang", "given": "Lihua", "initials": "L"}, {"family": "Wang", "given": "Yujie", "initials": "Y"}, {"family": "Wang", "given": "Zhe", "initials": "Z"}, {"family": "Wei", "given": "Wen Bin", "initials": "WB"}, {"family": "Williams", "given": "Christine", "initials": "C"}, {"family": "Wilson", "given": "Gregory", "initials": "G"}, {"family": "Wojczynski", "given": "Mary K", "initials": "MK"}, {"family": "Yao", "given": "Jie", "initials": "J"}, {"family": "Yu", "given": "Bing", "initials": "B"}, {"family": "Yu", "given": "Caizheng", "initials": "C"}, {"family": "Yuan", "given": "Jian-Min", "initials": "JM"}, {"family": "Zhao", "given": "Wei", "initials": "W"}, {"family": "Zonderman", "given": "Alan B", "initials": "AB"}, {"family": "Becker", "given": "Diane M", "initials": "DM"}, {"family": "Boehnke", "given": "Michael", "initials": "M"}, {"family": "Bowden", "given": "Donald W", "initials": "DW"}, {"family": "Chambers", "given": "John C", "initials": "JC"}, {"family": "Deary", "given": "Ian J", "initials": "IJ"}, {"family": "Esko", "given": "T\u00f5nu", "initials": "T"}, {"family": "Farrall", "given": "Martin", "initials": "M"}, {"family": "Franks", "given": "Paul W", "initials": "PW"}, {"family": "Freedman", "given": "Barry I", "initials": "BI"}, {"family": "Froguel", "given": "Philippe", "initials": "P"}, {"family": "Gasparini", "given": "Paolo", "initials": "P"}, {"family": "Gieger", "given": "Christian", "initials": "C"}, {"family": "Horta", "given": "Bernardo L", "initials": "BL"}, {"family": "Kamatani", "given": "Yoichiro", "initials": "Y"}, {"family": "Kato", "given": "Norihiro", "initials": "N"}, {"family": "Kooner", "given": "Jaspal S", "initials": "JS"}, {"family": "Laakso", "given": "Markku", "initials": "M"}, {"family": "Leander", "given": "Karin", "initials": "K"}, {"family": "Lehtim\u00e4ki", "given": "Terho", "initials": "T"}, {"family": "Lifelines Cohort, Groningen, The Netherlands (Lifelines Cohort Study)", "given": "", "initials": ""}, {"family": "Magnusson", "given": "Patrik K E", "initials": "PKE"}, {"family": "Penninx", "given": "Brenda", "initials": "B"}, {"family": "Pereira", "given": "Alexandre C", "initials": "AC"}, {"family": "Rauramaa", "given": "Rainer", "initials": "R"}, {"family": "Samani", "given": "Nilesh J", "initials": "NJ"}, {"family": "Scott", "given": "James", "initials": "J"}, {"family": "Shu", "given": "Xiao-Ou", "initials": "XO"}, {"family": "van der Harst", "given": "Pim", "initials": "P"}, {"family": "Wagenknecht", "given": "Lynne E", "initials": "LE"}, {"family": "Wang", "given": "Ya Xing", "initials": "YX"}, {"family": "Wareham", "given": "Nicholas J", "initials": "NJ"}, {"family": "Watkins", "given": "Hugh", "initials": "H"}, {"family": "Weir", "given": "David R", "initials": "DR"}, {"family": "Wickremasinghe", "given": "Ananda R", "initials": "AR"}, {"family": "Zheng", "given": "Wei", "initials": "W"}, {"family": "Elliott", "given": "Paul", "initials": "P"}, {"family": "North", "given": "Kari E", "initials": "KE"}, {"family": "Bouchard", "given": "Claude", "initials": "C"}, {"family": "Evans", "given": "Michele K", "initials": "MK"}, {"family": "Gudnason", "given": "Vilmundur", "initials": "V"}, {"family": "Liu", "given": "Ching-Ti", "initials": "CT"}, {"family": "Liu", "given": "Yongmei", "initials": "Y"}, {"family": "Psaty", "given": "Bruce M", "initials": "BM"}, {"family": "Ridker", "given": "Paul M", "initials": "PM"}, {"family": "van Dam", "given": "Rob M", "initials": "RM"}, {"family": "Kardia", "given": "Sharon L R", "initials": "SLR"}, {"family": "Zhu", "given": "Xiaofeng", "initials": "X"}, {"family": "Rotimi", "given": "Charles N", "initials": "CN"}, {"family": "Mook-Kanamori", "given": "Dennis O", "initials": "DO"}, {"family": "Fornage", "given": "Myriam", "initials": "M"}, {"family": "Kelly", "given": "Tanika N", "initials": "TN"}, {"family": "Fox", "given": "Ervin R", "initials": "ER"}, {"family": "Hayward", "given": "Caroline", "initials": "C"}, {"family": "van Duijn", "given": "Cornelia M", "initials": "CM"}, {"family": "Tai", "given": "E Shyong", "initials": "ES"}, {"family": "Wong", "given": "Tien Yin", "initials": "TY"}, {"family": "Liu", "given": "Jingmin", "initials": "J"}, {"family": "Rotter", "given": "Jerome I", "initials": "JI"}, {"family": "Gauderman", "given": "W James", "initials": "WJ"}, {"family": "Province", "given": "Michael A", "initials": "MA"}, {"family": "Munroe", "given": "Patricia B", "initials": "PB"}, {"family": "Rice", "given": "Kenneth", "initials": "K"}, {"family": "Chasman", "given": "Daniel I", "initials": "DI"}, {"family": "Cupples", "given": "L Adrienne", "initials": "LA"}, {"family": "Rao", "given": "Dabeeru C", "initials": "DC"}, {"family": "Morrison", "given": "Alanna C", "initials": "AC"}], "type": "journal article", "published": "2019-06-01", "journal": {"volume": "188", "issn": "1476-6256", "issue": "6", "pages": "1033-1054", "title": "Am. J. Epidemiol.", "issn-l": "0002-9262"}, "abstract": "A person's lipid profile is influenced by genetic variants and alcohol consumption, but the contribution of interactions between these exposures has not been studied. We therefore incorporated gene-alcohol interactions into a multiancestry genome-wide association study of levels of high-density lipoprotein cholesterol, low-density lipoprotein cholesterol, and triglycerides. We included 45 studies in stage 1 (genome-wide discovery) and 66 studies in stage 2 (focused follow-up), for a total of 394,584 individuals from 5 ancestry groups. Analyses covered the period July 2014-November 2017. Genetic main effects and interaction effects were jointly assessed by means of a 2-degrees-of-freedom (df) test, and a 1-df test was used to assess the interaction effects alone. Variants at 495 loci were at least suggestively associated (P < 1 \u00d7 10-6) with lipid levels in stage 1 and were evaluated in stage 2, followed by combined analyses of stage 1 and stage 2. In the combined analysis of stages 1 and 2, a total of 147 independent loci were associated with lipid levels at P < 5 \u00d7 10-8 using 2-df tests, of which 18 were novel. No genome-wide-significant associations were found testing the interaction effect alone. The novel loci included several genes (proprotein convertase subtilisin/kexin type 5 (PCSK5), vascular endothelial growth factor B (VEGFB), and apolipoprotein B mRNA editing enzyme, catalytic polypeptide 1 (APOBEC1) complementation factor (A1CF)) that have a putative role in lipid metabolism on the basis of existing evidence from cellular and experimental models.", "doi": "10.1093/aje/kwz005", "pmid": "30698716", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "5304469"}, {"db": "pmc", "key": "PMC6545280"}], "notes": [], "created": "2019-06-04T12:49:03.425Z", "modified": "2021-06-21T10:01:42.219Z"}, {"entity": "publication", "iuid": "39682f91aeb14ea7b76502635c21251f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/39682f91aeb14ea7b76502635c21251f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/39682f91aeb14ea7b76502635c21251f"}}, "title": "Integrated epigenomic and transcriptomic analysis reveals TP63 as a novel player in clinically aggressive chronic lymphocytic leukemia.", "authors": [{"family": "Papakonstantinou", "given": "Nikos", "initials": "N"}, {"family": "Ntoufa", "given": "Stavroula", "initials": "S"}, {"family": "Tsagiopoulou", "given": "Maria", "initials": "M"}, {"family": "Moysiadis", "given": "Theodoros", "initials": "T"}, {"family": "Bhoi", "given": "Sujata", "initials": "S"}, {"family": "Malousi", "given": "Andigoni", "initials": "A"}, {"family": "Psomopoulos", "given": "Fotis", "initials": "F"}, {"family": "Mansouri", "given": "Larry", "initials": "L"}, {"family": "Laidou", "given": "Stamatia", "initials": "S"}, {"family": "Papazoglou", "given": "Despoina", "initials": "D"}, {"family": "Gounari", "given": "Maria", "initials": "M"}, {"family": "Pasentsis", "given": "Konstantinos", "initials": "K"}, {"family": "Plevova", "given": "Karla", "initials": "K"}, {"family": "Kuci-Emruli", "given": "Venera", "initials": "V"}, {"family": "Duran-Ferrer", "given": "Marti", "initials": "M"}, {"family": "Davis", "given": "Zadie", "initials": "Z"}, {"family": "Ek", "given": "Sara", "initials": "S"}, {"family": "Rossi", "given": "Davide", "initials": "D"}, {"family": "Gaidano", "given": "Gianluca", "initials": "G"}, {"family": "Ritgen", "given": "Matthias", "initials": "M"}, {"family": "Oscier", "given": "David", "initials": "D"}, {"family": "Stavroyianni", "given": "Niki", "initials": "N"}, {"family": "Pospisilova", "given": "Sarka", "initials": "S"}, {"family": "Davi", "given": "Frederic", "initials": "F"}, {"family": "Ghia", "given": "Paolo", "initials": "P"}, {"family": "Hadzidimitriou", "given": "Anastasia", "initials": "A"}, {"family": "Belessi", "given": "Chrysoula", "initials": "C"}, {"family": "Martin-Subero", "given": "Jose I", "initials": "JI"}, {"family": "Pott", "given": "Christiane", "initials": "C"}, {"family": "Rosenquist", "given": "Richard", "initials": "R"}, {"family": "Stamatopoulos", "given": "Kostas", "initials": "K", "orcid": "0000-0001-8529-640X", "researcher": {"href": "https://publications.scilifelab.se/researcher/772756566c154559b2c70c8f0f44d1ad.json"}}], "type": "journal article", "published": "2019-06-01", "journal": {"volume": "144", "issn": "1097-0215", "issue": "11", "pages": "2695-2706", "title": "Int. J. Cancer", "issn-l": "0020-7136"}, "abstract": "Chronic lymphocytic leukemia (CLL) stereotyped subsets #6 and #8 include cases expressing unmutated B cell receptor immunoglobulin (BcR IG) (U-CLL). Subset #6 (IGHV1-69/IGKV3-20) is less aggressive compared to subset #8 (IGHV4-39/IGKV1(D)-39) which has the highest risk for Richter's transformation among all CLL. The underlying reasons for this divergent clinical behavior are not fully elucidated. To gain insight into this issue, here we focused on epigenomic signatures and their links with gene expression, particularly investigating genome-wide DNA methylation profiles in subsets #6 and #8 as well as other U-CLL cases not expressing stereotyped BcR IG. We found that subset #8 showed a distinctive DNA methylation profile compared to all other U-CLL cases, including subset #6. Integrated analysis of DNA methylation and gene expression revealed significant correlation for several genes, particularly highlighting a relevant role for the TP63 gene which was hypomethylated and overexpressed in subset #8. This observation was validated by quantitative PCR, which also revealed TP63 mRNA overexpression in additional nonsubset U-CLL cases. BcR stimulation had distinct effects on p63 protein expression, particularly leading to induction in subset #8, accompanied by increased CLL cell survival. This pro-survival effect was also supported by siRNA-mediated downregulation of p63 expression resulting in increased apoptosis. In conclusion, we report that DNA methylation profiles may vary even among CLL patients with similar somatic hypermutation status, supporting a compartmentalized approach to dissecting CLL biology. Furthermore, we highlight p63 as a novel prosurvival factor in CLL, thus identifying another piece of the complex puzzle of clinical aggressiveness.", "doi": "10.1002/ijc.31999", "pmid": "30447004", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [], "notes": [], "created": "2019-01-14T11:51:16.832Z", "modified": "2021-06-21T14:00:35.291Z"}, {"entity": "publication", "iuid": "8152d181864c494abdbe3a682fce8e68", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8152d181864c494abdbe3a682fce8e68.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8152d181864c494abdbe3a682fce8e68"}}, "title": "Identification of DNA methylation patterns predisposing for an efficient response to BCG vaccination in healthy BCG-na\u00efve subjects.", "authors": [{"family": "Das", "given": "Jyotirmoy", "initials": "J"}, {"family": "Verma", "given": "Deepti", "initials": "D"}, {"family": "Gustafsson", "given": "Mika", "initials": "M"}, {"family": "Lerm", "given": "Maria", "initials": "M"}], "type": "journal article", "published": "2019-06-00", "journal": {"volume": "14", "issn": "1559-2308", "issue": "6", "pages": "589-601", "title": "Epigenetics", "issn-l": "1559-2294"}, "abstract": "The protection against tuberculosis induced by the Bacille Calmette Gu\u00e9rin (BCG) vaccine is unpredictable. In our previous study, altered DNA methylation pattern in peripheral blood mononuclear cells (PBMCs) in response to BCG was observed in a subgroup of individuals, whose macrophages killed mycobacteria effectively ('responders'). These macrophages also showed production of Interleukin-1\u03b2 (IL-1\u03b2) in response to mycobacterial stimuli before vaccination. Here, we hypothesized that the propensity to respond to the BCG vaccine is reflected in the DNA methylome. We mapped the differentially methylated genes (DMGs) in PBMCs isolated from responders/non-responders at the time point before vaccination aiming to identify possible predictors of BCG responsiveness. We identified 43 DMGs and subsequent bioinformatic analyses showed that these were enriched for actin-modulating pathways, predicting differences in phagocytosis. This could be validated by experiments showing that phagocytosis of mycobacteria, which is an event preceding mycobacteria-induced IL-1\u03b2 production, was strongly correlated with the DMG pattern.", "doi": "10.1080/15592294.2019.1603963", "pmid": "31010371", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC6557603"}], "notes": [], "created": "2019-09-16T11:35:20.505Z", "modified": "2024-01-16T13:48:44.266Z"}, {"entity": "publication", "iuid": "375ef3c718aa48ee9437ba0daea30a63", "links": {"self": {"href": "https://publications.scilifelab.se/publication/375ef3c718aa48ee9437ba0daea30a63.json"}, "display": {"href": "https://publications.scilifelab.se/publication/375ef3c718aa48ee9437ba0daea30a63"}}, "title": "Genetic basis of amphibian larval development along a latitudinal gradient: Gene diversity, selection and links with phenotypic variation in transcription factor C/EBP-1.", "authors": [{"family": "Meyer-Lucht", "given": "Yvonne", "initials": "Y"}, {"family": "Luquet", "given": "Emilien", "initials": "E"}, {"family": "J\u00f3hannesd\u00f3ttir", "given": "Fr\u00ed\u00f0a", "initials": "F"}, {"family": "R\u00f6din-M\u00f6rch", "given": "Patrik", "initials": "P", "orcid": "0000-0001-6737-1488", "researcher": {"href": "https://publications.scilifelab.se/researcher/9e6abe040b284d67b11f45db1e58540e.json"}}, {"family": "Quintela", "given": "Mar\u00eda", "initials": "M"}, {"family": "Richter-Boix", "given": "Alex", "initials": "A"}, {"family": "H\u00f6glund", "given": "Jacob", "initials": "J", "orcid": "0000-0002-5840-779X", "researcher": {"href": "https://publications.scilifelab.se/researcher/8e1eb3c1903f4a97a4c585a2dee3b05f.json"}}, {"family": "Laurila", "given": "Anssi", "initials": "A", "orcid": "0000-0001-8090-3776", "researcher": {"href": "https://publications.scilifelab.se/researcher/1b55d6c459ef448c992a37db2a02c3ea.json"}}], "type": "journal article", "published": "2019-06-00", "journal": {"volume": "28", "issn": "1365-294X", "issue": "11", "pages": "2786-2801", "title": "Mol. Ecol.", "issn-l": "0962-1083"}, "abstract": "Ectotherm development rates often show adaptive divergence along climatic gradients, but the genetic basis for this variation is rarely studied. Here, we investigated the genetic basis for phenotypic variation in larval development in the moor frog Rana arvalis from five regions along a latitudinal gradient from Germany to northern Sweden. We focused on the C/EBP-1 gene, a transcription factor associated with larval development time. Allele frequencies at C/EBP-1 varied strongly among geographical regions. Overall, the distribution of alleles along the gradient was in concordance with the dual post-glacial colonization routes into Scandinavia, with a large number of alleles exclusively present along the southern colonization route. Only three of 38 alleles were shared between the routes. Analysis of contemporary selection on C/EBP-1 showed divergent selection among the regions, probably reflecting adaptation to the local environmental conditions, although this was especially strong between southern and northern regions coinciding also with lineages from different colonization routes. Overall, the C/EBP-1 gene has historically been under purifying selection, but two specific amino acid positions showed significant signals of positive selection. These positions showed divergence between southern and northern regions, and we suggest that they are functionally involved in the climatic adaptation of larval development. Using phenotypic data from a common garden experiment, we found evidence for specific C/EBP-1 alleles being correlated with larval development time, suggesting a functional role in adaptation of larval development to large-scale climatic variation.", "doi": "10.1111/mec.15123", "pmid": "31067349", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "GENBANK", "key": "U08604"}], "notes": [], "created": "2020-01-08T12:41:31.365Z", "modified": "2021-06-21T10:00:30.637Z"}, {"entity": "publication", "iuid": "3dd8803d595e43daa91b232ed5fd011f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3dd8803d595e43daa91b232ed5fd011f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3dd8803d595e43daa91b232ed5fd011f"}}, "title": "Detecting selection signatures in three Iranian sheep breeds.", "authors": [{"family": "Manzari", "given": "Z", "initials": "Z"}, {"family": "Mehrabani-Yeganeh", "given": "H", "initials": "H"}, {"family": "Nejati-Javaremi", "given": "A", "initials": "A"}, {"family": "Moradi", "given": "M H", "initials": "MH"}, {"family": "Gholizadeh", "given": "M", "initials": "M"}], "type": "journal article", "published": "2019-06-00", "journal": {"volume": "50", "issn": "1365-2052", "issue": "3", "pages": "298-302", "title": "Anim Genet", "issn-l": "0268-9146"}, "abstract": "The objective of genome mapping is to achieve valuable insight into the connection between gene variants (genotype) and observed traits (phenotype). Part of that objective is to understand the selective forces that have operated on a population. Finding links between genotype-phenotype changes makes it possible to identify selective sweeps by patterns of genetic variation and linkage disequilibrium. Based on Illumina 50KSNP chip data, two approaches, XP-EHH (cross-population extend haplotype homozygosity) and F ST (fixation index), were carried out in this research to identify selective sweeps in the genome of three Iranian local sheep breeds: Baluchi (n = 86), Lori-Bakhtiari (n = 45) and Zel (n = 45). Using both methods, 93 candidate genomic regions were identified as harboring putative selective sweeps. Bioinformatics analysis of the genomic regions showed that signatures of selection related to multiple candidate genes, such as HOXB9, HOXB13, ACAN, NPR2, TRIL, AOX1, CSF2, GHR, TNS2, SPAG8, HINT2, ALS2, AAAS, RARG, SYCP2, CAV1, PPP1R3D, PLA2G7, TTLL7 and C20orf10, that play a role in skeletal system and tail, sugar and energy metabolisms, growth, reproduction, immune and nervous system traits. Our findings indicated diverse genomic selection during the domestication of Iranian sheep breeds.", "doi": "10.1111/age.12772", "pmid": "30883840", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [], "notes": [], "created": "2019-04-12T14:00:39.415Z", "modified": "2021-06-21T13:28:49.858Z"}, {"entity": "publication", "iuid": "dbadcc071c0e4f37b4c693355956164f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/dbadcc071c0e4f37b4c693355956164f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/dbadcc071c0e4f37b4c693355956164f"}}, "title": "Can markers of biological age predict dependency in old age?", "authors": [{"family": "Jylh\u00e4v\u00e4", "given": "Juulia", "initials": "J"}, {"family": "Jiang", "given": "Miao", "initials": "M"}, {"family": "Foebel", "given": "Andrea D", "initials": "AD"}, {"family": "Pedersen", "given": "Nancy L", "initials": "NL"}, {"family": "H\u00e4gg", "given": "Sara", "initials": "S"}], "type": "journal article", "published": "2019-06-00", "journal": {"volume": "20", "issn": "1573-6768", "issue": "3", "pages": "321-329", "title": "Biogerontology", "issn-l": "1389-5729"}, "abstract": "Recent research has shown that markers of biological age, such as leukocyte telomere length (LTL), epigenetic clocks and the frailty index (FI) are predictive of mortality and age-related diseases. However, whether these markers associate with the need for care in old age, thereby having utility in reflecting dependency, is unclear. This study was undertaken to analyze whether LTL, two epigenetic clocks-the DNA methylation age (DNAmAge) and DNAm PhenoAge-and the FI are associated with the need for regular care in up to 604 individuals (aged 48-94\u00a0years) participating in the Swedish Adoption/Twin Study of Aging. Need for regular care was defined as receiving formal or informal help in daily routines at least once per week. Logistic regression adjusted for age, sex and education was used in the analysis. The predictive accuracies, assessed as the area under the curve (AUC) for the significant biological age measures were further compared to the accuracies of the limitations in activities of daily living (ADL) and instrumental ADL (IADL). Neither LTL nor the epigenetic clocks were associated with the need for care, whereas the FI was; odds ratio for 10% increase in FI 3.54 (95% confidence interval 2.32-5.41). The FI also demonstrated higher predictive accuracy than the ADL score (FI AUC 0.80 vs. ADL score AUC 0.62; p\u2009<\u20090.001 for equality of the AUCs), whereas the difference between FI AUC (0.80) and IADL score AUC (0.75) was not significant (p\u2009=\u20090.238). The FI might thus be a useful marker for the need for care.", "doi": "10.1007/s10522-019-09795-5", "pmid": "30666568", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1007/s10522-019-09795-5"}, {"db": "pmc", "key": "PMC6535415"}], "notes": [], "created": "2019-09-17T16:24:29.825Z", "modified": "2024-01-16T13:48:44.296Z"}, {"entity": "publication", "iuid": "a212f36b24ed408086fd6d1b5ab1eab5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a212f36b24ed408086fd6d1b5ab1eab5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a212f36b24ed408086fd6d1b5ab1eab5"}}, "title": "A catalog of genetic loci associated with kidney function from analyses of a million individuals.", "authors": [{"family": "Wuttke", "given": "Matthias", "initials": "M", "orcid": "0000-0003-3420-5082", "researcher": {"href": "https://publications.scilifelab.se/researcher/591c3f2263ba45feb7b31364f622f87a.json"}}, {"family": "Li", "given": "Yong", "initials": "Y", "orcid": "0000-0003-2651-8791", "researcher": {"href": "https://publications.scilifelab.se/researcher/1c15132ea27d43a097e4f2672f5b00ce.json"}}, {"family": "Li", "given": "Man", "initials": "M", "orcid": "0000-0002-3839-0281", "researcher": {"href": "https://publications.scilifelab.se/researcher/42c39506589c43b783f9e00c32882045.json"}}, {"family": "Sieber", "given": "Karsten B", "initials": "KB"}, {"family": "Feitosa", "given": "Mary F", "initials": "MF", "orcid": "0000-0002-0933-2410", "researcher": {"href": "https://publications.scilifelab.se/researcher/6e386c235834430eafaaca06e312aeb8.json"}}, {"family": "Gorski", "given": "Mathias", "initials": "M"}, {"family": "Tin", "given": "Adrienne", "initials": "A", "orcid": "0000-0002-4207-5866", "researcher": {"href": 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"Afaq", "given": "Saima", "initials": "S"}, {"family": "Ahluwalia", "given": "Tarunveer S", "initials": "TS"}, {"family": "Almgren", "given": "Peter", "initials": "P", "orcid": "0000-0002-0473-0241", "researcher": {"href": "https://publications.scilifelab.se/researcher/8c1a61189c4846eaa1de74d1fd79c8bb.json"}}, {"family": "Amin", "given": "Najaf", "initials": "N"}, {"family": "\u00c4rnl\u00f6v", "given": "Johan", "initials": "J"}, {"family": "Bakker", "given": "Stephan J L", "initials": "SJL"}, {"family": "Bansal", "given": "Nisha", "initials": "N"}, {"family": "Baptista", "given": "Daniela", "initials": "D"}, {"family": "Bergmann", "given": "Sven", "initials": "S", "orcid": "0000-0002-6785-9034", "researcher": {"href": "https://publications.scilifelab.se/researcher/07785d6cc5af460ca1901fe3819808fa.json"}}, {"family": "Biggs", "given": "Mary L", "initials": "ML"}, {"family": "Biino", "given": "Ginevra", "initials": "G", "orcid": "0000-0002-9936-946X", "researcher": {"href": 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"orcid": "0000-0003-1924-1202", "researcher": {"href": "https://publications.scilifelab.se/researcher/abe3ddd140b3478485f44119d18926b7.json"}}, {"family": "Butterworth", "given": "Adam S", "initials": "AS", "orcid": "0000-0002-6915-9015", "researcher": {"href": "https://publications.scilifelab.se/researcher/7b8c140c80d942c4b1b684876e4d6180.json"}}, {"family": "Campana", "given": "Eric", "initials": "E"}, {"family": "Campbell", "given": "Archie", "initials": "A", "orcid": "0000-0003-0198-5078", "researcher": {"href": "https://publications.scilifelab.se/researcher/89d6b9cb975246e5aa97c60035e2fdcc.json"}}, {"family": "Campbell", "given": "Harry", "initials": "H"}, {"family": "Canouil", "given": "Micka\u00ebl", "initials": "M", "orcid": "0000-0002-3396-4549", "researcher": {"href": "https://publications.scilifelab.se/researcher/d2bc5739e8e84ae08577977a71dd9b20.json"}}, {"family": "Carroll", "given": "Robert J", "initials": "RJ"}, {"family": "Catamo", "given": "Eulalia", "initials": "E"}, {"family": "Chambers", "given": "John C", "initials": "JC"}, {"family": "Chee", "given": "Miao-Ling", "initials": "ML"}, {"family": "Chee", "given": "Miao-Li", "initials": "ML"}, {"family": "Chen", "given": "Xu", "initials": "X", "orcid": "0000-0002-7299-3238", "researcher": {"href": "https://publications.scilifelab.se/researcher/9d354d5ca83c4059b8151c8e67b99405.json"}}, {"family": "Cheng", "given": "Ching-Yu", "initials": "CY"}, {"family": "Cheng", "given": "Yurong", "initials": "Y"}, {"family": "Christensen", "given": "Kaare", "initials": "K", "orcid": "0000-0002-5429-5292", "researcher": {"href": "https://publications.scilifelab.se/researcher/e79ea43d09544efc95351b52ac682910.json"}}, {"family": "Cifkova", "given": "Renata", "initials": "R"}, {"family": "Ciullo", "given": "Marina", "initials": "M"}, {"family": "Concas", "given": "Maria Pina", "initials": "MP", "orcid": "0000-0003-3598-2537", "researcher": {"href": 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"TB"}, {"family": "Hartman", "given": "Catharina A", "initials": "CA"}, {"family": "Hayward", "given": "Caroline", "initials": "C", "orcid": "0000-0002-9405-9550", "researcher": {"href": "https://publications.scilifelab.se/researcher/cd49e9ad5a024c7ca2f1aa97d9e58eba.json"}}, {"family": "Hellwege", "given": "Jacklyn N", "initials": "JN", "orcid": "0000-0001-7479-0920", "researcher": {"href": "https://publications.scilifelab.se/researcher/b9f81a674dae412bbd952bafdaa24a1a.json"}}, {"family": "Heng", "given": "Chew-Kiat", "initials": "CK", "orcid": "0000-0002-7309-9473", "researcher": {"href": "https://publications.scilifelab.se/researcher/a4e206bc73574cc1bcb4a9eb6c678d64.json"}}, {"family": "Hicks", "given": "Andrew A", "initials": "AA", "orcid": "0000-0001-6320-0411", "researcher": {"href": "https://publications.scilifelab.se/researcher/a679db3cfdb6408b8f1a009534d7b902.json"}}, {"family": "Hofer", "given": "Edith", "initials": "E"}, {"family": "Huang", "given": "Wei", "initials": "W"}, 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"https://publications.scilifelab.se/researcher/df3f5b6e8cb7470c880cff6dc960f283.json"}}, {"family": "Heid", "given": "Iris M", "initials": "IM"}, {"family": "Scholz", "given": "Markus", "initials": "M", "orcid": "0000-0002-4059-1779", "researcher": {"href": "https://publications.scilifelab.se/researcher/53d7b0e2dcdb4361b54016cb1550c5fe.json"}}, {"family": "Teumer", "given": "Alexander", "initials": "A", "orcid": "0000-0002-8309-094X", "researcher": {"href": "https://publications.scilifelab.se/researcher/dc9c2667a55b47a6a08aea764fab0946.json"}}, {"family": "K\u00f6ttgen", "given": "Anna", "initials": "A", "orcid": "0000-0002-4671-3714", "researcher": {"href": "https://publications.scilifelab.se/researcher/fe4cb85a14da4db6bc932a8bc4148efb.json"}}, {"family": "Pattaro", "given": "Cristian", "initials": "C", "orcid": "0000-0002-4119-0109", "researcher": {"href": "https://publications.scilifelab.se/researcher/3a6a570bbec647b188c4a7a5da03caac.json"}}], "type": "journal article", "published": "2019-06-00", "journal": {"volume": "51", "issn": "1546-1718", "issue": "6", "pages": "957-972", "title": "Nat. Genet.", "issn-l": "1061-4036"}, "abstract": "Chronic kidney disease (CKD) is responsible for a public health burden with multi-systemic complications. Through trans-ancestry meta-analysis of genome-wide association studies of estimated glomerular filtration rate (eGFR) and independent replication (n = 1,046,070), we identified 264 associated loci (166 new). Of these, 147 were likely to be relevant for kidney function on the basis of associations with the alternative kidney function marker blood urea nitrogen (n = 416,178). Pathway and enrichment analyses, including mouse models with renal phenotypes, support the kidney as the main target organ. A genetic risk score for lower eGFR was associated with clinically diagnosed CKD in 452,264 independent individuals. Colocalization analyses of associations with eGFR among 783,978 European-ancestry individuals and gene expression across 46 human tissues, including tubulo-interstitial and glomerular kidney compartments, identified 17 genes differentially expressed in kidney. Fine-mapping highlighted missense driver variants in 11 genes and kidney-specific regulatory variants. These results provide a comprehensive priority list of molecular targets for translational research.", "doi": "10.1038/s41588-019-0407-x", "pmid": "31152163", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41588-019-0407-x"}, {"db": "pmc", "key": "PMC6698888"}, {"db": "mid", "key": "NIHMS1038587"}], "notes": [], "created": "2019-06-04T12:49:02.356Z", "modified": "2021-06-21T11:50:41.587Z"}, {"entity": "publication", "iuid": "5c89b2604ecd4e0eb9cbc8a13f7b3b5a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5c89b2604ecd4e0eb9cbc8a13f7b3b5a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5c89b2604ecd4e0eb9cbc8a13f7b3b5a"}}, "title": "Genetic variation in CADM2 as a link between psychological traits and obesity.", "authors": [{"family": "Morris", "given": "Julia", "initials": "J"}, {"family": "Bailey", "given": "Mark E S", "initials": "MES", "orcid": "0000-0002-9788-2278", "researcher": {"href": "https://publications.scilifelab.se/researcher/3919edd84f254870a5644770152360b6.json"}}, {"family": "Baldassarre", "given": "Damiano", "initials": "D"}, {"family": "Cullen", "given": "Breda", "initials": "B", "orcid": "0000-0002-7259-9505", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff824f9a62154c718c075ad56b01177b.json"}}, {"family": "de Faire", "given": "Ulf", "initials": "U"}, {"family": "Ferguson", "given": "Amy", "initials": "A"}, {"family": "Gigante", "given": "Bruna", "initials": "B", "orcid": "0000-0003-4508-7990", "researcher": {"href": "https://publications.scilifelab.se/researcher/3ac1bdc52e3241ea9eb5645f603229a3.json"}}, {"family": "Giral", "given": "Philippe", "initials": "P"}, {"family": "Goel", "given": "Anuj", "initials": "A"}, {"family": "Graham", "given": "Nicholas", "initials": "N"}, {"family": "Hamsten", "given": "Anders", "initials": "A"}, {"family": "Humphries", "given": "Steve E", "initials": "SE"}, {"family": "Johnston", "given": "Keira J A", "initials": "KJA", "orcid": "0000-0002-1370-3149", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff151def49174d388b1b3e8619c2b329.json"}}, {"family": "Lyall", "given": "Donald M", "initials": "DM", "orcid": "0000-0003-3850-1487", "researcher": {"href": "https://publications.scilifelab.se/researcher/f1b08351693e4fb5b387edd6d9a9d347.json"}}, {"family": "Lyall", "given": "Laura M", "initials": "LM"}, {"family": "Sennblad", "given": "Bengt", "initials": "B"}, {"family": "Silveira", "given": "Angela", "initials": "A"}, {"family": "Smit", "given": "Andries J", "initials": "AJ"}, {"family": "Tremoli", "given": "Elena", "initials": "E"}, {"family": "Veglia", "given": "Fabrizio", "initials": "F"}, {"family": "Ward", "given": "Joey", "initials": "J"}, {"family": "Watkins", "given": "Hugh", "initials": "H"}, {"family": "Smith", "given": "Daniel J", "initials": "DJ", "orcid": "0000-0002-2267-1951", "researcher": {"href": "https://publications.scilifelab.se/researcher/1bba9787f512483d8eaf6cffc8743271.json"}}, {"family": "Strawbridge", "given": "Rona J", "initials": "RJ", "orcid": "0000-0001-8506-3585", "researcher": {"href": "https://publications.scilifelab.se/researcher/8ac5060a3b37466dae002d4ad8f4d0ac.json"}}], "type": "journal article", "published": "2019-05-14", "journal": {"volume": "9", "issn": "2045-2322", "issue": "1", "pages": "7339", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "CADM2 has been associated with a range of behavioural and metabolic traits, including physical activity, risk-taking, educational attainment, alcohol and cannabis use and obesity. Here, we set out to determine whether CADM2 contributes to mechanisms shared between mental and physical health disorders. We assessed genetic variants in the CADM2 locus for association with phenotypes in the UK Biobank, IMPROVE, PROCARDIS and SCARFSHEEP studies, before performing meta-analyses. A wide range of metabolic phenotypes were meta-analysed. Psychological phenotypes analysed in UK Biobank only were major depressive disorder, generalised anxiety disorder, bipolar disorder, neuroticism, mood instability and risk-taking behaviour. In UK Biobank, four, 88 and 172 genetic variants were significantly (p < 1 \u00d7 10 -5) associated with neuroticism, mood instability and risk-taking respectively. In meta-analyses of 4 cohorts, we identified 362, 63 and 11 genetic variants significantly (p < 1 \u00d7 10-5) associated with BMI, SBP and CRP respectively. Genetic effects on BMI, CRP and risk-taking were all positively correlated, and were consistently inversely correlated with genetic effects on SBP, mood instability and neuroticism. Conditional analyses suggested an overlap in the signals for physical and psychological traits. Many significant variants had genotype-specific effects on CADM2 expression levels in adult brain and adipose tissues. CADM2 variants influence a wide range of both psychological and metabolic traits, suggesting common biological mechanisms across phenotypes via regulation of CADM2 expression levels in adipose tissue. Functional studies of CADM2 are required to fully understand mechanisms connecting mental and physical health conditions.", "doi": "10.1038/s41598-019-43861-9", "pmid": "31089183", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-019-43861-9"}, {"db": "pmc", "key": "PMC6517397"}], "notes": [], "created": "2019-05-24T13:45:02.246Z", "modified": "2021-06-16T14:52:17.199Z"}, {"entity": "publication", "iuid": "d7571e14d8e34260a48b322d331e382e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d7571e14d8e34260a48b322d331e382e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d7571e14d8e34260a48b322d331e382e"}}, "title": "Shared Genetic Risk Factors Across Carbamazepine-Induced Hypersensitivity Reactions.", "authors": [{"family": "Nicoletti", "given": "Paola", "initials": "P"}, {"family": "Barrett", "given": "Sarah", "initials": "S"}, {"family": "McEvoy", "given": "Laurence", "initials": "L"}, {"family": "Daly", "given": "Ann K", "initials": "AK"}, {"family": "Aithal", "given": "Guruprasad", "initials": "G"}, {"family": "Lucena", "given": "M Isabel", "initials": "MI"}, {"family": "Andrade", "given": "Raul J", "initials": "RJ"}, {"family": "Wadelius", "given": "Mia", "initials": "M"}, {"family": "Hallberg", "given": "P\u00e4r", "initials": "P"}, {"family": "Stephens", "given": "Camilla", "initials": "C"}, {"family": "Bjornsson", "given": "Einar S", "initials": "ES"}, {"family": "Friedmann", "given": "Peter", "initials": "P"}, {"family": "Kainu", "given": "Kati", "initials": "K"}, {"family": "Laitinen", "given": "Tarja", "initials": "T"}, {"family": "Marson", "given": "Anthony", "initials": "A"}, {"family": "Molokhia", "given": "Mariam", "initials": "M"}, {"family": "Phillips", "given": "Elizabeth", "initials": "E"}, {"family": "Pichler", "given": "Werner", "initials": "W"}, {"family": "Romano", "given": "Antonino", "initials": "A"}, {"family": "Shear", "given": "Neil", "initials": "N"}, {"family": "Sills", "given": "Graeme", "initials": "G"}, {"family": "Tanno", "given": "Luciana K", "initials": "LK"}, {"family": "Swale", "given": "Ashley", "initials": "A"}, {"family": "Floratos", "given": "Aris", "initials": "A"}, {"family": "Shen", "given": "Yufeng", "initials": "Y"}, {"family": "Nelson", "given": "Matthew R", "initials": "MR"}, {"family": "Watkins", "given": "Paul B", "initials": "PB"}, {"family": "Daly", "given": "Mark J", "initials": "MJ"}, {"family": "Morris", "given": "Andrew P", "initials": "AP"}, {"family": "Alfirevic", "given": "Ana", "initials": "A"}, {"family": "Pirmohamed", "given": "Munir", "initials": "M"}], "type": "journal article", "published": "2019-05-07", "journal": {"volume": null, "issn": "1532-6535", "issue": null, "title": "Clin. Pharmacol. Ther.", "issn-l": "0009-9236"}, "abstract": "Carbamazepine (CBZ) causes life-threating T-cell-mediated hypersensitivity reactions, including serious cutaneous adverse reactions (SCARs) and drug-induced liver injury (CBZ-DILI). In order to evaluate shared or phenotype-specific genetic predisposing factors for CBZ hypersensitivity reactions, we performed a meta-analysis of two genomewide association studies (GWAS) on a total of 43 well-phenotyped Northern and Southern European CBZ-SCAR cases and 10,701 population controls and a GWAS on 12 CBZ-DILI cases and 8,438 ethnically matched population controls. HLA-A*31:01 was identified as the strongest genetic predisposing factor for both CBZ-SCAR (odds ratio (OR)\u00a0=\u00a08.0; 95% CI 4.10-15.80; P\u00a0=\u00a01.2\u00a0\u00d7\u00a010\n                -9 ) and CBZ-DILI (OR\u00a0=\u00a07.3; 95% CI 2.47-23.67; P\u00a0=\u00a00.0004) in European populations. The association with HLA-A*31:01 in patients with SCAR was mainly driven by hypersensitivity syndrome (OR\u00a0=\u00a012.9; P\u00a0=\u00a02.1\u00a0\u00d7\u00a010-9 ) rather than by Stevens-Johnson syndrome/toxic epidermal necrolysis cases, which showed an association with HLA-B*57:01. We also identified a novel risk locus mapping to ALK only for CBZ-SCAR cases, which needs replication in additional cohorts and functional evaluation.", "doi": "10.1002/cpt.1493", "pmid": "31066027", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [], "notes": [], "created": "2019-07-05T12:56:58.063Z", "modified": "2020-01-21T13:56:14.304Z"}, {"entity": "publication", "iuid": "c3611dc960cf4c7d90fcb7037f89a3b3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c3611dc960cf4c7d90fcb7037f89a3b3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c3611dc960cf4c7d90fcb7037f89a3b3"}}, "title": "Genetical Genomics of Tonic Immobility in the Chicken.", "authors": [{"family": "Fogelholm", "given": "Jesper", "initials": "J"}, {"family": "Inkabi", "given": "Samuel", "initials": "S"}, {"family": "H\u00f6glund", "given": "Andrey", "initials": "A"}, {"family": "Abbey-Lee", "given": "Robin", "initials": "R"}, {"family": "Johnsson", "given": "Martin", "initials": "M"}, {"family": "Jensen", "given": "Per", "initials": "P"}, {"family": "Henriksen", "given": "Rie", "initials": "R"}, {"family": "Wright", "given": "Dominic", "initials": "D"}], "type": "journal article", "published": "2019-05-07", "journal": {"volume": "10", "issn": "2073-4425", "issue": "5", "title": "Genes", "issn-l": "2073-4425"}, "abstract": "Identifying the molecular mechanisms of animal behaviour is an enduring goal for researchers. Gaining insight into these mechanisms enables us to gain a greater understanding of behaviour and their genetic control. In this paper, we perform Quantitative Trait Loci (QTL) mapping of tonic immobility behaviour in an advanced intercross line between wild and domestic chickens. Genes located within the QTL interval were further investigated using global expression QTL (eQTL) mapping from hypothalamus tissue, as well as causality analysis. This identified five candidate genes, with the genes \n            PRDX4 and ACOT9 emerging as the best supported candidates. In addition, we also investigated the connection between tonic immobility, meat pH and struggling behaviour, as the two candidate genes PRDX4 and ACOT9 have previously been implicated in controlling muscle pH at slaughter. We did not find any phenotypic correlations between tonic immobility, struggling behaviour and muscle pH in a smaller additional cohort, despite these behaviours being repeatable within-test.", "doi": "10.3390/genes10050341", "pmid": "31067744", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "genes10050341"}], "notes": [], "created": "2019-05-10T14:53:06.896Z", "modified": "2024-01-16T13:48:44.361Z"}, {"entity": "publication", "iuid": "c061cfb4e0ac42649fd2c7242bb1f8c9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c061cfb4e0ac42649fd2c7242bb1f8c9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c061cfb4e0ac42649fd2c7242bb1f8c9"}}, "title": "How Linked Selection Shapes the Diversity Landscape in Ficedula Flycatchers", "authors": [{"family": "Rettelbach", "given": "Agnes", "initials": "A"}, {"family": "Nater", "given": "Alexander", "initials": "A", "orcid": "0000-0002-4805-5575", "researcher": {"href": "https://publications.scilifelab.se/researcher/e92d7e509932438bbfccd2aa94c9c107.json"}}, {"family": "Ellegren", "given": "Hans", "initials": "H", "orcid": "0000-0002-5035-1736", "researcher": {"href": "https://publications.scilifelab.se/researcher/819e68cc7125446baec6165aabd2d19c.json"}}], "type": "journal-article", "published": "2019-05-01", "journal": {"volume": "212", "issn": "1943-2631", "issue": "1", "pages": "277-285", "title": "Genetics", "issn-l": "0016-6731"}, "abstract": "There is an increasing awareness that selection affecting linked neutral sites strongly influences on how diversity is distributed across the genome. In particular, linked selection is likely involved in the formation of heterogenous landscapes of genetic diversity, including genomic regions with locally reduced effective population sizes that manifest as dips in diversity, and \"islands\" of differentiation between closely related populations or species. Linked selection can be in the form of background selection or selective sweeps, and a long-standing quest in population genetics has been to unveil the relative importance of these processes. Here, we analyzed the theoretically expected reduction of diversity caused by linked selection in the collared flycatcher ( Ficedula albicollis) genome and compared this with population genomic data on the distribution of diversity across the flycatcher genome. By incorporating data on recombination rate variation and the density of target sites for selection (including both protein-coding genes and conserved noncoding elements), we found that background selection can explain most of the observed baseline variation in genetic diversity. However, positive selection was necessary to explain the pronounced local diversity dips in the collared flycatcher genome. We confirmed our analytical findings by comprehensive simulations. Therefore, our study demonstrates that even though both background selection and selective sweeps contribute to the heterogeneous diversity landscape seen in this avian system, they play different roles in shaping it.", "doi": "10.1534/genetics.119.301991", "pmid": "30872320", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "genetics.119.301991"}, {"db": "pmc", "key": "PMC6499528"}], "notes": [], "created": "2019-06-11T15:37:32.132Z", "modified": "2024-01-16T13:48:44.388Z"}, {"entity": "publication", "iuid": "eb2b54dae41a4478a0c3241adc1f0cc0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/eb2b54dae41a4478a0c3241adc1f0cc0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/eb2b54dae41a4478a0c3241adc1f0cc0"}}, "title": "Parental Education and Genetics of BMI from Infancy to Old Age: A Pooled Analysis of 29 Twin Cohorts.", "authors": [{"family": "Silventoinen", "given": "Karri", "initials": "K", "orcid": "0000-0003-1759-3079", "researcher": {"href": "https://publications.scilifelab.se/researcher/87ff661db88949b09e7b399c349a7e9d.json"}}, {"family": "Jelenkovic", "given": "Aline", "initials": "A"}, {"family": "Latvala", "given": "Antti", "initials": "A"}, {"family": "Yokoyama", "given": "Yoshie", "initials": "Y"}, {"family": "Sund", "given": "Reijo", "initials": "R"}, {"family": "Sugawara", "given": "Masumi", "initials": "M"}, {"family": "Tanaka", "given": "Mami", "initials": "M"}, {"family": "Matsumoto", "given": "Satoko", "initials": "S"}, {"family": "Aaltonen", "given": "Sari", "initials": "S"}, {"family": "Piirtola", "given": "Maarit", "initials": "M"}, {"family": "Freitas", "given": "Duarte L", "initials": "DL"}, {"family": "Maia", "given": "Jos\u00e9 A", "initials": "JA"}, {"family": "\u00d6ncel", "given": "Sevgi Y", "initials": "SY"}, {"family": "Aliev", "given": "Fazil", "initials": "F"}, {"family": "Ji", "given": "Fuling", "initials": "F", "orcid": "0000-0002-3261-0204", "researcher": {"href": "https://publications.scilifelab.se/researcher/e0fe35efe90044b0aa40828633d4f2be.json"}}, {"family": "Ning", "given": "Feng", "initials": "F"}, {"family": "Pang", "given": "Zengchang", "initials": "Z"}, {"family": "Rebato", "given": "Esther", "initials": "E"}, {"family": "Saudino", "given": "Kimberly J", "initials": "KJ"}, {"family": "Cutler", "given": "Tessa L", "initials": "TL"}, {"family": "Hopper", "given": "John L", "initials": "JL"}, {"family": "Ullemar", "given": "Vilhelmina", "initials": "V"}, {"family": "Almqvist", "given": "Catarina", "initials": "C"}, {"family": "Magnusson", "given": "Patrik K E", "initials": "PKE"}, {"family": "Cozen", "given": "Wendy", "initials": "W"}, {"family": "Hwang", "given": "Amie E", "initials": "AE"}, {"family": "Mack", "given": "Thomas M", "initials": "TM"}, {"family": "Willemsen", "given": "Gonneke", "initials": "G"}, {"family": "Bartels", "given": "Meike", "initials": "M"}, {"family": "van Beijsterveldt", "given": "Catharina E M", "initials": "CEM"}, {"family": "Nelson", "given": "Tracy L", "initials": "TL"}, {"family": "Whitfield", "given": "Keith E", "initials": "KE"}, {"family": "Sung", "given": "Joohon", "initials": "J"}, {"family": "Kim", "given": "Jina", "initials": "J"}, {"family": "Lee", "given": "Jooyeon", "initials": "J"}, {"family": "Lee", "given": "Sooji", "initials": "S"}, {"family": "Llewellyn", "given": "Clare H", "initials": "CH"}, {"family": "Fisher", "given": "Abigail", "initials": "A"}, {"family": "Medda", "given": "Emanuela", "initials": "E"}, {"family": "Nistic\u00f2", "given": "Lorenza", "initials": "L"}, {"family": "Toccaceli", "given": "Virgilia", "initials": "V"}, {"family": "Baker", "given": "Laura A", "initials": "LA"}, {"family": "Tuvblad", "given": "Catherine", "initials": "C"}, {"family": "Corley", "given": "Robin P", "initials": "RP"}, {"family": "Huibregtse", "given": "Brooke M", "initials": "BM", "orcid": "0000-0003-0977-7249", "researcher": {"href": "https://publications.scilifelab.se/researcher/e9df70acb87f443eb6da650b151a679c.json"}}, {"family": "Derom", "given": "Catherine A", "initials": "CA"}, {"family": "Vlietinck", "given": "Robert F", "initials": "RF"}, {"family": "Loos", "given": "Ruth J F", "initials": "RJF"}, {"family": "Knafo-Noam", "given": "Ariel", "initials": "A"}, {"family": "Mankuta", "given": "David", "initials": "D"}, {"family": "Abramson", "given": "Lior", "initials": "L"}, {"family": "Burt", "given": "S Alexandra", "initials": "SA"}, {"family": "Klump", "given": "Kelly L", "initials": "KL"}, {"family": "Silberg", "given": "Judy L", "initials": "JL"}, {"family": "Maes", "given": "Hermine H", "initials": "HH"}, {"family": "Krueger", "given": "Robert F", "initials": "RF"}, {"family": "McGue", "given": "Matt", "initials": "M"}, {"family": "Pahlen", "given": "Shandell", "initials": "S"}, {"family": "Gatz", "given": "Margaret", "initials": "M"}, {"family": "Butler", "given": "David A", "initials": "DA"}, {"family": "Harris", "given": "Jennifer R", "initials": "JR"}, {"family": "Nilsen", "given": "Thomas S", "initials": "TS"}, {"family": "Harden", "given": "K Paige", "initials": "KP"}, {"family": "Tucker-Drob", "given": "Elliot M", "initials": "EM"}, {"family": "Franz", "given": "Carol E", "initials": "CE"}, {"family": "Kremen", "given": "William S", "initials": "WS"}, {"family": "Lyons", "given": "Michael J", "initials": "MJ"}, {"family": "Lichtenstein", "given": "Paul", "initials": "P"}, {"family": "Jeong", "given": "Hoe-Uk", "initials": "HU"}, {"family": "Hur", "given": "Yoon-Mi", "initials": "YM"}, {"family": "Boomsma", "given": "Dorret I", "initials": "DI"}, {"family": "S\u00f8rensen", "given": "Thorkild I A", "initials": "TIA"}, {"family": "Kaprio", "given": "Jaakko", "initials": "J"}], "type": "journal article", "published": "2019-05-00", "journal": {"volume": "27", "issn": "1930-739X", "issue": "5", "pages": "855-865", "title": "Obesity (Silver Spring)", "issn-l": "1930-7381"}, "abstract": "The objective of this study was to analyze how parental education modifies the genetic and environmental variances of BMI from infancy to old age in three geographic-cultural regions.\n\nA pooled sample of 29 cohorts including 143,499 twin individuals with information on parental education and BMI from age 1 to 79 years (299,201 BMI measures) was analyzed by genetic twin modeling.\n\nUntil 4 years of age, parental education was not consistently associated with BMI. Thereafter, higher parental education level was associated with lower BMI in males and females. Total and additive genetic variances of BMI were smaller in the offspring of highly educated parents than in those whose parents had low education levels. Especially in North American and Australian children, environmental factors shared by co-twins also contributed to the higher BMI variation in the low education level category. In Europe and East Asia, the associations of parental education with mean BMI and BMI variance were weaker than in North America and Australia.\n\nLower parental education level is associated with higher mean BMI and larger genetic variance of BMI after early childhood, especially in the obesogenic macro-environment. The interplay among genetic predisposition, childhood social environment, and macro-social context is important for socioeconomic differences in BMI.", "doi": "10.1002/oby.22451", "pmid": "30950584", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC6478550"}, {"db": "mid", "key": "NIHMS1520745"}], "notes": [], "created": "2019-04-12T14:00:37.931Z", "modified": "2021-06-21T12:02:53.707Z"}, {"entity": "publication", "iuid": "e3d5472c01f14529be1d69c2d9cfefdb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e3d5472c01f14529be1d69c2d9cfefdb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e3d5472c01f14529be1d69c2d9cfefdb"}}, "title": "Interferon signature in patients with STAT1 gain-of-function mutation is epigenetically determined.", "authors": [{"family": "Kaleviste", "given": "Epp", "initials": "E"}, {"family": "Saare", "given": "Mario", "initials": "M"}, {"family": "Leahy", "given": "Timothy Ronan", "initials": "TR"}, {"family": "Bondet", "given": "Vincent", "initials": "V"}, {"family": "Duffy", "given": "Darragh", "initials": "D", "orcid": "0000-0002-8875-2308", "researcher": {"href": "https://publications.scilifelab.se/researcher/dce1a0fd17154c73b30f23c2a58bd390.json"}}, {"family": "Mogensen", "given": "Trine H", "initials": "TH", "orcid": "0000-0002-1853-9704", "researcher": {"href": "https://publications.scilifelab.se/researcher/a27f3f726f7546b7800c722348411cb9.json"}}, {"family": "J\u00f8rgensen", "given": "Sofie E", "initials": "SE"}, {"family": "Nurm", "given": "Helke", "initials": "H"}, {"family": "Ip", "given": "Winnie", "initials": "W"}, {"family": "Davies", "given": "E Graham", "initials": "EG"}, {"family": "Sauer", "given": "Sascha", "initials": "S"}, {"family": "Syv\u00e4nen", "given": "Ann-Christine", "initials": "AC", "orcid": "0000-0002-9681-9146", "researcher": {"href": "https://publications.scilifelab.se/researcher/f7012e35025543379380cb90efd71243.json"}}, {"family": "Milani", "given": "Lili", "initials": "L", "orcid": "0000-0002-5323-3102", "researcher": {"href": "https://publications.scilifelab.se/researcher/dec8d00c4b9d43458c5c895b164695d5.json"}}, {"family": "Peterson", "given": "P\u00e4rt", "initials": "P", "orcid": "0000-0001-6755-791X", "researcher": {"href": "https://publications.scilifelab.se/researcher/62e117ce0c4847c592011f09888326a3.json"}}, {"family": "Kisand", "given": "Kai", "initials": "K", "orcid": "0000-0002-5426-4648", "researcher": {"href": "https://publications.scilifelab.se/researcher/f3f676eacf9544b5b06ec3aafbf29899.json"}}], "type": "journal article", "published": "2019-05-00", "journal": {"volume": "49", "issn": "1521-4141", "issue": "5", "pages": "790-800", "title": "Eur. J. Immunol.", "issn-l": "0014-2980"}, "abstract": "STAT1 gain-of-function (GOF) variants lead to defective Th17 cell development and chronic mucocutaneous candidiasis (CMC), but frequently also to autoimmunity. Stimulation of cells with STAT1 inducing cytokines like interferons (IFN) result in hyperphosphorylation and delayed dephosphorylation of GOF STAT1. However, the mechanism how the delayed dephosphorylation exactly causes the increased expression of STAT1-dependent genes, and how the intracellular signal transduction from cytokine receptors is affected, remains unknown. In this study we show that the circulating levels of IFN-\u03b1 were not persistently elevated in STAT1 GOF patients. Nevertheless, the expression of interferon signature genes was evident even in the patient with low or undetectable serum IFN-\u03b1 levels. Chromatin immunoprecipitation (ChIP) experiments revealed that the active chromatin mark trimethylation of lysine 4 of histone 3 (H3K4me3), was significantly enriched in areas associated with interferon-stimulated genes in STAT1 GOF cells in comparison to cells from healthy donors. This suggests that the chromatin binding of GOF STAT1 variant promotes epigenetic changes compatible with higher gene expression and elevated reactivity to type I interferons, and possibly predisposes for interferon-related autoimmunity. The results also suggest that epigenetic rewiring may be responsible for treatment failure of Janus kinase 1/2 (JAK1/2) inhibitors in certain patients.", "doi": "10.1002/eji.201847955", "pmid": "30801692", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [], "notes": [], "created": "2019-12-03T13:21:31.593Z", "modified": "2023-06-19T10:56:15.956Z"}, {"entity": "publication", "iuid": "0cf9ba0976a24487bb1a3b38581f125b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0cf9ba0976a24487bb1a3b38581f125b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0cf9ba0976a24487bb1a3b38581f125b"}}, "title": "Genotype-free estimation of allele frequencies reduces bias and improves demographic inference from RADSeq data.", "authors": [{"family": "Warmuth", "given": "Vera M", "initials": "VM", "orcid": "0000-0002-0305-5125", "researcher": {"href": "https://publications.scilifelab.se/researcher/fee6013dc4c74608981a293e4bb8016b.json"}}, {"family": "Ellegren", "given": "Hans", "initials": "H", "orcid": "0000-0002-5035-1736", "researcher": {"href": "https://publications.scilifelab.se/researcher/819e68cc7125446baec6165aabd2d19c.json"}}], "type": "journal article", "published": "2019-05-00", "journal": {"volume": "19", "issn": "1755-0998", "issue": "3", "pages": "586-596", "title": "Mol Ecol Resour", "issn-l": "1755-098X"}, "abstract": "Restriction-site associated DNA sequencing (RADSeq) facilitates rapid generation of thousands of genetic markers at relatively low cost; however, several sources of error specific to RADSeq methods often lead to biased estimates of allele frequencies and thereby to erroneous population genetic inference. Estimating the distribution of sample allele frequencies without calling genotypes was shown to improve population inference from whole genome sequencing data, but the ability of this approach to account for RADSeq-specific biases remains unexplored. Here we assess in how far genotype-free methods of allele frequency estimation affect demographic inference from empirical RADSeq data. Using the well-studied pied flycatcher (Ficedula hypoleuca) as a study system, we compare allele frequency estimation and demographic inference from whole genome sequencing data with that from RADSeq data matched for samples using both genotype-based and genotype free methods. The demographic history of pied flycatchers as inferred from RADSeq data was highly congruent with that inferred from whole genome resequencing (WGS) data when allele frequencies were estimated directly from the read data. In contrast, when allele frequencies were derived from called genotypes, RADSeq-based estimates of most model parameters fell outside the 95% confidence interval of estimates derived from WGS data. Notably, more stringent filtering of the genotype calls tended to increase the discrepancy between parameter estimates from WGS and RADSeq data, respectively. The results from this study demonstrate the ability of genotype-free methods to improve allele frequency spectrum- (AFS-) based demographic inference from empirical RADSeq data and highlight the need to account for uncertainty in NGS data regardless of sequencing method.", "doi": "10.1111/1755-0998.12990", "pmid": "30633448", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2019-04-23T09:56:02.159Z", "modified": "2024-01-16T13:48:44.402Z"}, {"entity": "publication", "iuid": "e96e1b6ccf0f4364a2db800881b5dcf6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e96e1b6ccf0f4364a2db800881b5dcf6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e96e1b6ccf0f4364a2db800881b5dcf6"}}, "title": "Footprints of adaptive evolution revealed by whole Z chromosomes haplotypes in flycatchers.", "authors": [{"family": "Nadachowska-Brzyska", "given": "Krystyna", "initials": "K", "orcid": "0000-0002-8457-310X", "researcher": {"href": "https://publications.scilifelab.se/researcher/fc84301b6f3943058c16d3f644713078.json"}}, {"family": "Burri", "given": "Reto", "initials": "R", "orcid": "0000-0002-1813-0079", "researcher": {"href": "https://publications.scilifelab.se/researcher/68f21e70e2864b42ab9fc532c14c069c.json"}}, {"family": "Ellegren", "given": "Hans", "initials": "H", "orcid": "0000-0002-5035-1736", "researcher": {"href": "https://publications.scilifelab.se/researcher/819e68cc7125446baec6165aabd2d19c.json"}}], "type": "journal article", "published": "2019-05-00", "journal": {"volume": "28", "issn": "1365-294X", "issue": "9", "pages": "2290-2304", "title": "Mol. Ecol.", "issn-l": "0962-1083"}, "abstract": "Detecting positive selection using genomic data is critical to understanding the role of adaptive evolution. Of particular interest in this context is sex chromosomes since they are thought to play a special role in local adaptation and speciation. We sought to circumvent the challenges associated with statistical phasing when using haplotype-based statistics in sweep scans by benefitting from that whole chromosome haplotypes of the sex chromosomes can be obtained by resequencing of individuals of the hemizygous sex. We analyzed whole Z chromosome haplotypes from 100 females from several populations of four black and white flycatcher species (in birds, females are ZW and males ZZ). Based on integrated haplotype score (iHS) and number of segregating sites by length (nSL) statistics, we found strong and frequent haplotype structure in several regions of the Z chromosome in each species. Most of these sweep signals were population-specific, with essentially no evidence for regions under selection shared among species. Some completed sweeps were revealed by the cross-population extended haplotype homozygosity (XP-EHH) statistic. Importantly, by using statistically phased Z chromosome data from resequencing of males, we failed to recover the signals of selection detected in analyses based on whole chromosome haplotypes from females; instead, what likely represent false signals of selection were frequently seen. This highlights the power issues in statistical phasing and cautions against conclusions from selection scans using such data. The detection of frequent selective sweeps on the avian Z chromosome supports a large role of sex chromosomes in adaptive evolution.", "doi": "10.1111/mec.15021", "pmid": "30653779", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC6852393"}], "notes": [], "created": "2019-12-03T10:21:30.297Z", "modified": "2024-01-16T13:48:44.409Z"}, {"entity": "publication", "iuid": "d7d67ba83c054a63b3e9e39989da1cf5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d7d67ba83c054a63b3e9e39989da1cf5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d7d67ba83c054a63b3e9e39989da1cf5"}}, "title": "Exome sequencing in 51 early onset non-familial CRC cases.", "authors": [{"family": "Thutkawkorapin", "given": "Jessada", "initials": "J", "orcid": "0000-0001-9306-844X", "researcher": {"href": "https://publications.scilifelab.se/researcher/fa13464dfebd4c868fe4eb1f0186a41b.json"}}, {"family": "Lindblom", "given": "Annika", "initials": "A"}, {"family": "Tham", "given": "Emma", "initials": "E", "orcid": "0000-0001-6079-164X", "researcher": {"href": "https://publications.scilifelab.se/researcher/6689dd9aff584082a57398141a538111.json"}}], "type": "journal article", "published": "2019-05-00", "journal": {"volume": "7", "issn": "2324-9269", "issue": "5", "pages": "e605", "title": "Mol Genet Genomic Med", "issn-l": "2324-9269"}, "abstract": "Colorectal cancer (CRC) cases with an age of onset <40 years suggests a germline genetic cause. In total, 51 simplex cases were included to test the hypothesis of CRC as a mendelian trait caused by either heterozygous autosomal dominant or bi-allelic autosomal recessive pathogenic variants.\n\nThe cohort was whole exome sequenced (WES) at 100\u00d7 coverage. Both a dominant- and recessive model were used for searching predisposing genetic factors. In addition, we assayed recessive variants of potential moderate risk that were enriched in our young-onset CRC cohort. Variants were filtered using a candidate cancer gene list or by selecting variants more likely to be pathogenic based on variant type (e.g., loss-of-function) or allele frequency.\n\nWe identified one pathogenic variant in PTEN in a patient subsequently confirmed to have a hereditary hamartoma tumor syndrome (Cowden syndrome) and one patient with a pathogenic heterozygous variant in PMS2 that was originally not identified by WES due to low quality reads resulting from pseudogenes. In addition, we identified three heterozygous candidate missense variants in known cancer susceptibility genes (BMPR1A, BRIP1, and SRC), three truncating variants in possibly novel cancer genes (CLSPN, SEC24B, SSH2) and four candidate missense variants in ACACA, NR2C2, INPP4A, and DIDO1. We also identify five possible autosomal recessive candidate genes: ATP10B, PKHD1, UGGT2, MYH13, TFF3.\n\nTwo clear pathogenic variants were identified in patients that had not been identified clinically. Thus, the chance of detecting a hereditary cancer syndrome in patients with CRC at young age but without family history is 2/51 (4%) and therefore the clinical benefit of genetic testing in this patient group is low. Of note, using stringent filtering, we have identified a total of ten candidate heterozygous variants and five possibly biallelic autosomal recessive candidate genes that warrant further study.", "doi": "10.1002/mgg3.605", "pmid": "30809968", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC6503031"}], "notes": [], "created": "2019-04-23T10:00:11.219Z", "modified": "2024-01-16T13:48:44.415Z"}, {"entity": "publication", "iuid": "a57bfe6b48a545ef9ba6b9d8fcaa6843", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a57bfe6b48a545ef9ba6b9d8fcaa6843.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a57bfe6b48a545ef9ba6b9d8fcaa6843"}}, "title": "Asthma and affective traits in adults: a genetically informative study.", "authors": [{"family": "Lehto", "given": "Kelli", "initials": "K"}, {"family": "Pedersen", "given": "Nancy L", "initials": "NL"}, {"family": "Almqvist", "given": "Catarina", "initials": "C"}, {"family": "Lu", "given": "Yi", "initials": "Y"}, {"family": "Brew", "given": "Bronwyn K", "initials": "BK"}], "type": "journal article", "published": "2019-05-00", "journal": {"volume": "53", "issn": "1399-3003", "issue": "5", "pages": "1802142", "title": "Eur. Respir. J.", "issn-l": "0903-1936"}, "abstract": "Depression, anxiety and high neuroticism (affective traits) are often comorbid with asthma. A causal direction between the affective traits and asthma is difficult to determine; however, there may be a common underlying pathway attributable to shared genetic factors. Our aim was to determine whether a common genetic susceptibility exists for asthma and each of the affective traits.An adult cohort from the Swedish Twin Registry underwent questionnaire-based health assessments (n=23 693) and genotyping (n=15 908). Firstly, questionnaire-based associations between asthma and affective traits were explored. This was followed by genetic analyses: 1) polygenic risk scores (PRS) for affective traits were used as predictors of asthma in the cohort, and 2) genome-wide association results from UK Biobank were used in linkage-disequilibrium score regression (LDSC) to quantify genetic correlations between asthma and affective traits. Analyses found associations between questionnaire-based asthma and affective traits (OR 1.67, 95% CI 1.50-1.86 major depression; OR 1.45, 95% CI 1.30-1.61 anxiety; and OR 1.60, 95% CI 1.40-1.82 high neuroticism). Genetic susceptibility for neuroticism explained the variance in asthma with a dose-response effect; that is, study participants in the highest neuroticism PRS quartile were more likely to have asthma than those in the lowest quartile (OR 1.37, 95% CI 1.17-1.61). Genetic correlations were found between depression and asthma (r g=0.17), but not for anxiety or neuroticism.We conclude that the observed comorbidity between asthma and the affective traits may in part be due to shared genetic influences between asthma and depression (LDSC) and neuroticism (PRS), but not anxiety.", "doi": "10.1183/13993003.02142-2018", "pmid": "30956207", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "13993003.02142-2018"}], "notes": [], "created": "2019-04-12T14:00:37.475Z", "modified": "2021-06-21T12:02:25.827Z"}, {"entity": "publication", "iuid": "94f532b12f2647cf94b08ca109b6ba63", "links": {"self": {"href": "https://publications.scilifelab.se/publication/94f532b12f2647cf94b08ca109b6ba63.json"}, "display": {"href": "https://publications.scilifelab.se/publication/94f532b12f2647cf94b08ca109b6ba63"}}, "title": "EnsembleCNV: an ensemble machine learning algorithm to identify and genotype copy number variation using SNP array data.", "authors": [{"family": "Zhang", "given": "Zhongyang", "initials": "Z"}, {"family": "Cheng", "given": "Haoxiang", "initials": "H"}, {"family": "Hong", "given": "Xiumei", "initials": "X"}, {"family": "Di Narzo", "given": "Antonio F", "initials": "AF"}, {"family": "Franzen", "given": "Oscar", "initials": "O"}, {"family": "Peng", "given": "Shouneng", "initials": "S"}, {"family": "Ruusalepp", "given": "Arno", "initials": "A"}, {"family": "Kovacic", "given": "Jason C", "initials": "JC"}, {"family": "Bjorkegren", "given": "Johan L M", "initials": "JLM"}, {"family": "Wang", "given": "Xiaobin", "initials": "X"}, {"family": "Hao", "given": "Ke", "initials": "K"}], "type": "journal article", "published": "2019-04-23", "journal": {"volume": "47", "issn": "1362-4962", "issue": "7", "pages": "e39", "title": "Nucleic Acids Res.", "issn-l": "0305-1048"}, "abstract": "The associations between diseases/traits and copy number variants (CNVs) have not been systematically investigated in genome-wide association studies (GWASs), primarily due to a lack of robust and accurate tools for CNV genotyping. Herein, we propose a novel ensemble learning framework, ensembleCNV, to detect and genotype CNVs using single nucleotide polymorphism (SNP) array data. EnsembleCNV (a) identifies and eliminates batch effects at raw data level; (b) assembles individual CNV calls into CNV regions (CNVRs) from multiple existing callers with complementary strengths by a heuristic algorithm; (c) re-genotypes each CNVR with local likelihood model adjusted by global information across multiple CNVRs; (d) refines CNVR boundaries by local correlation structure in copy number intensities; (e) provides direct CNV genotyping accompanied with confidence score, directly accessible for downstream quality control and association analysis. Benchmarked on two large datasets, ensembleCNV outperformed competing methods and achieved a high call rate (93.3%) and reproducibility (98.6%), while concurrently achieving high sensitivity by capturing 85% of common CNVs documented in the 1000 Genomes Project. Given this CNV call rate and accuracy, which are comparable to SNP genotyping, we suggest ensembleCNV holds significant promise for performing genome-wide CNV association studies and investigating how CNVs predispose to human diseases.", "doi": "10.1093/nar/gkz068", "pmid": "30722045", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "5306576"}, {"db": "pmc", "key": "PMC6468244"}], "notes": [], "created": "2019-04-30T11:34:33.446Z", "modified": "2020-01-21T13:56:14.195Z"}, {"entity": "publication", "iuid": "2c82a9ea57f64c3e9eb8c9106277dc9c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2c82a9ea57f64c3e9eb8c9106277dc9c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2c82a9ea57f64c3e9eb8c9106277dc9c"}}, "title": "A Genome-Wide Association Study of Bisphosphonate-Associated Atypical Femoral Fracture.", "authors": [{"family": "Kharazmi", "given": "Mohammad", "initials": "M"}, {"family": "Micha\u00eblsson", "given": "Karl", "initials": "K"}, {"family": "Schilcher", "given": "J\u00f6rg", "initials": "J"}, {"family": "Eriksson", "given": "Niclas", "initials": "N"}, {"family": "Melhus", "given": "H\u00e5kan", "initials": "H"}, {"family": "Wadelius", "given": "Mia", "initials": "M"}, {"family": "Hallberg", "given": "P\u00e4r", "initials": "P"}], "type": "journal article", "published": "2019-04-20", "journal": {"volume": null, "issn": "1432-0827", "issue": null, "title": "Calcif. Tissue Int.", "issn-l": "0171-967X"}, "abstract": "Atypical femoral fracture is a well-documented adverse reaction to bisphosphonates. It is strongly related to duration of bisphosphonate use, and the risk declines rapidly after drug withdrawal. The mechanism behind bisphosphonate-associated atypical femoral fracture is unclear, but a genetic predisposition has been suggested. With the aim to identify common genetic variants that could be used for preemptive genetic testing, we performed a genome-wide association study. Cases were recruited mainly through reports of adverse drug reactions sent to the Swedish Medical Products Agency on a nation-wide basis. We compared atypical femoral fracture cases (n\u2009=\u200951) with population-based controls (n\u2009=\u20094891), and to reduce the possibility of confounding by indication, we also compared with bisphosphonate-treated controls without a current diagnosis of cancer (n\u2009=\u2009324). The total number of single-nucleotide polymorphisms after imputation was 7,585,874. A genome-wide significance threshold of p\u2009<\u20095\u00a0\u00d7\u00a010\n            -8 was used to correct for multiple testing. In addition, we performed candidate gene analyses for a panel of 29 genes previously implicated in atypical femoral fractures (significance threshold of p\u2009<\u20095.7\u00a0\u00d7\u00a010-6). Compared with population controls, bisphosphonate-associated atypical femoral fracture was associated with four isolated, uncommon single-nucleotide polymorphisms. When cases were compared with bisphosphonate-treated controls, no statistically significant genome-wide association remained. We conclude that the detected associations were either false positives or related to the underlying disease, i.e., treatment indication. Furthermore, there was no significant association with single-nucleotide polymorphisms in the 29 candidate genes. In conclusion, this study found no evidence of a common genetic predisposition for bisphosphonate-associated atypical femoral fracture. Further studies of larger sample size to identify possible weakly associated genetic traits, as well as whole exome or whole-genome sequencing studies to identify possible rare genetic variation conferring a risk are warranted.", "doi": "10.1007/s00223-019-00546-9", "pmid": "31006051", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1007/s00223-019-00546-9"}], "notes": [], "created": "2019-04-30T11:28:45.369Z", "modified": "2024-01-16T13:48:44.463Z"}, {"entity": "publication", "iuid": "7c9ca836b2d640fe827a0c70884fbbe0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7c9ca836b2d640fe827a0c70884fbbe0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7c9ca836b2d640fe827a0c70884fbbe0"}}, "title": "RNA Sequencing Provides Novel Insights into the Transcriptome of Aldosterone Producing Adenomas.", "authors": [{"family": "Backman", "given": "Samuel", "initials": "S"}, {"family": "\u00c5kerstr\u00f6m", "given": "Tobias", "initials": "T"}, {"family": "Maharjan", "given": "Rajani", "initials": "R", "orcid": "0000-0001-8171-5451", "researcher": {"href": "https://publications.scilifelab.se/researcher/18e62885ee4d4f1987cb2b03f483f005.json"}}, {"family": "Cupisti", "given": "Kenko", "initials": "K"}, {"family": "Willenberg", "given": "Holger S", "initials": "HS"}, {"family": "Hellman", "given": "Per", "initials": "P"}, {"family": "Bj\u00f6rklund", "given": "Peyman", "initials": "P"}], "type": "journal article", "published": "2019-04-18", "journal": {"volume": "9", "issn": "2045-2322", "issue": "1", "pages": "6269", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "Aldosterone producing adenomas (APAs) occur in the adrenal glands of around 30% of patients with primary aldosteronism, the most common form of secondary hypertension. Somatic mutations in KCNJ5, ATP1A1, ATP2B3, CACNA1D and CTNNB1 have been described in ~60% of these tumours. We subjected 15 aldosterone producing adenomas (13 with known mutations and two without) to RNA Sequencing and Whole Genome Sequencing (n = 2). All known mutations were detected in the RNA-Seq reads, and mutations in ATP2B3 (G123R) and CACNA1D (S410L) were discovered in the tumours without known mutations. Adenomas with CTNNB1 mutations showed a large number of differentially expressed genes (1360 compared to 106 and 75 for KCNJ5 and ATP1A1/ATP2B3 respectively) and clustered together in a hierarchical clustering analysis. RT-PCR in an extended cohort of 49 APAs confirmed higher expression of AFF3 and ISM1 in APAs with CTNNB1 mutations. Investigation of the expression of genes involved in proliferation and apoptosis revealed subtle differences between tumours with and without CTNNB1 mutations. Together our results consolidate the notion that CTNNB1 mutations characterize a distinct subgroup of APAs.", "doi": "10.1038/s41598-019-41525-2", "pmid": "31000732", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-019-41525-2"}, {"db": "pmc", "key": "PMC6472367"}], "notes": [], "created": "2019-04-23T10:02:48.530Z", "modified": "2024-01-16T13:48:44.470Z"}, {"entity": "publication", "iuid": "b0c567853e634255a4771fc7b22cca55", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b0c567853e634255a4771fc7b22cca55.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b0c567853e634255a4771fc7b22cca55"}}, "title": "A multi-ancestry genome-wide study incorporating gene-smoking interactions identifies multiple new loci for pulse pressure and mean arterial pressure.", 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"Ching-Yu", "initials": "CY"}, {"family": "Sim", "given": "Xueling", "initials": "X"}, {"family": "Vojinovic", "given": "Dina", "initials": "D"}, {"family": "Marten", "given": "Jonathan", "initials": "J"}, {"family": "Musani", "given": "Solomon K", "initials": "SK"}, {"family": "Kilpel\u00e4inen", "given": "Tuomas O", "initials": "TO"}, {"family": "Richard", "given": "Melissa A", "initials": "MA"}, {"family": "Aslibekyan", "given": "Stella", "initials": "S"}, {"family": "Bartz", "given": "Traci M", "initials": "TM"}, {"family": "Dorajoo", "given": "Rajkumar", "initials": "R"}, {"family": "Li", "given": "Changwei", "initials": "C"}, {"family": "Liu", "given": "Yongmei", "initials": "Y"}, {"family": "Rankinen", "given": "Tuomo", "initials": "T"}, {"family": "Smith", "given": "Albert Vernon", "initials": "AV"}, {"family": "Tajuddin", "given": "Salman M", "initials": "SM"}, {"family": "Tayo", "given": "Bamidele O", "initials": "BO"}, {"family": "Zhao", "given": "Wei", "initials": "W"}, 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{"family": "Esko", "given": "T\u00f5nu", "initials": "T"}, {"family": "Farrall", "given": "Martin", "initials": "M"}, {"family": "Forrester", "given": "Terrence", "initials": "T"}, {"family": "Freedman", "given": "Barry I", "initials": "BI"}, {"family": "Froguel", "given": "Philippe", "initials": "P"}, {"family": "Gasparini", "given": "Paolo", "initials": "P"}, {"family": "Gieger", "given": "Christian", "initials": "C"}, {"family": "Horta", "given": "Bernardo Lessa", "initials": "BL"}, {"family": "Hung", "given": "Yi-Jen", "initials": "YJ"}, {"family": "Jonas", "given": "Jost Bruno", "initials": "JB"}, {"family": "Kato", "given": "Norihiro", "initials": "N"}, {"family": "Kooner", "given": "Jaspal S", "initials": "JS"}, {"family": "Laakso", "given": "Markku", "initials": "M"}, {"family": "Lehtim\u00e4ki", "given": "Terho", "initials": "T"}, {"family": "Liang", "given": "Kae-Woei", "initials": "KW"}, {"family": "Magnusson", "given": "Patrik K E", "initials": "PKE"}, {"family": "Oldehinkel", "given": "Albertine J", "initials": "AJ"}, {"family": "Pereira", "given": "Alexandre C", "initials": "AC"}, {"family": "Perls", "given": "Thomas", "initials": "T"}, {"family": "Rauramaa", "given": "Rainer", "initials": "R"}, {"family": "Redline", "given": "Susan", "initials": "S"}, {"family": "Rettig", "given": "Rainer", "initials": "R"}, {"family": "Samani", "given": "Nilesh J", "initials": "NJ"}, {"family": "Scott", "given": "James", "initials": "J"}, {"family": "Shu", "given": "Xiao-Ou", "initials": "XO"}, {"family": "van der Harst", "given": "Pim", "initials": "P"}, {"family": "Wagenknecht", "given": "Lynne E", "initials": "LE"}, {"family": "Wareham", "given": "Nicholas J", "initials": "NJ"}, {"family": "Watkins", "given": "Hugh", "initials": "H"}, {"family": "Wickremasinghe", "given": "Ananda R", "initials": "AR"}, {"family": "Wu", "given": "Tangchun", "initials": "T"}, {"family": "Kamatani", "given": "Yoichiro", "initials": "Y"}, {"family": "Laurie", "given": "Cathy C", "initials": "CC"}, {"family": "Bouchard", "given": "Claude", "initials": "C"}, {"family": "Cooper", "given": "Richard S", "initials": "RS"}, {"family": "Evans", "given": "Michele K", "initials": "MK"}, {"family": "Gudnason", "given": "Vilmundur", "initials": "V"}, {"family": "Hixson", "given": "James", "initials": "J"}, {"family": "Kardia", "given": "Sharon L R", "initials": "SLR"}, {"family": "Kritchevsky", "given": "Stephen B", "initials": "SB"}, {"family": "Psaty", "given": "Bruce M", "initials": "BM"}, {"family": "van Dam", "given": "Rob M", "initials": "RM"}, {"family": "Arnett", "given": "Donna K", "initials": "DK"}, {"family": "Mook-Kanamori", "given": "Dennis O", "initials": "DO"}, {"family": "Fornage", "given": "Myriam", "initials": "M"}, {"family": "Fox", "given": "Ervin R", "initials": "ER"}, {"family": "Hayward", "given": "Caroline", "initials": "C"}, {"family": "van Duijn", "given": "Cornelia M", "initials": "CM"}, {"family": "Tai", "given": "E Shyong", "initials": "ES"}, {"family": "Wong", "given": "Tien Yin", "initials": "TY"}, {"family": "Loos", "given": "Ruth J F", "initials": "RJF"}, {"family": "Reiner", "given": "Alex P", "initials": "AP"}, {"family": "Rotimi", "given": "Charles N", "initials": "CN"}, {"family": "Bierut", "given": "Laura J", "initials": "LJ"}, {"family": "Zhu", "given": "Xiaofeng", "initials": "X"}, {"family": "Cupples", "given": "L Adrienne", "initials": "LA"}, {"family": "Province", "given": "Michael A", "initials": "MA"}, {"family": "Rotter", "given": "Jerome I", "initials": "JI"}, {"family": "Franks", "given": "Paul W", "initials": "PW"}, {"family": "Rice", "given": "Kenneth", "initials": "K"}, {"family": "Elliott", "given": "Paul", "initials": "P"}, {"family": "Caulfield", "given": "Mark J", "initials": "MJ"}, {"family": "Gauderman", "given": "W James", "initials": "WJ"}, {"family": "Munroe", "given": "Patricia B", "initials": "PB"}, {"family": "Rao", "given": "Dabeeru C", "initials": "DC"}, {"family": "Morrison", "given": "Alanna C", "initials": "AC"}], "type": "journal article", "published": "2019-04-10", "journal": {"volume": null, "issn": "1460-2083", "issue": null, "title": "Hum. Mol. Genet.", "issn-l": "0964-6906"}, "abstract": "Elevated blood pressure (BP), a leading cause of global morbidity and mortality, is influenced by both genetic and lifestyle factors. Cigarette smoking is one such lifestyle factor. Across five ancestries, we performed a genome-wide gene-smoking interaction study of mean arterial pressure (MAP) and pulse pressure (PP) in 129\u2009913 individuals in stage 1 and follow-up analysis in 480\u2009178 additional individuals in stage 2. We report here 136 loci significantly associated with MAP and/or PP. Of these, 61 were previously published through main-effect analysis of BP traits, 37 were recently reported by us for systolic BP and/or diastolic BP through gene-smoking interaction analysis and 38 were newly identified (P\u2009<\u20095\u2009\u00d7\u200910-8, false discovery rate\u2009<\u20090.05). We also identified nine new signals near known loci. Of the 136 loci, 8 showed significant interaction with smoking status. They include CSMD1 previously reported for insulin resistance and BP in the spontaneously hypertensive rats. Many of the 38 new loci show biologic plausibility for a role in BP regulation. SLC26A7 encodes a chloride/bicarbonate exchanger expressed in the renal outer medullary collecting duct. AVPR1A is widely expressed, including in vascular smooth muscle cells, kidney, myocardium and brain. FHAD1 is a long non-coding RNA overexpressed in heart failure. TMEM51 was associated with contractile function in cardiomyocytes. CASP9 plays a central role in cardiomyocyte apoptosis. Identified only in African ancestry were 30 novel loci. Our findings highlight the value of multi-ancestry investigations, particularly in studies of interaction with lifestyle factors, where genomic and lifestyle differences may contribute to novel findings.", "doi": "10.1093/hmg/ddz070", "pmid": "31127295", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "5439584"}, {"db": "pmc", "key": "PMC6644157"}], "notes": [], "created": "2019-09-16T12:23:13.319Z", "modified": "2020-01-21T13:56:14.421Z"}, {"entity": "publication", "iuid": "fde78c4e8a6e4f4bb18faa285e9b451c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/fde78c4e8a6e4f4bb18faa285e9b451c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/fde78c4e8a6e4f4bb18faa285e9b451c"}}, "title": "Bidirectional Selection for Body Weight on Standing Genetic Variation in a Chicken Model.", "authors": [{"family": "Lillie", "given": "Mette", "initials": "M", "orcid": "0000-0001-8714-0812", "researcher": {"href": "https://publications.scilifelab.se/researcher/3ce02b2116c0417e8a4dcd578f45983b.json"}}, {"family": "Honaker", "given": "Christa F", "initials": "CF"}, {"family": "Siegel", "given": "Paul B", "initials": "PB"}, {"family": "Carlborg", "given": "\u00d6rjan", "initials": "\u00d6", "orcid": "0000-0002-2722-5264", "researcher": {"href": "https://publications.scilifelab.se/researcher/4efb0861e6144f00b8b4f5dd8a83c75b.json"}}], "type": "journal article", "published": "2019-04-09", "journal": {"volume": "9", "issn": "2160-1836", "issue": "4", "pages": "1165-1173", "title": "G3 (Bethesda)", "issn-l": "2160-1836"}, "abstract": "Experimental populations of model organisms provide valuable opportunities to unravel the genomic impact of selection in a controlled system. The Virginia body weight chicken lines represent a unique resource to investigate signatures of selection in a system where long-term, single-trait, bidirectional selection has been carried out for more than 60 generations. At 55 generations of divergent selection, earlier analyses of pooled genome resequencing data from these lines revealed that 14.2% of the genome showed extreme differentiation between the selected lines, contained within 395 genomic regions. Here, we report more detailed analyses of these data exploring the regions displaying within- and between-line genomic signatures of the bidirectional selection applied in these lines. Despite the strict selection regime for opposite extremes in body weight, this did not result in opposite genomic signatures between the lines. The lines often displayed a duality of the sweep signatures, where an extended region of homozygosity in one line, in contrast to mosaic pattern of heterozygosity in the other line. These haplotype mosaics consisted of short, distinct haploblocks of variable between-line divergence, likely the results of a complex demographic history involving bottlenecks, introgressions and moderate inbreeding. We demonstrate this using the example of complex haplotype mosaicism in the growth1 QTL. These mosaics represent the standing genetic variation available at the onset of selection in the founder population. Selection on standing genetic variation can thus result in different signatures depending on the intensity and direction of selection.", "doi": "10.1534/g3.119.400038", "pmid": "30737239", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "g3.119.400038"}, {"db": "pmc", "key": "PMC6469407"}, {"db": "figshare", "key": "10.25387/g3.7674281"}], "notes": [], "created": "2020-01-08T12:43:07.761Z", "modified": "2021-06-21T13:34:06.686Z"}, {"entity": "publication", "iuid": "4678681995a049ef9f7b56ce8b425c73", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4678681995a049ef9f7b56ce8b425c73.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4678681995a049ef9f7b56ce8b425c73"}}, "title": "Genetic Architectures of Childhood- and Adult-Onset Asthma Are Partly Distinct.", "authors": [{"family": "Ferreira", "given": "Manuel A R", "initials": "MAR"}, {"family": "Mathur", "given": "Riddhima", "initials": "R"}, {"family": "Vonk", "given": "Judith M", "initials": "JM"}, {"family": "Szwajda", "given": "Agnieszka", "initials": "A"}, {"family": "Brumpton", "given": "Ben", "initials": "B"}, {"family": "Granell", "given": "Raquel", "initials": "R"}, {"family": "Brew", "given": "Bronwyn K", "initials": "BK"}, {"family": "Ullemar", "given": "Vilhelmina", "initials": "V"}, {"family": "Lu", "given": "Yi", "initials": "Y"}, {"family": "Jiang", "given": "Yunxuan", "initials": "Y"}, {"family": "23andMe Research Team", "given": "", "initials": ""}, {"family": "eQTLGen Consortium", "given": "", "initials": ""}, {"family": "BIOS Consortium", "given": "", "initials": ""}, {"family": "Magnusson", "given": "Patrik K E", "initials": "PKE"}, {"family": "Karlsson", "given": "Robert", "initials": "R"}, {"family": "Hinds", "given": "David A", "initials": "DA"}, {"family": "Paternoster", "given": "Lavinia", "initials": "L"}, {"family": "Koppelman", "given": "Gerard H", "initials": "GH"}, {"family": "Almqvist", "given": "Catarina", "initials": "C"}], "type": "journal article", "published": "2019-04-04", "journal": {"volume": "104", "issn": "1537-6605", "issue": "4", "pages": "665-684", "title": "Am. J. Hum. Genet.", "issn-l": "0002-9297"}, "abstract": "The extent to which genetic risk factors are shared between childhood-onset (COA) and adult-onset (AOA) asthma has not been estimated. On the basis of data from the UK Biobank study (n = 447,628), we found that the variance in disease liability explained by common variants is higher for COA (onset at ages between 0 and 19 years; h 2g = 25.6%) than for AOA (onset at ages between 20 and 60 years; h2g = 10.6%). The genetic correlation (rg) between COA and AOA was 0.67. Variation in age of onset among COA-affected individuals had a low heritability (h2g = 5%), which we confirmed in independent studies and also among AOA-affected individuals. To identify subtype-specific genetic associations, we performed a genome-wide association study (GWAS) in the UK Biobank for COA (13,962 affected individuals) and a separate GWAS for AOA (26,582 affected individuals) by using a common set of 300,671 controls for both studies. We identified 123 independent associations for COA and 56 for AOA (37 overlapped); of these, 98 and 34, respectively, were reproducible in an independent study (n = 262,767). Collectively, 28 associations were not previously reported. For 96 COA-associated variants, including five variants that represent COA-specific risk factors, the risk allele was more common in COA- than in AOA-affected individuals. Conversely, we identified three variants that are stronger risk factors for AOA. Variants associated with obesity and smoking had a stronger contribution to the risk of AOA than to the risk of COA. Lastly, we identified 109 likely target genes of the associated variants, primarily on the basis of correlated expression quantitative trait loci (up to n = 31,684). GWAS informed by age of onset can identify subtype-specific risk variants, which can help us understand differences in pathophysiology between COA and AOA and so can be informative for drug development.", "doi": "10.1016/j.ajhg.2019.02.022", "pmid": "30929738", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "S0002-9297(19)30067-9"}, {"db": "pmc", "key": "PMC6451732"}], "notes": [], "created": "2019-04-12T14:00:38.338Z", "modified": "2021-06-21T12:08:57.171Z"}, {"entity": "publication", "iuid": "60647a4009af4347902f106baab2bf7c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/60647a4009af4347902f106baab2bf7c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/60647a4009af4347902f106baab2bf7c"}}, "title": "Post-glacial colonization routes coincide with a life-history breakpoint along a latitudinal gradient.", "authors": [{"family": "Luquet", "given": "Emilien", "initials": "E", "orcid": "0000-0002-9550-8899", "researcher": {"href": "https://publications.scilifelab.se/researcher/fd7a705353f6475e8b6b8621d9f205c9.json"}}, {"family": "R\u00f6din M\u00f6rch", "given": "Patrik", "initials": "P"}, {"family": "Cort\u00e1zar-Chinarro", "given": "Maria", "initials": "M"}, {"family": "Meyer-Lucht", "given": "Yvonne", "initials": "Y"}, {"family": "H\u00f6glund", "given": "Jacob", "initials": "J"}, {"family": "Laurila", "given": "Anssi", "initials": "A", "orcid": "0000-0001-8090-3776", "researcher": {"href": "https://publications.scilifelab.se/researcher/1b55d6c459ef448c992a37db2a02c3ea.json"}}], "type": "journal article", "published": "2019-04-00", "journal": {"volume": "32", "issn": "1420-9101", "issue": "4", "pages": "356-368", "title": "J. Evol. Biol.", "issn-l": "1010-061X"}, "abstract": "Although adaptive divergence along environmental gradients has repeatedly been demonstrated, the role of post-glacial colonization routes in determining phenotypic variation along gradients has received little attention. Here, we used a hierarchical Q ST -FST approach to separate the roles of adaptive and neutral processes in shaping phenotypic variation in moor frog (Rana arvalis) larval life histories along a 1,700 km latitudinal gradient across northern Europe. This species has colonized Scandinavia via two routes with a contact zone in northern Sweden. By using neutral SNP and common garden phenotypic data from 13 populations at two temperatures, we showed that most of the variation along the gradient occurred between the two colonizing lineages. We found little phenotypic divergence within the lineages; however, all phenotypic traits were strongly diverged between the southern and northern colonization routes, with higher growth and development rates and larger body size in the north. The QST estimates between the colonization routes were four times higher than FST , indicating a prominent role for natural selection. QST within the colonization routes did not generally differ from FST , but we found temperature-dependent adaptive divergence close to the contact zone. These results indicate that lineage-specific variation can account for much of the adaptive divergence along a latitudinal gradient.", "doi": "10.1111/jeb.13419", "pmid": "30703260", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "Dryad", "key": "10.5061/dryad.fn38f87"}], "notes": [], "created": "2020-01-08T12:39:54.536Z", "modified": "2021-06-21T12:08:42.895Z"}, {"entity": "publication", "iuid": "b9b71a4c6139494dbeedba7da68e5c49", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b9b71a4c6139494dbeedba7da68e5c49.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b9b71a4c6139494dbeedba7da68e5c49"}}, "title": "Mutation patterns in a population-based non-small cell lung cancer cohort and prognostic impact of concomitant mutations in KRAS and TP53 or STK11.", "authors": [{"family": "La Fleur", "given": "Linn\u00e9a", "initials": "L"}, {"family": "Falk-S\u00f6rqvist", "given": "Elin", "initials": "E"}, {"family": "Smeds", "given": "Patrik", "initials": "P"}, {"family": "Berglund", "given": "Anders", "initials": "A"}, {"family": "Sundstr\u00f6m", "given": "Magnus", "initials": "M"}, {"family": "Mattsson", "given": "Johanna Sm", "initials": "JS"}, {"family": "Brand\u00e9n", "given": "Eva", "initials": "E"}, {"family": "Koyi", "given": "Hirsh", "initials": "H", "orcid": "0000-0002-4960-1232", "researcher": {"href": "https://publications.scilifelab.se/researcher/952a87a3216c44baa33286c842c10d22.json"}}, {"family": "Isaksson", "given": "Johan", "initials": "J"}, {"family": "Brunnstr\u00f6m", "given": "Hans", "initials": "H"}, {"family": "Nilsson", "given": "Mats", "initials": "M", "orcid": "0000-0001-9985-0387", "researcher": {"href": "https://publications.scilifelab.se/researcher/197cf8ba83ba430f9712b2f4d94dc3e5.json"}}, {"family": "Micke", "given": "Patrick", "initials": "P", "orcid": "0000-0003-1210-5961", "researcher": {"href": "https://publications.scilifelab.se/researcher/fc0cba74e74a4c39a8f96319cb9a3034.json"}}, {"family": "Moens", "given": "Lotte", "initials": "L"}, {"family": "Botling", "given": "Johan", "initials": "J"}], "type": "journal article", "published": "2019-04-00", "journal": {"volume": "130", "issn": "1872-8332", "issue": null, "pages": "50-58", "title": "Lung Cancer", "issn-l": "0169-5002"}, "abstract": "Non-small cell lung cancer (NSCLC) is a heterogeneous disease with unique combinations of somatic molecular alterations in individual patients, as well as significant differences in populations across the world with regard to mutation spectra and mutation frequencies. Here we aim to describe mutational patterns and linked clinical parameters in a population-based NSCLC cohort.\n\nUsing targeted resequencing the mutational status of 82 genes was evaluated in a consecutive Swedish surgical NSCLC cohort, consisting of 352 patient samples from either fresh frozen or formalin fixed paraffin embedded (FFPE) tissues. The panel covers all exons of the 82 genes and utilizes reduced target fragment length and two-strand capture making it compatible with degraded FFPE samples.\n\nWe obtained a uniform sequencing coverage and mutation load across the fresh frozen and FFPE samples by adaption of sequencing depth and bioinformatic pipeline, thereby avoiding a technical bias between these two sample types. At large, the mutation frequencies resembled the frequencies seen in other western populations, except for a high frequency of KRAS hotspot mutations (43%) in adenocarcinoma patients. Worse overall survival was observed for adenocarcinoma patients with a mutation in either TP53, STK11 or SMARCA4. In the adenocarcinoma KRAS-mutated group poor survival appeared to be linked to concomitant TP53 or STK11 mutations, and not to KRAS mutation as a single aberration. Similar results were seen in the analysis of publicly available data from the cBioPortal. In squamous cell carcinoma a worse prognosis could be observed for patients with MLL2 mutations, while CSMD3 mutations were linked to a better prognosis.\n\nHere we have evaluated the mutational status of a NSCLC cohort. We could not confirm any survival impact of isolated driver mutations. Instead, concurrent mutations in TP53 and STK11 were shown to confer poor survival in the KRAS-positive adenocarcinoma subgroup.", "doi": "10.1016/j.lungcan.2019.01.003", "pmid": "30885352", "labels": {"National Genomics Infrastructure": "Service", "Clinical Genomics Uppsala": "Collaborative", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service", "Clinical Genomics": "Collaborative"}, "xrefs": [{"db": "pii", "key": "S0169-5002(19)30005-4"}], "notes": [], "created": "2019-11-29T13:21:46.345Z", "modified": "2024-01-16T13:48:44.581Z"}, {"entity": "publication", "iuid": "7a40ff4fb7e14b518f09678e19c9c8e1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7a40ff4fb7e14b518f09678e19c9c8e1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7a40ff4fb7e14b518f09678e19c9c8e1"}}, "title": "Multi-ancestry genome-wide gene-smoking interaction study of 387,272 individuals identifies new loci associated with serum lipids.", "authors": [{"family": "Bentley", "given": "Amy R", "initials": "AR", "orcid": "0000-0002-0827-9101", "researcher": {"href": "https://publications.scilifelab.se/researcher/da79fd53be004c09b1ff6c81d1fb709c.json"}}, {"family": "Sung", "given": "Yun J", "initials": "YJ"}, {"family": "Brown", "given": "Michael R", "initials": "MR"}, {"family": "Winkler", "given": "Thomas W", "initials": "TW"}, {"family": "Kraja", "given": "Aldi T", "initials": "AT"}, {"family": "Ntalla", "given": "Ioanna", "initials": "I"}, {"family": "Schwander", "given": "Karen", "initials": "K"}, {"family": "Chasman", "given": "Daniel I", "initials": "DI"}, {"family": "Lim", "given": "Elise", "initials": "E"}, {"family": "Deng", "given": "Xuan", "initials": "X"}, {"family": "Guo", "given": "Xiuqing", "initials": "X"}, {"family": "Liu", "given": "Jingmin", "initials": "J", "orcid": "0000-0002-3255-3019", "researcher": {"href": 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{"family": "Samani", "given": "Nilesh J", "initials": "NJ"}, {"family": "Scott", "given": "James", "initials": "J"}, {"family": "Shu", "given": "Xiao-Ou", "initials": "XO"}, {"family": "van der Harst", "given": "Pim", "initials": "P", "orcid": "0000-0002-2713-686X", "researcher": {"href": "https://publications.scilifelab.se/researcher/a710eb0e12344e8fb5083599c95a1b2e.json"}}, {"family": "Wagenknecht", "given": "Lynne E", "initials": "LE"}, {"family": "Wang", "given": "Jun-Sing", "initials": "JS"}, {"family": "Wang", "given": "Ya Xing", "initials": "YX", "orcid": "0000-0003-2749-7793", "researcher": {"href": "https://publications.scilifelab.se/researcher/a335d5361052470689def030e03e597b.json"}}, {"family": "Wareham", "given": "Nicholas J", "initials": "NJ"}, {"family": "Watkins", "given": "Hugh", "initials": "H"}, {"family": "Weir", "given": "David R", "initials": "DR"}, {"family": "Wickremasinghe", "given": "Ananda R", "initials": "AR"}, {"family": "Wu", "given": "Tangchun", "initials": "T"}, {"family": "Zeggini", "given": "Eleftheria", "initials": "E"}, {"family": "Zheng", "given": "Wei", "initials": "W", "orcid": "0000-0003-1226-070X", "researcher": {"href": "https://publications.scilifelab.se/researcher/f627ad7a8b2740cd9efc88a79157f29e.json"}}, {"family": "Bouchard", "given": "Claude", "initials": "C"}, {"family": "Evans", "given": "Michele K", "initials": "MK"}, {"family": "Gudnason", "given": "Vilmundur", "initials": "V", "orcid": "0000-0001-5696-0084", "researcher": {"href": "https://publications.scilifelab.se/researcher/d18327939c1541acba054b2340ac174f.json"}}, {"family": "Kardia", "given": "Sharon L R", "initials": "SLR"}, {"family": "Liu", "given": "Yongmei", "initials": "Y"}, {"family": "Psaty", "given": "Bruce M", "initials": "BM"}, {"family": "Ridker", "given": "Paul M", "initials": "PM"}, {"family": "van Dam", "given": "Rob M", "initials": "RM"}, {"family": "Mook-Kanamori", "given": "Dennis O", "initials": "DO"}, {"family": "Fornage", "given": "Myriam", "initials": "M"}, {"family": "Province", "given": "Michael A", "initials": "MA"}, {"family": "Kelly", "given": "Tanika N", "initials": "TN"}, {"family": "Fox", "given": "Ervin R", "initials": "ER"}, {"family": "Hayward", "given": "Caroline", "initials": "C", "orcid": "0000-0002-9405-9550", "researcher": {"href": "https://publications.scilifelab.se/researcher/cd49e9ad5a024c7ca2f1aa97d9e58eba.json"}}, {"family": "van Duijn", "given": "Cornelia M", "initials": "CM"}, {"family": "Tai", "given": "E Shyong", "initials": "ES"}, {"family": "Wong", "given": "Tien Yin", "initials": "TY"}, {"family": "Loos", "given": "Ruth J F", "initials": "RJF", "orcid": "0000-0002-8532-5087", "researcher": {"href": "https://publications.scilifelab.se/researcher/e5b6c24c302d42828806076ded81afe1.json"}}, {"family": "Franceschini", "given": "Nora", "initials": "N"}, {"family": "Rotter", "given": "Jerome I", "initials": "JI"}, {"family": "Zhu", "given": "Xiaofeng", "initials": "X"}, {"family": "Bierut", "given": "Laura J", "initials": "LJ"}, {"family": "Gauderman", "given": "W James", "initials": "WJ"}, {"family": "Rice", "given": "Kenneth", "initials": "K", "orcid": "0000-0002-3071-7278", "researcher": {"href": "https://publications.scilifelab.se/researcher/5affb61f3ef141e8a6e7c7bfd2477ae3.json"}}, {"family": "Munroe", "given": "Patricia B", "initials": "PB", "orcid": "0000-0002-4176-2947", "researcher": {"href": "https://publications.scilifelab.se/researcher/657544a7f921459f926aae5cd0e2065c.json"}}, {"family": "Morrison", "given": "Alanna C", "initials": "AC"}, {"family": "Rao", "given": "Dabeeru C", "initials": "DC"}, {"family": "Rotimi", "given": "Charles N", "initials": "CN", "orcid": "0000-0001-5759-053X", "researcher": {"href": "https://publications.scilifelab.se/researcher/7fa2951fdebf4fddaad296d49b8f3f2b.json"}}, {"family": "Cupples", "given": "L Adrienne", "initials": "LA", "orcid": "0000-0003-0273-7965", "researcher": {"href": "https://publications.scilifelab.se/researcher/b931b673086a471e9fd17728b97fb83e.json"}}], "type": "journal article", "published": "2019-04-00", "journal": {"volume": "51", "issn": "1546-1718", "issue": "4", "pages": "636-648", "title": "Nat. Genet.", "issn-l": "1061-4036"}, "abstract": "The concentrations of high- and low-density-lipoprotein cholesterol and triglycerides are influenced by smoking, but it is unknown whether genetic associations with lipids may be modified by smoking. We conducted a multi-ancestry genome-wide gene-smoking interaction study in 133,805 individuals with follow-up in an additional 253,467 individuals. Combined meta-analyses identified 13 new loci associated with lipids, some of which were detected only because association differed by smoking status. Additionally, we demonstrate the importance of including diverse populations, particularly in studies of interactions with lifestyle factors, where genomic and lifestyle differences by ancestry may contribute to novel findings.", "doi": "10.1038/s41588-019-0378-y", "pmid": "30926973", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41588-019-0378-y"}, {"db": "pmc", "key": "PMC6467258"}, {"db": "mid", "key": "NIHMS1521094"}], "notes": [], "created": "2019-04-12T14:00:38.931Z", "modified": "2021-06-21T12:08:20.267Z"}, {"entity": "publication", "iuid": "bd2759fb45af4bd9a9e69a0e7f2e9d24", "links": {"self": {"href": "https://publications.scilifelab.se/publication/bd2759fb45af4bd9a9e69a0e7f2e9d24.json"}, "display": {"href": "https://publications.scilifelab.se/publication/bd2759fb45af4bd9a9e69a0e7f2e9d24"}}, "title": "A geographically matched control population efficiently limits the number of candidate disease-causing variants in an unbiased whole-genome analysis", "authors": [{"family": "Rentoft", "given": "Matilda", "initials": "M"}, {"family": "Svensson", "given": "Daniel", "initials": "D"}, {"family": "Sj\u00f6din", "given": "Andreas", "initials": "A"}, {"family": "Olason", "given": "Pall I", "initials": "PI"}, {"family": "Sj\u00f6str\u00f6m", "given": "Olle", "initials": "O"}, {"family": "Nylander", "given": "Carin", "initials": "C"}, {"family": "Osterman", "given": "Pia", "initials": "P"}, {"family": "Sj\u00f6gren", "given": "Rickard", "initials": "R"}, {"family": "Netotea", "given": "Sergiu", "initials": "S"}, {"family": "Wibom", "given": "Carl", "initials": "C"}, {"family": "Cederquist", "given": "Kristina", "initials": "K"}, {"family": "Chabes", "given": "Andrei", "initials": "A"}, {"family": "Trygg", "given": "Johan", "initials": "J"}, {"family": "Melin", "given": "Beatrice S", "initials": "BS"}, {"family": "Johansson", "given": "Erik", "initials": "E"}], "type": "journal-article", "published": "2019-03-27", "journal": {"volume": "14", "issn": "1932-6203", "issue": "3", "pages": "e0213350", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "Whole-genome sequencing is a promising approach for human autosomal dominant disease studies. However, the vast number of genetic variants observed by this method constitutes a challenge when trying to identify the causal variants. This is often handled by restricting disease studies to the most damaging variants, e.g. those found in coding regions, and overlooking the remaining genetic variation. Such a biased approach explains in part why the genetic causes of many families with dominantly inherited diseases, in spite of being included in whole-genome sequencing studies, are left unsolved today. Here we explore the use of a geographically matched control population to minimize the number of candidate disease-causing variants without excluding variants based on assumptions on genomic position or functional predictions. To exemplify the benefit of the geographically matched control population we apply a typical disease variant filtering strategy in a family with an autosomal dominant form of colorectal cancer. With the use of the geographically matched control population we end up with 26 candidate variants genome wide. This is in contrast to the tens of thousands of candidates left when only making use of available public variant datasets. The effect of the local control population is dual, it (1) reduces the total number of candidate variants shared between affected individuals, and more importantly (2) increases the rate by which the number of candidate variants are reduced as additional affected family members are included in the filtering strategy. We demonstrate that the application of a geographically matched control population effectively limits the number of candidate disease-causing variants and may provide the means by which variants suitable for functional studies are identified genome wide.", "doi": "10.1371/journal.pone.0213350", "pmid": "30917156", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "Systems Biology": "Collaborative", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [], "notes": [], "created": "2019-04-04T19:12:26.169Z", "modified": "2024-01-16T13:48:44.593Z"}, {"entity": "publication", "iuid": "245c154fe70e44399677dc677d54a1f0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/245c154fe70e44399677dc677d54a1f0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/245c154fe70e44399677dc677d54a1f0"}}, "title": "Subsequent Event Risk in Individuals with Established Coronary Heart Disease: Design and Rationale of the GENIUS-CHD Consortium.", "authors": [{"family": "Patel", "given": "Riyaz", "initials": "R"}, {"family": "Tragante", "given": "Vinicius", "initials": "V"}, {"family": "Schmidt", "given": "Amand F", "initials": "AF"}, {"family": "McCubrey", "given": "Raymond O", "initials": "RO"}, {"family": "Holmes", "given": "Michael V", "initials": "MV"}, {"family": "Howe", "given": "Laurence J", "initials": "LJ"}, {"family": "Direk", "given": "Kenan", "initials": "K"}, {"family": "\u00c5kerblom", "given": "Axel", "initials": "A"}, {"family": "Leander", "given": "Karin", "initials": "K"}, {"family": "Virani", "given": "Salim S", "initials": "SS"}, {"family": "Kaminski", "given": "Karol A", "initials": "KA"}, {"family": "Muehlschlegel", "given": "Jochen D", "initials": "JD"}, {"family": "Allayee", "given": "Hooman", "initials": "H"}, {"family": "Almgren", "given": "Peter", "initials": "P"}, {"family": "Alver", "given": "Maris", "initials": "M"}, {"family": "Baranova", "given": "Ekaterina V", "initials": "EV"}, {"family": "Behlouli", "given": "Hassan", "initials": "H"}, {"family": "Boeckx", "given": "Bram", "initials": "B"}, {"family": "Braund", "given": "Peter S", "initials": "PS"}, {"family": "Breitling", "given": "Lutz P", "initials": "LP"}, {"family": "Delgado", "given": "Graciela", "initials": "G"}, {"family": "Duarte", "given": "Nubia E", "initials": "NE"}, {"family": "Dub\u00e9", "given": "Marie-Pierre", "initials": "MP"}, {"family": "Dufresne", "given": "Line", "initials": "L"}, {"family": "Eriksson", "given": "Niclas", "initials": "N"}, {"family": "Foco", "given": "Luisa", "initials": "L"}, {"family": "Scholz", "given": "Markus", "initials": "M"}, {"family": 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"initials": "U"}, {"family": "Nelson", "given": "Christopher P", "initials": "CP"}, {"family": "Nikus", "given": "Kjell", "initials": "K"}, {"family": "Pilbrow", "given": "Anna P", "initials": "AP"}, {"family": "Ploski", "given": "Rafal", "initials": "R"}, {"family": "Sun", "given": "Yan V", "initials": "YV"}, {"family": "Tanck", "given": "Michael W T", "initials": "MWT"}, {"family": "Tang", "given": "W H Wilson", "initials": "WHW"}, {"family": "Trompet", "given": "Stella", "initials": "S"}, {"family": "van der Laan", "given": "Sander W", "initials": "SW"}, {"family": "Van Setten", "given": "Jessica", "initials": "J"}, {"family": "Vilmundarson", "given": "Ragnar O", "initials": "RO"}, {"family": "Viviani Anselmi", "given": "Chiara", "initials": "C"}, {"family": "Vlachopoulou", "given": "Efthymia", "initials": "E"}, {"family": "Al Ali", "given": "Lawien", "initials": "L"}, {"family": "Boerwinkle", "given": "Eric", "initials": "E"}, {"family": "Briguori", "given": "Carlo", "initials": "C"}, {"family": "Carlquist", "given": "John F", "initials": "JF"}, {"family": "Carruthers", "given": "Kathryn F", "initials": "KF"}, {"family": "Casu", "given": "Gavino", "initials": "G"}, {"family": "Deanfield", "given": "John", "initials": "J"}, {"family": "Deloukas", "given": "Panos", "initials": "P"}, {"family": "Dudbridge", "given": "Frank", "initials": "F"}, {"family": "Engstr\u00f6m", "given": "Thomas", "initials": "T"}, {"family": "Fitzpatrick", "given": "Natalie", "initials": "N"}, {"family": "Fox", "given": "Kim", "initials": "K"}, {"family": "Gigante", "given": "Bruna", "initials": "B"}, {"family": "James", "given": "Stefan", "initials": "S"}, {"family": "Lokki", "given": "Marja-Liisa", "initials": "ML"}, {"family": "Lotufo", "given": "Paulo A", "initials": "PA"}, {"family": "Marziliano", "given": "Nicola", "initials": "N"}, {"family": "Mordi", "given": "Ify R", "initials": "IR"}, {"family": "Muhlestein", "given": "Joseph B", "initials": "JB"}, {"family": "Newton-Cheh", "given": "Christopher", "initials": "C"}, {"family": "Pitha", "given": "Jan", "initials": "J"}, {"family": "Saely", "given": "Christoph H", "initials": "CH"}, {"family": "Samman-Tahhan", "given": "Ayman", "initials": "A"}, {"family": "Sandesara", "given": "Pratik B", "initials": "PB"}, {"family": "Teren", "given": "Andrej", "initials": "A"}, {"family": "Timmis", "given": "Adam", "initials": "A"}, {"family": "Van de Werf", "given": "Frans", "initials": "F"}, {"family": "Wauters", "given": "Els", "initials": "E"}, {"family": "Wilde", "given": "Arthur A M", "initials": "AAM"}, {"family": "Ford", "given": "Ian", "initials": "I"}, {"family": "Stott", "given": "David J", "initials": "DJ"}, {"family": "Algra", "given": "Ale", "initials": "A"}, {"family": "Andreassi", "given": "Maria G", "initials": "MG"}, {"family": "Ardissino", "given": "Diego", "initials": "D"}, {"family": "Arsenault", "given": "Benoit J", "initials": "BJ"}, {"family": "Ballantyne", "given": "Christie M", "initials": "CM"}, {"family": "Bergmeijer", "given": "Thomas O", "initials": "TO"}, {"family": "Bezzina", "given": "Connie R", "initials": "CR"}, {"family": "Body", "given": "Simon C", "initials": "SC"}, {"family": "Boersma", "given": "Eric H", "initials": "EH"}, {"family": "Bogaty", "given": "Peter", "initials": "P"}, {"family": "Bots", "given": "Michiel", "initials": "M"}, {"family": "Brenner", "given": "Hermann", "initials": "H"}, {"family": "Brugts", "given": "Jasper J", "initials": "JJ"}, {"family": "Burkhardt", "given": "Ralph", "initials": "R"}, {"family": "Carpeggiani", "given": "Clara", "initials": "C"}, {"family": "Condorelli", "given": "Gianluigi", "initials": "G"}, {"family": "Cooper-DeHoff", "given": "Rhonda M", "initials": "RM"}, {"family": "Cresci", "given": "Sharon", "initials": "S"}, {"family": "Danchin", "given": "Nicolas", "initials": "N"}, {"family": "de Faire", "given": "Ulf", "initials": "U"}, {"family": "Doughty", "given": "Robert N", "initials": "RN"}, {"family": "Drexel", "given": "Heinz", "initials": "H"}, {"family": "Engert", "given": "James C", "initials": "JC"}, {"family": "Fox", "given": "Keith A A", "initials": "KAA"}, {"family": "Girelli", "given": "Domenico", "initials": "D"}, {"family": "Grobbee", "given": "Diederick E", "initials": "DE"}, {"family": "Hagstr\u00f6m", "given": "Emil", "initials": "E"}, {"family": "Hazen", "given": "Stanley L", "initials": "SL"}, {"family": "Held", "given": "Claes", "initials": "C"}, {"family": "Hemingway", "given": "Harry", "initials": "H"}, {"family": "Hoefer", "given": "Imo E", "initials": "IE"}, {"family": "Hovingh", "given": "G Kees", "initials": "GK"}, {"family": "Jabbari", "given": "Reza", "initials": "R"}, {"family": "Johnson", "given": "Julie A", "initials": "JA"}, {"family": "Jukema", "given": "J Wouter", "initials": "JW"}, {"family": "Kaczor", "given": "Marcin P", "initials": "MP"}, {"family": "K\u00e4h\u00f6nen", "given": "Mika", "initials": "M"}, {"family": "Kettner", "given": "Jiri", "initials": "J"}, {"family": "Kiliszek", "given": "Marek", "initials": "M"}, {"family": "Klungel", "given": "Olaf H", "initials": "OH"}, {"family": "Lagerqvist", "given": "Bo", "initials": "B"}, {"family": "Lambrechts", "given": "Diether", "initials": "D"}, {"family": "Laurikka", "given": "Jari O", "initials": "JO"}, {"family": "Lehtim\u00e4ki", "given": "Terho", "initials": "T"}, {"family": "Lindholm", "given": "Daniel", "initials": "D"}, {"family": "Mahmoodi", "given": "B K", "initials": "BK"}, {"family": "Maitland-van der Zee", "given": "Anke H", "initials": "AH"}, {"family": "McPherson", "given": "Ruth", "initials": "R"}, {"family": "Melander", "given": "Olle", "initials": "O"}, {"family": "Metspalu", "given": "Andres", "initials": "A"}, {"family": "Niemcunowicz-Janica", "given": "Anna", "initials": "A"}, {"family": "Olivieri", "given": "Oliviero", "initials": "O"}, {"family": "Opolski", "given": "Grzegorz", "initials": "G"}, {"family": "Palmer", "given": "Colin N", "initials": "CN"}, {"family": "Pasterkamp", "given": "Gerard", "initials": "G"}, {"family": "Pepine", "given": "Carl J", "initials": "CJ"}, {"family": "Pereira", "given": "Alexandre C", "initials": "AC"}, {"family": "Pilote", "given": "Louise", "initials": "L"}, {"family": "Quyyumi", "given": "Arshed A", "initials": "AA"}, {"family": "Richards", "given": "A Mark", "initials": "AM"}, {"family": "Sanak", "given": "Marek", "initials": "M"}, {"family": "Siegbahn", "given": "Agneta", "initials": "A"}, {"family": "Simon", "given": "Tabassome", "initials": "T"}, {"family": "Sinisalo", "given": "Juha", "initials": "J"}, {"family": "Smith", "given": "J Gustav", "initials": "JG"}, {"family": "Spertus", "given": "John A", "initials": "JA"}, {"family": "Stender", "given": "Steen", "initials": "S"}, {"family": "Stewart", "given": "Alexandre F R", "initials": "AFR"}, {"family": "Szczeklik", "given": "Wojciech", "initials": "W"}, {"family": "Szpakowicz", "given": "Anna", "initials": "A"}, {"family": "Tardif", "given": "Jean-Claude", "initials": "JC"}, {"family": "Ten Berg", "given": "Jurri\u00ebn M", "initials": "JM"}, {"family": "Tfelt-Hansen", "given": "Jacob", "initials": "J"}, {"family": "Thanassoulis", "given": "George", "initials": "G"}, {"family": "Thiery", "given": "Joachim", "initials": "J"}, {"family": "Torp-Pedersen", "given": "Christian", "initials": "C"}, {"family": "van der Graaf", "given": "Yolanda", "initials": "Y"}, {"family": "Visseren", "given": "Frank L J", "initials": "FLJ"}, {"family": "Waltenberger", "given": "Johannes", "initials": "J"}, {"family": "Weeke", "given": "Peter E", "initials": "PE"}, {"family": "Van der Harst", "given": "Pim", "initials": "P"}, {"family": "Lang", "given": "Chim C", "initials": "CC"}, {"family": "Sattar", "given": "Naveed", "initials": "N"}, {"family": "Cameron", "given": "Vicky A", "initials": "VA"}, {"family": "Anderson", "given": "Jeffrey L", "initials": "JL"}, {"family": "Brophy", "given": "James M", "initials": "JM"}, {"family": "Par\u00e9", "given": "Guillaume", "initials": "G"}, {"family": "Horne", "given": "Benjamin D", "initials": "BD"}, {"family": "M\u00e4rz", "given": "Winfried", "initials": "W"}, {"family": "Wallentin", "given": "Lars", "initials": "L"}, {"family": "Samani", "given": "Nilesh J", "initials": "NJ"}, {"family": "Hingorani", "given": "Aroon D", "initials": "AD"}, {"family": "Asselbergs", "given": "Folkert W", "initials": "FW"}], "type": "journal article", "published": "2019-03-21", "journal": {"volume": null, "issn": "2574-8300", "issue": null, "title": "Circ Genom Precis Med", "issn-l": "2574-8300"}, "abstract": "The \"GENetIcs of sUbSequent Coronary Heart Disease\" (GENIUS-CHD) consortium was established to facilitate discovery and validation of genetic variants and biomarkers for risk of subsequent CHD events, in individuals with established CHD.\n\nThe consortium currently includes 57 studies from 18 countries, recruiting 185,614 participants with either acute coronary syndrome, stable CHD or a mixture of both at baseline. All studies collected biological samples and followed-up study participants prospectively for subsequent events.\n\nEnrollment into the individual studies took place between 1985 to present day with duration of follow up ranging from 9 months to 15 years. Within each study, participants with CHD are predominantly of self-reported European descent (38%-100%), mostly male (44%-91%) with mean ages at recruitment ranging from 40 to 75 years. Initial feasibility analyses, using a federated analysis approach, yielded expected associations between age (HR 1.15 95% CI 1.14-1.16) per 5-year increase, male sex (HR 1.17, 95% CI 1.13-1.21) and smoking (HR 1.43, 95% CI 1.35-1.51) with risk of subsequent CHD death or myocardial infarction, and differing associations with other individual and composite cardiovascular endpoints.\n\nGENIUS-CHD is a global collaboration seeking to elucidate genetic and non-genetic determinants of subsequent event risk in individuals with established CHD, in order to improve residual risk prediction and identify novel drug targets for secondary prevention. Initial analyses demonstrate the feasibility and reliability of a federated analysis approach. The consortium now plans to initiate and test novel hypotheses as well as supporting replication and validation analyses for other investigators.", "doi": "10.1161/CIRCGEN.119.002470", "pmid": "30896328", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [], "notes": [], "created": "2019-04-30T11:25:58.584Z", "modified": "2020-01-21T13:56:14.170Z"}, {"entity": "publication", "iuid": "33ff715f09eb42d3ab347fdb1f582366", "links": {"self": {"href": "https://publications.scilifelab.se/publication/33ff715f09eb42d3ab347fdb1f582366.json"}, "display": {"href": "https://publications.scilifelab.se/publication/33ff715f09eb42d3ab347fdb1f582366"}}, "title": "Association of Chromosome 9p21 with Subsequent Coronary Heart Disease Events: A GENIUS-CHD Study of Individual Participant Data.", "authors": [{"family": "Patel", "given": "Riyaz S", "initials": "RS"}, {"family": "Schmidt", "given": "Amand F", "initials": "AF"}, {"family": "Tragante", "given": "Vinicius", "initials": "V"}, {"family": "McCubrey", "given": "Raymond O", "initials": "RO"}, {"family": "Holmes", "given": "Michael V", "initials": "MV"}, {"family": "Howe", "given": "Laurence J", "initials": "LJ"}, {"family": "Direk", "given": "Kenan", "initials": "K"}, {"family": "\u00c5kerblom", "given": "Axel", "initials": "A"}, {"family": "Leander", "given": "Karin", "initials": "K"}, {"family": "Virani", "given": "Salim S", "initials": "SS"}, {"family": "Kaminski", "given": "Karol A", "initials": "KA"}, {"family": "Muehlschlegel", "given": "Jochen D", "initials": "JD"}, {"family": "Dub\u00e9", "given": "Marie-Pierre", "initials": "MP"}, {"family": "Allayee", "given": "Hooman", "initials": "H"}, {"family": "Almgren", "given": "Peter", "initials": "P"}, {"family": "Alver", "given": "Maris", "initials": "M"}, {"family": "Baranova", "given": "Ekaterina V", "initials": "EV"}, {"family": "Behlouli", "given": "Hassan", "initials": "H"}, {"family": "Boeckx", "given": "Bram", "initials": "B"}, {"family": "Braund", "given": "Peter S", "initials": "PS"}, {"family": "Breitling", "given": "Lutz P", "initials": "LP"}, {"family": "Delgado", "given": "Graciela", "initials": "G"}, {"family": "Duarte", "given": "Nubia E", "initials": "NE"}, {"family": "Dufresne", "given": "Line", "initials": "L"}, {"family": "Eriksson", "given": "Niclas", "initials": "N"}, {"family": "Foco", "given": "Luisa", "initials": "L"}, {"family": "Gijsberts", "given": "Crystel M", "initials": "CM"}, {"family": "Gong", "given": "Yan", "initials": "Y"}, {"family": "Hartiala", "given": "Jaana", "initials": "J"}, {"family": "Heydarpour", "given": "Mahyar", "initials": "M"}, {"family": "Hubacek", "given": "Jaroslav A", "initials": "JA"}, {"family": "Kleber", "given": "Marcus", "initials": "M"}, {"family": "Kofink", "given": "Daniel", "initials": "D"}, {"family": "Kuukasj\u00e4rvi", "given": "Pekka", "initials": "P"}, {"family": "Lee", "given": "Vei-Vei", "initials": "VV"}, {"family": "Leiherer", "given": "Andreas", "initials": "A"}, {"family": "Lenzini", "given": "Petra A", "initials": "PA"}, {"family": "Levin", "given": "Daniel", "initials": "D"}, {"family": "Lyytik\u00e4inen", "given": "Leo-Pekka", "initials": "LP"}, {"family": "Martinelli", "given": "Nicola", "initials": "N"}, {"family": "Mons", "given": "Ute", "initials": "U"}, {"family": "Nelson", "given": "Christopher P", "initials": "CP"}, {"family": "Nikus", "given": "Kjell", "initials": "K"}, {"family": "Pilbrow", "given": "Anna P", "initials": "AP"}, {"family": "Ploski", "given": "Rafal", "initials": "R"}, {"family": "Sun", "given": "Yan V", "initials": "YV"}, {"family": "Tanck", "given": "Michael W T", "initials": "MWT"}, {"family": "Tang", "given": "W H Wilson", "initials": "WHW"}, {"family": "Trompet", "given": "Stella", "initials": "S"}, {"family": "van der Laan", "given": "Sander W", "initials": "SW"}, {"family": "Van Setten", "given": "Jessica", "initials": "J"}, {"family": "Vilmundarson", "given": "Ragnar O", "initials": "RO"}, {"family": "Viviani Anselmi", "given": "Chiara", "initials": "C"}, {"family": "Vlachopoulou", "given": "Efthymia", "initials": "E"}, {"family": "Boerwinkle", "given": "Eric", "initials": "E"}, {"family": "Briguori", "given": "Carlo", "initials": "C"}, {"family": "Carlquist", "given": "John F", "initials": "JF"}, {"family": "Carruthers", "given": "Kathryn F", "initials": "KF"}, {"family": "Casu", "given": "Gavino", "initials": "G"}, {"family": "Deanfield", "given": "John", "initials": "J"}, {"family": "Deloukas", "given": "Panos", "initials": "P"}, {"family": "Dudbridge", "given": "Frank", "initials": "F"}, {"family": "Fitzpatrick", "given": "Natalie", "initials": "N"}, {"family": "Gigante", "given": "Bruna", "initials": "B"}, {"family": "James", "given": "Stefan", "initials": "S"}, {"family": "Lokki", "given": "Marja-Liisa", "initials": "ML"}, {"family": "Lotufo", "given": "Paulo A", "initials": "PA"}, {"family": "Marziliano", "given": "Nicola", "initials": "N"}, {"family": "Mordi", "given": "Ify R", "initials": "IR"}, {"family": "Muhlestein", "given": "Joseph B", "initials": "JB"}, {"family": "Newton-Cheh", "given": "Christopher", "initials": "C"}, {"family": "Pitha", "given": "Jan", "initials": "J"}, {"family": "Saely", "given": "Christoph H", "initials": "CH"}, {"family": "Samman-Tahhan", "given": "Ayman", "initials": "A"}, {"family": "Sandesara", "given": "Pratik B", "initials": "PB"}, {"family": "Teren", "given": "Andrej", "initials": "A"}, {"family": "Timmis", "given": "Adam", "initials": "A"}, {"family": "Van de Werf", "given": "Frans", "initials": "F"}, {"family": "Wauters", "given": "Els", "initials": "E"}, {"family": "Wilde", "given": "Arthur A M", "initials": "AAM"}, {"family": "Ford", "given": "Ian", "initials": "I"}, {"family": "Stott", "given": "David J", "initials": "DJ"}, {"family": "Algra", "given": "Ale", "initials": "A"}, {"family": "Andreassi", "given": "Maria G", "initials": "MG"}, {"family": "Ardissino", "given": "Diego", "initials": "D"}, {"family": "Arsenault", "given": "Benoit J", "initials": "BJ"}, {"family": "Ballantyne", "given": "Christie M", "initials": "CM"}, {"family": "Bergmeijer", "given": "Thomas O", "initials": "TO"}, {"family": "Bezzina", "given": "Connie R", "initials": "CR"}, {"family": "Body", "given": "Simon C", "initials": "SC"}, {"family": "Bogaty", "given": "Peter", "initials": "P"}, {"family": "de Borst", "given": "Gert J", "initials": "GJ"}, {"family": "Brenner", "given": "Hermann", "initials": "H"}, {"family": "Burkhardt", "given": "Ralph", "initials": "R"}, {"family": "Carpeggiani", "given": "Clara", "initials": "C"}, {"family": "Condorelli", "given": "Gianluigi", "initials": "G"}, {"family": "Cooper-DeHoff", "given": "Rhonda M", "initials": "RM"}, {"family": "Cresci", "given": "Sharon", "initials": "S"}, {"family": "de Faire", "given": "Ulf", "initials": "U"}, {"family": "Doughty", "given": "Robert N", "initials": "RN"}, {"family": "Drexel", "given": "Heinz", "initials": "H"}, {"family": "Engert", "given": "James C", "initials": "JC"}, {"family": "Fox", "given": "Keith A A", "initials": "KAA"}, {"family": "Girelli", "given": "Domenico", "initials": "D"}, {"family": "Hagstr\u00f6m", "given": "Emil", "initials": "E"}, {"family": "Hazen", "given": "Stanley L", "initials": "SL"}, {"family": "Held", "given": "Claes", "initials": "C"}, {"family": "Hemingway", "given": "Harry", "initials": "H"}, {"family": "Hoefer", "given": "Imo E", "initials": "IE"}, {"family": "Hovingh", "given": "G Kees", "initials": "GK"}, {"family": "Johnson", "given": "Julie A", "initials": "JA"}, {"family": "de Jong", "given": "Pim A", "initials": "PA"}, {"family": "Jukema", "given": "J Wouter", "initials": "JW"}, {"family": "Kaczor", "given": "Marcin P", "initials": "MP"}, {"family": "K\u00e4h\u00f6nen", "given": "Mika", "initials": "M"}, {"family": "Kettner", "given": "Jiri", "initials": "J"}, {"family": "Kiliszek", "given": "Marek", "initials": "M"}, {"family": "Klungel", "given": "Olaf H", "initials": "OH"}, {"family": "Lagerqvist", "given": "Bo", "initials": "B"}, {"family": "Lambrechts", "given": "Diether", "initials": "D"}, {"family": "Laurikka", "given": "Jari O", "initials": "JO"}, {"family": "Lehtim\u00e4ki", "given": "Terho", "initials": "T"}, {"family": "Lindholm", "given": "Daniel", "initials": "D"}, {"family": "Mahmoodi", "given": "B K", "initials": "BK"}, {"family": "Maitland-van der Zee", "given": "Anke H", "initials": "AH"}, {"family": "McPherson", "given": "Ruth", "initials": "R"}, {"family": "Melander", "given": "Olle", "initials": "O"}, {"family": "Metspalu", "given": "Andres", "initials": "A"}, {"family": "Pepinski", "given": "Witold", "initials": "W"}, {"family": "Olivieri", "given": "Oliviero", "initials": "O"}, {"family": "Opolski", "given": "Grzegorz", "initials": "G"}, {"family": "Palmer", "given": "Colin N", "initials": "CN"}, {"family": "Pasterkamp", "given": "Gerard", "initials": "G"}, {"family": "Pepine", "given": "Carl J", "initials": "CJ"}, {"family": "Pereira", "given": "Alexandre C", "initials": "AC"}, {"family": "Pilote", "given": "Louise", "initials": "L"}, {"family": "Quyyumi", "given": "Arshed A", "initials": "AA"}, {"family": "Richards", "given": "A Mark", "initials": "AM"}, {"family": "Sanak", "given": "Marek", "initials": "M"}, {"family": "Scholz", "given": "Markus", "initials": "M"}, {"family": "Siegbahn", "given": "Agneta", "initials": "A"}, {"family": "Sinisalo", "given": "Juha", "initials": "J"}, {"family": "Smith", "given": "J Gustav", "initials": "JG"}, {"family": "Spertus", "given": "John A", "initials": "JA"}, {"family": "Stewart", "given": "Alexandre F R", "initials": "AFR"}, {"family": "Szczeklik", "given": "Wojciech", "initials": "W"}, {"family": "Szpakowicz", "given": "Anna", "initials": "A"}, {"family": "Ten Berg", "given": "Jurri\u00ebn M", "initials": "JM"}, {"family": "Thanassoulis", "given": "George", "initials": "G"}, {"family": "Thiery", "given": "Joachim", "initials": "J"}, {"family": "van der Graaf", "given": "Yolanda", "initials": "Y"}, {"family": "Visseren", "given": "Frank L J", "initials": "FLJ"}, {"family": "Waltenberger", "given": "Johannes", "initials": "J"}, {"family": "Van der Harst", "given": "Pim", "initials": "P"}, {"family": "Tardif", "given": "Jean-Claude", "initials": "JC"}, {"family": "Sattar", "given": "Naveed", "initials": "N"}, {"family": "Lang", "given": "Chim C", "initials": "CC"}, {"family": "Par\u00e9", "given": "Guillaume", "initials": "G"}, {"family": "Brophy", "given": "James M", "initials": "JM"}, {"family": "Anderson", "given": "Jeffrey L", "initials": "JL"}, {"family": "M\u00e4rz", "given": "Winfried", "initials": "W"}, {"family": "Wallentin", "given": "Lars", "initials": "L"}, {"family": "Cameron", "given": "Vicky A", "initials": "VA"}, {"family": "Horne", "given": "Benjamin D", "initials": "BD"}, {"family": "Samani", "given": "Nilesh J", "initials": "NJ"}, {"family": "Hingorani", "given": "Aroon D", "initials": "AD"}, {"family": "Asselbergs", "given": "Folkert W", "initials": "FW"}], "type": "journal article", "published": "2019-03-21", "journal": {"volume": null, "issn": "2574-8300", "issue": null, "title": "Circ Genom Precis Med", "issn-l": "2574-8300"}, "abstract": "Genetic variation at chromosome 9p21 is a recognized risk factor for coronary heart disease (CHD). However, its effect on disease progression and subsequent events is unclear, raising questions about its value for stratification of residual risk.\n\nA variant at chromosome 9p21 (rs1333049) was tested for association with subsequent events during follow-up in 103,357 Europeans with established CHD at baseline from the GENIUS-CHD Consortium (73.1% male, mean age 62.9 years). The primary outcome, subsequent CHD death or myocardial infarction (CHD death/MI), occurred in 13,040 of the 93,115 participants with available outcome data. Effect estimates were compared to case/control risk obtained from CARDIoGRAMPlusC4D including 47,222 CHD cases and 122,264 controls free of CHD.\n\nMeta-analyses revealed no significant association between chromosome 9p21 and the primary outcome of CHD death/MI among those with established CHD at baseline (GENIUS-CHD OR 1.02; 95% CI 0.99-1.05). This contrasted with a strong association in CARDIoGRAMPlusC4D OR 1.20; 95% CI 1.18-1.22; p for interaction Conclusions: In contrast to studies comparing individuals with CHD to disease free controls, we found no clear association between genetic variation at chromosome 9p21 and risk of subsequent acute CHD events when all individuals had CHD at baseline. However, the association with subsequent revascularization may support the postulated mechanism of chromosome 9p21 for promoting atheroma development.", "doi": "10.1161/CIRCGEN.119.002471", "pmid": "30897348", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [], "notes": [], "created": "2019-04-30T11:25:57.570Z", "modified": "2020-01-21T13:56:14.153Z"}, {"entity": "publication", "iuid": "9d4a6d1f011642a5b37d753122fb5053", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9d4a6d1f011642a5b37d753122fb5053.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9d4a6d1f011642a5b37d753122fb5053"}}, "title": "Extended insight into the Mycobacterium chelonae-abscessus complex through whole genome sequencing of Mycobacterium salmoniphilum outbreak and Mycobacterium salmoniphilum-like strains.", "authors": [{"family": "Behra", "given": "Phani Rama Krishna", "initials": "PRK"}, {"family": "Das", "given": "Sarbashis", "initials": "S"}, {"family": "Pettersson", "given": "B M Fredrik", "initials": "BMF"}, {"family": "Shirreff", "given": "Lisa", "initials": "L"}, {"family": "DuCote", "given": "Tanner", "initials": "T"}, {"family": "Jacobsson", "given": "Karl-Gustav", "initials": "K"}, {"family": "Ennis", "given": "Don G", "initials": "DG"}, {"family": "Kirsebom", "given": "Leif A", "initials": "LA", "orcid": "0000-0002-5092-512X", "researcher": {"href": "https://publications.scilifelab.se/researcher/e80849a89d0043b0b4daff9804c67332.json"}}], "type": "journal article", "published": "2019-03-14", "journal": {"volume": "9", "issn": "2045-2322", "issue": "1", "pages": "4603", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "Members of the Mycobacterium chelonae-abscessus complex (MCAC) are close to the mycobacterial ancestor and includes both human, animal and fish pathogens. We present the genomes of 14 members of this complex: the complete genomes of Mycobacterium salmoniphilum and Mycobacterium chelonae type strains, seven M. salmoniphilum isolates, and five M. salmoniphilum-like strains including strains isolated during an outbreak in an animal facility at Uppsala University. Average nucleotide identity (ANI) analysis and core gene phylogeny revealed that the M. salmoniphilum-like strains are variants of the human pathogen Mycobacterium franklinii and phylogenetically close to Mycobacterium abscessus. Our data further suggested that M. salmoniphilum separates into three branches named group I, II and III with the M. salmoniphilum type strain belonging to group II. Among predicted virulence factors, the presence of phospholipase C (plcC), which is a major virulence factor that makes M. abscessus highly cytotoxic to mouse macrophages, and that M. franklinii originally was isolated from infected humans make it plausible that the outbreak in the animal facility was caused by a M. salmoniphilum-like strain. Interestingly, M. salmoniphilum-like was isolated from tap water suggesting that it can be present in the environment. Moreover, we predicted the presence of mutational hotspots in the M. salmoniphilum isolates and 26% of these hotspots overlap with genes categorized as having roles in virulence, disease and defense. We also provide data about key genes involved in transcription and translation such as sigma factor, ribosomal protein and tRNA genes.", "doi": "10.1038/s41598-019-40922-x", "pmid": "30872669", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-019-40922-x"}, {"db": "pmc", "key": "PMC6418233"}], "notes": [], "created": "2019-04-10T09:37:39.069Z", "modified": "2024-01-16T13:48:44.610Z"}, {"entity": "publication", "iuid": "d50103cc28a443cbb19050234fc11364", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d50103cc28a443cbb19050234fc11364.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d50103cc28a443cbb19050234fc11364"}}, "title": "Oxygen induces the expression of invasion and stress response genes in the anaerobic salmon parasite Spironucleus salmonicida.", "authors": [{"family": "Stairs", "given": "Courtney W", "initials": "CW", "orcid": "0000-0001-6650-0970", "researcher": {"href": "https://publications.scilifelab.se/researcher/618e83e896494c7bb6cbe06350baf0a5.json"}}, {"family": "Kokla", "given": "Anna", "initials": "A"}, {"family": "\u00c1stvaldsson", "given": "\u00c1sgeir", "initials": "\u00c1"}, {"family": "Jerlstr\u00f6m-Hultqvist", "given": "Jon", "initials": "J"}, {"family": "Sv\u00e4rd", "given": "Staffan", "initials": "S"}, {"family": "Ettema", "given": "Thijs J G", "initials": "TJG"}], "type": "journal article", "published": "2019-03-01", "journal": {"volume": "17", "issn": "1741-7007", "issue": "1", "pages": "19", "title": "BMC Biol.", "issn-l": "1741-7007"}, "abstract": "Spironucleus salmonicida is an anaerobic parasite that can cause systemic infections in Atlantic salmon. Unlike other diplomonad parasites, such as the human pathogen Giardia intestinalis, Spironucleus species can infiltrate the blood stream of their hosts eventually colonizing organs, skin and gills. How this presumed anaerobe can persist and invade oxygenated tissues, despite having a strictly anaerobic metabolism, remains elusive.\n\nTo investigate how S. salmonicida response to oxygen stress, we performed RNAseq transcriptomic analyses of cells grown in the presence of oxygen or antioxidant-free medium. We found that over 20% of the transcriptome is differentially regulated in oxygen (1705 genes) and antioxidant-depleted (2280 genes) conditions. These differentially regulated transcripts encode proteins related to anaerobic metabolism, cysteine and Fe-S cluster biosynthesis, as well as a large number of proteins of unknown function. S. salmonicida does not encode genes involved in the classical elements of oxygen metabolism (e.g., catalases, superoxide dismutase, glutathione biosynthesis, oxidative phosphorylation). Instead, we found that genes encoding bacterial-like oxidoreductases were upregulated in response to oxygen stress. Phylogenetic analysis revealed some of these oxygen-responsive genes (e.g., nadh oxidase, rubrerythrin, superoxide reductase) are rare in eukaryotes and likely derived from lateral gene transfer (LGT) events into diplomonads from prokaryotes. Unexpectedly, we observed that many host evasion- and invasion-related genes were also upregulated under oxidative stress suggesting that oxygen might be an important signal for pathogenesis.\n\nWhile oxygen is toxic for related organisms, such as G. intestinalis, we find that oxygen is likely a gene induction signal for host invasion- and evasion-related pathways in S. salmonicida. These data provide the first molecular evidence for how S. salmonicida could tolerate oxic host environments and demonstrate how LGT can have a profound impact on the biology of anaerobic parasites.", "doi": "10.1186/s12915-019-0634-8", "pmid": "30823887", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1186/s12915-019-0634-8"}, {"db": "pmc", "key": "PMC6397501"}], "notes": [], "created": "2019-12-03T12:58:12.091Z", "modified": "2021-06-16T14:41:22.388Z"}, {"entity": "publication", "iuid": "0bb8912b1be1418985a2639354012484", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0bb8912b1be1418985a2639354012484.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0bb8912b1be1418985a2639354012484"}}, "title": "Association of Genetic Risk Factors for Psychiatric Disorders and Traits of These Disorders in a Swedish Population Twin Sample.", "authors": [{"family": "Taylor", "given": "Mark J", "initials": "MJ"}, {"family": "Martin", "given": "Joanna", "initials": "J"}, {"family": "Lu", "given": "Yi", "initials": "Y"}, {"family": "Brikell", "given": "Isabell", "initials": "I"}, {"family": "Lundstr\u00f6m", "given": "Sebastian", "initials": "S"}, {"family": "Larsson", "given": "Henrik", "initials": "H"}, {"family": "Lichtenstein", "given": "Paul", "initials": "P"}], "type": "journal article", "published": "2019-03-01", "journal": {"volume": "76", "issn": "2168-6238", "issue": "3", "pages": "280-289", "title": "JAMA Psychiatry", "issn-l": "2168-622X"}, "abstract": "Psychiatric traits associated with categorically defined psychiatric disorders are heritable and present to varying degrees in the general population. It is commonly assumed that diagnoses represent the extreme end of continuously distributed traits in the population, but this assumption has yet to be robustly tested for many psychiatric phenotypes.\n\nTo assess whether genetic risk factors associated with psychiatric disorders are also associated with continuous variation in milder population traits.\n\nThis study combined a novel twin analytic approach with polygenic risk score (PRS) analyses in a large population-based twin sample. Phenotypic and genetic data were available from the Child and Adolescent Twin Study in Sweden. Inpatient data were available for January 1, 1987, to December 31, 2014, and outpatient data for January 1, 2001, to December 31, 2013. The last day of follow-up was December 31, 2014. Data analysis was performed from January 1, 2017, to September 30, 2017.\n\nQuestionnaires that assessed traits of autism spectrum disorder (ASD), attention-deficit/hyperactivity disorder (ADHD), learning difficulties, tic disorders (TDs), obsessive-compulsive disorder (OCD), anxiety, major depressive disorder (MDD), mania, and psychotic experiences were administered to a large Swedish twin sample. Individuals with clinical psychiatric diagnoses were identified using the Swedish National Patient Register. Joint categorical/continuous twin modeling was used to estimate genetic correlations between psychiatric diagnoses and continuous traits. The PRSs for psychiatric disorders were calculated based on independent discovery genetic data. The association between PRSs for each disorder and associated continuous traits was tested.\n\nPhenotype data were available for 13 923 twin pairs (35.1% opposite sex and 31.7% same-sex females) at 9 years of age, 5165 pairs (36.9% opposite sex and 34.0% same-sex females) at 15 years of age, and 4273 pairs (36.5% opposite sex and 34.4% same-sex females) at 18 years of age. Genetic data were available for 13 412 individuals (50.2% females). Twin genetic correlations between numerous psychiatric diagnoses and corresponding traits ranged from 0.31 to 0.69. Disorder PRSs were associated with related population traits for ASD (\u03b2 [SE] = 0.04 [0.01] at 9 years of age), ADHD (\u03b2 [SE] = 0.27 [0.03] at 9 years of age), TDs (\u03b2 [SE] = 0.02 [0.004] at 9 years of age), OCD (\u03b2 [SE] = 0.13 [0.05] at 18 years of age), anxiety (\u03b2 [SE] = 0.18 [0.08] at 9 years of age; \u03b2 [SE] = 0.07 [0.02] at 15 years of age; and \u03b2 [SE] = 0.40 [0.17] at 18 years of age), MDD (\u03b2 [SE] = 0.10 [0.03] at 9 years of age; \u03b2 [SE] = 0.11 [0.02] at 15 years of age; and \u03b2 [SE] = 0.41 [0.10] at 18 years of age), and schizophrenia (\u03b2 [SE] = 0.02 [0.01] at 18 years of age). Polygenic risk scores for depressive symptoms were associated with MDD diagnoses (odds ratio, 1.16; 95% CI, 1.02-1.32).\n\nThese results suggest that genetic factors associated with psychiatric disorders are also associated with milder variation in characteristic traits throughout the general population for many psychiatric phenotypes. This study suggests that many psychiatric disorders are likely to be continuous phenotypes rather than the categorical entities currently defined in diagnostic manuals, which has strong implications for genetic research in particular.", "doi": "10.1001/jamapsychiatry.2018.3652", "pmid": "30566181", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "2718628"}, {"db": "pmc", "key": "PMC6439816"}], "notes": [], "created": "2019-01-04T09:53:06.069Z", "modified": "2021-06-21T13:52:28.878Z"}, {"entity": "publication", "iuid": "a83f57593e954660884b10ae5e2254a4", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a83f57593e954660884b10ae5e2254a4.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a83f57593e954660884b10ae5e2254a4"}}, "title": "Whole genome sequencing of consanguineous families reveals novel pathogenic variants in intellectual disability.", "authors": [{"family": "Thuresson", "given": "Ann-Charlotte", "initials": "AC", "orcid": "0000-0002-4018-5551", "researcher": {"href": "https://publications.scilifelab.se/researcher/829bcbc2bb734d848f7b370546aca35c.json"}}, {"family": "Soussi Zander", "given": "Cecilia", "initials": "C"}, {"family": "Zhao", "given": "Jin J", "initials": "JJ"}, {"family": "Halvardson", "given": "Jonatan", "initials": "J"}, {"family": "Maqbool", "given": "Khurram", "initials": "K", "orcid": "0000-0003-2981-2582", "researcher": {"href": "https://publications.scilifelab.se/researcher/7ea06b85057744018f754c373fef3ca5.json"}}, {"family": "M\u00e5nsson", "given": "Else", "initials": "E"}, {"family": "Stenninger", "given": "Eric", "initials": "E"}, {"family": "Holmlund", "given": "Ulrika", "initials": "U"}, {"family": "\u00d6hrner", "given": "Ylva", "initials": "Y"}, {"family": "Feuk", "given": "Lars", "initials": "L", "orcid": "0000-0003-2355-2919", "researcher": {"href": "https://publications.scilifelab.se/researcher/3eb2f826b3554d4b9971bf0766b275c4.json"}}], "type": "letter", "published": "2019-03-00", "journal": {"volume": "95", "issn": "1399-0004", "issue": "3", "pages": "436-439", "title": "Clin. Genet.", "issn-l": "0009-9163"}, "abstract": null, "doi": "10.1111/cge.13470", "pmid": "30525197", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Clinical Genomics Uppsala": "Collaborative", "Clinical Genomics": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC6392105"}], "notes": [], "created": "2019-01-07T18:03:32.030Z", "modified": "2021-06-21T13:53:42.462Z"}, {"entity": "publication", "iuid": "63053cd763f14b46bffe7d397270205a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/63053cd763f14b46bffe7d397270205a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/63053cd763f14b46bffe7d397270205a"}}, "title": "Protein-coding variants implicate novel genes related to lipid homeostasis contributing to body-fat distribution.", "authors": [{"family": "Justice", "given": "Anne E", "initials": "AE"}, {"family": "Karaderi", "given": "Tugce", "initials": "T"}, {"family": "Highland", "given": "Heather M", "initials": "HM"}, {"family": "Young", "given": "Kristin L", "initials": "KL"}, {"family": "Graff", "given": "Mariaelisa", "initials": "M"}, {"family": "Lu", "given": "Yingchang", "initials": "Y"}, {"family": "Turcot", "given": "Val\u00e9rie", "initials": "V"}, {"family": "Auer", "given": "Paul L", "initials": "PL"}, {"family": "Fine", "given": "Rebecca S", "initials": "RS"}, {"family": "Guo", "given": "Xiuqing", "initials": "X"}, {"family": "Schurmann", "given": "Claudia", "initials": "C"}, {"family": "Lempradl", "given": "Adelheid", "initials": "A"}, {"family": "Marouli", "given": "Eirini", "initials": "E"}, {"family": "Mahajan", "given": "Anubha", "initials": "A"}, {"family": "Winkler", "given": "Thomas W", "initials": "TW"}, {"family": "Locke", "given": "Adam E", "initials": "AE"}, {"family": "Medina-Gomez", "given": "Carolina", "initials": "C"}, {"family": "Esko", "given": "T\u00f5nu", "initials": "T"}, {"family": "Vedantam", "given": "Sailaja", "initials": "S"}, {"family": "Giri", "given": "Ayush", "initials": "A"}, {"family": "Lo", "given": "Ken Sin", "initials": "KS"}, {"family": "Alfred", "given": "Tamuno", "initials": "T"}, {"family": "Mudgal", "given": "Poorva", "initials": "P"}, {"family": "Ng", "given": "Maggie C Y", "initials": "MCY"}, {"family": "Heard-Costa", "given": "Nancy L", "initials": "NL"}, {"family": "Feitosa", "given": "Mary F", "initials": "MF"}, {"family": "Manning", "given": "Alisa K", "initials": "AK"}, {"family": "Willems", "given": "Sara M", "initials": "SM"}, {"family": "Sivapalaratnam", "given": "Suthesh", "initials": "S"}, {"family": "Abecasis", "given": "Goncalo", "initials": "G"}, {"family": "Alam", "given": "Dewan S", "initials": "DS"}, {"family": "Allison", "given": "Matthew", "initials": "M"}, {"family": "Amouyel", "given": "Philippe", "initials": "P"}, {"family": "Arzumanyan", "given": "Zorayr", "initials": "Z"}, {"family": "Balkau", "given": "Beverley", "initials": "B"}, {"family": "Bastarache", "given": "Lisa", "initials": "L"}, {"family": "Bergmann", "given": "Sven", "initials": "S"}, {"family": "Bielak", "given": "Lawrence F", "initials": "LF"}, {"family": "Bl\u00fcher", "given": "Matthias", "initials": "M"}, {"family": "Boehnke", "given": "Michael", "initials": "M"}, {"family": "Boeing", "given": "Heiner", "initials": "H"}, {"family": "Boerwinkle", "given": "Eric", "initials": "E"}, {"family": "B\u00f6ger", "given": "Carsten A", "initials": "CA"}, {"family": "Bork-Jensen", "given": "Jette", "initials": "J"}, {"family": "Bottinger", "given": "Erwin P", "initials": "EP"}, {"family": "Bowden", "given": "Donald W", "initials": "DW"}, {"family": "Brandslund", "given": "Ivan", "initials": "I"}, {"family": "Broer", "given": "Linda", "initials": "L"}, {"family": "Burt", "given": "Amber A", "initials": "AA"}, {"family": "Butterworth", "given": "Adam S", "initials": "AS"}, {"family": "Caulfield", "given": "Mark J", "initials": "MJ"}, {"family": "Cesana", "given": "Giancarlo", "initials": "G"}, {"family": "Chambers", "given": "John C", "initials": "JC"}, {"family": "Chasman", "given": "Daniel I", "initials": "DI"}, {"family": "Chen", "given": "Yii-Der Ida", "initials": "YI"}, {"family": "Chowdhury", "given": "Rajiv", "initials": "R"}, {"family": "Christensen", "given": "Cramer", "initials": "C"}, {"family": "Chu", "given": "Audrey Y", "initials": "AY"}, {"family": "Collins", "given": "Francis S", "initials": "FS"}, {"family": "Cook", "given": "James P", "initials": "JP"}, {"family": "Cox", "given": "Amanda J", "initials": "AJ"}, {"family": "Crosslin", "given": "David S", "initials": "DS"}, {"family": "Danesh", "given": "John", "initials": "J"}, {"family": "de Bakker", "given": "Paul I W", "initials": "PIW"}, {"family": "Denus", "given": "Simon de", "initials": "S"}, {"family": "Mutsert", "given": "Ren\u00e9e de", "initials": "R"}, {"family": "Dedoussis", "given": "George", "initials": "G"}, {"family": "Demerath", "given": "Ellen W", "initials": "EW"}, {"family": "Dennis", "given": "Joe G", "initials": "JG"}, {"family": "Denny", "given": "Josh C", "initials": "JC"}, {"family": "Angelantonio", "given": "Emanuele Di", "initials": "ED"}, {"family": "D\u00f6rr", "given": "Marcus", "initials": "M"}, {"family": "Drenos", "given": "Fotios", "initials": "F"}, {"family": "Dub\u00e9", "given": "Marie-Pierre", "initials": "MP"}, {"family": "Dunning", "given": "Alison M", "initials": "AM"}, {"family": "Easton", "given": "Douglas F", "initials": "DF"}, {"family": "Elliott", "given": "Paul", "initials": "P"}, {"family": "Evangelou", "given": "Evangelos", "initials": "E"}, {"family": "Farmaki", "given": "Aliki-Eleni", "initials": "AE"}, {"family": "Feng", "given": "Shuang", "initials": "S"}, {"family": "Ferrannini", "given": "Ele", "initials": "E"}, {"family": "Ferrieres", "given": "Jean", "initials": "J"}, {"family": "Florez", "given": "Jose C", "initials": "JC"}, {"family": "Fornage", "given": "Myriam", "initials": "M"}, {"family": "Fox", "given": "Caroline S", "initials": "CS"}, {"family": "Franks", "given": "Paul W", "initials": "PW"}, {"family": "Friedrich", "given": "Nele", "initials": "N"}, {"family": "Gan", "given": "Wei", "initials": "W"}, {"family": "Gandin", "given": "Ilaria", "initials": "I"}, {"family": "Gasparini", "given": "Paolo", "initials": "P"}, {"family": "Giedraitis", "given": "Vilmantas", "initials": "V"}, {"family": "Girotto", "given": "Giorgia", "initials": "G"}, {"family": "Gorski", "given": "Mathias", "initials": "M"}, {"family": "Grallert", "given": "Harald", "initials": "H"}, {"family": "Grarup", "given": "Niels", "initials": "N"}, {"family": "Grove", "given": "Megan L", "initials": "ML"}, {"family": "Gustafsson", "given": "Stefan", "initials": "S"}, {"family": "Haessler", "given": "Jeff", "initials": "J"}, {"family": "Hansen", "given": "Torben", "initials": "T"}, {"family": "Hattersley", "given": "Andrew T", "initials": "AT"}, {"family": "Hayward", "given": "Caroline", "initials": "C"}, {"family": "Heid", "given": "Iris M", "initials": "IM"}, {"family": "Holmen", "given": "Oddgeir L", "initials": "OL"}, {"family": "Hovingh", "given": "G Kees", "initials": "GK"}, {"family": "Howson", "given": "Joanna M M", "initials": "JMM"}, {"family": "Hu", "given": "Yao", "initials": "Y"}, {"family": "Hung", "given": "Yi-Jen", "initials": "YJ"}, {"family": "Hveem", "given": "Kristian", "initials": "K"}, {"family": "Ikram", "given": "M Arfan", "initials": "MA"}, {"family": "Ingelsson", "given": "Erik", "initials": "E"}, {"family": "Jackson", "given": "Anne U", "initials": "AU"}, {"family": "Jarvik", "given": "Gail P", "initials": "GP"}, {"family": "Jia", "given": "Yucheng", "initials": "Y"}, {"family": "J\u00f8rgensen", "given": "Torben", "initials": "T"}, {"family": "Jousilahti", "given": "Pekka", "initials": "P"}, {"family": "Justesen", "given": "Johanne M", "initials": "JM"}, {"family": "Kahali", "given": "Bratati", "initials": "B"}, {"family": "Karaleftheri", "given": "Maria", "initials": "M"}, {"family": "Kardia", "given": "Sharon L R", "initials": "SLR"}, {"family": "Karpe", "given": "Fredrik", "initials": "F"}, {"family": "Kee", "given": "Frank", "initials": "F"}, {"family": "Kitajima", "given": "Hidetoshi", "initials": "H"}, {"family": "Komulainen", "given": "Pirjo", "initials": "P"}, {"family": "Kooner", "given": "Jaspal S", "initials": "JS"}, {"family": "Kovacs", "given": "Peter", "initials": "P"}, {"family": "Kr\u00e4mer", "given": "Bernhard K", "initials": "BK"}, {"family": "Kuulasmaa", "given": "Kari", "initials": "K"}, {"family": "Kuusisto", "given": "Johanna", "initials": "J"}, {"family": "Laakso", "given": "Markku", "initials": "M"}, {"family": "Lakka", "given": "Timo A", "initials": "TA"}, {"family": "Lamparter", "given": "David", "initials": "D"}, {"family": "Lange", "given": "Leslie A", "initials": "LA"}, {"family": "Langenberg", "given": "Claudia", "initials": "C"}, {"family": "Larson", "given": "Eric B", "initials": "EB"}, {"family": "Lee", 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{"family": "Sim", "given": "Xueling", "initials": "X"}, {"family": "Slater", "given": "Andrew J", "initials": "AJ"}, {"family": "Small", "given": "Kerrin S", "initials": "KS"}, {"family": "Smith", "given": "Blair H", "initials": "BH"}, {"family": "Smith", "given": "Jennifer A", "initials": "JA"}, {"family": "Southam", "given": "Lorraine", "initials": "L"}, {"family": "Spector", "given": "Timothy D", "initials": "TD"}, {"family": "Speliotes", "given": "Elizabeth K", "initials": "EK"}, {"family": "Stefansson", "given": "Kari", "initials": "K"}, {"family": "Steinthorsdottir", "given": "Valgerdur", "initials": "V"}, {"family": "Stirrups", "given": "Kathleen E", "initials": "KE"}, {"family": "Strauch", "given": "Konstantin", "initials": "K"}, {"family": "Stringham", "given": "Heather M", "initials": "HM"}, {"family": "Stumvoll", "given": "Michael", "initials": "M"}, {"family": "Sun", "given": "Liang", "initials": "L"}, {"family": "Surendran", "given": "Praveen", "initials": "P"}, {"family": "Swart", "given": "Karin M A", "initials": "KMA"}, {"family": "Tardif", "given": "Jean-Claude", "initials": "JC"}, {"family": "Taylor", "given": "Kent D", "initials": "KD"}, {"family": "Teumer", "given": "Alexander", "initials": "A"}, {"family": "Thompson", "given": "Deborah J", "initials": "DJ"}, {"family": "Thorleifsson", "given": "Gudmar", "initials": "G"}, {"family": "Thorsteinsdottir", "given": "Unnur", "initials": "U"}, {"family": "Thuesen", "given": "Betina H", "initials": "BH"}, {"family": "T\u00f6njes", "given": "Anke", "initials": "A"}, {"family": "Torres", "given": "Mina", "initials": "M"}, {"family": "Tsafantakis", "given": "Emmanouil", "initials": "E"}, {"family": "Tuomilehto", "given": "Jaakko", "initials": "J"}, {"family": "Uitterlinden", "given": "Andr\u00e9 G", "initials": "AG"}, {"family": "Uusitupa", "given": "Matti", "initials": "M"}, {"family": "van Duijn", "given": "Cornelia M", "initials": "CM"}, {"family": "Vanhala", "given": "Mauno", "initials": "M"}, {"family": "Varma", "given": "Rohit", "initials": "R"}, {"family": "Vermeulen", "given": "Sita H", "initials": "SH"}, {"family": "Vestergaard", "given": "Henrik", "initials": "H"}, {"family": "Vitart", "given": "Veronique", "initials": "V"}, {"family": "Vogt", "given": "Thomas F", "initials": "TF"}, {"family": "Vuckovic", "given": "Dragana", "initials": "D"}, {"family": "Wagenknecht", "given": "Lynne E", "initials": "LE"}, {"family": "Walker", "given": "Mark", "initials": "M"}, {"family": "Wallentin", "given": "Lars", "initials": "L"}, {"family": "Wang", "given": "Feijie", "initials": "F"}, {"family": "Wang", "given": "Carol A", "initials": "CA"}, {"family": "Wang", "given": "Shuai", "initials": "S"}, {"family": "Wareham", "given": "Nicholas J", "initials": "NJ"}, {"family": "Warren", "given": "Helen R", "initials": "HR"}, {"family": "Waterworth", "given": "Dawn M", "initials": "DM"}, {"family": "Wessel", "given": "Jennifer", "initials": "J"}, {"family": "White", "given": "Harvey D", "initials": "HD"}, {"family": "Willer", "given": "Cristen J", "initials": "CJ"}, {"family": "Wilson", "given": "James G", "initials": "JG"}, {"family": "Wood", "given": "Andrew R", "initials": "AR"}, {"family": "Wu", "given": "Ying", "initials": "Y"}, {"family": "Yaghootkar", "given": "Hanieh", "initials": "H"}, {"family": "Yao", "given": "Jie", "initials": "J"}, {"family": "Yerges-Armstrong", "given": "Laura M", "initials": "LM"}, {"family": "Young", "given": "Robin", "initials": "R"}, {"family": "Zeggini", "given": "Eleftheria", "initials": "E"}, {"family": "Zhan", "given": "Xiaowei", "initials": "X"}, {"family": "Zhang", "given": "Weihua", "initials": "W"}, {"family": "Zhao", "given": "Jing Hua", "initials": "JH"}, {"family": "Zhao", "given": "Wei", "initials": "W"}, {"family": "Zheng", "given": "He", "initials": "H"}, {"family": "Zhou", "given": "Wei", "initials": "W"}, {"family": "Zillikens", "given": "M Carola", "initials": "MC"}, {"family": "CHD Exome+ Consortium", "given": "", "initials": ""}, {"family": "Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) Consortium", "given": "", "initials": ""}, {"family": "EPIC-CVD Consortium", "given": "", "initials": ""}, {"family": "ExomeBP Consortium", "given": "", "initials": ""}, {"family": "Global Lipids Genetic Consortium", "given": "", "initials": ""}, {"family": "GoT2D Genes Consortium", "given": "", "initials": ""}, {"family": "InterAct", "given": "", "initials": ""}, {"family": "ReproGen Consortium", "given": "", "initials": ""}, {"family": "T2D-Genes Consortium", "given": "", "initials": ""}, {"family": "MAGIC Investigators", "given": "", "initials": ""}, {"family": "Rivadeneira", "given": "Fernando", "initials": "F"}, {"family": "Borecki", "given": "Ingrid B", "initials": "IB"}, {"family": "Pospisilik", "given": "J Andrew", "initials": "JA"}, {"family": "Deloukas", "given": "Panos", "initials": "P"}, {"family": "Frayling", "given": "Timothy M", "initials": "TM"}, {"family": "Lettre", "given": "Guillaume", "initials": "G"}, {"family": "Mohlke", "given": "Karen L", "initials": "KL"}, {"family": "Rotter", "given": "Jerome I", "initials": "JI"}, {"family": "Kutalik", "given": "Zolt\u00e1n", "initials": "Z"}, {"family": "Hirschhorn", "given": "Joel N", "initials": "JN"}, {"family": "Cupples", "given": "L Adrienne", "initials": "LA"}, {"family": "Loos", "given": "Ruth J F", "initials": "RJF"}, {"family": "North", "given": "Kari E", "initials": "KE"}, {"family": "Lindgren", "given": "Cecilia M", "initials": "CM"}], "type": "journal article", "published": "2019-03-00", "journal": {"volume": "51", "issn": "1546-1718", "issue": "3", "pages": "452-469", "title": "Nat. Genet.", "issn-l": "1061-4036"}, "abstract": "Body-fat distribution is a risk factor for adverse cardiovascular health consequences. We analyzed the association of body-fat distribution, assessed by waist-to-hip ratio adjusted for body mass index, with 228,985 predicted coding and splice site variants available on exome arrays in up to 344,369 individuals from five major ancestries (discovery) and 132,177 European-ancestry individuals (validation). We identified 15 common (minor allele frequency, MAF \u22655%) and nine low-frequency or rare (MAF <5%) coding novel variants. Pathway/gene set enrichment analyses identified lipid particle, adiponectin, abnormal white adipose tissue physiology and bone development and morphology as important contributors to fat distribution, while cross-trait associations highlight cardiometabolic traits. In functional follow-up analyses, specifically in Drosophila RNAi-knockdowns, we observed a significant increase in the total body triglyceride levels for two genes (DNAH10 and PLXND1). We implicate novel genes in fat distribution, stressing the importance of interrogating low-frequency and protein-coding variants.", "doi": "10.1038/s41588-018-0334-2", "pmid": "30778226", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41588-018-0334-2"}], "notes": [], "created": "2019-03-13T09:21:21.215Z", "modified": "2020-01-21T13:56:13.837Z"}, {"entity": "publication", "iuid": "a70b7ac96cdf46c7bd2ff8d1ca75b907", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a70b7ac96cdf46c7bd2ff8d1ca75b907.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a70b7ac96cdf46c7bd2ff8d1ca75b907"}}, "title": "New genetic signals for lung function highlight pathways and chronic obstructive pulmonary disease associations across multiple ancestries.", "authors": [{"family": "Shrine", "given": "Nick", "initials": "N"}, {"family": "Guyatt", "given": "Anna L", "initials": "AL"}, {"family": "Erzurumluoglu", "given": "A Mesut", "initials": "AM"}, {"family": "Jackson", "given": "Victoria E", "initials": "VE"}, {"family": "Hobbs", "given": "Brian D", "initials": "BD"}, {"family": "Melbourne", "given": "Carl A", "initials": "CA"}, {"family": "Batini", "given": "Chiara", "initials": "C"}, {"family": "Fawcett", "given": "Katherine A", "initials": "KA"}, {"family": "Song", "given": "Kijoung", "initials": "K"}, {"family": "Sakornsakolpat", "given": "Phuwanat", "initials": "P"}, {"family": "Li", "given": "Xingnan", "initials": "X"}, {"family": "Boxall", "given": "Ruth", "initials": "R"}, {"family": "Reeve", "given": "Nicola F", "initials": "NF"}, {"family": "Obeidat", "given": "Ma'en", "initials": "M"}, {"family": "Zhao", "given": "Jing Hua", "initials": "JH"}, {"family": "Wielscher", "given": "Matthias", "initials": "M"}, {"family": "Understanding Society Scientific Group", "given": "", "initials": ""}, {"family": "Weiss", "given": "Stefan", "initials": "S"}, {"family": "Kentistou", "given": "Katherine A", "initials": "KA"}, {"family": "Cook", "given": "James P", "initials": "JP"}, {"family": "Sun", "given": "Benjamin B", "initials": "BB"}, {"family": "Zhou", "given": "Jian", "initials": "J"}, {"family": "Hui", "given": "Jennie", "initials": "J"}, {"family": "Karrasch", "given": "Stefan", "initials": "S"}, {"family": "Imboden", "given": "Medea", "initials": "M"}, {"family": "Harris", "given": "Sarah E", "initials": "SE"}, {"family": "Marten", "given": "Jonathan", "initials": "J"}, {"family": "Enroth", "given": "Stefan", "initials": "S"}, {"family": "Kerr", "given": "Shona M", "initials": "SM"}, {"family": "Surakka", "given": "Ida", "initials": "I"}, {"family": "Vitart", "given": "Veronique", "initials": "V"}, {"family": "Lehtim\u00e4ki", "given": "Terho", "initials": "T"}, {"family": "Allen", "given": "Richard J", "initials": "RJ"}, {"family": "Bakke", "given": "Per S", "initials": "PS"}, {"family": "Beaty", "given": "Terri H", "initials": "TH"}, {"family": "Bleecker", "given": "Eugene R", "initials": "ER"}, {"family": "Boss\u00e9", "given": "Yohan", "initials": "Y"}, {"family": "Brandsma", "given": "Corry-Anke", "initials": "CA"}, {"family": "Chen", "given": "Zhengming", "initials": "Z"}, {"family": "Crapo", "given": "James D", "initials": "JD"}, {"family": "Danesh", "given": "John", "initials": "J"}, {"family": "DeMeo", "given": "Dawn L", "initials": "DL"}, {"family": "Dudbridge", "given": "Frank", "initials": "F"}, {"family": "Ewert", "given": "Ralf", "initials": "R"}, {"family": "Gieger", "given": "Christian", "initials": "C"}, {"family": "Gulsvik", "given": "Amund", "initials": "A"}, {"family": "Hansell", "given": "Anna L", "initials": "AL"}, {"family": "Hao", "given": "Ke", "initials": "K"}, {"family": "Hoffman", "given": "Joshua D", "initials": "JD"}, {"family": "Hokanson", "given": "John E", "initials": "JE"}, {"family": "Homuth", "given": "Georg", "initials": "G"}, {"family": "Joshi", "given": "Peter K", "initials": "PK"}, {"family": "Joubert", "given": "Philippe", "initials": "P"}, {"family": "Langenberg", "given": "Claudia", "initials": "C"}, {"family": "Li", "given": "Xuan", "initials": "X"}, {"family": "Li", "given": "Liming", "initials": "L"}, {"family": "Lin", "given": "Kuang", "initials": "K"}, {"family": "Lind", "given": "Lars", "initials": "L"}, {"family": "Locantore", "given": "Nicholas", "initials": "N"}, {"family": "Luan", "given": "Jian'an", "initials": "J"}, {"family": "Mahajan", "given": "Anubha", "initials": "A"}, {"family": "Maranville", "given": "Joseph C", "initials": "JC"}, {"family": "Murray", "given": "Alison", "initials": "A"}, {"family": "Nickle", "given": "David C", "initials": "DC"}, {"family": "Packer", "given": "Richard", "initials": "R"}, {"family": "Parker", "given": "Margaret M", "initials": "MM"}, {"family": "Paynton", "given": "Megan L", "initials": "ML"}, {"family": "Porteous", "given": "David J", "initials": "DJ"}, {"family": "Prokopenko", "given": "Dmitry", "initials": "D"}, {"family": "Qiao", "given": "Dandi", "initials": "D"}, {"family": "Rawal", "given": "Rajesh", "initials": "R"}, {"family": "Runz", "given": "Heiko", "initials": "H"}, {"family": "Sayers", "given": "Ian", "initials": "I"}, {"family": "Sin", "given": "Don D", "initials": "DD"}, {"family": "Smith", "given": "Blair H", "initials": "BH"}, {"family": "Soler Artigas", "given": "Mar\u00eda", "initials": "M"}, {"family": "Sparrow", "given": "David", "initials": "D"}, {"family": "Tal-Singer", "given": "Ruth", "initials": "R"}, {"family": "Timmers", "given": "Paul R H J", "initials": "PRHJ"}, {"family": "Van den Berge", "given": "Maarten", "initials": "M"}, {"family": "Whittaker", "given": "John C", "initials": "JC"}, {"family": "Woodruff", "given": "Prescott G", "initials": "PG"}, {"family": "Yerges-Armstrong", "given": "Laura M", "initials": "LM"}, {"family": "Troyanskaya", "given": "Olga G", "initials": "OG"}, {"family": "Raitakari", "given": "Olli T", "initials": "OT"}, {"family": "K\u00e4h\u00f6nen", "given": "Mika", "initials": "M"}, {"family": "Pola\u0161ek", "given": "Ozren", "initials": "O"}, {"family": "Gyllensten", "given": "Ulf", "initials": "U"}, {"family": "Rudan", "given": "Igor", "initials": "I"}, {"family": "Deary", "given": "Ian J", "initials": "IJ"}, {"family": "Probst-Hensch", "given": "Nicole M", "initials": "NM"}, {"family": "Schulz", "given": "Holger", "initials": "H"}, {"family": "James", "given": "Alan L", "initials": "AL"}, {"family": "Wilson", "given": "James F", "initials": "JF"}, {"family": "Stubbe", "given": "Beate", "initials": "B"}, {"family": "Zeggini", "given": "Eleftheria", "initials": "E"}, {"family": "Jarvelin", "given": "Marjo-Riitta", "initials": "MR"}, {"family": "Wareham", "given": "Nick", "initials": "N"}, {"family": "Silverman", "given": "Edwin K", "initials": "EK"}, {"family": "Hayward", "given": "Caroline", "initials": "C"}, {"family": "Morris", "given": "Andrew P", "initials": "AP"}, {"family": "Butterworth", "given": "Adam S", "initials": "AS"}, {"family": "Scott", "given": "Robert A", "initials": "RA"}, {"family": "Walters", "given": "Robin G", "initials": "RG"}, {"family": "Meyers", "given": "Deborah A", "initials": "DA"}, {"family": "Cho", "given": "Michael H", "initials": "MH"}, {"family": "Strachan", "given": "David P", "initials": "DP"}, {"family": "Hall", "given": "Ian P", "initials": "IP"}, {"family": "Tobin", "given": "Martin D", "initials": "MD"}, {"family": "Wain", "given": "Louise V", "initials": "LV"}], "type": "journal article", "published": "2019-03-00", "journal": {"volume": "51", "issn": "1546-1718", "issue": "3", "pages": "481-493", "title": "Nat. Genet.", "issn-l": "1061-4036"}, "abstract": "Reduced lung function predicts mortality and is key to the diagnosis of chronic obstructive pulmonary disease (COPD). In a genome-wide association study in 400,102 individuals of European ancestry, we define 279 lung function signals, 139 of which are new. In combination, these variants strongly predict COPD in independent populations. Furthermore, the combined effect of these variants showed generalizability across smokers and never smokers, and across ancestral groups. We highlight biological pathways, known and potential drug targets for COPD and, in phenome-wide association studies, autoimmune-related and other pleiotropic effects of lung function-associated variants. This new genetic evidence has potential to improve future preventive and therapeutic strategies for COPD.", "doi": "10.1038/s41588-018-0321-7", "pmid": "30804560", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41588-018-0321-7"}, {"db": "pmc", "key": "PMC6397078"}, {"db": "mid", "key": "NIHMS1514965"}], "notes": [], "created": "2019-03-13T09:21:19.890Z", "modified": "2020-01-21T13:56:13.826Z"}, {"entity": "publication", "iuid": "402d0d7732444ebebd30ab0e35ac2d10", "links": {"self": {"href": "https://publications.scilifelab.se/publication/402d0d7732444ebebd30ab0e35ac2d10.json"}, "display": {"href": "https://publications.scilifelab.se/publication/402d0d7732444ebebd30ab0e35ac2d10"}}, "title": "Genome-wide meta-analysis reveals shared new loci in systemic seropositive rheumatic diseases.", "authors": [{"family": "Acosta-Herrera", "given": "Marialbert", "initials": "M"}, {"family": "Kerick", "given": "Martin", "initials": "M"}, {"family": "Gonz\u00e1lez-Serna", "given": "David", "initials": "D"}, {"family": "Myositis Genetics Consortium", "given": "", "initials": ""}, {"family": "Scleroderma Genetics Consortium", "given": "", "initials": ""}, {"family": "Wijmenga", "given": "Cisca", "initials": "C"}, {"family": "Franke", "given": "Andre", "initials": "A"}, {"family": "Gregersen", "given": "Peter K", "initials": "PK"}, {"family": "Padyukov", "given": "Leonid", "initials": "L"}, {"family": "Worthington", "given": "Jane", "initials": "J"}, {"family": "Vyse", "given": "Timothy James", "initials": "TJ"}, {"family": "Alarc\u00f3n-Riquelme", "given": "Marta Eugenia", "initials": "ME"}, {"family": "Mayes", "given": "Maureen D", "initials": "MD"}, {"family": "Martin", "given": "Javier", "initials": "J"}], "type": "journal article", "published": "2019-03-00", "journal": {"volume": "78", "issn": "1468-2060", "issue": "3", "pages": "311-319", "title": "Ann. Rheum. Dis.", "issn-l": "0003-4967"}, "abstract": "Immune-mediated inflammatory diseases (IMIDs) are heterogeneous and complex conditions with overlapping clinical symptoms and elevated familial aggregation, which suggests the existence of a shared genetic component. In order to identify this genetic background in a systematic fashion, we performed the first cross-disease genome-wide meta-analysis in systemic seropositive rheumatic diseases, namely, systemic sclerosis, systemic lupus erythematosus, rheumatoid arthritis and idiopathic inflammatory myopathies.\r\n\r\nWe meta-analysed ~6.5\u2009million single nucleotide polymorphisms in 11\u2009678 cases and 19\u2009704 non-affected controls of European descent populations. The functional roles of the associated variants were interrogated using publicly available databases.\r\n\r\nOur analysis revealed five shared genome-wide significant independent \r\n                loci that had not been previously associated with these diseases: NAB1, KPNA4-ARL14, DGQK, LIMK1 and PRR12. All of these loci are related with immune processes such as interferon and epidermal growth factor signalling, response to methotrexate, cytoskeleton dynamics and coagulation cascade. Remarkably, several of the associated loci are known key players in autoimmunity, which supports the validity of our results. All the associated variants showed significant functional enrichment in DNase hypersensitivity sites, chromatin states and histone marks in relevant immune cells, including shared expression quantitative trait loci. Additionally, our results were significantly enriched in drugs that are being tested for the treatment of the diseases under study.\r\n\r\nWe have identified shared new risk \r\n                loci with functional value across diseases and pinpoint new potential candidate loci that could be further investigated. Our results highlight the potential of drug repositioning among related systemic seropositive rheumatic IMIDs.", "doi": "10.1136/annrheumdis-2018-214127", "pmid": "30573655", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "annrheumdis-2018-214127"}], "notes": [], "created": "2019-09-17T16:24:30.655Z", "modified": "2020-01-21T13:56:14.764Z"}, {"entity": "publication", "iuid": "ad07a7341fca458f96005a035573c8ce", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ad07a7341fca458f96005a035573c8ce.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ad07a7341fca458f96005a035573c8ce"}}, "title": "Genome-wide meta-analysis identifies new loci and functional pathways influencing Alzheimer's disease risk.", "authors": [{"family": "Jansen", "given": "Iris E", "initials": "IE", "orcid": "0000-0003-1901-8131", "researcher": {"href": "https://publications.scilifelab.se/researcher/0023d0046d8844abac6b071beabf71b8.json"}}, {"family": "Savage", "given": "Jeanne E", "initials": "JE", "orcid": "0000-0002-2034-8341", "researcher": {"href": "https://publications.scilifelab.se/researcher/d8768341f7f44f449c2f70a493cc556d.json"}}, {"family": "Watanabe", "given": "Kyoko", "initials": "K"}, {"family": "Bryois", "given": "Julien", "initials": "J"}, {"family": "Williams", "given": "Dylan M", "initials": "DM"}, {"family": "Steinberg", "given": "Stacy", "initials": "S", "orcid": "0000-0001-7726-5152", "researcher": {"href": "https://publications.scilifelab.se/researcher/9051c5beba2742ffabdd386bf9939fd3.json"}}, {"family": "Sealock", "given": "Julia", "initials": "J"}, {"family": "Karlsson", "given": "Ida K", "initials": "IK"}, {"family": "H\u00e4gg", "given": "Sara", "initials": "S", "orcid": "0000-0002-2452-1500", "researcher": {"href": "https://publications.scilifelab.se/researcher/e1d010dfe5d84a33b6a6c7ec815ca3dc.json"}}, {"family": "Athanasiu", "given": "Lavinia", "initials": "L"}, {"family": "Voyle", "given": "Nicola", "initials": "N"}, {"family": "Proitsi", "given": "Petroula", "initials": "P", "orcid": "0000-0002-2553-6974", "researcher": {"href": "https://publications.scilifelab.se/researcher/724f31ac8bc746e7801728be49ab9cc2.json"}}, {"family": "Witoelar", "given": "Aree", "initials": "A"}, {"family": "Stringer", "given": "Sven", "initials": "S", "orcid": "0000-0003-3115-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/f7e6ae56d0474688b3722f58d33f385d.json"}}, {"family": "Aarsland", "given": "Dag", "initials": "D", "orcid": "0000-0001-6314-216X", "researcher": {"href": "https://publications.scilifelab.se/researcher/121af6702db54d68b1ca94e8c22a8688.json"}}, {"family": "Almdahl", "given": "Ina S", "initials": "IS", "orcid": "0000-0001-6070-4921", "researcher": {"href": "https://publications.scilifelab.se/researcher/8c99e3bce167471ba669e820cc6e0839.json"}}, {"family": "Andersen", "given": "Fred", "initials": "F"}, {"family": "Bergh", "given": "Sverre", "initials": "S"}, {"family": "Bettella", "given": "Francesco", "initials": "F"}, {"family": "Bjornsson", "given": "Sigurbjorn", "initials": "S"}, {"family": "Br\u00e6khus", "given": "Anne", "initials": "A"}, {"family": "Br\u00e5then", "given": "Geir", "initials": "G", "orcid": "0000-0003-3224-7983", "researcher": {"href": "https://publications.scilifelab.se/researcher/52e7ea4ab30548829139064396d7c044.json"}}, {"family": "de Leeuw", "given": "Christiaan", "initials": "C", "orcid": "0000-0003-1076-9828", "researcher": {"href": "https://publications.scilifelab.se/researcher/54a93840c735496c81a9514bbc564849.json"}}, {"family": "Desikan", "given": "Rahul S", "initials": "RS"}, {"family": "Djurovic", "given": "Srdjan", "initials": "S", "orcid": "0000-0002-8140-8061", "researcher": {"href": "https://publications.scilifelab.se/researcher/906538321c8e4f38b6bb4a7b0bc18fa3.json"}}, {"family": "Dumitrescu", "given": "Logan", "initials": "L"}, {"family": "Fladby", "given": "Tormod", "initials": "T"}, {"family": "Hohman", "given": "Timothy J", "initials": "TJ", "orcid": "0000-0002-3377-7014", "researcher": {"href": "https://publications.scilifelab.se/researcher/079a5de2cf894db3b46faa3f6ba1e04e.json"}}, {"family": "Jonsson", "given": "Palmi V", "initials": "PV"}, {"family": "Kiddle", "given": "Steven J", "initials": "SJ", "orcid": "0000-0003-4350-7437", "researcher": {"href": "https://publications.scilifelab.se/researcher/6f86c2bca0014cf9aef8c215d97ce39c.json"}}, {"family": "Rongve", "given": "Arvid", "initials": "A"}, {"family": "Saltvedt", "given": "Ingvild", "initials": "I"}, {"family": "Sando", "given": "Sigrid B", "initials": "SB"}, {"family": "Selb\u00e6k", "given": "Geir", "initials": "G"}, {"family": "Shoai", "given": "Maryam", "initials": "M"}, {"family": "Skene", "given": "Nathan G", "initials": "NG", "orcid": "0000-0002-6807-3180", "researcher": {"href": "https://publications.scilifelab.se/researcher/0b4340cc0fa948eda26ce5618ebc0693.json"}}, {"family": "Snaedal", "given": "Jon", "initials": "J"}, {"family": "Stordal", "given": "Eystein", "initials": "E", "orcid": "0000-0002-2443-7923", "researcher": {"href": "https://publications.scilifelab.se/researcher/6eacc414991448c38cee92ac328eb4d3.json"}}, {"family": "Ulstein", "given": "Ingun D", "initials": "ID"}, {"family": "Wang", "given": "Yunpeng", "initials": "Y"}, {"family": "White", "given": "Linda R", "initials": "LR"}, {"family": "Hardy", "given": "John", "initials": "J"}, {"family": "Hjerling-Leffler", "given": "Jens", "initials": "J", "orcid": "0000-0002-4539-1776", "researcher": {"href": "https://publications.scilifelab.se/researcher/51675f0ff9aa47d89d6b2eb84a14820a.json"}}, {"family": "Sullivan", "given": "Patrick F", "initials": "PF"}, {"family": "van der Flier", "given": "Wiesje M", "initials": "WM"}, {"family": "Dobson", "given": "Richard", "initials": "R", "orcid": "0000-0003-4224-9245", "researcher": {"href": "https://publications.scilifelab.se/researcher/098ba38a51a64ba89362ed2a2e51455f.json"}}, {"family": "Davis", "given": "Lea K", "initials": "LK", "orcid": "0000-0001-5143-2282", "researcher": {"href": "https://publications.scilifelab.se/researcher/60132a034c8d412dbbb7fedbc9743d81.json"}}, {"family": "Stefansson", "given": "Hreinn", "initials": "H"}, {"family": "Stefansson", "given": "Kari", "initials": "K", "orcid": "0000-0003-1676-864X", "researcher": {"href": "https://publications.scilifelab.se/researcher/679465193fba4887a68e2aec34ccfd8e.json"}}, {"family": "Pedersen", "given": "Nancy L", "initials": "NL"}, {"family": "Ripke", "given": "Stephan", "initials": "S"}, {"family": "Andreassen", "given": "Ole A", "initials": "OA", "orcid": "0000-0002-4461-3568", "researcher": {"href": "https://publications.scilifelab.se/researcher/56f384e8e2fd4a7383c7b26e88a828b2.json"}}, {"family": "Posthuma", "given": "Danielle", "initials": "D", "orcid": "0000-0001-7582-2365", "researcher": {"href": "https://publications.scilifelab.se/researcher/406e98180d174e8ca087f50074c025c9.json"}}], "type": "journal article", "published": "2019-03-00", "journal": {"volume": "51", "issn": "1546-1718", "issue": "3", "pages": "404-413", "title": "Nat. Genet.", "issn-l": "1061-4036"}, "abstract": "Alzheimer's disease (AD) is highly heritable and recent studies have identified over 20 disease-associated genomic loci. Yet these only explain a small proportion of the genetic variance, indicating that undiscovered loci remain. Here, we performed a large genome-wide association study of clinically diagnosed AD and AD-by-proxy (71,880 cases, 383,378 controls). AD-by-proxy, based on parental diagnoses, showed strong genetic correlation with AD (rg = 0.81). Meta-analysis identified 29 risk loci, implicating 215 potential causative genes. Associated genes are strongly expressed in immune-related tissues and cell types (spleen, liver, and microglia). Gene-set analyses indicate biological mechanisms involved in lipid-related processes and degradation of amyloid precursor proteins. We show strong genetic correlations with multiple health-related outcomes, and Mendelian randomization results suggest a protective effect of cognitive ability on AD risk. These results are a step forward in identifying the genetic factors that contribute to AD risk and add novel insights into the neurobiology of AD.", "doi": "10.1038/s41588-018-0311-9", "pmid": "30617256", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "mid", "key": "NIHMS1031924"}, {"db": "pmc", "key": "PMC6836675"}, {"db": "pii", "key": "10.1038/s41588-018-0311-9"}], "notes": [], "created": "2019-03-13T09:21:28.969Z", "modified": "2023-06-20T15:57:06.709Z"}, {"entity": "publication", "iuid": "c411673d88f94ce68794635c59d1eb32", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c411673d88f94ce68794635c59d1eb32.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c411673d88f94ce68794635c59d1eb32"}}, "title": "Estimating the Fitness Effect of Deleterious Mutations During the Two Phases of the Life Cycle: A New Method Applied to the Root-Rot Fungus Heterobasidion parviporum.", "authors": [{"family": "Clergeot", "given": "Pierre-Henri", "initials": "PH"}, {"family": "Rode", "given": "Nicolas O", "initials": "NO", "orcid": "0000-0002-1121-4202", "researcher": {"href": "https://publications.scilifelab.se/researcher/6cf02c27d37f4f67be76b9ba4cd5686f.json"}}, {"family": "Gl\u00e9min", "given": "Sylvain", "initials": "S", "orcid": "0000-0001-7260-4573", "researcher": {"href": "https://publications.scilifelab.se/researcher/0ce5a8d7ac9a490eb2e261aeb75088d4.json"}}, {"family": "Brandstr\u00f6m Durling", "given": "Mikael", "initials": "M", "orcid": "0000-0001-6485-197X", "researcher": {"href": "https://publications.scilifelab.se/researcher/7be72d0dcc48489495509b23c7ad3d38.json"}}, {"family": "Ihrmark", "given": "Katarina", "initials": "K"}, {"family": "Olson", "given": "\u00c5ke", "initials": "\u00c5", "orcid": "0000-0001-8998-6096", "researcher": {"href": "https://publications.scilifelab.se/researcher/83a79139c2b94d9f97cf038e1cab8c03.json"}}], "type": "journal article", "published": "2019-03-00", "journal": {"volume": "211", "issn": "1943-2631", "issue": "3", "pages": "963-976", "title": "Genetics", "issn-l": "0016-6731"}, "abstract": "Many eukaryote species, including taxa such as fungi or algae, have a lifecycle with substantial haploid and diploid phases. A recent theoretical model predicts that such haploid-diploid lifecycles are stable over long evolutionary time scales when segregating deleterious mutations have stronger effects in homozygous diploids than in haploids and when they are partially recessive in heterozygous diploids. The model predicts that effective dominance-a measure that accounts for these two effects-should be close to 0.5 in these species. It also predicts that diploids should have higher fitness than haploids on average. However, an appropriate statistical framework to conjointly investigate these predictions is currently lacking. In this study, we derive a new quantitative genetic model to test these predictions using fitness data of two haploid parents and their diploid offspring, and genome-wide genetic distance between haploid parents. We apply this model to the root-rot basidiomycete fungus Heterobasidion parviporum-a species where the heterokaryotic (equivalent to the diploid) phase is longer than the homokaryotic (haploid) phase. We measured two fitness-related traits (mycelium growth rate and the ability to degrade wood) in both homokaryons and heterokaryons, and we used whole-genome sequencing to estimate nuclear genetic distance between parents. Possibly due to a lack of power, we did not find that deleterious mutations were recessive or more deleterious when expressed during the heterokaryotic phase. Using this model to compare effective dominance among haploid-diploid species where the relative importance of the two phases varies should help better understand the evolution of haploid-diploid life cycles.", "doi": "10.1534/genetics.118.301855", "pmid": "30598467", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "genetics.118.301855"}, {"db": "pmc", "key": "PMC6404244"}, {"db": "figshare", "key": "10.25386/genetics.6941477"}], "notes": [], "created": "2020-01-08T12:44:32.500Z", "modified": "2021-06-21T13:30:12.874Z"}, {"entity": "publication", "iuid": "970a4233ec8f488880a8e2ccf62dc529", "links": {"self": {"href": "https://publications.scilifelab.se/publication/970a4233ec8f488880a8e2ccf62dc529.json"}, "display": {"href": "https://publications.scilifelab.se/publication/970a4233ec8f488880a8e2ccf62dc529"}}, "title": "Endosperm-specific transcriptome analysis by applying the INTACT system.", "authors": [{"family": "Del Toro-De Le\u00f3n", "given": "Gerardo", "initials": "G", "orcid": "0000-0003-2079-1746", "researcher": {"href": "https://publications.scilifelab.se/researcher/f765f9578882429d9d86f646bbbb6169.json"}}, {"family": "K\u00f6hler", "given": "Claudia", "initials": "C", "orcid": "0000-0002-2619-4857", "researcher": {"href": "https://publications.scilifelab.se/researcher/accd3f9307614c8ab67154dd5e50cdac.json"}}], "type": "equivalence trial", "published": "2019-03-00", "journal": {"volume": "32", "issn": "2194-7961", "issue": "1", "pages": "55-61", "title": "Plant Reprod", "issn-l": "2194-7953"}, "abstract": "We report the adaptation of the INTACT method for RNA-sequencing in the endosperm and demonstrate its feasibility for allele-specific expression analysis. Tissue-specific transcriptome analyses provide important insights into the developmental programs of defined cell types. The isolation of nuclei tagged in specific cell types (INTACT) is a versatile method that allows to isolate highly pure nuclei from defined tissue types that can be used for several downstream applications. Here, we describe the adaptation of INTACT from endosperm nuclei for high-throughput RNA-sequencing. By analyzing the ratio of parental reads and tissue-specific gene expression in the endosperm, we could assess the contamination level of our samples. Based on this analysis, we estimate that in most of the samples the contamination level is lower than in previously published datasets. We further show that the nuclear transcriptome and total transcriptome of the endosperm are well correlated. Together, our data show that INTACT of the endosperm is a reliable methodology for endosperm-specific transcriptome analysis that overcomes the limitation of time-consuming manual endosperm dissection that is connected with high levels of maternal tissue contamination. INTACT does not rely on expensive equipment and can be set up in every standard molecular biology laboratory, making it the method of choice for future molecular studies of the endosperm.", "doi": "10.1007/s00497-018-00356-3", "pmid": "30588542", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1007/s00497-018-00356-3"}], "notes": [], "created": "2019-01-07T18:04:05.802Z", "modified": "2021-06-21T13:50:08.358Z"}, {"entity": "publication", "iuid": "6d28ace9457d4629bb9f751492ef60e0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6d28ace9457d4629bb9f751492ef60e0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6d28ace9457d4629bb9f751492ef60e0"}}, "title": "Asexual reproduction and growth rate: independent and plastic life history traits in Neurospora crassa.", "authors": [{"family": "Anderson", "given": "Jennifer L", "initials": "JL", "orcid": "0000-0002-0713-6897", "researcher": {"href": "https://publications.scilifelab.se/researcher/925e9736bd84401ca54158c320ed0b55.json"}}, {"family": "Nieuwenhuis", "given": "Bart P S", "initials": "BPS", "orcid": "0000-0001-8159-4784", "researcher": {"href": "https://publications.scilifelab.se/researcher/8e3278c557ff403aa061ee99a8631d6e.json"}}, {"family": "Johannesson", "given": "Hanna", "initials": "H", "orcid": "0000-0001-6359-9856", "researcher": {"href": "https://publications.scilifelab.se/researcher/36e8fe278e01470e8cddaaccc5dad596.json"}}], "type": "journal article", "published": "2019-03-00", "journal": {"volume": "13", "issn": "1751-7370", "issue": "3", "pages": "780-788", "title": "ISME J", "issn-l": "1751-7362"}, "abstract": "Trade-offs among traits influencing fitness are predicted by life history theory because resources allocated to one function are unavailable to another. Here we examine the relationship between two such traits, asexual reproduction and growth rate, in the filamentous fungus Neurospora crassa, where shared genetic and physiological factors and a source-sink energetic relationship between growth and reproduction may constrain the evolution of these traits. To test growth-reproduction relationships in this species, we independently selected on mycelial growth rate or asexual spore production in a heterogeneous lab-derived population and evaluated the response of the non-selected traits. Combined with phenotypes for the 20 wild strains used to produce the heterogeneous population and the genome-wide genotypes of 468 strains, these data show that growth and reproduction are highly plastic in N. crassa and do not trade off either among wild strains or after laboratory selection in two environments. Rather, we find no predictable growth-reproduction relationship in the environments tested, indicating an effective absence of genetic constraint between these traits. Our results suggest that growth rate and asexual reproduction may not respond predictably to environmental change and suggest that reliance on a single trait as a proxy for fitness in fungal studies may be inadvisable.", "doi": "10.1038/s41396-018-0294-7", "pmid": "30413765", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41396-018-0294-7"}, {"db": "pmc", "key": "PMC6462030"}], "notes": [], "created": "2019-01-07T22:49:26.024Z", "modified": "2021-06-21T14:01:01.937Z"}, {"entity": "publication", "iuid": "231ea4382fec40589e362e641083fa78", "links": {"self": {"href": "https://publications.scilifelab.se/publication/231ea4382fec40589e362e641083fa78.json"}, "display": {"href": "https://publications.scilifelab.se/publication/231ea4382fec40589e362e641083fa78"}}, "title": "A rare regulatory variant in the MEF2D gene affects gene regulation and splicing and is associated with a SLE sub-phenotype in Swedish cohorts.", "authors": [{"family": "Farias", "given": "Fabiana H G", "initials": "FHG"}, {"family": "Dahlqvist", "given": "Johanna", "initials": "J"}, {"family": "Kozyrev", "given": "Sergey V", "initials": "SV"}, {"family": "Leonard", "given": "Dag", "initials": "D"}, {"family": "Wilbe", "given": "Maria", "initials": "M"}, {"family": "Abramov", "given": "Sergei N", "initials": "SN"}, {"family": "Alexsson", "given": "Andrei", "initials": "A"}, {"family": "Pielberg", "given": "Gerli R", "initials": "GR"}, {"family": "Hansson-Hamlin", "given": "Helene", "initials": "H"}, {"family": "Andersson", "given": "G\u00f6ran", "initials": "G"}, {"family": "Tandre", "given": "Karolina", "initials": "K"}, {"family": "Bengtsson", "given": "Anders A", "initials": "AA"}, {"family": "Sj\u00f6wall", "given": "Christopher", "initials": "C", "orcid": "0000-0003-0900-2048", "researcher": {"href": "https://publications.scilifelab.se/researcher/fe4dd47b8ca1436e8a26fdea33f5e7f6.json"}}, {"family": "Svenungsson", "given": "Elisabet", "initials": "E"}, {"family": "Gunnarsson", "given": "Iva", "initials": "I"}, {"family": "Rantap\u00e4\u00e4-Dahlqvist", "given": "Solbritt", "initials": "S"}, {"family": "Syv\u00e4nen", "given": "Ann-Christine", "initials": "AC", "orcid": "0000-0002-9681-9146", "researcher": {"href": "https://publications.scilifelab.se/researcher/f7012e35025543379380cb90efd71243.json"}}, {"family": "Sandling", "given": "Johanna K", "initials": "JK"}, {"family": "Eloranta", "given": "Maija-Leena", "initials": "ML"}, {"family": "R\u00f6nnblom", "given": "Lars", "initials": "L"}, {"family": "Lindblad-Toh", "given": "Kerstin", "initials": "K", "orcid": "0000-0001-8338-0253", "researcher": {"href": "https://publications.scilifelab.se/researcher/e0063145f7d6476f80ab42f94833f4cf.json"}}], "type": "journal article", "published": "2019-03-00", "journal": {"volume": "27", "issn": "1476-5438", "issue": "3", "pages": "432-441", "title": "Eur. J. Hum. Genet.", "issn-l": "1018-4813"}, "abstract": "Systemic lupus erythematosus (SLE) is an autoimmune disorder with heterogeneous clinical presentation and complex etiology involving the interplay between genetic, epigenetic, environmental and hormonal factors. Many common SNPs identified by genome wide-association studies (GWAS) explain only a small part of the disease heritability suggesting the contribution from rare genetic variants, undetectable in GWAS, and complex epistatic interactions. Using targeted re-sequencing of coding and conserved regulatory regions within and around 215 candidate genes selected on the basis of their known role in autoimmunity and genes associated with canine immune-mediated diseases, we identified a rare regulatory variant rs200395694:G > T located in intron 4 of the MEF2D gene encoding the myocyte-specific enhancer factor 2D transcription factor and associated with SLE in Swedish cohorts (504 SLE patients and 839 healthy controls, p = 0.014, CI = 1.1-10). Fisher's exact test revealed an association between the genetic variant and a triad of disease manifestations including Raynaud, anti-U1-ribonucleoprotein (anti-RNP), and anti-Smith (anti-Sm) antibodies (p = 0.00037) among the patients. The DNA-binding activity of the allele was further studied by EMSA, reporter assays, and minigenes. The region has properties of an active cell-specific enhancer, differentially affected by the alleles of rs200395694:G > T. In addition, the risk allele exerts an inhibitory effect on the splicing of the alternative tissue-specific isoform, and thus may modify the target gene set regulated by this isoform. These findings emphasize the potential of dissecting traits of complex diseases and correlating them with rare risk alleles with strong biological effects.", "doi": "10.1038/s41431-018-0297-x", "pmid": "30459414", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41431-018-0297-x"}, {"db": "pmc", "key": "PMC6460566"}], "notes": [], "created": "2018-11-28T07:46:41.045Z", "modified": "2024-01-16T13:48:44.647Z"}, {"entity": "publication", "iuid": "b06725ea3ccc41b7a6cfe3ab0c4e3c0a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b06725ea3ccc41b7a6cfe3ab0c4e3c0a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b06725ea3ccc41b7a6cfe3ab0c4e3c0a"}}, "title": "A genome-wide association study identifies new loci for factor VII and implicates factor VII in ischemic stroke etiology.", "authors": [{"family": "de Vries", "given": "Paul S", "initials": "PS"}, {"family": "Sabater-Lleal", "given": "Maria", "initials": "M"}, {"family": "Huffman", "given": "Jennifer E", "initials": "JE"}, {"family": "Marten", "given": "Jonathan", "initials": "J"}, {"family": "Song", "given": "Ci", "initials": "C"}, {"family": "Pankratz", "given": "Nathan", "initials": "N"}, {"family": "Bartz", "given": "Traci M", "initials": "TM"}, {"family": "de Haan", "given": "Hugoline G", "initials": "HG"}, {"family": "Delgado", "given": "Graciela E", "initials": "GE"}, {"family": "Eicher", "given": "John D", "initials": "JD"}, {"family": "Martinez-Perez", "given": "Angel", "initials": "A"}, {"family": "Ward-Caviness", "given": "Cavin K", "initials": "CK"}, {"family": "Brody", "given": "Jennifer A", "initials": "JA"}, {"family": "Chen", "given": "Ming-Huei", "initials": "MH"}, {"family": "de Maat", "given": "Moniek P M", "initials": "MPM"}, {"family": "Fr\u00e5nberg", "given": "Mattias", "initials": "M"}, {"family": "Gill", "given": "Dipender", "initials": "D"}, {"family": "Kleber", "given": "Marcus E", "initials": "ME"}, {"family": "Rivadeneira", "given": "Fernando", "initials": "F"}, {"family": "Soria", "given": "Jos\u00e9 Manuel", "initials": "JM"}, {"family": "Tang", "given": "Weihong", "initials": "W"}, {"family": "Tofler", "given": "Geoffrey H", "initials": "GH"}, {"family": "Uitterlinden", "given": "Andr\u00e9 G", "initials": "AG"}, {"family": "van Hylckama Vlieg", "given": "Astrid", "initials": "A"}, {"family": "Seshadri", "given": "Sudha", "initials": "S"}, {"family": "Boerwinkle", "given": "Eric", "initials": "E"}, {"family": "Davies", "given": "Neil M", "initials": "NM"}, {"family": "Giese", "given": "Anne-Katrin", "initials": "AK"}, {"family": "Ikram", "given": "M Kamran", "initials": "MK"}, {"family": "Kittner", "given": "Steven J", "initials": "SJ"}, {"family": "McKnight", "given": "Barbara", "initials": "B"}, {"family": "Psaty", "given": "Bruce M", "initials": "BM"}, {"family": "Reiner", "given": "Alex P", "initials": "AP"}, {"family": "Sargurupremraj", "given": "Muralidharan", "initials": "M"}, {"family": "Taylor", "given": "Kent D", "initials": "KD"}, {"family": "INVENT Consortium", "given": "", "initials": ""}, {"family": "MEGASTROKE Consortium of the International Stroke Genetics Consortium", "given": "", "initials": ""}, {"family": "Fornage", "given": "Myriam", "initials": "M"}, {"family": "Hamsten", "given": "Anders", "initials": "A"}, {"family": "M\u00e4rz", "given": "Winfried", "initials": "W"}, {"family": "Rosendaal", "given": "Frits R", "initials": "FR"}, {"family": "Souto", "given": "Juan Carlos", "initials": "JC"}, {"family": "Dehghan", "given": "Abbas", "initials": "A"}, {"family": "Johnson", "given": "Andrew D", "initials": "AD"}, {"family": "Morrison", "given": "Alanna C", "initials": "AC"}, {"family": "O'Donnell", "given": "Christopher J", "initials": "CJ"}, {"family": "Smith", "given": "Nicholas L", "initials": "NL"}], "type": "journal article", "published": "2019-02-28", "journal": {"volume": "133", "issn": "1528-0020", "issue": "9", "pages": "967-977", "title": "Blood", "issn-l": "0006-4971"}, "abstract": "Factor VII (FVII) is an important component of the coagulation cascade. Few genetic loci regulating FVII activity and/or levels have been discovered to date. We conducted a meta-analysis of 9 genome-wide association studies of plasma FVII levels (7 FVII activity and 2 FVII antigen) among 27\u2009495 participants of European and African ancestry. Each study performed ancestry-specific association analyses. Inverse variance weighted meta-analysis was performed within each ancestry group and then combined for a \n            trans-ancestry meta-analysis. Our primary analysis included the 7 studies that measured FVII activity, and a secondary analysis included all 9 studies. We provided functional genomic validation for newly identified significant loci by silencing candidate genes in a human liver cell line (HuH7) using small-interfering RNA and then measuring F7 messenger RNA and FVII protein expression. Lastly, we used meta-analysis results to perform Mendelian randomization analysis to estimate the causal effect of FVII activity on coronary artery disease, ischemic stroke (IS), and venous thromboembolism. We identified 2 novel (REEP3 and JAZF1-AS1) and 6 known loci associated with FVII activity, explaining 19.0% of the phenotypic variance. Adding FVII antigen data to the meta-analysis did not result in the discovery of further loci. Silencing REEP3 in HuH7 cells upregulated FVII, whereas silencing JAZF1 downregulated FVII. Mendelian randomization analyses suggest that FVII activity has a positive causal effect on the risk of IS. Variants at REEP3 and JAZF1 contribute to FVII activity by regulating F7 expression levels. FVII activity appears to contribute to the etiology of IS in the general population.", "doi": "10.1182/blood-2018-05-849240", "pmid": "30642921", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "blood-2018-05-849240"}], "notes": [], "created": "2019-03-13T09:21:27.986Z", "modified": "2020-01-21T13:56:13.895Z"}, {"entity": "publication", "iuid": "79c087299ab448418fad91a86e9a6d2e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/79c087299ab448418fad91a86e9a6d2e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/79c087299ab448418fad91a86e9a6d2e"}}, "title": "Genetics and epigenetics in primary Sj\u00f6gren's syndrome.", "authors": [{"family": "Imgenberg-Kreuz", "given": "Juliana", "initials": "J"}, {"family": "Rasmussen", "given": "Astrid", "initials": "A"}, {"family": "Sivils", "given": "Kathy", "initials": "K"}, {"family": "Nordmark", "given": "Gunnel", "initials": "G"}], "type": "journal article", "published": "2019-02-15", "journal": {"volume": null, "issn": "1462-0332", "issue": null, "title": "Rheumatology (Oxford)", "issn-l": "1462-0324"}, "abstract": "Primary Sj\u00f6gren's syndrome (pSS) is considered to be a multifactorial disease, where underlying genetic predisposition, epigenetic mechanisms and environmental factors contribute to disease development. In the last 5 years, the first genome-wide association studies in pSS have been completed. The strongest signal of association lies within the HLA genes, whereas the non-HLA genes IRF5 and STAT4 show consistent associations in multiple ethnicities but with a smaller effect size. The majority of the genetic risk variants are found at intergenic regions and their functional impact has in most cases not been elucidated. Epigenetic mechanisms such as DNA methylation, histone modifications and non-coding RNAs play a role in the pathogenesis of pSS by their modulating effects on gene expression and may constitute a dynamic link between the genome and phenotypic manifestations. This article reviews the hitherto published genetic studies and our current understanding of epigenetic mechanisms in pSS.", "doi": "10.1093/rheumatology/key330", "pmid": "30770922", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "5321203"}], "notes": [], "created": "2019-03-13T09:21:22.219Z", "modified": "2020-01-21T13:56:13.854Z"}, {"entity": "publication", "iuid": "450f8da69f4542c8a4a21da72c872a4a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/450f8da69f4542c8a4a21da72c872a4a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/450f8da69f4542c8a4a21da72c872a4a"}}, "title": "Fine-Tuning of Sox17 and Canonical Wnt Coordinates the Permeability Properties of the Blood-Brain Barrier.", "authors": [{"family": "Corada", "given": "Monica", "initials": "M"}, {"family": "Orsenigo", "given": "Fabrizio", "initials": "F"}, {"family": "Bhat", "given": "Ganesh Parameshwar", "initials": "GP"}, {"family": "Conze", "given": "Lei Liu", "initials": "LL"}, {"family": "Breviario", "given": "Ferruccio", "initials": "F"}, {"family": "Cunha", "given": "Sara Isabel", "initials": "SI"}, {"family": "Claesson-Welsh", "given": "Lena", "initials": "L"}, {"family": "Beznoussenko", "given": "Galina V", "initials": "GV"}, {"family": "Mironov", "given": "Alexander A", "initials": "AA"}, {"family": "Bacigaluppi", "given": "Marco", "initials": "M"}, {"family": "Martino", "given": "Gianvito", "initials": "G"}, {"family": "Pitulescu", "given": "Mara E", "initials": "ME"}, {"family": "Adams", "given": "Ralf H", "initials": "RH"}, {"family": "Magnusson", "given": "Peetra", "initials": "P"}, {"family": "Dejana", "given": "Elisabetta", "initials": "E"}], "type": "journal article", "published": "2019-02-15", "journal": {"volume": "124", "issn": "1524-4571", "issue": "4", "pages": "511-525", "title": "Circ. Res.", "issn-l": "0009-7330"}, "abstract": "The microvasculature of the central nervous system includes the blood-brain barrier (BBB), which regulates the permeability to nutrients and restricts the passage of toxic agents and inflammatory cells. Canonical Wnt/\u03b2-catenin signaling is responsible for the early phases of brain vascularization and BBB differentiation. However, this signal declines after birth, and other signaling pathways able to maintain barrier integrity at postnatal stage are still unknown.\n\nSox17 (SRY [sex-determining region Y]-box 17) constitutes a major downstream target of Wnt/\u03b2-catenin in endothelial cells and regulates arterial differentiation. In the present article, we asked whether Sox17 may act downstream of Wnt/\u03b2-catenin in inducing BBB differentiation and maintenance.\n\nUsing reporter mice and nuclear staining of Sox17 and \u03b2-catenin, we report that although \u03b2-catenin signaling declines after birth, Sox17 activation increases and remains high in the adult. Endothelial-specific inactivation of Sox17 leads to increase of permeability of the brain microcirculation. The severity of this effect depends on the degree of BBB maturation: it is strong in the embryo and progressively declines after birth. In search of Sox17 mechanism of action, RNA sequencing analysis of gene expression of brain endothelial cells has identified members of the Wnt/\u03b2-catenin signaling pathway as downstream targets of Sox17. Consistently, we found that Sox17 is a positive inducer of Wnt/\u03b2-catenin signaling, and it acts in concert with this pathway to induce and maintain BBB properties. In vivo, inhibition of the \u03b2-catenin destruction complex or expression of a degradation-resistant \u03b2-catenin mutant, prevent the increase in permeability and retina vascular malformations observed in the absence of Sox17.\n\nOur data highlight a novel role for Sox17 in the induction and maintenance of the BBB, and they underline the strict reciprocal tuning of this transcription factor and Wnt/\u03b2-catenin pathway. Modulation of Sox17 activity may be relevant to control BBB permeability in pathological conditions.", "doi": "10.1161/CIRCRESAHA.118.313316", "pmid": "30591003", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC6407809"}], "notes": [], "created": "2020-01-08T12:41:49.709Z", "modified": "2021-06-21T13:33:14.416Z"}, {"entity": "publication", "iuid": "cc74f4cd8d9b4314b59b768ea493f52f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/cc74f4cd8d9b4314b59b768ea493f52f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/cc74f4cd8d9b4314b59b768ea493f52f"}}, "title": "Association of the coronary artery disease risk gene GUCY1A3 with ischaemic events after coronary intervention.", "authors": [{"family": "Kessler", "given": "Thorsten", "initials": "T"}, {"family": "Wolf", "given": "Bernhard", "initials": "B"}, {"family": "Eriksson", "given": "Niclas", "initials": "N"}, {"family": "Kofink", "given": "Daniel", "initials": "D"}, {"family": "Mahmoodi", "given": "Bakhtawar K", "initials": "BK"}, {"family": "Rai", "given": "Himanshu", "initials": "H"}, {"family": "Tragante", "given": "Vinicius", "initials": "V"}, {"family": "\u00c5kerblom", "given": "Axel", "initials": "A"}, {"family": "Becker", "given": "Richard C", "initials": "RC"}, {"family": "Bernlochner", "given": "Isabell", "initials": "I"}, {"family": "Bopp", "given": "Roman", "initials": "R"}, {"family": "James", "given": "Stefan", "initials": "S"}, {"family": "Katus", "given": "Hugo A", "initials": "HA"}, {"family": "Mayer", "given": "Katharina", "initials": "K"}, {"family": "Munz", "given": "Matthias", "initials": "M"}, {"family": "Nordio", "given": "Francesco", "initials": "F"}, {"family": "O'Donoghue", "given": "Michelle L", "initials": "ML"}, {"family": "Sager", "given": "Hendrik B", "initials": "HB"}, {"family": "Sibbing", "given": "Dirk", "initials": "D"}, {"family": "Solakov", "given": "Linda", "initials": "L"}, {"family": "Storey", "given": "Robert F", "initials": "RF"}, {"family": "Wobst", "given": "Jana", "initials": "J"}, {"family": "Asselbergs", "given": "Folkert W", "initials": "FW"}, {"family": "Byrne", "given": "Robert A", "initials": "RA"}, {"family": "Erdmann", "given": "Jeanette", "initials": "J"}, {"family": "Koenig", "given": "Wolfgang", "initials": "W"}, {"family": "Laugwitz", "given": "Karl-Ludwig", "initials": "KL"}, {"family": "Ten Berg", "given": "Jurrien M", "initials": "JM"}, {"family": "Wallentin", "given": "Lars", "initials": "L"}, {"family": "Kastrati", "given": "Adnan", "initials": "A"}, {"family": "Schunkert", "given": "Heribert", "initials": "H"}], "type": "journal article", "published": "2019-02-14", "journal": {"volume": null, "issn": "1755-3245", "issue": null, "title": "Cardiovasc. Res.", "issn-l": "0008-6363"}, "abstract": "A common genetic variant at the GUCY1A3 coronary artery disease locus has been shown to influence platelet aggregation. The risk of ischaemic events including stent thrombosis varies with the efficacy of aspirin to inhibit platelet reactivity. This study sought to investigate whether homozygous GUCY1A3 (rs7692387) risk allele carriers display higher on-aspirin platelet reactivity and risk of ischaemic events early after coronary intervention.\n\nThe association of GUCY1A3 genotype and on-aspirin platelet reactivity was analysed in the genetics substudy of the ISAR-ASPI registry (n\u2009=\u20091678) using impedance aggregometry. The clinical outcome cardiovascular death or stent thrombosis within 30\u2009days after stenting was investigated in a meta-analysis of substudies of the ISAR-ASPI registry, the PLATO trial (n\u2009=\u20093236), and the Utrecht Coronary Biobank (n\u2009=\u20091003) comprising a total 5917 patients. Homozygous GUCY1A3 risk allele carriers (GG) displayed increased on-aspirin platelet reactivity compared with non-risk allele (AA/AG) carriers [150 (interquartile range 91-209) vs. 134 (85-194) AU\u22c5min, P\u2009<\u20090.01]. More homozygous risk allele carriers, compared with non-risk allele carriers, were assigned to the high-risk group for ischaemic events (>203\u2009AU\u22c5min; 29.5 vs. 24.2%, P\u2009=\u20090.02). Homozygous risk allele carriers were also at higher risk for cardiovascular death or stent thrombosis (hazard ratio 1.70, 95% confidence interval 1.08-2.68; P\u2009=\u20090.02). Bleeding risk was not altered.\n\nWe conclude that homozygous GUCY1A3 risk allele carriers are at increased risk of cardiovascular death or stent thrombosis within 30\u2009days after coronary stenting, likely due to higher on-aspirin platelet reactivity. Whether GUCY1A3 genotype helps to tailor antiplatelet treatment remains to be investigated.", "doi": "10.1093/cvr/cvz015", "pmid": "30768153", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "5320311"}], "notes": [], "created": "2019-03-13T09:21:23.117Z", "modified": "2020-01-21T13:56:14.318Z"}, {"entity": "publication", "iuid": "5d538c9fd747401885a3756a374d7e28", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5d538c9fd747401885a3756a374d7e28.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5d538c9fd747401885a3756a374d7e28"}}, "title": "Two Basidiomycete Fungi in the Cortex of Wolf Lichens.", "authors": [{"family": "Tuovinen", "given": "Veera", "initials": "V"}, {"family": "Ekman", "given": "Stefan", "initials": "S"}, {"family": "Thor", "given": "G\u00f6ran", "initials": "G"}, {"family": "Vanderpool", "given": "Dan", "initials": "D"}, {"family": "Spribille", "given": "Toby", "initials": "T"}, {"family": "Johannesson", "given": "Hanna", "initials": "H"}], "type": "journal article", "published": "2019-02-04", "journal": {"volume": "29", "issn": "1879-0445", "issue": "3", "pages": "476-483.e5", "title": "Curr. Biol.", "issn-l": "0960-9822"}, "abstract": "Since the late 1800s, mycologists have been detecting fungi above and beyond the assumed single fungus in lichen thalli [1-6]. Over the last century, these fungi have been accorded roles ranging from commensalists to pathogens. Recently, Cyphobasidiales yeasts were shown to be ubiquitous in the cortex layer of many macrolichens [7], but for most species, little is known of their cellular distribution and constancy beyond visible fruiting structures. Here, we demonstrate the occurrence of an additional and distantly related basidiomycete, Tremella, in 95% of studied thalli in a global sample of one of the most intensively studied groups of lichens, the wolf lichens (genus Letharia). Tremella species are reported from a wide range of lichen genera [8], but until now, their biology was deduced from fruiting bodies (basidiomata) formed on lichen thalli. Based on this, they have been thought to be uncommon to rare, to occur exclusively in a hyphal form, and to be parasitic on the dominant fungal partner [9, 10]. We show that, in wolf lichens, Tremella occurs as yeast cells also in thalli that lack basidiomata and infer that this is its dominant stage in nature. We further show that the hyphal stage, when present in Letharia, is in close contact with algal cells, challenging the assumption that lichen-associated Tremella species are uniformly mycoparasites. Our results suggest that extent of occurrence and cellular interactions of known fungi within lichens have historically been underestimated and raise new questions about their function in specific lichen symbioses.", "doi": "10.1016/j.cub.2018.12.022", "pmid": "30661799", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "S0960-9822(18)31654-3"}], "notes": [], "created": "2019-04-23T09:57:20.875Z", "modified": "2024-01-16T13:48:44.697Z"}, {"entity": "publication", "iuid": "d76d3e51f0094752b0b8b525a73f55a8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d76d3e51f0094752b0b8b525a73f55a8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d76d3e51f0094752b0b8b525a73f55a8"}}, "title": "The genomics of major psychiatric disorders in a large pedigree from Northern Sweden.", "authors": [{"family": "Szatkiewicz", "given": "Jin", "initials": "J"}, {"family": "Crowley", "given": "James J", "initials": "JJ"}, {"family": "Adolfsson", "given": "Annelie Nordin", "initials": "AN"}, {"family": "\u00c5berg", "given": "Karolina A", "initials": "KA"}, {"family": "Alaerts", "given": "Maaike", "initials": "M"}, {"family": "Genovese", "given": "Giulio", "initials": "G"}, {"family": "McCarroll", "given": "Steven", "initials": "S"}, {"family": "Del-Favero", "given": "Jurgen", "initials": "J"}, {"family": "Adolfsson", "given": "Rolf", "initials": "R"}, {"family": "Sullivan", "given": "Patrick F", "initials": "PF", "orcid": "0000-0002-6619-873X", "researcher": {"href": "https://publications.scilifelab.se/researcher/4d95de0b5ab14586980a6a13c8299346.json"}}], "type": "journal article", "published": "2019-02-04", "journal": {"volume": "9", "issn": "2158-3188", "issue": "1", "pages": "60", "title": "Transl Psychiatry", "issn-l": "2158-3188"}, "abstract": "We searched for genetic causes of major psychiatric disorders (bipolar disorder, schizoaffective disorder, and schizophrenia) in a large, densely affected pedigree from Northern Sweden that originated with three pairs of founders born around 1650. We applied a systematic genomic approach to the pedigree via karyotyping (N = 9), genome-wide SNP arrays (N = 418), whole-exome sequencing (N = 26), and whole-genome sequencing (N = 10). Comprehensive analysis did not identify plausible variants of strong effect. Rather, pedigree cases had significantly higher genetic risk scores compared to pedigree and community controls.", "doi": "10.1038/s41398-019-0414-9", "pmid": "30718465", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41398-019-0414-9"}, {"db": "pmc", "key": "PMC6362018"}], "notes": [], "created": "2019-04-23T09:58:54.570Z", "modified": "2024-01-16T13:48:44.705Z"}, {"entity": "publication", "iuid": "4ab972d262af414cae7747417e8fbeb0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4ab972d262af414cae7747417e8fbeb0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4ab972d262af414cae7747417e8fbeb0"}}, "title": "Exploring the genetics of trotting racing ability in horses using a unique Nordic horse model.", "authors": [{"family": "Velie", "given": "Brandon D", "initials": "BD", "orcid": "0000-0001-9359-6138", "researcher": {"href": "https://publications.scilifelab.se/researcher/c39a4ff0532345f58201d6d40a691a46.json"}}, {"family": "Lillie", "given": "Mette", "initials": "M"}, {"family": "Fegraeus", "given": "Kim J\u00e4derkvist", "initials": "KJ"}, {"family": "Rosengren", "given": "Maria K", "initials": "MK"}, {"family": "Sol\u00e9", "given": "Marina", "initials": "M"}, {"family": "Wiklund", "given": "Maja", "initials": "M"}, {"family": "Ihler", "given": "Carl-Fredrik", "initials": "CF"}, {"family": "Strand", "given": "Eric", "initials": "E"}, {"family": "Lindgren", "given": "Gabriella", "initials": "G"}], "type": "journal article", "published": "2019-02-04", "journal": {"volume": "20", "issn": "1471-2164", "issue": "1", "pages": "104", "title": "BMC Genomics", "issn-l": "1471-2164"}, "abstract": "Horses have been strongly selected for speed, strength, and endurance-exercise traits since the onset of domestication. As a result, highly specialized horse breeds have developed with many modern horse breeds often representing closed populations with high phenotypic and genetic uniformity. However, a great deal of variation still exists between breeds, making the horse particularly well suited for genetic studies of athleticism. To identify genomic regions associated with athleticism as it pertains to trotting racing ability in the horse, the current study applies a pooled sequence analysis approach using a unique Nordic horse model.\n\nPooled sequence data from three Nordic horse populations were used for F ST analysis. After strict filtering, FST analysis yielded 580 differentiated regions for trotting racing ability. Candidate regions on equine chromosomes 7 and 11 contained the largest number of SNPs (n = 214 and 147, respectively). GO analyses identified multiple genes related to intelligence, energy metabolism, and skeletal development as potential candidate genes. However, only one candidate region for trotting racing ability overlapped a known racing ability QTL.\n\nNot unexpected for genomic investigations of complex traits, the current study identified hundreds of candidate regions contributing to trotting racing ability in the horse. Likely resulting from the cumulative effects of many variants across the genome, racing ability continues to demonstrate its polygenic nature with candidate regions implicating genes influencing both musculature and neurological development.", "doi": "10.1186/s12864-019-5484-9", "pmid": "30717660", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1186/s12864-019-5484-9"}, {"db": "pmc", "key": "PMC6360714"}], "notes": [], "created": "2019-04-23T09:58:32.755Z", "modified": "2024-01-16T13:48:44.722Z"}, {"entity": "publication", "iuid": "68743e5b18c84dccb5ae3d1e44e83dc3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/68743e5b18c84dccb5ae3d1e44e83dc3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/68743e5b18c84dccb5ae3d1e44e83dc3"}}, "title": "Introgression of resistance to Rhopalosiphum padi L. from wild barley into cultivated barley facilitated by doubled haploid and molecular marker techniques.", "authors": [{"family": "\u00c5hman", "given": "Inger", "initials": "I"}, {"family": "Bengtsson", "given": "Ther\u00e9se", "initials": "T"}], "type": "journal article", "published": "2019-02-02", "journal": {"volume": null, "issn": "1432-2242", "issue": null, "title": "Theor. Appl. Genet.", "issn-l": "0040-5752"}, "abstract": "Long-term pre-breeding using Hordeum vulgare ssp. spontaneum as a donor of bird cherry-oat aphid resistance has resulted in agronomically improved resistance sources of barley along with easy-to-use molecular markers. Bird cherry-oat aphid (Rhopalosiphum padi L.) is a pest and a virus vector in barley to which there are no bred-resistant cultivars. The present study describes how resistance from Hordeum vulgare ssp. spontaneum has been introgressed in cultivated barley via five successive crosses with the same cultivar Lina (BC) and in parallel with other more modern barley cultivars. Most of the selections for resistance are based on measurements of individual aphid growth in the laboratory. This very slow phenotyping method has been complemented by molecular marker evaluation and application in part of the breeding material. Doubled haploid production in each generation has been crucial for more precise selection of lines with the quantitatively expressed resistance. A field trial of selected \"BC\n            3\"-generation lines essentially confirmed the laboratory results, so did genotyping of the whole pedigree of parents and selected \"BC2\" and \"BC4\" offspring lines. The Infinium iSelect 50\u00a0K SNP assay confirmed relationships between lines and discerned several new markers for a resistance QTL on chromosome 2H.", "doi": "10.1007/s00122-019-03287-3", "pmid": "30712072", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1007/s00122-019-03287-3"}], "notes": [], "created": "2019-03-13T09:21:25.129Z", "modified": "2020-01-21T13:56:13.872Z"}, {"entity": "publication", "iuid": "d68baa0a66714860bfbb5829877af33f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d68baa0a66714860bfbb5829877af33f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d68baa0a66714860bfbb5829877af33f"}}, "title": "Disentangling the genetics of lean mass.", "authors": [{"family": "Karasik", "given": "David", "initials": "D"}, {"family": "Zillikens", "given": "M Carola", "initials": "MC"}, {"family": "Hsu", "given": "Yi-Hsiang", "initials": "YH"}, {"family": "Aghdassi", "given": "Ali", "initials": "A"}, {"family": "Akesson", "given": "Kristina", "initials": "K"}, {"family": "Amin", "given": "Najaf", "initials": "N"}, {"family": "Barroso", "given": "In\u00eas", "initials": "I"}, {"family": "Bennett", "given": "David A", "initials": "DA"}, {"family": "Bertram", "given": "Lars", "initials": "L"}, {"family": "Bochud", "given": "Murielle", "initials": "M"}, {"family": "Borecki", "given": "Ingrid B", "initials": "IB"}, {"family": "Broer", "given": "Linda", "initials": "L"}, {"family": "Buchman", "given": "Aron S", "initials": "AS"}, {"family": "Byberg", "given": "Liisa", "initials": "L"}, {"family": "Campbell", "given": "Harry", "initials": "H"}, {"family": "Campos-Obando", "given": "Natalia", "initials": "N"}, {"family": "Cauley", "given": "Jane A", "initials": "JA"}, {"family": "Cawthon", "given": "Peggy M", "initials": "PM"}, {"family": "Chambers", "given": "John C", "initials": "JC"}, {"family": "Chen", "given": "Zhao", "initials": "Z"}, {"family": "Cho", "given": "Nam H", "initials": "NH"}, {"family": "Choi", "given": "Hyung Jin", "initials": "HJ"}, {"family": "Chou", "given": "Wen-Chi", "initials": "WC"}, {"family": "Cummings", "given": "Steven R", "initials": "SR"}, {"family": "de Groot", "given": "Lisette C P G M", "initials": "LCPGM"}, {"family": "De Jager", "given": "Phillip L", "initials": "PL"}, {"family": "Demuth", "given": "Ilja", "initials": "I"}, {"family": "Diatchenko", "given": "Luda", "initials": "L"}, {"family": "Econs", "given": "Michael J", "initials": "MJ"}, {"family": "Eiriksdottir", "given": "Gudny", "initials": "G"}, {"family": "Enneman", "given": "Anke W", "initials": "AW"}, {"family": "Eriksson", "given": "Joel", "initials": "J"}, {"family": "Eriksson", "given": "Johan G", "initials": "JG"}, {"family": "Estrada", "given": "Karol", "initials": "K"}, {"family": "Evans", "given": "Daniel S", "initials": "DS"}, {"family": "Feitosa", "given": "Mary F", "initials": "MF"}, {"family": "Fu", "given": "Mao", "initials": "M"}, {"family": "Gieger", "given": "Christian", "initials": "C"}, {"family": "Grallert", "given": "Harald", "initials": "H"}, {"family": "Gudnason", "given": "Vilmundur", "initials": "V"}, {"family": "Lenore", "given": "Launer J", "initials": "LJ"}, {"family": "Hayward", "given": "Caroline", "initials": "C"}, {"family": "Hofman", "given": "Albert", "initials": "A"}, {"family": "Homuth", "given": "Georg", "initials": "G"}, {"family": "Huffman", "given": "Kim M", "initials": "KM"}, {"family": "Husted", "given": "Lise B", "initials": "LB"}, {"family": "Illig", "given": "Thomas", "initials": "T"}, {"family": "Ingelsson", "given": "Erik", "initials": "E"}, {"family": "Ittermann", "given": "Till", "initials": "T"}, {"family": "Jansson", "given": "John-Olov", "initials": "JO"}, {"family": "Johnson", "given": "Toby", "initials": "T"}, {"family": "Biffar", "given": "Reiner", "initials": "R"}, {"family": "Jordan", "given": "Joanne M", "initials": "JM"}, {"family": "Jula", "given": "Antti", "initials": "A"}, {"family": "Karlsson", "given": "Magnus", "initials": "M"}, {"family": "Khaw", "given": "Kay-Tee", "initials": "KT"}, {"family": "Kilpel\u00e4inen", "given": "Tuomas O", "initials": "TO"}, {"family": "Klopp", "given": "Norman", "initials": "N"}, {"family": "Kloth", "given": "Jacqueline S L", "initials": "JSL"}, {"family": "Koller", "given": "Daniel L", "initials": "DL"}, {"family": "Kooner", "given": "Jaspal S", "initials": "JS"}, {"family": "Kraus", "given": "William E", "initials": "WE"}, {"family": "Kritchevsky", "given": "Stephen", "initials": "S"}, {"family": "Kutalik", "given": "Zolt\u00e1n", "initials": "Z"}, {"family": "Kuulasmaa", "given": "Teemu", "initials": "T"}, {"family": "Kuusisto", "given": "Johanna", "initials": "J"}, {"family": "Laakso", "given": "Markku", "initials": "M"}, {"family": "Lahti", "given": "Jari", "initials": "J"}, {"family": "Lang", "given": "Thomas", "initials": "T"}, {"family": "Langdahl", "given": "Bente L", "initials": "BL"}, {"family": "Lerch", "given": "Markus M", "initials": "MM"}, {"family": "Lewis", "given": "Joshua R", "initials": "JR"}, {"family": "Lill", "given": "Christina", "initials": "C"}, {"family": "Lind", "given": "Lars", "initials": "L"}, {"family": "Lindgren", "given": "Cecilia", "initials": "C"}, {"family": "Liu", "given": "Yongmei", "initials": "Y"}, {"family": "Livshits", "given": "Gregory", "initials": "G"}, {"family": "Ljunggren", "given": "\u00d6sten", "initials": "\u00d6"}, {"family": "Loos", "given": "Ruth J F", "initials": "RJF"}, {"family": "Lorentzon", "given": "Mattias", "initials": "M"}, {"family": "Luan", "given": "Jian'an", "initials": "J"}, {"family": "Luben", "given": "Robert N", "initials": "RN"}, {"family": "Malkin", "given": "Ida", "initials": "I"}, {"family": "McGuigan", "given": "Fiona E", "initials": "FE"}, {"family": "Medina-Gomez", "given": "Carolina", "initials": "C"}, {"family": "Meitinger", "given": "Thomas", "initials": "T"}, {"family": "Melhus", "given": "H\u00e5kan", "initials": "H"}, {"family": "Mellstr\u00f6m", "given": "Dan", "initials": "D"}, {"family": "Micha\u00eblsson", "given": "Karl", "initials": "K"}, {"family": "Mitchell", "given": "Braxton D", "initials": "BD"}, {"family": "Morris", "given": "Andrew P", "initials": "AP"}, {"family": "Mosekilde", "given": "Leif", "initials": "L"}, {"family": "Nethander", "given": "Maria", "initials": "M"}, {"family": "Newman", "given": "Anne B", "initials": "AB"}, {"family": "O'Connell", "given": "Jeffery R", "initials": "JR"}, {"family": "Oostra", "given": "Ben A", "initials": "BA"}, {"family": "Orwoll", "given": "Eric S", "initials": "ES"}, {"family": "Palotie", "given": "Aarno", "initials": "A"}, {"family": "Peacock", "given": "Munro", "initials": "M"}, {"family": "Perola", "given": "Markus", "initials": "M"}, {"family": "Peters", "given": "Annette", "initials": "A"}, {"family": "Prince", "given": "Richard L", "initials": "RL"}, {"family": "Psaty", "given": "Bruce M", "initials": "BM"}, {"family": "R\u00e4ikk\u00f6nen", "given": "Katri", "initials": "K"}, {"family": "Ralston", "given": "Stuart H", "initials": "SH"}, {"family": "Ripatti", "given": "Samuli", "initials": "S"}, {"family": "Rivadeneira", "given": "Fernando", "initials": "F"}, {"family": "Robbins", "given": "John A", "initials": "JA"}, {"family": "Rotter", "given": "Jerome I", "initials": "JI"}, {"family": "Rudan", "given": "Igor", "initials": "I"}, {"family": "Salomaa", "given": "Veikko", "initials": "V"}, {"family": "Satterfield", "given": "Suzanne", "initials": "S"}, {"family": "Schipf", "given": "Sabine", "initials": "S"}, {"family": "Shin", "given": "Chan Soo", "initials": "CS"}, {"family": "Smith", "given": "Albert V", "initials": "AV"}, {"family": "Smith", "given": "Shad B", "initials": "SB"}, {"family": "Soranzo", "given": "Nicole", "initials": "N"}, {"family": "Spector", "given": "Timothy D", "initials": "TD"}, {"family": "Stanc\u00e1kov\u00e1", "given": "Alena", "initials": "A"}, {"family": "Stefansson", "given": "Kari", "initials": "K"}, {"family": "Steinhagen-Thiessen", "given": "Elisabeth", "initials": "E"}, {"family": "Stolk", "given": "Lisette", "initials": "L"}, {"family": "Streeten", "given": "Elizabeth A", "initials": "EA"}, {"family": "Styrkarsdottir", "given": "Unnur", "initials": "U"}, {"family": "Swart", "given": "Karin M A", "initials": "KMA"}, {"family": "Thompson", "given": "Patricia", "initials": "P"}, {"family": "Thomson", "given": "Cynthia A", "initials": "CA"}, {"family": "Thorleifsson", "given": "Gudmar", "initials": "G"}, {"family": "Thorsteinsdottir", "given": "Unnur", "initials": "U"}, {"family": "Tikkanen", "given": "Emmi", "initials": "E"}, {"family": "Tranah", "given": "Gregory J", "initials": "GJ"}, {"family": "Uitterlinden", "given": "Andr\u00e9 G", "initials": "AG"}, {"family": "van Duijn", "given": "Cornelia M", "initials": "CM"}, {"family": "van Schoor", "given": "Natasja M", "initials": "NM"}, {"family": "Vandenput", "given": "Liesbeth", "initials": "L"}, {"family": "Vollenweider", "given": "Peter", "initials": "P"}, {"family": "V\u00f6lzke", "given": "Henry", "initials": "H"}, {"family": "Wactawski-Wende", "given": "Jean", "initials": "J"}, {"family": "Walker", "given": "Mark", "initials": "M"}, {"family": "J Wareham", "given": "Nicholas", "initials": "N"}, {"family": "Waterworth", "given": "Dawn", "initials": "D"}, {"family": "Weedon", "given": "Michael N", "initials": "MN"}, {"family": "Wichmann", "given": "H-Erich", "initials": "HE"}, {"family": "Widen", "given": "Elisabeth", "initials": "E"}, {"family": "Williams", "given": "Frances M K", "initials": "FMK"}, {"family": "Wilson", "given": "James F", "initials": "JF"}, {"family": "Wright", "given": "Nicole C", "initials": "NC"}, {"family": "Yerges-Armstrong", "given": "Laura M", "initials": "LM"}, {"family": "Yu", "given": "Lei", "initials": "L"}, {"family": "Zhang", "given": "Weihua", "initials": "W"}, {"family": "Zhao", "given": "Jing Hua", "initials": "JH"}, {"family": "Zhou", "given": "Yanhua", "initials": "Y"}, {"family": "Nielson", "given": "Carrie M", "initials": "CM"}, {"family": "Harris", "given": "Tamara B", "initials": "TB"}, {"family": "Demissie", "given": "Serkalem", "initials": "S"}, {"family": "Kiel", "given": "Douglas P", "initials": "DP"}, {"family": "Ohlsson", "given": "Claes", "initials": "C"}], "type": "journal article", "published": "2019-02-01", "journal": {"volume": "109", "issn": "1938-3207", "issue": "2", "pages": "276-287", "title": "Am. J. Clin. Nutr.", "issn-l": "0002-9165"}, "abstract": "Lean body mass (LM) plays an important role in mobility and metabolic function. We previously identified five loci associated with LM adjusted for fat mass in kilograms. Such an adjustment may reduce the power to identify genetic signals having an association with both lean mass and fat mass.\n\nTo determine the impact of different fat mass adjustments on genetic architecture of LM and identify additional LM loci.\n\nWe performed genome-wide association analyses for whole-body LM (20 cohorts of European ancestry with n\u00a0=\u00a038,292) measured using dual-energy X-ray absorptiometry) or bioelectrical impedance analysis, adjusted for sex, age, age2, and height with or without fat mass adjustments (Model 1 no fat adjustment; Model 2 adjustment for fat mass as a percentage of body mass; Model 3 adjustment for fat mass in kilograms).\n\nSeven single-nucleotide polymorphisms (SNPs) in separate loci, including one novel LM locus (TNRC6B), were successfully replicated in an additional 47,227 individuals from 29 cohorts. Based on the strengths of the associations in Model 1 vs Model 3, we divided the LM loci into those with an effect on both lean mass and fat mass in the same direction and refer to those as \"sumo wrestler\" loci (FTO and MC4R). In contrast, loci with an impact specifically on LM were termed \"body builder\" loci (VCAN and ADAMTSL3). Using existing available genome-wide association study databases, LM increasing alleles of SNPs in sumo wrestler loci were associated with an adverse metabolic profile, whereas LM increasing alleles of SNPs in \"body builder\" loci were associated with metabolic protection.\n\nIn conclusion, we identified one novel LM locus (TNRC6B). Our results suggest that a genetically determined increase in lean mass might exert either harmful or protective effects on metabolic traits, depending on its relation to fat mass.", "doi": "10.1093/ajcn/nqy272", "pmid": "30721968", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "5307112"}], "notes": [], "created": "2019-03-13T09:21:24.166Z", "modified": "2020-01-21T13:56:13.860Z"}, {"entity": "publication", "iuid": "9f6015e49aac403f94de4b7cc0b5d8e1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9f6015e49aac403f94de4b7cc0b5d8e1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9f6015e49aac403f94de4b7cc0b5d8e1"}}, "title": "Allele-Specific Methylation of SPDEF: A Novel Moderator of Psychosocial Stress and Substance Abuse.", "authors": [{"family": "Tay", "given": "Nicole", "initials": "N"}, {"family": "Macare", "given": "Christine", "initials": "C"}, {"family": "Liu", "given": "Yun", "initials": "Y"}, {"family": "Ruggeri", "given": "Barbara", "initials": "B"}, {"family": "Jia", "given": "Tianye", "initials": "T"}, {"family": "Chu", "given": "Congying", "initials": "C"}, {"family": "Biondo", "given": "Francesca", "initials": "F"}, {"family": "Ing", "given": "Alex", "initials": "A"}, {"family": "Luo", "given": "Qiang", "initials": "Q"}, {"family": "Sarkysian", "given": "Daniil", "initials": "D"}, {"family": "Banaschewski", "given": "Tobias", "initials": "T"}, {"family": "Barker", "given": "Gareth J", "initials": "GJ"}, {"family": "Bokde", "given": "Arun L W", "initials": "ALW"}, {"family": "Bromberg", "given": "Uli", "initials": "U"}, {"family": "B\u00fcchel", "given": "Christian", "initials": "C"}, {"family": "Quinlan", "given": "Erin Burke", "initials": "EB"}, {"family": "Desrivi\u00e8res", "given": "Sylvane", "initials": "S"}, {"family": "Flor", "given": "Herta", "initials": "H"}, {"family": "Frouin", "given": "Vincent", "initials": "V"}, {"family": "Garavan", "given": "Hugh", "initials": "H"}, {"family": "Gowland", "given": "Penny", "initials": "P"}, {"family": "Heinz", "given": "Andreas", "initials": "A"}, {"family": "Ittermann", "given": "Bernd", "initials": "B"}, {"family": "Martinot", "given": "Jean-Luc", "initials": "JL"}, {"family": "Artiges", "given": "Eric", "initials": "E"}, {"family": "Nees", "given": "Frauke", "initials": "F"}, {"family": "Orfanos", "given": "Dimitri Papadopoulos", "initials": "DP"}, {"family": "Paus", "given": "Tom\u00e1\u0161", "initials": "T"}, {"family": "Poustka", "given": "Luise", "initials": "L"}, {"family": "Hohmann", "given": "Sarah", "initials": "S"}, {"family": "Fr\u00f6hner", "given": "Juliane H", "initials": "JH"}, {"family": "Smolka", "given": "Michael N", "initials": "MN"}, {"family": "Walter", "given": "Henrik", "initials": "H"}, {"family": "Whelan", "given": "Robert", "initials": "R"}, {"family": "Frieling", "given": "Helge", "initials": "H"}, {"family": "Bleich", "given": "Stefan", "initials": "S"}, {"family": "Barker", "given": "Edward D", "initials": "ED"}, {"family": "Syv\u00e4nen", "given": "Ann-Christine", "initials": "AC", "orcid": "0000-0002-9681-9146", "researcher": {"href": "https://publications.scilifelab.se/researcher/f7012e35025543379380cb90efd71243.json"}}, {"family": "R\u00fcegg", "given": "Jo\u00eblle", "initials": "J"}, {"family": "Ekstr\u00f6m", "given": "Tomas J", "initials": "TJ"}, {"family": "Bakalkin", "given": "Georgy", "initials": "G"}, {"family": "Schumann", "given": "Gunter", "initials": "G"}, {"family": "IMAGEN Consortium", "given": "", "initials": ""}], "type": "journal article", "published": "2019-02-01", "journal": {"volume": "176", "issn": "1535-7228", "issue": "2", "pages": "146-155", "title": "Am J Psychiatry", "issn-l": "0002-953X"}, "abstract": "Psychosocial stress is a key risk factor for substance abuse among adolescents. Recently, epigenetic processes such as DNA methylation have emerged as potential mechanisms that could mediate this relationship. The authors conducted a genome-wide methylation analysis to investigate whether differentially methylated regions are associated with psychosocial stress in an adolescent population.\n\nA methylome-wide analysis of differentially methylated regions was used to examine a sample of 1,287 14-year-old adolescents (50.7% of them female) from the European IMAGEN study. The Illumina 450k array was used to assess DNA methylation, pyrosequencing was used for technical replication, and linear regression analyses were used to identify associations with psychosocial stress and substance use (alcohol and tobacco). Findings were replicated by pyrosequencing a test sample of 413 participants from the IMAGEN study.\n\nHypermethylation in the sterile alpha motif/pointed domain containing the ETS transcription factor (SPDEF) gene locus was associated with a greater number of stressful life events in an allele-dependent way. Among individuals with the minor G-allele, SPDEF methylation moderated the association between psychosocial stress and substance abuse. SPDEF methylation interacted with lifetime stress in gray matter volume in the right cuneus, which in turn was associated with the frequency of alcohol and tobacco use. SPDEF was involved in the regulation of trans-genes linked to substance use.\n\nTaken together, the study findings describe a novel epigenetic mechanism that helps explain how psychosocial stress exposure influences adolescent substance abuse.", "doi": "10.1176/appi.ajp.2018.17121360", "pmid": "30525907", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [], "notes": [], "created": "2018-12-12T12:15:08.429Z", "modified": "2021-07-07T14:57:20.017Z"}, {"entity": "publication", "iuid": "5b3289292c7d4469a46d995dc7709d64", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5b3289292c7d4469a46d995dc7709d64.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5b3289292c7d4469a46d995dc7709d64"}}, "title": "Whole-genome sequencing identifies complex contributions to genetic risk by variants in genes causing monogenic systemic lupus erythematosus.", "authors": [{"family": "Alml\u00f6f", "given": "Jonas Carlsson", "initials": "JC", "orcid": "0000-0002-1211-9821", "researcher": {"href": "https://publications.scilifelab.se/researcher/046904cd12eb4764bd2dcadc876f65d7.json"}}, {"family": "Nystedt", "given": "Sara", "initials": "S"}, {"family": "Leonard", "given": "Dag", "initials": "D"}, {"family": "Eloranta", "given": "Maija-Leena", "initials": "ML"}, {"family": "Grosso", "given": "Giorgia", "initials": "G"}, {"family": "Sj\u00f6wall", "given": "Christopher", "initials": "C"}, {"family": "Bengtsson", "given": "Anders A", "initials": "AA"}, {"family": "J\u00f6nsen", "given": "Andreas", "initials": "A"}, {"family": "Gunnarsson", "given": "Iva", "initials": "I"}, {"family": "Svenungsson", "given": "Elisabet", "initials": "E"}, {"family": "R\u00f6nnblom", "given": "Lars", "initials": "L"}, {"family": "Sandling", "given": "Johanna K", "initials": "JK"}, {"family": "Syv\u00e4nen", "given": "Ann-Christine", "initials": "AC", "orcid": "0000-0002-9681-9146", "researcher": {"href": "https://publications.scilifelab.se/researcher/f7012e35025543379380cb90efd71243.json"}}], "type": "journal article", "published": "2019-02-00", "journal": {"volume": "138", "issn": "1432-1203", "issue": "2", "pages": "141-150", "title": "Hum. Genet.", "issn-l": "0340-6717"}, "abstract": "Systemic lupus erythematosus (SLE, OMIM 152700) is a systemic autoimmune disease with a complex etiology. The mode of inheritance of the genetic risk beyond familial SLE cases is currently unknown. Additionally, the contribution of heterozygous variants in genes known to cause monogenic SLE is not fully understood. Whole-genome sequencing of DNA samples from 71 Swedish patients with SLE and their healthy biological parents was performed to investigate the general genetic risk of SLE using known SLE GWAS risk loci identified using the ImmunoChip, variants in genes associated to monogenic SLE, and the mode of inheritance of SLE risk alleles in these families. A random forest model for predicting genetic risk for SLE showed that the SLE risk variants were mainly inherited from one of the parents. In the 71 patients, we detected a significant enrichment of ultra-rare ( \u2264 0.1%) missense and nonsense mutations in 22 genes known to cause monogenic forms of SLE. We identified one previously reported homozygous nonsense mutation in the C1QC (Complement C1q C Chain) gene, which explains the immunodeficiency and severe SLE phenotype of that patient. We also identified seven ultra-rare, coding heterozygous variants in five genes (C1S, DNASE1L3, DNASE1, IFIH1, and RNASEH2A) involved in monogenic SLE. Our findings indicate a complex contribution to the overall genetic risk of SLE by rare variants in genes associated with monogenic forms of SLE. The rare variants were inherited from the other parent than the one who passed on the more common risk variants leading to an increased genetic burden for SLE in the child. Higher frequency SLE risk variants are mostly passed from one of the parents to the offspring affected with SLE. In contrast, the other parent, in seven cases, contributed heterozygous rare variants in genes associated with monogenic forms of SLE, suggesting a larger impact of rare variants in SLE than hitherto reported.", "doi": "10.1007/s00439-018-01966-7", "pmid": "30707351", "labels": {"National Genomics Infrastructure": "Collaborative", "NGI Uppsala (SNP&SEQ Technology Platform)": "Collaborative", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1007/s00439-018-01966-7"}, {"db": "pmc", "key": "PMC6373277"}], "notes": [], "created": "2019-04-23T09:58:00.211Z", "modified": "2024-01-16T13:48:44.732Z"}, {"entity": "publication", "iuid": "a9aa7d58238e4af99f61a9de99617bd4", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a9aa7d58238e4af99f61a9de99617bd4.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a9aa7d58238e4af99f61a9de99617bd4"}}, "title": "Longitudinal changes in the genetic and environmental influences on the epigenetic clocks across old age: Evidence from two twin cohorts.", "authors": [{"family": "Jylh\u00e4v\u00e4", "given": "Juulia", "initials": "J"}, {"family": "Hjelmborg", "given": "Jacob", "initials": "J"}, {"family": "Soerensen", "given": "Mette", "initials": "M"}, {"family": "Munoz", "given": "Elizabeth", "initials": "E"}, {"family": "Tan", "given": "Qihua", "initials": "Q"}, {"family": "Kuja-Halkola", "given": "Ralf", "initials": "R"}, {"family": "Mengel-From", "given": "Jonas", "initials": "J"}, {"family": "Christensen", "given": "Kaare", "initials": "K"}, {"family": "Christiansen", "given": "Lene", "initials": "L"}, {"family": "H\u00e4gg", "given": "Sara", "initials": "S"}, {"family": "Pedersen", "given": "Nancy L", "initials": "NL"}, {"family": "Reynolds", "given": "Chandra A", "initials": "CA"}], "type": "journal article", "published": "2019-02-00", "journal": {"volume": "40", "issn": "2352-3964", "issue": null, "pages": "710-716", "title": "EBioMedicine", "issn-l": "2352-3964"}, "abstract": "Measures based on DNA methylation, epigenetic clocks, have recently gained attraction as predictors of mortality and age-related pathologies. However, the origins of variation in these measures are not well understood.\n\nIn a pooled sample of 104 Swedish and Danish twin pairs, we estimated, at the mean age of 70 (baseline) and 79\u202fyears (follow-up), the genetic and environmental influences on the Horvath and Levine clocks.\n\nA model incorporating additive genetic (A) and person-specific environmental (E) influences best explained the variation in both clocks. Heritability was estimated at 55% at baseline and at 51% at follow-up for the Horvath clock and 34% at baseline and 41% at follow-up for the Levine clock. For the Horvath clock, new sources of A influences emerged at follow-up, whereas for the Levine clock, the same A influences accounted for the genetic variance at both measurement occasions. The cross-time phenotypic correlations, 0\u00b752 for the Horvath clock and 0\u00b736 for the Levine clock, were mediated primarily by genetic factors, whereas the person-specific environmental factors were completely different at the two measurement occasions.\n\nFor both clocks, new sources of person-specific environmental influences emerge with age. The epigenetic clocks might thus be responsive to new environmental stimuli even at old age. FUND: NIH (R01;AG04563;AG10175;AG028555) the MacArthur Foundation Research Network on Successful Aging, FAS/FORTE (97:0147:1B;2009-0795), Swedish Research Council (825-2007-7460;825-2009-6141;521-2013-8689;2015-03255;2015-06796;2018-02077), FORTE (2013-2292), the Strategic Research Program in Epidemiology at KI, VELUX FOUNDATION, NIA (P01-AG08761), the EU (FP7/2007-2011;259679) and The Danish National Program for Research Infrastructure 2007 (9-063256).", "doi": "10.1016/j.ebiom.2019.01.040", "pmid": "30704927", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "S2352-3964(19)30047-7"}, {"db": "pmc", "key": "PMC6413471"}], "notes": [], "created": "2019-09-17T16:24:28.329Z", "modified": "2020-01-21T13:56:14.517Z"}, {"entity": "publication", "iuid": "47fa055782d94bfaaa8cc696b134f6d4", "links": {"self": {"href": "https://publications.scilifelab.se/publication/47fa055782d94bfaaa8cc696b134f6d4.json"}, "display": {"href": "https://publications.scilifelab.se/publication/47fa055782d94bfaaa8cc696b134f6d4"}}, "title": "Genome-wide association analyses of risk tolerance and risky behaviors in over 1 million individuals identify hundreds of loci and shared genetic influences.", "authors": [{"family": "Karlsson Linn\u00e9r", "given": "Richard", "initials": "R"}, {"family": "Biroli", "given": "Pietro", "initials": "P"}, {"family": "Kong", "given": "Edward", "initials": "E"}, {"family": "Meddens", "given": "S Fleur W", "initials": "SFW"}, {"family": "Wedow", "given": "Robbee", "initials": "R"}, {"family": "Fontana", "given": "Mark Alan", "initials": "MA"}, {"family": "Lebreton", "given": "Ma\u00ebl", "initials": "M"}, {"family": "Tino", "given": "Stephen P", "initials": "SP"}, {"family": "Abdellaoui", "given": "Abdel", "initials": "A"}, {"family": "Hammerschlag", "given": "Anke R", "initials": "AR"}, {"family": "Nivard", "given": "Michel G", "initials": "MG"}, {"family": "Okbay", "given": "Aysu", "initials": "A"}, {"family": "Rietveld", "given": "Cornelius A", "initials": "CA"}, {"family": "Timshel", "given": "Pascal N", "initials": "PN"}, {"family": "Trzaskowski", "given": "Maciej", "initials": "M"}, {"family": "Vlaming", "given": "Ronald de", "initials": "R"}, {"family": "Z\u00fcnd", "given": "Christian L", "initials": "CL"}, {"family": "Bao", "given": "Yanchun", "initials": "Y"}, {"family": "Buzdugan", "given": "Laura", "initials": "L"}, {"family": "Caplin", "given": "Ann H", "initials": "AH"}, {"family": "Chen", "given": "Chia-Yen", "initials": "CY"}, {"family": "Eibich", "given": "Peter", "initials": "P"}, {"family": "Fontanillas", "given": "Pierre", "initials": "P"}, {"family": "Gonzalez", "given": "Juan R", "initials": "JR"}, {"family": "Joshi", "given": "Peter K", "initials": "PK"}, {"family": "Karhunen", "given": "Ville", "initials": "V"}, {"family": "Kleinman", "given": "Aaron", "initials": "A"}, {"family": "Levin", "given": "Remy Z", "initials": "RZ"}, {"family": "Lill", "given": "Christina M", "initials": "CM"}, {"family": "Meddens", "given": "Gerardus A", "initials": "GA"}, {"family": "Muntan\u00e9", "given": "Gerard", "initials": "G"}, {"family": "Sanchez-Roige", "given": "Sandra", "initials": "S"}, {"family": "Rooij", "given": "Frank J van", "initials": "FJV"}, {"family": "Taskesen", "given": "Erdogan", "initials": "E"}, {"family": "Wu", "given": "Yang", "initials": "Y"}, {"family": "Zhang", "given": "Futao", "initials": "F"}, {"family": "23and Me Research Team", "given": "", "initials": ""}, {"family": "eQTLgen Consortium", "given": "", "initials": ""}, {"family": "International Cannabis Consortium", "given": "", "initials": ""}, {"family": "Social Science Genetic Association Consortium", "given": "", "initials": ""}, {"family": "Auton", "given": "Adam", "initials": "A"}, {"family": "Boardman", "given": "Jason D", "initials": "JD"}, {"family": "Clark", "given": "David W", "initials": "DW"}, {"family": "Conlin", "given": "Andrew", "initials": "A"}, {"family": "Dolan", "given": "Conor C", "initials": "CC"}, {"family": "Fischbacher", "given": "Urs", "initials": "U"}, {"family": "Groenen", "given": "Patrick J F", "initials": "PJF"}, {"family": "Harris", "given": "Kathleen Mullan", "initials": "KM"}, {"family": "Hasler", "given": "Gregor", "initials": "G"}, {"family": "Hofman", "given": "Albert", "initials": "A"}, {"family": "Ikram", "given": "Mohammad A", "initials": "MA"}, {"family": "Jain", "given": "Sonia", "initials": "S"}, {"family": "Karlsson", "given": "Robert", "initials": "R"}, {"family": "Kessler", "given": "Ronald C", "initials": "RC"}, {"family": "Kooyman", "given": "Maarten", "initials": "M"}, {"family": "MacKillop", "given": "James", "initials": "J"}, {"family": "M\u00e4nnikk\u00f6", "given": "Minna", "initials": "M"}, {"family": "Morcillo-Suarez", "given": "Carlos", "initials": "C"}, {"family": "McQueen", "given": "Matthew B", "initials": "MB"}, {"family": "Schmidt", "given": "Klaus M", "initials": "KM"}, {"family": "Smart", "given": "Melissa C", "initials": "MC"}, {"family": "Sutter", "given": "Matthias", "initials": "M"}, {"family": "Thurik", "given": "A Roy", "initials": "AR"}, {"family": "Uitterlinden", "given": "Andr\u00e9 G", "initials": "AG"}, {"family": "White", "given": "Jon", "initials": "J"}, {"family": "Wit", "given": "Harriet de", "initials": "H"}, {"family": "Yang", "given": "Jian", "initials": "J"}, {"family": "Bertram", "given": "Lars", "initials": "L"}, {"family": "Boomsma", "given": "Dorret I", "initials": "DI"}, {"family": "Esko", "given": "T\u00f5nu", "initials": "T"}, {"family": "Fehr", "given": "Ernst", "initials": "E"}, {"family": "Hinds", "given": "David A", "initials": "DA"}, {"family": "Johannesson", "given": "Magnus", "initials": "M"}, {"family": "Kumari", "given": "Meena", "initials": "M"}, {"family": "Laibson", "given": "David", "initials": "D"}, {"family": "Magnusson", "given": "Patrik K E", "initials": "PKE"}, {"family": "Meyer", "given": "Michelle N", "initials": "MN"}, {"family": "Navarro", "given": "Arcadi", "initials": "A"}, {"family": "Palmer", "given": "Abraham A", "initials": "AA"}, {"family": "Pers", "given": "Tune H", "initials": "TH"}, {"family": "Posthuma", "given": "Danielle", "initials": "D"}, {"family": "Schunk", "given": "Daniel", "initials": "D"}, {"family": "Stein", "given": "Murray B", "initials": "MB"}, {"family": "Svento", "given": "Rauli", "initials": "R"}, {"family": "Tiemeier", "given": "Henning", "initials": "H"}, {"family": "Timmers", "given": "Paul R H J", "initials": "PRHJ"}, {"family": "Turley", "given": "Patrick", "initials": "P"}, {"family": "Ursano", "given": "Robert J", "initials": "RJ"}, {"family": "Wagner", "given": "Gert G", "initials": "GG"}, {"family": "Wilson", "given": "James F", "initials": "JF"}, {"family": "Gratten", "given": "Jacob", "initials": "J"}, {"family": "Lee", "given": "James J", "initials": "JJ"}, {"family": "Cesarini", "given": "David", "initials": "D"}, {"family": "Benjamin", "given": "Daniel J", "initials": "DJ"}, {"family": "Koellinger", "given": "Philipp D", "initials": "PD"}, {"family": "Beauchamp", "given": "Jonathan P", "initials": "JP"}], "type": "journal article", "published": "2019-02-00", "journal": {"volume": "51", "issn": "1546-1718", "issue": "2", "pages": "245-257", "title": "Nat. Genet.", "issn-l": "1061-4036"}, "abstract": "Humans vary substantially in their willingness to take risks. In a combined sample of over 1 million individuals, we conducted genome-wide association studies (GWAS) of general risk tolerance, adventurousness, and risky behaviors in the driving, drinking, smoking, and sexual domains. Across all GWAS, we identified hundreds of associated loci, including 99 loci associated with general risk tolerance. We report evidence of substantial shared genetic influences across risk tolerance and the risky behaviors: 46 of the 99 general risk tolerance loci contain a lead SNP for at least one of our other GWAS, and general risk tolerance is genetically correlated ([Formula: see text]\u2009~\u20090.25 to 0.50) with a range of risky behaviors. Bioinformatics analyses imply that genes near SNPs associated with general risk tolerance are highly expressed in brain tissues and point to a role for glutamatergic and GABAergic neurotransmission. We found no evidence of enrichment for genes previously hypothesized to relate to risk tolerance.", "doi": "10.1038/s41588-018-0309-3", "pmid": "30643258", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41588-018-0309-3"}], "notes": [], "created": "2019-03-13T09:21:27.036Z", "modified": "2020-01-21T13:56:13.886Z"}, {"entity": "publication", "iuid": "3c98cc52c63142efaaa374c5f15eeb91", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3c98cc52c63142efaaa374c5f15eeb91.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3c98cc52c63142efaaa374c5f15eeb91"}}, "title": "Eleven loci with new reproducible genetic associations with allergic disease risk", "authors": [{"family": "Ferreira", "given": "Manuel A R", "initials": "MAR"}, {"family": "Vonk", "given": "Judith M", "initials": "JM"}, {"family": "Baurecht", "given": "Hansj\u00f6rg", "initials": "H"}, {"family": "Marenholz", "given": "Ingo", "initials": "I"}, {"family": "Tian", "given": "Chao", "initials": "C"}, {"family": "Hoffman", "given": "Joshua D", "initials": "JD"}, {"family": "Helmer", "given": "Quinta", "initials": "Q"}, {"family": "Tillander", "given": "Annika", "initials": "A"}, {"family": "Ullemar", "given": "Vilhelmina", "initials": "V"}, {"family": "Lu", "given": "Yi", "initials": "Y"}, {"family": "R\u00fcschendorf", "given": "Franz", "initials": "F"}, {"family": "Hinds", "given": "David A", "initials": "DA"}, {"family": "H\u00fcbner", "given": "Norbert", "initials": "N"}, {"family": "Weidinger", "given": "Stephan", "initials": "S"}, {"family": "Magnusson", "given": "Patrik K E", "initials": "PKE"}, {"family": "Jorgenson", "given": "Eric", "initials": "E"}, {"family": "Lee", "given": "Young Ae", "initials": "YA"}, {"family": "Boomsma", "given": "Dorret I", "initials": "DI"}, {"family": "Karlsson", "given": "Robert", "initials": "R"}, {"family": "Almqvist", "given": "Catarina", "initials": "C"}, {"family": "Koppelman", "given": "Gerard H", "initials": "GH"}, {"family": "Paternoster", "given": "Lavinia", "initials": "L"}], "type": "journal-article", "published": "2019-02-00", "journal": {"volume": "143", "issn": "1085-8725", "issue": "2", "title": "Journal of Allergy and Clinical Immunology", "pages": "691-699", "issn-l": "0091-6749"}, "abstract": "A recent genome-wide association study (GWAS) identified 99 loci that contain genetic risk variants shared between asthma, hay fever, and eczema. Many more risk loci shared between these common allergic diseases remain to be discovered, which could point to new therapeutic opportunities.\n\nWe sought to identify novel risk loci shared between asthma, hay fever, and eczema by applying a gene-based test of association to results from a published GWAS that included data from 360,838 subjects.\n\nWe used approximate conditional analysis to adjust the results from the published GWAS for the effects of the top risk variants identified in that study. We then analyzed the adjusted GWAS results with the EUGENE gene-based approach, which combines evidence for association with disease risk across regulatory variants identified in different tissues. Novel gene-based associations were followed up in an independent sample of 233,898 subjects from the UK Biobank study.\n\nOf the 19,432 genes tested, 30 had a significant gene-based association at a Bonferroni-corrected P value of 2.5 \u00d7 10-6. Of these, 20 were also significantly associated (P < .05/30 = .0016) with disease risk in the replication sample, including 19 that were located in 11 loci not reported to contain allergy risk variants in previous GWASs. Among these were 9 genes with a known function that is directly relevant to allergic disease: FOSL2, VPRBP, IPCEF1, PRR5L, NCF4, APOBR, IL27, ATXN2L, and LAT. For 4 genes (eg, ATXN2L), a genetically determined decrease in gene expression was associated with decreased allergy risk, and therefore drugs that inhibit gene expression or function are predicted to ameliorate disease symptoms. The opposite directional effect was observed for 14 genes, including IL27, a cytokine known to suppress TH2 responses.\n\nUsing a gene-based approach, we identified 11 risk loci for allergic disease that were not reported in previous GWASs. Functional studies that investigate the contribution of the 19 associated genes to the pathophysiology of allergic disease and assess their therapeutic potential are warranted.", "doi": "10.1016/j.jaci.2018.03.012", "pmid": "29679657", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "mid", "key": "NIHMS966504"}, {"db": "pmc", "key": "PMC7189804"}, {"db": "pii", "key": "S0091-6749(18)30558-X"}], "notes": [], "created": "2018-05-25T13:37:49.128Z", "modified": "2024-01-16T13:48:44.763Z"}, {"entity": "publication", "iuid": "c01d9bc8b2964021b55b8b03a23fb836", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c01d9bc8b2964021b55b8b03a23fb836.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c01d9bc8b2964021b55b8b03a23fb836"}}, "title": "CD99 expression is strongly associated with clinical outcome in children with B-cell precursor acute lymphoblastic leukaemia.", "authors": [{"family": "Chen", "given": "Dongfeng", "initials": "D", "orcid": "0000-0003-1910-1234", "researcher": {"href": "https://publications.scilifelab.se/researcher/530bf9a48f9448998663d51dc9d33df2.json"}}, {"family": "Camponeschi", "given": "Alessandro", "initials": "A"}, {"family": "Wu", "given": "Qingqing", "initials": "Q"}, {"family": "Gerasimcik", "given": "Natalija", "initials": "N"}, {"family": "Li", "given": "Huiqi", "initials": "H"}, {"family": "Shen", "given": "Xue", "initials": "X"}, {"family": "Tan", "given": "Yujie", "initials": "Y"}, {"family": "Sj\u00f6gren", "given": "Helene", "initials": "H"}, {"family": "Nordlund", "given": "Jessica", "initials": "J", "orcid": "0000-0001-8699-9959", "researcher": {"href": "https://publications.scilifelab.se/researcher/ddf48c9262134821bcc6ce1180049753.json"}}, {"family": "L\u00f6nnerholm", "given": "Gudmar", "initials": "G"}, {"family": "Abrahamsson", "given": "Jonas", "initials": "J"}, {"family": "Fogelstrand", "given": "Linda", "initials": "L"}, {"family": "M\u00e5rtensson", "given": "Inga-Lill", "initials": "IL"}], "type": "journal article", "published": "2019-02-00", "journal": {"volume": "184", "issn": "1365-2141", "issue": "3", "pages": "418-423", "title": "Br. J. Haematol.", "issn-l": "0007-1048"}, "abstract": "Our study aimed to determine the expression pattern and clinical relevance of CD99 in paediatric B-cell precursor acute lymphoblastic leukaemia (BCP-ALL). Our findings demonstrate that high expression levels of CD99 are mainly found in high-risk BCP-ALL, e.g. BCR-ABL1 and CRLF2Re/Hi , and that high CD99 mRNA levels are strongly associated with a high frequency of relapse, high proportion of positive for minimal residual disease at day 29 and poor overall survival in paediatric cohorts, which indicate that CD99 is a potential biomarker for BCP-ALL.", "doi": "10.1111/bjh.15683", "pmid": "30484860", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [], "notes": [], "created": "2019-12-03T12:29:13.462Z", "modified": "2021-07-07T14:48:21.918Z"}, {"entity": "publication", "iuid": "5dcc907f38414467976927bd7619e5b6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5dcc907f38414467976927bd7619e5b6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5dcc907f38414467976927bd7619e5b6"}}, "title": "Pandemrix-induced narcolepsy is associated with genes related to immunity and neuronal survival.", "authors": [{"family": "Hallberg", "given": "P\u00e4r", "initials": "P"}, {"family": "Smedje", "given": "Hans", "initials": "H"}, {"family": "Eriksson", "given": "Niclas", "initials": "N"}, {"family": "Kohnke", "given": "Hugo", "initials": "H"}, {"family": "Daniilidou", "given": "Makrina", "initials": "M"}, {"family": "\u00d6hman", "given": "Inger", "initials": "I"}, {"family": "Yue", "given": "Qun-Ying", "initials": "QY"}, {"family": "Cavalli", "given": "Marco", "initials": "M"}, {"family": "Wadelius", "given": "Claes", "initials": "C"}, {"family": "Magnusson", "given": "Patrik K E", "initials": "PKE"}, {"family": "Landtblom", "given": "Anne-Marie", "initials": "AM"}, {"family": "Wadelius", "given": "Mia", "initials": "M"}, {"family": "Swedegene", "given": "", "initials": ""}], "type": "journal article", "published": "2019-01-30", "journal": {"volume": null, "issn": "2352-3964", "issue": null, "title": "EBioMedicine", "issn-l": "2352-3964"}, "abstract": "The incidence of narcolepsy rose sharply after the swine influenza A (H1N1) vaccination campaign with Pandemrix. Narcolepsy is an immune-related disorder with excessive daytime sleepiness. The most frequent form is strongly associated with HLA-DQB1*06:02, but only a minority of carriers develop narcolepsy. We aimed to identify genetic markers that predispose to Pandemrix-induced narcolepsy.\n\nWe tested for genome-wide and candidate gene associations in 42 narcolepsy cases and 4981 controls. Genotyping was performed on Illumina arrays, HLA alleles were imputed using SNP2HLA, and single nucleotide polymorphisms were imputed using the haplotype reference consortium panel. The genome-wide significance threshold was p\u202f<\u202f5\u202f\u00d7\u202f10\n                -8, and the nominal threshold was p\u202f<\u202f0.05. Results were replicated in 32 cases and 7125 controls. Chromatin data was used for functional annotation.\n\nCarrying HLA-DQB1*06:02 was significantly associated with narcolepsy, odds ratio (OR) 39.4 [95% confidence interval (CI) 11.3, 137], p\u202f=\u202f7.9\u202f\u00d7\u202f10\n                -9. After adjustment for HLA, GDNF-AS1 (rs62360233) was significantly associated, OR\u202f=\u202f8.7 [95% CI 4.2, 17.5], p\u202f=\u202f2.6\u202f\u00d7\u202f10-9, and this was replicated, OR\u202f=\u202f3.4 [95% CI 1.2-9.6], p\u202f=\u202f0.022. Functional analysis revealed variants in high LD with rs62360233 that might explain the detected association. The candidate immune-gene locus TRAJ (rs1154155) was nominally associated in both the discovery and replication cohorts, meta-analysis OR\u202f=\u202f2.0 [95% CI 1.4, 2.8], p\u202f=\u202f0.0002.\n\nWe found a novel association between Pandemrix-induced narcolepsy and the non-coding RNA gene GDNF-AS1, which has been shown to regulate expression of the essential neurotrophic factor GDNF. Changes in regulation of GDNF have been associated with neurodegenerative diseases. This finding may increase the understanding of disease mechanisms underlying narcolepsy. Associations between Pandemrix-induced narcolepsy and immune-related genes were replicated.", "doi": "10.1016/j.ebiom.2019.01.041", "pmid": "30711515", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "S2352-3964(19)30048-9"}], "notes": [], "created": "2019-03-13T09:21:25.995Z", "modified": "2024-01-16T13:48:44.788Z"}, {"entity": "publication", "iuid": "6cc66373dc394583886020d0a1ba7c07", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6cc66373dc394583886020d0a1ba7c07.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6cc66373dc394583886020d0a1ba7c07"}}, "title": "Genomic regions of speciation and adaptation among three species of grouse.", "authors": [{"family": "Kozma", "given": "Radoslav", "initials": "R"}, {"family": "R\u00f6din-M\u00f6rch", "given": "Patrik", "initials": "P"}, {"family": "H\u00f6glund", "given": "Jacob", "initials": "J", "orcid": "0000-0002-5840-779X", "researcher": {"href": "https://publications.scilifelab.se/researcher/8e1eb3c1903f4a97a4c585a2dee3b05f.json"}}], "type": "journal article", "published": "2019-01-28", "journal": {"volume": "9", "issn": "2045-2322", "issue": "1", "pages": "812", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "Understanding the molecular basis of adaption is one of the central goals in evolutionary biology and when investigated across sister species it can provide detailed insight into the mechanisms of speciation. Here, we sequence the genomes of 34 individuals from three closely related grouse species in order to uncover the genomic architecture of speciation and the genes involved in adaptation. We identify 6 regions, containing 7 genes that show lineage specific signs of differential selection across the species. These genes are involved in a variety of cell processes ranging from stress response to neural, gut, olfactory and limb development. Genome wide neutrality test statistics reveal a strong signal of population expansion acting across the genomes. Additionally, we uncover a 3.5 Mb region on chromosome 20 that shows considerably lower levels of differentiation across the three grouse lineages, indicating possible action of uniform selection in this region.", "doi": "10.1038/s41598-018-36880-5", "pmid": "30692562", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-018-36880-5"}, {"db": "pmc", "key": "PMC6349846"}], "notes": [], "created": "2020-01-08T12:37:53.909Z", "modified": "2021-06-16T14:50:59.101Z"}, {"entity": "publication", "iuid": "c18905fcb7164ee28fa05a65c5c65439", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c18905fcb7164ee28fa05a65c5c65439.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c18905fcb7164ee28fa05a65c5c65439"}}, "title": "Mercury methylating microbial communities of boreal forest soils.", "authors": [{"family": "Xu", "given": "Jingying", "initials": "J"}, {"family": "Buck", "given": "Moritz", "initials": "M"}, {"family": "Ekl\u00f6f", "given": "Karin", "initials": "K"}, {"family": "Ahmed", "given": "Omneya O", "initials": "OO"}, {"family": "Schaefer", "given": "Jeffra K", "initials": "JK"}, {"family": "Bishop", "given": "Kevin", "initials": "K", "orcid": "0000-0002-8057-1051", "researcher": {"href": "https://publications.scilifelab.se/researcher/2cf39f8ead0744f591dcdbcb6caee99a.json"}}, {"family": "Skyllberg", "given": "Ulf", "initials": "U"}, {"family": "Bj\u00f6rn", "given": "Erik", "initials": "E"}, {"family": "Bertilsson", "given": "Stefan", "initials": "S"}, {"family": "Bravo", "given": "Andrea G", "initials": "AG", "orcid": "0000-0002-8341-3462", "researcher": {"href": "https://publications.scilifelab.se/researcher/749bb106ca6b452d82603ef8cf3cbdee.json"}}], "type": "journal article", "published": "2019-01-24", "journal": {"volume": "9", "issn": "2045-2322", "issue": "1", "pages": "518", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "The formation of the potent neurotoxic methylmercury (MeHg) is a microbially mediated process that has raised much concern because MeHg poses threats to wildlife and human health. Since boreal forest soils can be a source of MeHg in aquatic networks, it is crucial to understand the biogeochemical processes involved in the formation of this pollutant. High-throughput sequencing of 16S rRNA and the mercury methyltransferase, hgcA, combined with geochemical characterisation of soils, were used to determine the microbial populations contributing to MeHg formation in forest soils across Sweden. The hgcA sequences obtained were distributed among diverse clades, including Proteobacteria, Firmicutes, and Methanomicrobia, with Deltaproteobacteria, particularly Geobacteraceae, dominating the libraries across all soils examined. Our results also suggest that MeHg formation is also linked to the composition of non-mercury methylating bacterial communities, likely providing growth substrate (e.g. acetate) for the hgcA-carrying microorganisms responsible for the actual methylation process. While previous research focused on mercury methylating microbial communities of wetlands, this study provides some first insights into the diversity of mercury methylating microorganisms in boreal forest soils.", "doi": "10.1038/s41598-018-37383-z", "pmid": "30679728", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-018-37383-z"}, {"db": "pmc", "key": "PMC6345997"}], "notes": [], "created": "2019-04-23T10:00:57.684Z", "modified": "2024-01-16T13:48:44.797Z"}, {"entity": "publication", "iuid": "2c7b5a8890f74a13b826cafed1ac185b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2c7b5a8890f74a13b826cafed1ac185b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2c7b5a8890f74a13b826cafed1ac185b"}}, "title": "Carbonic Anhydrase 6 Gene Variation influences Oral Microbiota Composition and Caries Risk in Swedish adolescents.", "authors": [{"family": "Esberg", "given": "A", "initials": "A"}, {"family": "Haworth", "given": "S", "initials": "S"}, {"family": "Brunius", "given": "C", "initials": "C"}, {"family": "Lif Holgerson", "given": "P", "initials": "P"}, {"family": "Johansson", "given": "I", "initials": "I"}], "type": "journal article", "published": "2019-01-24", "journal": {"volume": "9", "issn": "2045-2322", "issue": "1", "pages": "452", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "Carbonic anhydrase VI (CA6) catalyses the reversible hydration of carbon dioxide in saliva with possible pH regulation, taste perception, and tooth formation effects. This study assessed effects of variation in the CA6 gene on oral microbiota and specifically the acidophilic and caries-associated Streptococcus mutans in 17-year old Swedish adolescents (n\u2009=\u2009154). Associations with caries status and secreted CA6 protein were also evaluated. Single Nucleotide Polymorphisms (27 SNPs in 5 haploblocks) and saliva and tooth biofilm microbiota from Illumina MiSeq 16S rDNA (V3-V4) sequencing and culturing were analysed. Haploblock 4 (rs10864376, rs3737665, rs12138897) CCC associated with low prevalence of S. mutans (OR (95% CI): 0.5 (0.3, 0.8)), and caries (OR 0.6 (0.3, 0.9)), whereas haploblock 4 TTG associated with high prevalence of S. mutans (OR: 2.7 (1.2, 5.9)) and caries (OR: 2.3 (1.2, 4.4)). The TTG-haploblock 4 (represented by rs12138897(G)) was characterized by S. mutans, Scardovia wiggsiae, Treponema sp. HOT268, Tannerella sp. HOT286, Veillonella gp.1 compared with the CCC-haploblock 4 (represented by rs12138897(C)). Secreted CA6 in saliva was weakly linked to CA6 gene variation. In conclusion, the results indicate that CA6 gene polymorphisms influence S. mutans colonization, tooth biofilm microbiota composition and risk of dental caries in Swedish adolescents.", "doi": "10.1038/s41598-018-36832-z", "pmid": "30679524", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-018-36832-z"}, {"db": "pmc", "key": "PMC6345836"}], "notes": [], "created": "2019-09-17T16:24:29.013Z", "modified": "2024-01-16T13:48:44.805Z"}, {"entity": "publication", "iuid": "d827751fe5bd40ffb8ceda3c1052fc64", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d827751fe5bd40ffb8ceda3c1052fc64.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d827751fe5bd40ffb8ceda3c1052fc64"}}, "title": "Multi-ancestry study of blood lipid levels identifies four loci interacting with physical activity.", "authors": [{"family": "Kilpel\u00e4inen", "given": "Tuomas O", "initials": "TO"}, {"family": "Bentley", "given": "Amy R", "initials": "AR"}, {"family": "Noordam", "given": "Raymond", "initials": "R"}, {"family": "Sung", "given": "Yun Ju", "initials": "YJ"}, {"family": "Schwander", "given": "Karen", "initials": "K"}, {"family": "Winkler", "given": "Thomas W", "initials": "TW"}, {"family": "Jakupovi\u0107", "given": "Hermina", "initials": "H"}, {"family": "Chasman", "given": "Daniel I", "initials": "DI"}, {"family": "Manning", "given": "Alisa", "initials": "A"}, {"family": "Ntalla", "given": "Ioanna", "initials": "I"}, {"family": "Aschard", "given": "Hugues", "initials": "H"}, {"family": "Brown", "given": "Michael R", "initials": "MR"}, {"family": "de Las Fuentes", "given": "Lisa", "initials": "L"}, {"family": "Franceschini", "given": "Nora", "initials": "N"}, {"family": "Guo", "given": "Xiuqing", "initials": "X"}, {"family": "Vojinovic", "given": "Dina", "initials": "D"}, {"family": "Aslibekyan", "given": "Stella", "initials": "S"}, {"family": "Feitosa", "given": "Mary F", "initials": "MF"}, {"family": "Kho", "given": "Minjung", "initials": "M"}, {"family": "Musani", "given": "Solomon K", "initials": "SK"}, {"family": "Richard", "given": "Melissa", "initials": "M"}, {"family": "Wang", "given": "Heming", "initials": "H"}, {"family": "Wang", "given": "Zhe", "initials": "Z"}, {"family": "Bartz", "given": "Traci M", "initials": "TM"}, {"family": "Bielak", "given": "Lawrence F", "initials": "LF"}, {"family": "Campbell", "given": "Archie", "initials": "A"}, {"family": "Dorajoo", "given": "Rajkumar", "initials": "R"}, {"family": "Fisher", "given": "Virginia", "initials": "V"}, {"family": "Hartwig", "given": "Fernando P", "initials": "FP"}, {"family": "Horimoto", "given": "Andrea R V R", "initials": "ARVR"}, {"family": "Li", "given": "Changwei", "initials": "C"}, {"family": "Lohman", "given": "Kurt K", "initials": "KK"}, {"family": "Marten", "given": "Jonathan", "initials": "J"}, {"family": "Sim", "given": "Xueling", "initials": "X"}, {"family": "Smith", "given": "Albert V", "initials": "AV"}, {"family": "Tajuddin", "given": "Salman M", "initials": "SM"}, {"family": "Alver", "given": "Maris", "initials": "M"}, {"family": "Amini", "given": "Marzyeh", "initials": "M"}, {"family": "Boissel", "given": "Mathilde", "initials": "M"}, {"family": "Chai", "given": "Jin Fang", "initials": "JF"}, {"family": "Chen", "given": "Xu", "initials": "X"}, {"family": "Divers", "given": "Jasmin", "initials": "J"}, {"family": "Evangelou", "given": "Evangelos", "initials": "E"}, {"family": "Gao", "given": "Chuan", "initials": "C"}, {"family": "Graff", "given": "Mariaelisa", "initials": "M"}, {"family": "Harris", "given": "Sarah E", "initials": "SE"}, {"family": "He", "given": "Meian", "initials": "M"}, {"family": "Hsu", "given": "Fang-Chi", "initials": "FC"}, {"family": "Jackson", "given": "Anne U", "initials": "AU"}, {"family": "Zhao", "given": "Jing Hua", "initials": "JH"}, {"family": "Kraja", "given": "Aldi T", "initials": "AT"}, {"family": "K\u00fchnel", "given": "Brigitte", "initials": "B"}, {"family": "Laguzzi", "given": "Federica", "initials": "F"}, {"family": "Lyytik\u00e4inen", "given": "Leo-Pekka", "initials": "LP"}, {"family": "Nolte", "given": "Ilja M", "initials": "IM"}, {"family": "Rauramaa", "given": "Rainer", "initials": "R"}, {"family": "Riaz", "given": "Muhammad", "initials": "M"}, {"family": "Robino", "given": "Antonietta", "initials": "A"}, {"family": "Rueedi", "given": "Rico", "initials": "R"}, {"family": "Stringham", "given": "Heather M", "initials": "HM"}, {"family": "Takeuchi", "given": "Fumihiko", "initials": "F"}, {"family": "van der Most", "given": "Peter J", "initials": "PJ"}, {"family": "Varga", "given": "Tibor V", "initials": "TV"}, {"family": "Verweij", "given": "Niek", "initials": "N"}, {"family": "Ware", "given": "Erin B", "initials": "EB"}, {"family": "Wen", "given": "Wanqing", "initials": 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"initials": "W"}, {"family": "Zhu", "given": "Xiaofeng", "initials": "X"}, {"family": "Evans", "given": "Michele K", "initials": "MK"}, {"family": "Franks", "given": "Paul W", "initials": "PW"}, {"family": "Gudnason", "given": "Vilmundur", "initials": "V"}, {"family": "Hayward", "given": "Caroline", "initials": "C"}, {"family": "Horta", "given": "Bernardo L", "initials": "BL"}, {"family": "Kelly", "given": "Tanika N", "initials": "TN"}, {"family": "Liu", "given": "Yongmei", "initials": "Y"}, {"family": "North", "given": "Kari E", "initials": "KE"}, {"family": "Pereira", "given": "Alexandre C", "initials": "AC"}, {"family": "Ridker", "given": "Paul M", "initials": "PM"}, {"family": "Tai", "given": "E Shyong", "initials": "ES"}, {"family": "van Dam", "given": "Rob M", "initials": "RM"}, {"family": "Fox", "given": "Ervin R", "initials": "ER"}, {"family": "Kardia", "given": "Sharon L R", "initials": "SLR"}, {"family": "Liu", "given": "Ching-Ti", "initials": "CT"}, {"family": "Mook-Kanamori", "given": "Dennis O", "initials": "DO"}, {"family": "Province", "given": "Michael A", "initials": "MA"}, {"family": "Redline", "given": "Susan", "initials": "S"}, {"family": "van Duijn", "given": "Cornelia M", "initials": "CM"}, {"family": "Rotter", "given": "Jerome I", "initials": "JI"}, {"family": "Kooperberg", "given": "Charles B", "initials": "CB"}, {"family": "Gauderman", "given": "W James", "initials": "WJ"}, {"family": "Psaty", "given": "Bruce M", "initials": "BM"}, {"family": "Rice", "given": "Kenneth", "initials": "K"}, {"family": "Munroe", "given": "Patricia B", "initials": "PB"}, {"family": "Fornage", "given": "Myriam", "initials": "M"}, {"family": "Cupples", "given": "L Adrienne", "initials": "LA"}, {"family": "Rotimi", "given": "Charles N", "initials": "CN"}, {"family": "Morrison", "given": "Alanna C", "initials": "AC"}, {"family": "Rao", "given": "Dabeeru C", "initials": "DC"}, {"family": "Loos", "given": "Ruth J F", "initials": "RJF"}], "type": "journal article", "published": "2019-01-22", "journal": {"volume": "10", "issn": "2041-1723", "issue": "1", "pages": "376", "title": "Nat Commun", "issn-l": "2041-1723"}, "abstract": "Many genetic loci affect circulating lipid levels, but it remains unknown whether lifestyle factors, such as physical activity, modify these genetic effects. To identify lipid loci interacting with physical activity, we performed genome-wide analyses of circulating HDL cholesterol, LDL cholesterol, and triglyceride levels in up to 120,979 individuals of European, African, Asian, Hispanic, and Brazilian ancestry, with follow-up of suggestive associations in an additional 131,012 individuals. We find four loci, in/near CLASP1, LHX1, SNTA1, and CNTNAP2, that are associated with circulating lipid levels through interaction with physical activity; higher levels of physical activity enhance the HDL cholesterol-increasing effects of the CLASP1, LHX1, and SNTA1 loci and attenuate the LDL cholesterol-increasing effect of the CNTNAP2 locus. The CLASP1, LHX1, and SNTA1 regions harbor genes linked to muscle function and lipid metabolism. Our results elucidate the role of physical activity interactions in the genetic contribution to blood lipid levels.", "doi": "10.1038/s41467-018-08008-w", "pmid": "30670697", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-018-08008-w"}, {"db": "pmc", "key": "PMC6342931"}], "notes": [], "created": "2019-10-16T15:10:15.717Z", "modified": "2020-01-21T13:56:14.665Z"}, {"entity": "publication", "iuid": "d40e946f30574dbfa823bd9b2f4d0e51", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d40e946f30574dbfa823bd9b2f4d0e51.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d40e946f30574dbfa823bd9b2f4d0e51"}}, "title": "Genetic and lifestyle risk factors for MRI-defined brain infarcts in a population-based setting.", "authors": [{"family": "Chauhan", "given": "Ganesh", "initials": "G"}, {"family": "Adams", "given": "Hieab H H", 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{"family": "Sharma", "given": "Pankaj", "initials": "P"}, {"family": "Sudlow", "given": "Cathie L M", "initials": "CLM"}, {"family": "Rosand", "given": "Jonathan", "initials": "J"}, {"family": "Woo", "given": "Daniel", "initials": "D"}, {"family": "Cole", "given": "John W", "initials": "JW"}, {"family": "Meschia", "given": "James F", "initials": "JF"}, {"family": "Slowik", "given": "Agnieszka", "initials": "A"}, {"family": "Thijs", "given": "Vincent", "initials": "V"}, {"family": "Lindgren", "given": "Arne", "initials": "A"}, {"family": "Melander", "given": "Olle", "initials": "O"}, {"family": "Grewal", "given": "Raji P", "initials": "RP"}, {"family": "Rundek", "given": "Tatjana", "initials": "T"}, {"family": "Rexrode", "given": "Kathy", "initials": "K"}, {"family": "Rothwell", "given": "Peter M", "initials": "PM"}, {"family": "Arnett", "given": "Donna K", "initials": "DK"}, {"family": "Jern", "given": "Christina", "initials": "C"}, {"family": "Johnson", "given": "Julie A", "initials": "JA"}, {"family": "Benavente", "given": "Oscar R", "initials": "OR"}, {"family": "Wasssertheil-Smoller", "given": "Sylvia", "initials": "S"}, {"family": "Lee", "given": "Jin-Moo", "initials": "JM"}, {"family": "Wong", "given": "Quenna", "initials": "Q"}, {"family": "Mitchell", "given": "Braxton D", "initials": "BD"}, {"family": "Rich", "given": "Stephen S", "initials": "SS"}, {"family": "McArdle", "given": "Patrick F", "initials": "PF"}, {"family": "Geerlings", "given": "Mirjam I", "initials": "MI"}, {"family": "van der Graaf", "given": "Yolanda", "initials": "Y"}, {"family": "de Bakker", "given": "Paul I W", "initials": "PIW"}, {"family": "Asselbergs", "given": "Folkert W", "initials": "FW"}, {"family": "Srikanth", "given": "Velandai", "initials": "V"}, {"family": "Thomson", "given": "Russell", "initials": "R"}, {"family": "McWhirter", "given": "Rebekah", "initials": "R"}, {"family": "Moran", "given": "Chris", "initials": "C"}, {"family": "Callisaya", "given": "Michele", "initials": "M"}, {"family": "Phan", "given": "Thanh", "initials": "T"}, {"family": "Rutten-Jacobs", "given": "Loes C A", "initials": "LCA"}, {"family": "Bevan", "given": "Steve", "initials": "S"}, {"family": "Tzourio", "given": "Christophe", "initials": "C"}, {"family": "Mather", "given": "Karen A", "initials": "KA"}, {"family": "Sachdev", "given": "Perminder S", "initials": "PS"}, {"family": "van Duijn", "given": "Cornelia M", "initials": "CM"}, {"family": "Worrall", "given": "Bradford B", "initials": "BB"}, {"family": "Dichgans", "given": "Martin", "initials": "M"}, {"family": "Kittner", "given": "Steven J", "initials": "SJ"}, {"family": "Markus", "given": "Hugh S", "initials": "HS"}, {"family": "Ikram", "given": "Mohammad A", "initials": "MA"}, {"family": "Fornage", "given": "Myriam", "initials": "M"}, {"family": "Launer", "given": "Lenore J", "initials": "LJ"}, {"family": "Seshadri", "given": "Sudha", "initials": "S"}, {"family": "Longstreth", "given": "W T", "initials": "WT"}, {"family": "Debette", "given": "St\u00e9phanie", "initials": "S"}, {"family": "Stroke Genetics Network (SiGN), the International Stroke Genetics Consortium (ISGC), METASTROKE, Alzheimer's Disease Genetics Consortium (ADGC), and the Neurology Working Group of the Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) Consortium", "given": "", "initials": ""}], "type": "journal article", "published": "2019-01-16", "journal": {"volume": null, "issn": "1526-632X", "issue": null, "title": "Neurology", "issn-l": "0028-3878"}, "abstract": "To explore genetic and lifestyle risk factors of MRI-defined brain infarcts (BI) in large population-based cohorts.\n\nWe performed meta-analyses of genome-wide association studies (GWAS) and examined associations of vascular risk factors and their genetic risk scores (GRS) with MRI-defined BI and a subset of BI, namely, small subcortical BI (SSBI), in 18 population-based cohorts (n = 20,949) from 5 ethnicities (3,726 with BI, 2,021 with SSBI). Top loci were followed up in 7 population-based cohorts (n = 6,862; 1,483 with BI, 630 with SBBI), and we tested associations with related phenotypes including ischemic stroke and pathologically defined BI.\n\nThe mean prevalence was 17.7% for BI and 10.5% for SSBI, steeply rising after age 65. Two loci showed genome-wide significant association with BI: FBN2, \n                p = 1.77 \u00d7 10-8; and LINC00539/ZDHHC20, p = 5.82 \u00d7 10-9. Both have been associated with blood pressure (BP)-related phenotypes, but did not replicate in the smaller follow-up sample or show associations with related phenotypes. Age- and sex-adjusted associations with BI and SSBI were observed for BP traits (p value for BI, p[BI] = 9.38 \u00d7 10-25; p[SSBI] = 5.23 \u00d7 10-14 for hypertension), smoking (p[BI] = 4.4 \u00d7 10-10; p[SSBI] = 1.2 \u00d7 10-4), diabetes (p[BI] = 1.7 \u00d7 10-8; p[SSBI] = 2.8 \u00d7 10-3), previous cardiovascular disease (p[BI] = 1.0 \u00d7 10-18; p[SSBI] = 2.3 \u00d7 10-7), stroke (p[BI] = 3.9 \u00d7 10-69; p[SSBI] = 3.2 \u00d7 10-24), and MRI-defined white matter hyperintensity burden (p[BI] = 1.43 \u00d7 10-157; p[SSBI] = 3.16 \u00d7 10-106), but not with body mass index or cholesterol. GRS of BP traits were associated with BI and SSBI (p \u2264 0.0022), without indication of directional pleiotropy.\n\nIn this multiethnic GWAS meta-analysis, including over 20,000 population-based participants, we identified genetic risk loci for BI requiring validation once additional large datasets become available. High BP, including genetically determined, was the most significant modifiable, causal risk factor for BI.", "doi": "10.1212/WNL.0000000000006851", "pmid": "30651383", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "WNL.0000000000006851"}, {"db": "pmc", "key": "PMC6369905"}], "notes": [], "created": "2019-09-16T14:28:27.947Z", "modified": "2020-01-21T13:56:14.686Z"}, {"entity": "publication", "iuid": "28e9976dd34d4b74925aac29d26d0dcb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/28e9976dd34d4b74925aac29d26d0dcb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/28e9976dd34d4b74925aac29d26d0dcb"}}, "title": "Transcriptomic and proteomic analyses reveal new insights into the regulation of immune pathways during adenovirus type 2 infection.", "authors": [{"family": "Zhao", "given": "Hongxing", "initials": "H", "orcid": "0000-0002-6915-2729", "researcher": {"href": "https://publications.scilifelab.se/researcher/ce92393b5ec7435eae512f37cce8f895.json"}}, {"family": "Chen", "given": "Maoshan", "initials": "M"}, {"family": "Vald\u00e9s", "given": "Alberto", "initials": "A"}, {"family": "Lind", "given": "Sara Bergstr\u00f6m", "initials": "SB"}, {"family": "Pettersson", "given": "Ulf", "initials": "U"}], "type": "journal article", "published": "2019-01-14", "journal": {"volume": "19", "issn": "1471-2180", "issue": "1", "pages": "15", "title": "BMC Microbiol.", "issn-l": "1471-2180"}, "abstract": "Human adenovirus (Ad) infection leads to the changes of host cell gene expression and biosynthetic processes. Transcriptomics in adenovirus type 2 (Ad2)-infected lung fibroblasts (IMR-90) cells has previously been studied using RNA sequencing. However, this study included only two time points (12 and 24 hpi) using constrained 76 bp long sequencing reads. Therefore, a more detailed study of transcription at different phases of infection using an up-graded sequencing technique is recalled. Furthermore, the correlation between transcription and protein expression needs to be addressed.\n\nIn total, 3556 unique cellular genes were identified as differentially expressed at the transcriptional level with more than 2-fold changes in Ad2-infected cells as compared to non-infected cells by using paired-end sequencing. Based on the kinetics of the gene expression changes at different times after infection, these RNAs fell into 20 clusters. Among them, cellular genes involved in immune response were highly up-regulated in the early phase before becoming down-regulated in the late phase. Comparison of differentially expressed genes at transcriptional and posttranscriptional levels revealed low correlation. Particularly genes involved in cellular immune pathways showed a negative correlation. Here, we highlight the genes which expose inconsistent expression profiles with an emphasis on key factors in cellular immune pathways including NF\u03baB, JAK/STAT, caspases and MAVS. Different from their transcriptional profiles with up- and down-regulation in the early and late phase, respectively, these proteins were up-regulated in the early phase and were sustained in the late phase. A surprising finding was that the target genes of the sustained activators failed to show response.\n\nThere were features common to genes which play important roles in cellular immune pathways. Their expression was stimulated at both RNA and protein levels during the early phase. In the late phase however, their transcription was suppressed while protein levels remained stable. These results indicate that Ad2 and the host cell use different strategies to regulate cellular immune pathways. A control mechanism at the post-translational level must thus exist which is under the control of Ad2.", "doi": "10.1186/s12866-018-1375-5", "pmid": "30642258", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1186/s12866-018-1375-5"}, {"db": "pmc", "key": "PMC6332865"}], "notes": [], "created": "2019-04-23T09:56:25.854Z", "modified": "2021-06-16T14:57:18.495Z"}, {"entity": "publication", "iuid": "3ceba61f89834bd284538a521f2c5781", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3ceba61f89834bd284538a521f2c5781.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3ceba61f89834bd284538a521f2c5781"}}, "title": "Decreased Snow Cover Stimulates Under-Ice Primary Producers but Impairs Methanotrophic Capacity.", "authors": [{"family": "Garcia", "given": "Sarahi L", "initials": "SL", "orcid": "0000-0002-8622-0308", "researcher": {"href": "https://publications.scilifelab.se/researcher/8aabc8c17d5b4ad7872c7380301d4562.json"}}, {"family": "Szekely", "given": "Anna J", "initials": "AJ"}, {"family": "Bergvall", "given": "Christoffer", "initials": "C"}, {"family": "Schattenhofer", "given": "Martha", "initials": "M"}, {"family": "Peura", "given": "Sari", "initials": "S", "orcid": "0000-0003-3892-8157", "researcher": {"href": "https://publications.scilifelab.se/researcher/c430ad5c3bd14387b768c588a9b12ce0.json"}}], "type": "journal article", "published": "2019-01-09", "journal": {"volume": "4", "issn": "2379-5042", "issue": "1", "pages": null, "title": "mSphere", "issn-l": "2379-5042"}, "abstract": "Climate change scenarios anticipate decreased spring snow cover in boreal and subarctic regions. Forest lakes are abundant in these regions and substantial contributors of methane emissions. To investigate the effect of reduced snow cover, we experimentally removed snow from an anoxic frozen lake. We observed that the removal of snow increased light penetration through the ice, increasing water temperature and modifying microbial composition in the different depths. Chlorophyll a and b concentrations increased in the upper water column, suggesting activation of algal primary producers. At the same time, Chlorobiaceae, one of the key photosynthetic bacterial families in anoxic lakes, shifted to lower depths. Moreover, a decrease in the relative abundance of methanotrophs within the bacterial family Methylococcaceae was detected, concurrent with an increase in methane concentration in the water column. These results indicate that decreased snow cover impacts both primary production and methane production and/or consumption, which may ultimately lead to increased methane emissions after spring ice off.IMPORTANCE Small lakes are an important source of greenhouse gases in the boreal zone. These lakes are severely impacted by the winter season, when ice and snow cover obstruct gas exchange between the lake and the atmosphere and diminish light availability in the water column. Currently, climate change is resulting in reduced spring snow cover. A short-term removal of the snow from the ice stimulated algal primary producers and subsequently heterotrophic bacteria. Concurrently, the relative abundance of methanotrophic bacteria decreased and methane concentrations increased. Our results increase the general knowledge of microbial life under ice and, specifically, the understanding of the potential impact of climate change on boreal lakes.", "doi": "10.1128/mSphere.00626-18", "pmid": "30626619", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "4/1/e00626-18"}, {"db": "pmc", "key": "PMC6327105"}], "notes": [], "created": "2019-04-23T10:01:18.250Z", "modified": "2024-01-16T13:48:44.837Z"}, {"entity": "publication", "iuid": "58d22ea9779545d3bb67e719d15ac7d5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/58d22ea9779545d3bb67e719d15ac7d5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/58d22ea9779545d3bb67e719d15ac7d5"}}, "title": "Trans-ethnic kidney function association study reveals putative causal genes and effects on kidney-specific disease aetiologies.", "authors": [{"family": "Morris", "given": "Andrew P", "initials": "AP"}, {"family": "Le", "given": "Thu H", "initials": "TH"}, {"family": "Wu", "given": "Haojia", "initials": "H"}, {"family": "Akbarov", "given": "Artur", "initials": "A"}, {"family": "van der Most", "given": "Peter J", "initials": "PJ"}, {"family": "Hemani", "given": "Gibran", "initials": "G"}, {"family": "Smith", "given": "George Davey", "initials": "GD"}, {"family": "Mahajan", "given": "Anubha", "initials": "A"}, {"family": "Gaulton", "given": "Kyle J", "initials": "KJ"}, {"family": "Nadkarni", "given": "Girish N", "initials": "GN"}, {"family": "Valladares-Salgado", "given": "Adan", "initials": "A"}, {"family": "Wacher-Rodarte", "given": "Niels", "initials": "N"}, {"family": "Mychaleckyj", "given": "Josyf C", "initials": "JC"}, {"family": "Dueker", "given": "Nicole D", "initials": "ND"}, {"family": "Guo", "given": "Xiuqing", "initials": "X"}, {"family": "Hai", "given": "Yang", "initials": "Y"}, {"family": "Haessler", "given": "Jeffrey", "initials": "J"}, {"family": "Kamatani", "given": "Yoichiro", "initials": "Y"}, {"family": "Stilp", "given": "Adrienne M", "initials": "AM"}, {"family": "Zhu", "given": "Gu", "initials": "G"}, {"family": "Cook", "given": "James P", "initials": "JP"}, {"family": "\u00c4rnl\u00f6v", "given": "Johan", "initials": "J"}, {"family": "Blanton", "given": "Susan H", "initials": "SH"}, {"family": "de Borst", "given": "Martin H", "initials": "MH"}, {"family": "Bottinger", "given": "Erwin P", "initials": "EP"}, {"family": "Buchanan", "given": "Thomas A", "initials": "TA"}, {"family": "Cechova", "given": "Sylvia", "initials": "S"}, {"family": "Charchar", "given": "Fadi J", "initials": "FJ"}, {"family": "Chu", "given": "Pei-Lun", "initials": "PL"}, {"family": "Damman", "given": "Jeffrey", "initials": "J"}, {"family": "Eales", "given": "James", "initials": "J"}, {"family": "Gharavi", "given": "Ali G", "initials": "AG"}, {"family": "Giedraitis", "given": "Vilmantas", "initials": "V"}, {"family": "Heath", "given": "Andrew C", "initials": "AC"}, {"family": "Ipp", "given": "Eli", "initials": "E"}, {"family": "Kiryluk", "given": "Krzysztof", "initials": "K"}, {"family": "Kramer", "given": "Holly J", "initials": "HJ"}, {"family": "Kubo", "given": "Michiaki", "initials": "M"}, {"family": "Larsson", "given": "Anders", "initials": "A"}, {"family": "Lindgren", "given": "Cecilia M", "initials": "CM"}, {"family": "Lu", "given": "Yingchang", "initials": "Y"}, {"family": "Madden", "given": "Pamela A F", "initials": "PAF"}, {"family": "Montgomery", "given": "Grant W", "initials": "GW"}, {"family": "Papanicolaou", "given": "George J", "initials": "GJ"}, {"family": "Raffel", "given": "Leslie J", "initials": "LJ"}, {"family": "Sacco", "given": "Ralph L", "initials": "RL"}, {"family": "Sanchez", "given": "Elena", "initials": "E"}, {"family": "Stark", "given": "Holger", "initials": "H"}, {"family": "Sundstrom", "given": "Johan", "initials": "J"}, {"family": "Taylor", "given": "Kent D", "initials": "KD"}, {"family": "Xiang", "given": "Anny H", "initials": "AH"}, {"family": "Zivkovic", "given": "Aleksandra", "initials": "A"}, {"family": "Lind", "given": "Lars", "initials": "L"}, {"family": "Ingelsson", "given": "Erik", "initials": "E"}, {"family": "Martin", "given": "Nicholas G", "initials": "NG"}, {"family": "Whitfield", "given": "John B", "initials": "JB"}, {"family": "Cai", "given": "Jianwen", "initials": "J"}, {"family": "Laurie", "given": "Cathy C", "initials": "CC"}, {"family": "Okada", "given": "Yukinori", "initials": "Y"}, {"family": "Matsuda", "given": "Koichi", "initials": "K"}, {"family": "Kooperberg", "given": "Charles", "initials": "C"}, {"family": "Chen", "given": "Yii-Der Ida", "initials": "YI"}, {"family": "Rundek", "given": "Tatjana", "initials": "T"}, {"family": "Rich", "given": "Stephen S", "initials": "SS"}, {"family": "Loos", "given": "Ruth J F", "initials": "RJF"}, {"family": "Parra", "given": "Esteban J", "initials": "EJ"}, {"family": "Cruz", "given": "Miguel", "initials": "M"}, {"family": "Rotter", "given": "Jerome I", "initials": "JI"}, {"family": "Snieder", "given": "Harold", "initials": "H"}, {"family": "Tomaszewski", "given": "Maciej", "initials": "M"}, {"family": "Humphreys", "given": "Benjamin D", "initials": "BD"}, {"family": "Franceschini", "given": "Nora", "initials": "N"}], "type": "journal article", "published": "2019-01-03", "journal": {"volume": "10", "issn": "2041-1723", "issue": "1", "pages": "29", "title": "Nat Commun", "issn-l": "2041-1723"}, "abstract": "Chronic kidney disease (CKD) affects ~10% of the global population, with considerable ethnic differences in prevalence and aetiology. We assemble genome-wide association studies of estimated glomerular filtration rate (eGFR), a measure of kidney function that defines CKD, in 312,468 individuals of diverse ancestry. We identify 127 distinct association signals with homogeneous effects on eGFR across ancestries and enrichment in genomic annotations including kidney-specific histone modifications. Fine-mapping reveals 40 high-confidence variants driving eGFR associations and highlights putative causal genes with cell-type specific expression in glomerulus, and in\u00a0proximal and distal nephron. Mendelian randomisation supports causal effects of eGFR on overall and cause-specific CKD, kidney stone formation, diastolic blood pressure and hypertension. These results define novel molecular mechanisms and putative causal genes for eGFR, offering insight into clinical outcomes and routes to CKD treatment development.", "doi": "10.1038/s41467-018-07867-7", "pmid": "30604766", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-018-07867-7"}, {"db": "pmc", "key": "PMC6318312"}], "notes": [], "created": "2019-09-16T14:28:28.864Z", "modified": "2024-01-16T13:48:44.852Z"}, {"entity": "publication", "iuid": "9864571076894519bcfdf7ef49a0fb3f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9864571076894519bcfdf7ef49a0fb3f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9864571076894519bcfdf7ef49a0fb3f"}}, "title": "Tracking the Epigenetic Clock Across the Human Life Course: A Meta-analysis of Longitudinal Cohort Data.", "authors": [{"family": "Marioni", "given": "Riccardo E", "initials": "RE"}, {"family": "Suderman", "given": "Matthew", "initials": "M"}, {"family": "Chen", "given": "Brian H", "initials": "BH"}, {"family": "Horvath", "given": "Steve", "initials": "S"}, {"family": "Bandinelli", "given": "Stefania", "initials": "S"}, {"family": "Morris", "given": "Tiffany", "initials": "T"}, {"family": "Beck", "given": "Stephan", "initials": "S"}, {"family": "Ferrucci", "given": "Luigi", "initials": "L"}, {"family": "Pedersen", "given": "Nancy L", "initials": "NL"}, {"family": "Relton", "given": "Caroline L", "initials": "CL"}, {"family": "Deary", "given": "Ian J", "initials": "IJ"}, {"family": "H\u00e4gg", "given": "Sara", "initials": "S"}], "type": "journal article", "published": "2019-01-01", "journal": {"volume": "74", "issn": "1758-535X", "issue": "1", "pages": "57-61", "title": "J. Gerontol. A Biol. Sci. Med. Sci.", "issn-l": "1079-5006"}, "abstract": "Epigenetic clocks based on DNA methylation yield high correlations with chronological age in cross-sectional data. Due to a paucity of longitudinal data, it is not known how \u0394age (epigenetic age - chronological age) changes over time or if it remains constant from childhood to old age. Here, we investigate this using longitudinal DNA methylation data from five datasets, covering most of the human life course.\n\nTwo measures of the epigenetic clock (Hannum and Horvath) are used to calculate \u0394age in the following cohorts: Avon Longitudinal Study of Parents and Children (ALSPAC) offspring (n = 986, total age-range 7-19 years, 2 waves), ALSPAC mothers (n = 982, 16-60 years, 2 waves), InCHIANTI (n = 460, 21-100 years, 2 waves), SATSA (n = 373, 48-99 years, 5 waves), Lothian Birth Cohort 1936 (n = 1,054, 70-76 years, 3 waves), and Lothian Birth Cohort 1921 (n = 476, 79-90 years, 3 waves). Linear mixed models were used to track longitudinal change in \u0394age within each cohort.\n\nFor both epigenetic age measures, \u0394age showed a declining trend in almost all of the cohorts. The correlation between \u0394age across waves ranged from 0.22 to 0.82 for Horvath and 0.25 to 0.71 for Hannum, with stronger associations in samples collected closer in time.\n\nEpigenetic age increases at a slower rate than chronological age across the life course, especially in the oldest population. Some of the effect is likely driven by survival bias, where healthy individuals are those maintained within a longitudinal study, although other factors like the age distribution of the underlying training population may also have influenced this trend.", "doi": "10.1093/gerona/gly060", "pmid": "29718110", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "4944478"}, {"db": "pmc", "key": "PMC6298183"}], "notes": [], "created": "2019-09-17T16:24:48.771Z", "modified": "2024-01-16T13:48:44.869Z"}, {"entity": "publication", "iuid": "ee17531a7dba4f3ebbab13b2486302cb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ee17531a7dba4f3ebbab13b2486302cb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ee17531a7dba4f3ebbab13b2486302cb"}}, "title": "ZBED6 negatively regulates insulin production, neuronal differentiation, and cell aggregation in MIN6 cells.", "authors": [{"family": "Wang", "given": "Xuan", "initials": "X"}, {"family": "Jiang", "given": "Lin", "initials": "L"}, {"family": "Wallerman", "given": "Ola", "initials": "O"}, {"family": "Younis", "given": "Shady", "initials": "S"}, {"family": "Yu", "given": "Qian", "initials": "Q"}, {"family": "Klaesson", "given": "Axel", "initials": "A"}, {"family": "Tengholm", "given": "Anders", "initials": "A"}, {"family": "Welsh", "given": "Nils", "initials": "N"}, {"family": "Andersson", "given": "Leif", "initials": "L"}], "type": "journal article", "published": "2019-01-00", "journal": {"volume": "33", "issn": "1530-6860", "issue": "1", "pages": "88-100", "title": "FASEB J.", "issn-l": "0892-6638"}, "abstract": "Zinc finger BED domain containing protein 6 ( Zbed6) has evolved from a domesticated DNA transposon and encodes a transcription factor unique to placental mammals. The aim of the present study was to investigate further the role of ZBED6 in insulin-producing cells, using mouse MIN6 cells, and to evaluate the effects of Zbed6 knockdown on basal \u03b2-cell functions, such as morphology, transcriptional regulation, insulin content, and release. Zbed6-silenced cells and controls were characterized with a range of methods, including RNA sequencing, chromatin immunoprecipitation sequencing, insulin content and release, subplasma membrane Ca 2+ measurements, cAMP determination, and morphologic studies. More than 700 genes showed differential expression in response to Zbed6 knockdown, which was paralleled by increased capacity to generate cAMP, as well as by augmented subplasmalemmal calcium concentration and insulin secretion in response to glucose stimulation. We identified >4000 putative ZBED6-binding sites in the MIN6 genome, with an enrichment of ZBED6 sites at upregulated genes, such as the \u03b2-cell transcription factors v-maf musculoaponeurotic fibrosarcoma oncogene homolog A and Nk6 homeobox 1. We also observed altered morphology/growth patterns, as indicated by increased cell clustering, and in the appearance of axon-like Neurofilament, medium polypeptide and tubulin \u03b2 3, class III-positive protrusions. We conclude that ZBED6 acts as a transcriptional regulator in MIN6 cells and that its activity suppresses insulin production, cell aggregation, and neuronal-like differentiation.-Wang, X., Jiang, L., Wallerman, O., Younis, S., Yu, Q., Klaesson, A., Tengholm, A., Welsh, N., Andersson, L. ZBED6 negatively regulates insulin production, neuronal differentiation, and cell aggregation in MIN6 cells.", "doi": "10.1096/fj.201600835R", "pmid": "29957057", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2019-01-07T18:07:46.759Z", "modified": "2024-01-16T13:48:44.878Z"}, {"entity": "publication", "iuid": "c7a5555be6be478eb44a55046f81e128", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c7a5555be6be478eb44a55046f81e128.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c7a5555be6be478eb44a55046f81e128"}}, "title": "Mosaic loss of chromosome Y in leukocytes matters.", "authors": [{"family": "Forsberg", "given": "Lars A", "initials": "LA"}, {"family": "Halvardson", "given": "Jonatan", "initials": "J"}, {"family": "Rychlicka-Buniowska", "given": "Edyta", "initials": "E"}, {"family": "Danielsson", "given": "Marcus", "initials": "M"}, {"family": "Moghadam", "given": "Behrooz Torabi", "initials": "BT"}, {"family": "Mattisson", "given": "Jonas", "initials": "J"}, {"family": "Rasi", "given": "Chiara", "initials": "C"}, {"family": "Davies", "given": "Hanna", "initials": "H"}, {"family": "Lind", "given": "Lars", "initials": "L"}, {"family": "Giedraitis", "given": "Vilmantas", "initials": "V"}, {"family": "Lannfelt", "given": "Lars", "initials": "L"}, {"family": "Kilander", "given": "Lena", "initials": "L"}, {"family": "Ingelsson", "given": "Martin", "initials": "M"}, {"family": "Dumanski", "given": "Jan P", "initials": "JP"}], "type": "letter", "published": "2019-01-00", "journal": {"volume": "51", "issn": "1546-1718", "issue": "1", "pages": "4-7", "title": "Nat. Genet.", "issn-l": "1061-4036"}, "abstract": null, "doi": "10.1038/s41588-018-0267-9", "pmid": "30374072", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41588-018-0267-9"}], "notes": [], "created": "2019-01-07T17:59:08.474Z", "modified": "2024-01-16T13:48:44.894Z"}, {"entity": "publication", "iuid": "88f530d9a18040d2a24f397f4025ca13", "links": {"self": {"href": "https://publications.scilifelab.se/publication/88f530d9a18040d2a24f397f4025ca13.json"}, "display": {"href": "https://publications.scilifelab.se/publication/88f530d9a18040d2a24f397f4025ca13"}}, "title": "Genetic risk for neuroticism predicts emotional health depending on childhood adversity.", "authors": [{"family": "Lehto", "given": "Kelli", "initials": "K"}, {"family": "Karlsson", "given": "Ida", "initials": "I"}, {"family": "Lundholm", "given": "Cecilia", "initials": "C"}, {"family": "Pedersen", "given": "Nancy L", "initials": "NL"}], "type": "journal article", "published": "2019-01-00", "journal": {"volume": "49", "issn": "1469-8978", "issue": "2", "pages": "260-267", "title": "Psychol Med", "issn-l": "0033-2917"}, "abstract": "Existing evidence for gene \u00d7 environment interaction (G \u00d7 E) in neuroticism largely relies on candidate gene studies, although neuroticism is highly polygenic. This study aimed to investigate the long-term associations between polygenic risk scores for neuroticism (PRSN), objective childhood adversity and their interplay on emotional health aspects such as neuroticism itself, depressive symptoms, anxiety symptoms, loneliness and life satisfaction.\n\nThe sample consisted of reared-apart (TRA) and reared-together (TRT) middle- and old age twins (N = 699; median age at separation = 2). PRSN were created under nine p value cut-off thresholds (pT-s) and the pT with the highest degree of neuroticism variance explained was chosen for subsequent analyses. Linear regressions were used to assess the associations between PRSN, childhood adversity (being reared apart) and emotional health. G \u00d7 E was further investigated using a discordant twin design.\n\nPRSN explained up to 1.7% (pT &lt; 0.01) of phenotypic neuroticism in the total sample. Analyses across two separation groups revealed substantial heterogeneity in the variance explained by PRSN; 4.3% was explained in TRT, but almost no effect was observed in TRA. Similarly, PRSN explained 4% and 1.7% of the variance in depressive symptoms and loneliness, respectively, only in TRT. A significant G \u00d7 E interaction was identified for depressive symptoms.\n\nBy taking advantage of a unique sample of adopted twins, we demonstrated the presence of G \u00d7 E in neuroticism and emotional health using PRSN and childhood adversity. Our results may indicate that genome-wide association studies are detecting genetic main effects associated with neuroticism, but not those susceptible to early environmental influences.", "doi": "10.1017/S0033291718000715", "pmid": "29576022", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "S0033291718000715"}], "notes": [], "created": "2019-01-04T09:53:06.432Z", "modified": "2024-01-16T13:48:44.919Z"}, {"entity": "publication", "iuid": "7891dd32a0fe42cda198089b6b8552e4", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7891dd32a0fe42cda198089b6b8552e4.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7891dd32a0fe42cda198089b6b8552e4"}}, "title": "Exploring rare and low-frequency variants in the Saguenay-Lac-Saint-Jean population identified genes associated with asthma and allergy traits.", "authors": [{"family": "Morin", "given": "Andr\u00e9anne", "initials": "A"}, {"family": "Madore", "given": "Anne-Marie", "initials": "AM"}, {"family": "Kwan", "given": "Tony", "initials": "T"}, {"family": "Ban", "given": "Maria", "initials": "M"}, {"family": "Partanen", "given": "Jukka", "initials": "J"}, {"family": "R\u00f6nnblom", "given": "Lars", "initials": "L"}, {"family": "Syv\u00e4nen", "given": "Ann-Christine", "initials": "AC", "orcid": "0000-0002-9681-9146", "researcher": {"href": "https://publications.scilifelab.se/researcher/f7012e35025543379380cb90efd71243.json"}}, {"family": "Sawcer", "given": "Stephen", "initials": "S"}, {"family": "Stunnenberg", "given": "Hendrik", "initials": "H"}, {"family": "Lathrop", "given": "Mark", "initials": "M"}, {"family": "Pastinen", "given": "Tomi", "initials": "T"}, {"family": "Laprise", "given": "Catherine", "initials": "C"}], "type": "journal article", "published": "2019-01-00", "journal": {"volume": "27", "issn": "1476-5438", "issue": "1", "pages": "90-101", "title": "Eur. J. Hum. Genet.", "issn-l": "1018-4813"}, "abstract": "The Saguenay-Lac-Saint-Jean (SLSJ) region is located in northeastern Quebec and is known for its unique demographic history and founder effect. As founder populations are enriched with population-specific variants, we characterized the variants distribution in SLSJ and compared it with four European populations (Finnish, Sweden, United Kingdom and France), of which the Finnish population is another founder population. Targeted sequencing of the coding and non-coding immune regulatory regions of the SLSJ asthma familial cohort and the four European populations were performed. Rare and low-frequency coding and non-coding regulatory variants identified in the SLSJ population were then investigated for variant- and gene-level associations with asthma and allergy-related traits (eosinophil percentage, immunoglobulin (Ig) E levels and lung function). Our data showed that (1) rare or deleterious variants were not enriched in the two founder populations as compared with the three non-founder European populations; (2) a larger proportion of founder population-specific variants occurred with higher frequencies; and (3) low-frequency variants appeared to be more deleterious. Furthermore, a rare variant, rs1386931, located in the 3'-UTR of CXCR6 and intron of FYCO1 was found to be associated with eosinophil percentage. Gene-based analyses identified NRP2, MRPL44 and SERPINE2 to be associated with various asthma and allergy-related traits. Our study demonstrated the usefulness of using a founder population to identify new genes associated with asthma and allergy-related traits; thus better understand the genes and pathways implicated in pathophysiology.", "doi": "10.1038/s41431-018-0266-4", "pmid": "30206357", "labels": {"National Genomics Infrastructure": "Collaborative", "NGI Uppsala (SNP&SEQ Technology Platform)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1038/s41431-018-0266-4"}, {"db": "pmc", "key": "PMC6303288"}], "notes": [], "created": "2019-04-23T09:51:30.738Z", "modified": "2021-07-07T14:57:19.973Z"}, {"entity": "publication", "iuid": "4f4066ac61b044a88ea46c8424c17c55", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4f4066ac61b044a88ea46c8424c17c55.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4f4066ac61b044a88ea46c8424c17c55"}}, "title": "Significantly altered peripheral blood cell DNA methylation profile as a result of immediate effect of metformin use in healthy individuals.", "authors": [{"family": "Elbere", "given": "Ilze", "initials": "I"}, {"family": "Silamikelis", "given": "Ivars", "initials": "I"}, {"family": "Ustinova", "given": "Monta", "initials": "M"}, {"family": "Kalnina", "given": "Ineta", "initials": "I"}, {"family": "Zaharenko", "given": "Linda", "initials": "L"}, {"family": "Peculis", "given": "Raitis", "initials": "R"}, {"family": "Konrade", "given": "Ilze", "initials": "I"}, {"family": "Ciuculete", "given": "Diana Maria", "initials": "DM"}, {"family": "Zhukovsky", "given": "Christina", "initials": "C"}, {"family": "Gudra", "given": "Dita", "initials": "D"}, {"family": "Radovica-Spalvina", "given": "Ilze", "initials": "I"}, {"family": "Fridmanis", "given": "Davids", "initials": "D"}, {"family": "Pirags", "given": "Valdis", "initials": "V"}, {"family": "Schi\u00f6th", "given": "Helgi B", "initials": "HB"}, {"family": "Klovins", "given": "Janis", "initials": "J", "orcid": "0000-0001-8362-5505", "researcher": {"href": "https://publications.scilifelab.se/researcher/fa29507790e14761b99d789df9f1b9a6.json"}}], "type": "clinical trial", "published": "2018-12-13", "journal": {"volume": "10", "issn": "1868-7083", "issue": "1", "pages": "156", "title": "Clin Epigenetics", "issn-l": "1868-7075"}, "abstract": "Metformin is a widely prescribed antihyperglycemic agent that has been also associated with multiple therapeutic effects in various diseases, including several types of malignancies. There is growing evidence regarding the contribution of the epigenetic mechanisms in reaching metformin's therapeutic goals; however, the effect of metformin on human cells in vivo is not comprehensively studied. The aim of our study was to examine metformin-induced alterations of DNA methylation profiles in white blood cells of healthy volunteers, employing a longitudinal study design.\n\nTwelve healthy metformin-na\u00efve individuals where enrolled in the study. Genome-wide DNA methylation pattern was estimated at baseline, 10 h and 7 days after the start of metformin administration. The whole-genome DNA methylation analysis in total revealed 125 differentially methylated CpGs, of which 11 CpGs and their associated genes with the most consistent changes in the DNA methylation profile were selected: POFUT2, CAMKK1, EML3, KIAA1614, UPF1, MUC4, LOC727982, SIX3, ADAM8, SNORD12B, VPS8, and several differentially methylated regions as novel potential epigenetic targets of metformin. The main functions of the majority of top-ranked differentially methylated loci and their representative cell signaling pathways were linked to the well-known metformin therapy targets: regulatory processes of energy homeostasis, inflammatory responses, tumorigenesis, and neurodegenerative diseases.\n\nHere we demonstrate for the first time the immediate effect of short-term metformin administration at therapeutic doses on epigenetic regulation in human white blood cells. These findings suggest the DNA methylation process as one of the mechanisms involved in the action of metformin, thereby revealing novel targets and directions of the molecular mechanisms underlying the various beneficial effects of metformin.\n\nEU Clinical Trials Register, 2016-001092-74. Registered 23 March 2017, https://www.clinicaltrialsregister.eu/ctr-search/trial/2016-001092-74/LV .", "doi": "10.1186/s13148-018-0593-x", "pmid": "30545422", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1186/s13148-018-0593-x"}, {"db": "pmc", "key": "PMC6293577"}], "notes": [], "created": "2019-01-04T14:47:43.898Z", "modified": "2021-06-21T13:58:55.242Z"}, {"entity": "publication", "iuid": "03e089f784674cf0b6532fb717803809", "links": {"self": {"href": "https://publications.scilifelab.se/publication/03e089f784674cf0b6532fb717803809.json"}, "display": {"href": "https://publications.scilifelab.se/publication/03e089f784674cf0b6532fb717803809"}}, "title": "Transancestral GWAS of alcohol dependence reveals common genetic underpinnings with psychiatric disorders", "authors": [{"family": "Walters", "given": "Raymond K", "initials": "RK"}, {"family": null, "given": "", "initials": ""}, {"family": "Polimanti", "given": "Renato", "initials": "R"}, {"family": "Johnson", "given": "Emma C", "initials": "EC"}, {"family": "McClintick", "given": "Jeanette N", "initials": "JN"}, {"family": "Adams", "given": "Mark J", "initials": "MJ"}, {"family": "Adkins", "given": "Amy E", "initials": "AE"}, {"family": "Aliev", "given": "Fazil", "initials": "F"}, {"family": "Bacanu", "given": "Silviu Alin", "initials": "SA"}, {"family": "Batzler", "given": "Anthony", "initials": "A"}, {"family": "Bertelsen", "given": "Sarah", "initials": "S"}, {"family": "Biernacka", "given": "Joanna M", "initials": "JM"}, {"family": "Bigdeli", "given": "Tim B", "initials": "TB"}, {"family": "Chen", "given": "Li Shiun", "initials": "LS"}, {"family": "Clarke", "given": "Toni Kim", "initials": "TK"}, {"family": "Chou", "given": "Yi Ling", "initials": "YL"}, {"family": "Degenhardt", "given": "Franziska", "initials": "F"}, {"family": "Docherty", "given": "Anna R", "initials": "AR"}, {"family": "Edwards", "given": "Alexis C", "initials": "AC"}, {"family": "Fontanillas", "given": "Pierre", "initials": "P"}, {"family": "Foo", "given": "Jerome C", "initials": "JC"}, {"family": "Fox", "given": "Louis", "initials": "L"}, {"family": "Frank", "given": "Josef", "initials": "J"}, {"family": "Giegling", "given": "Ina", "initials": "I"}, {"family": "Gordon", "given": "Scott", "initials": "S"}, {"family": "Hack", "given": "Laura M", "initials": "LM"}, {"family": "Hartmann", "given": "Annette M", "initials": "AM"}, {"family": "Hartz", "given": "Sarah M", "initials": "SM"}, {"family": "Heilmann-Heimbach", "given": "Stefanie", "initials": "S"}, {"family": "Herms", "given": "Stefan", "initials": "S"}, {"family": "Hodgkinson", "given": "Colin", "initials": "C"}, {"family": "Hoffmann", "given": "Per", "initials": "P"}, {"family": "Jan Hottenga", "given": "Jouke", "initials": "J"}, {"family": "Kennedy", "given": "Martin A", "initials": "MA"}, {"family": "Alanne-Kinnunen", "given": "Mervi", "initials": "M"}, {"family": "Konte", "given": "Bettina", "initials": "B"}, {"family": "Lahti", "given": "Jari", "initials": "J"}, {"family": "Lahti-Pulkkinen", "given": "Marius", "initials": "M"}, {"family": "Lai", "given": "Dongbing", "initials": "D"}, {"family": "Ligthart", "given": "Lannie", "initials": "L"}, {"family": "Loukola", "given": "Anu", "initials": "A"}, {"family": "Maher", "given": "Brion S", "initials": "BS"}, {"family": "Mbarek", "given": "Hamdi", "initials": "H"}, {"family": "McIntosh", "given": "Andrew M", "initials": "AM"}, {"family": "McQueen", "given": "Matthew B", "initials": "MB"}, {"family": "Meyers", "given": "Jacquelyn L", "initials": "JL"}, {"family": "Milaneschi", "given": "Yuri", "initials": "Y"}, {"family": "Palviainen", "given": "Teemu", "initials": "T"}, {"family": "Pearson", "given": "John F", "initials": "JF"}, {"family": "Peterson", "given": "Roseann E", "initials": "RE"}, {"family": "Ripatti", "given": "Samuli", "initials": "S"}, {"family": "Ryu", "given": "Euijung", "initials": "E"}, {"family": "Saccone", "given": "Nancy L", "initials": "NL"}, {"family": "Salvatore", "given": "Jessica E", "initials": "JE"}, {"family": "Sanchez-Roige", "given": "Sandra", "initials": "S"}, {"family": "Schwandt", "given": "Melanie", "initials": "M"}, {"family": "Sherva", "given": "Richard", "initials": "R"}, {"family": "Streit", "given": "Fabian", "initials": "F"}, {"family": "Strohmaier", "given": "Jana", "initials": "J"}, {"family": "Thomas", "given": "Nathaniel", "initials": "N"}, {"family": "Wang", "given": "Jen Chyong", "initials": "JC"}, {"family": "Webb", "given": "Bradley T", "initials": "BT"}, {"family": "Wedow", "given": "Robbee", "initials": "R"}, {"family": "Wetherill", "given": "Leah", "initials": "L"}, {"family": "Wills", "given": "Amanda G", "initials": "AG"}, {"family": "Boardman", "given": "Jason D", "initials": "JD"}, {"family": "Chen", "given": "Danfeng", "initials": "D"}, {"family": "Choi", "given": "Doo Sup", "initials": "DS"}, {"family": "Copeland", "given": "William E", "initials": "WE"}, {"family": "Culverhouse", "given": "Robert C", "initials": "RC"}, {"family": "Dahmen", "given": "Norbert", "initials": "N"}, {"family": "Degenhardt", "given": "Louisa", "initials": "L"}, {"family": "Domingue", "given": "Benjamin W", "initials": "BW"}, {"family": "Elson", "given": "Sarah L", "initials": "SL"}, {"family": "Frye", "given": "Mark A", "initials": "MA"}, {"family": "G\u00e4bel", "given": "Wolfgang", "initials": "W"}, {"family": "Hayward", "given": "Caroline", "initials": "C"}, {"family": "Ising", "given": "Marcus", "initials": "M"}, {"family": "Keyes", "given": "Margaret", "initials": "M"}, {"family": "Kiefer", "given": "Falk", "initials": "F"}, {"family": "Kramer", "given": "John", "initials": "J"}, {"family": "Kuperman", "given": "Samuel", "initials": "S"}, {"family": "Lucae", "given": "Susanne", "initials": "S"}, {"family": "Lynskey", "given": "Michael T", "initials": "MT"}, {"family": "Maier", "given": "Wolfgang", "initials": "W"}, {"family": "Mann", "given": "Karl", "initials": "K"}, {"family": "M\u00e4nnist\u00f6", "given": "Satu", "initials": "S"}, {"family": "M\u00fcller-Myhsok", "given": "Bertram", "initials": "B"}, {"family": "Murray", "given": "Alison D", "initials": "AD"}, {"family": "Nurnberger", "given": "John I", "initials": "JI"}, {"family": "Palotie", "given": "Aarno", "initials": "A"}, {"family": "Preuss", "given": "Ulrich", "initials": "U"}, {"family": "R\u00e4ikk\u00f6nen", "given": "Katri", "initials": "K"}, {"family": "Reynolds", "given": "Maureen D", "initials": "MD"}, {"family": "Ridinger", "given": "Monika", "initials": "M"}, {"family": "Scherbaum", "given": "Norbert", "initials": "N"}, {"family": "Schuckit", "given": "Marc A", "initials": "MA"}, {"family": "Soyka", "given": "Michael", "initials": "M"}, {"family": "Treutlein", "given": "Jens", "initials": "J"}, {"family": "Witt", "given": "Stephanie", "initials": "S"}, {"family": "Wodarz", "given": "Norbert", "initials": "N"}, {"family": "Zill", "given": "Peter", "initials": "P"}, {"family": "Adkins", "given": "Daniel E", "initials": "DE"}, {"family": "Boden", "given": "Joseph M", "initials": "JM"}, {"family": "Boomsma", "given": "Dorret I", "initials": "DI"}, {"family": "Bierut", "given": "Laura J", "initials": "LJ"}, {"family": "Brown", "given": "Sandra A", "initials": "SA"}, {"family": "Bucholz", "given": "Kathleen K", "initials": "KK"}, {"family": "Cichon", "given": "Sven", "initials": "S"}, {"family": "Costello", "given": "E Jane", "initials": "EJ"}, {"family": "de Wit", "given": "Harriet", "initials": "H"}, {"family": "Diazgranados", "given": "Nancy", "initials": "N"}, {"family": "Dick", "given": "Danielle M", "initials": "DM"}, {"family": "Eriksson", "given": "Johan G", "initials": "JG"}, {"family": "Farrer", "given": "Lindsay A", "initials": "LA"}, {"family": "Foroud", "given": "Tatiana M", "initials": "TM"}, {"family": "Gillespie", "given": "Nathan A", "initials": "NA"}, {"family": "Goate", "given": "Alison M", "initials": "AM"}, {"family": "Goldman", "given": "David", "initials": "D"}, {"family": "Grucza", "given": "Richard A", "initials": "RA"}, {"family": "Hancock", "given": "Dana B", "initials": "DB"}, {"family": "Harris", "given": "Kathleen Mullan", "initials": "KM"}, {"family": "Heath", "given": "Andrew C", "initials": "AC"}, {"family": "Hesselbrock", "given": "Victor", "initials": "V"}, {"family": "Hewitt", "given": "John K", "initials": "JK"}, {"family": "Hopfer", "given": "Christian J", "initials": "CJ"}, {"family": "Horwood", "given": "John", "initials": "J"}, {"family": "Iacono", "given": "William", "initials": "W"}, {"family": "Johnson", "given": "Eric O", "initials": "EO"}, {"family": "Kaprio", "given": "Jaakko A", "initials": "JA"}, {"family": "Karpyak", "given": "Victor M", "initials": "VM"}, {"family": "Kendler", "given": "Kenneth S", "initials": "KS"}, {"family": "Kranzler", "given": "Henry R", "initials": "HR"}, {"family": "Krauter", "given": "Kenneth", "initials": "K"}, {"family": "Lichtenstein", "given": "Paul", "initials": "P"}, {"family": "Lind", "given": "Penelope A", "initials": "PA"}, {"family": "McGue", "given": "Matt", "initials": "M"}, {"family": "MacKillop", "given": "James", "initials": "J"}, {"family": "Madden", "given": "Pamela A F", "initials": "PAF"}, {"family": "Maes", "given": "Hermine H", "initials": "HH"}, {"family": "Magnusson", "given": "Patrik", "initials": "P"}, {"family": "Martin", "given": "Nicholas G", "initials": "NG"}, {"family": "Medland", "given": "Sarah E", "initials": "SE"}, {"family": "Montgomery", "given": "Grant W", "initials": "GW"}, {"family": "Nelson", "given": "Elliot C", "initials": "EC"}, {"family": "N\u00f6then", "given": "Markus M", "initials": "MM"}, {"family": "Palmer", "given": "Abraham A", "initials": "AA"}, {"family": "Pedersen", "given": "Nancy L", "initials": "NL"}, {"family": "Penninx", "given": "Brenda W J H", "initials": "BWJH"}, {"family": "Porjesz", "given": "Bernice", "initials": "B"}, {"family": "Rice", "given": "John P", "initials": "JP"}, {"family": "Rietschel", "given": "Marcella", "initials": "M"}, {"family": "Riley", "given": "Brien P", "initials": "BP"}, {"family": "Rose", "given": "Richard", "initials": "R"}, {"family": "Rujescu", "given": "Dan", "initials": "D"}, {"family": "Shen", "given": "Pei Hong", "initials": "PH"}, {"family": "Silberg", "given": "Judy", "initials": "J"}, {"family": "Stallings", "given": "Michael C", "initials": "MC"}, {"family": "Tarter", "given": "Ralph E", "initials": "RE"}, {"family": "Vanyukov", "given": "Michael M", "initials": "MM"}, {"family": "Vrieze", "given": "Scott", "initials": "S"}, {"family": "Wall", "given": "Tamara L", "initials": "TL"}, {"family": "Whitfield", "given": "John B", "initials": "JB"}, {"family": "Zhao", "given": "Hongyu", "initials": "H"}, {"family": "Neale", "given": "Benjamin M", "initials": "BM"}, {"family": "Gelernter", "given": "Joel", "initials": "J"}, {"family": "Edenberg", "given": "Howard J", "initials": "HJ"}, {"family": "Agrawal", "given": "Arpana", "initials": "A"}], "type": "journal-article", "published": "2018-12-00", "journal": {"volume": "21", "issn": "1097-6256", "issue": "12", "pages": "1656-1669", "title": "Nat Neurosci", "issn-l": "1097-6256"}, "abstract": null, "doi": "10.1038/s41593-018-0275-1", "pmid": "30482948", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2018-12-06T16:14:41.933Z", "modified": "2024-01-16T13:48:44.950Z"}, {"entity": "publication", "iuid": "11a38fc77c6d4ef9ac5c86685799c062", "links": {"self": {"href": "https://publications.scilifelab.se/publication/11a38fc77c6d4ef9ac5c86685799c062.json"}, "display": {"href": "https://publications.scilifelab.se/publication/11a38fc77c6d4ef9ac5c86685799c062"}}, "title": "The gut microbiome participates in transgenerational inheritance of low-temperature responses in Drosophila melanogaster.", "authors": [{"family": "Zare", "given": "Aman", "initials": "A", "orcid": "0000-0003-1642-0301", "researcher": {"href": "https://publications.scilifelab.se/researcher/b33d062437a14b39affbcff0277d7979.json"}}, {"family": "Johansson", "given": "Anna-Mia", "initials": "AM"}, {"family": "Karlsson", "given": "Edvin", "initials": "E"}, {"family": "Delhomme", "given": "Nicolas", "initials": "N"}, {"family": "Stenberg", "given": "Per", "initials": "P"}], "type": "journal article", "published": "2018-12-00", "journal": {"volume": "592", "issn": "1873-3468", "issue": "24", "pages": "4078-4086", "title": "FEBS Lett.", "issn-l": "0014-5793"}, "abstract": "Environmental perturbations induce transcriptional changes, some of which may be inherited even in the absence of the initial stimulus. Previous studies have focused on transfers through the germline although microbiota is also passed on to the offspring. Thus, we inspected the involvement of the gut microbiome in transgenerational inheritance of environmental exposures in Drosophila melanogaster. We grew flies in the cold versus control temperatures and compared their transcriptional patterns in both conditions as well as in their offspring. F2 flies grew in control temperature, while we controlled their microbiota acquisition from either F1 sets. Transcriptional status of some genes was conserved transgenerationally, and a subset of these genes, mainly expressed in the gut, was transcriptionally dependent on the acquired microbiome.", "doi": "10.1002/1873-3468.13278", "pmid": "30372516", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC6587461"}], "notes": [], "created": "2019-01-07T18:01:48.764Z", "modified": "2021-06-21T13:59:27.690Z"}, {"entity": "publication", "iuid": "8458130c02a944ca87945d52163f75c7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8458130c02a944ca87945d52163f75c7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8458130c02a944ca87945d52163f75c7"}}, "title": "T-cell transcriptomics from peripheral blood highlights differences between polymyositis and dermatomyositis patients", "authors": [{"family": "Houtman", "given": "Miranda", "initials": "M"}, {"family": "Ekholm", "given": "Louise", "initials": "L"}, {"family": "Hesselberg", "given": "Espen", "initials": "E"}, {"family": "Chemin", "given": "Karine", "initials": "K"}, {"family": "Malmstr\u00f6m", "given": "Vivianne", "initials": "V"}, {"family": "Reed", "given": "Ann M", "initials": "AM"}, {"family": "Lundberg", "given": "Ingrid E", "initials": "IE"}, {"family": "Padyukov", "given": "Leonid", "initials": "L"}], "type": "journal-article", "published": "2018-12-00", "journal": {"volume": "20", "issn": "1478-6362", "issue": "1", "pages": null, "title": "Arthritis Res. Ther.", "issn-l": "1478-6354"}, "abstract": null, "doi": "10.1186/s13075-018-1688-7", "pmid": "30157932", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2018-09-14T12:06:42.130Z", "modified": "2024-01-16T13:48:44.982Z"}, {"entity": "publication", "iuid": "af907f6acd284aba883ef8032157b0fa", "links": {"self": {"href": "https://publications.scilifelab.se/publication/af907f6acd284aba883ef8032157b0fa.json"}, "display": {"href": "https://publications.scilifelab.se/publication/af907f6acd284aba883ef8032157b0fa"}}, "title": "Molecular Investigation of the Ciliate Spirostomum semivirescens, with First Transcriptome and New Geographical Records", "authors": [{"family": "Hines", "given": "Hunter N", "initials": "HN"}, {"family": "Onsbring", "given": "Henning", "initials": "H"}, {"family": "Ettema", "given": "Thijs J G", "initials": "TJG"}, {"family": "Esteban", "given": "Genoveva F", "initials": "GF"}], "type": "journal-article", "published": "2018-12-00", "journal": {"volume": "169", "issn": "1434-4610", "issue": "6", "pages": "875-886", "title": "Protist", "issn-l": null}, "abstract": null, "doi": "10.1016/j.protis.2018.08.001", "pmid": "30447617", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [], "notes": [], "created": "2018-12-10T06:26:43.617Z", "modified": "2020-01-21T13:56:12.178Z"}, {"entity": "publication", "iuid": "e9dcc8c6cfb543bd9d2439e6e883fbb3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e9dcc8c6cfb543bd9d2439e6e883fbb3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e9dcc8c6cfb543bd9d2439e6e883fbb3"}}, "title": "Linking FOXO3, NCOA3, and TCF7L2 to Ras pathway phenotypes through a genome-wide forward genetic screen in human colorectal cancer cells", "authors": [{"family": "Kundu", "given": "Snehangshu", "initials": "S"}, {"family": "Ali", "given": "Muhammad Akhtar", "initials": "MA"}, {"family": "Handin", "given": "Niklas", "initials": "N"}, {"family": "Padhan", "given": "Narendra", "initials": "N"}, {"family": "Larsson", "given": "Jimmy", "initials": "J"}, {"family": "Karoutsou", "given": "Maria", "initials": "M"}, {"family": "Ban", "given": "Kenneth", "initials": "K"}, {"family": "Wi\u015bniewski", "given": "Jacek R", "initials": "JR"}, {"family": "Artursson", "given": "Per", "initials": "P"}, {"family": "He", "given": "Liqun", "initials": "L"}, {"family": "Hellstr\u00f6m", "given": "Mats", "initials": "M"}, {"family": "Sj\u00f6blom", "given": "Tobias", "initials": "T"}], "type": "journal-article", "published": "2018-12-00", "journal": {"volume": "10", "issn": "1756-994X", "issue": "1", "pages": null, "title": "Genome Med", "issn-l": "1756-994X"}, "abstract": null, "doi": "10.1186/s13073-017-0511-4", "pmid": "29301589", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "BioProject", "description": "A genome-wide forward genetic screen in transposon mutagenized human colorectal carcinomas cells", "key": "PRJNA419878"}, {"db": "https://www.ebi.ac.uk/pride/archive/", "description": "https://www.ebi.ac.uk/pride/archive/projects/PXD008382", "key": "PXD008382"}], "notes": [], "created": "2018-01-09T20:57:49.046Z", "modified": "2024-01-16T13:48:45.035Z"}, {"entity": "publication", "iuid": "fc866c628b2c41bd8a241148f5c3c739", "links": {"self": {"href": "https://publications.scilifelab.se/publication/fc866c628b2c41bd8a241148f5c3c739.json"}, "display": {"href": "https://publications.scilifelab.se/publication/fc866c628b2c41bd8a241148f5c3c739"}}, "title": "Individual Genetic Variation Might Predict Acute Skin Reactions in Women Undergoing Adjuvant Breast Cancer Radiotherapy.", "authors": [{"family": "Oliva", "given": "Delmy", "initials": "D"}, {"family": "Nilsson", "given": "Mats", "initials": "M"}, {"family": "Strand\u00e9us", "given": "Michael", "initials": "M"}, {"family": "Andersson", "given": "Bengt-\u00c5ke", "initials": "B\u00c5"}, {"family": "Sharp", "given": "Lena", "initials": "L"}, {"family": "Laytragoon-Lewin", "given": "Nongnit", "initials": "N"}, {"family": "Lewin", "given": "Freddi", "initials": "F"}], "type": "journal article", "published": "2018-12-00", "journal": {"volume": "38", "issn": "1791-7530", "issue": "12", "pages": "6763-6770", "title": "Anticancer Res.", "issn-l": "0250-7005"}, "abstract": "Adverse skin reactions during radiotherapy (RT) are common. The aim of this study was to explore whether genetic variation might be linked to acute radiation skin reactions (ARSR).\n\nOne hundred and nineteen women undergoing adjuvant RT for breast cancer were included. The symptoms of itching, burning and irritation were self-reported twice using the visual analogue scale. Assessments used the Radiation Therapy Oncology Group scoring system for acute RT skin reaction (RTOG scale). Blood-based single nucleotide polymorphism (SNP) analysis was performed. Thirty SNPs of well-defined functional genes were investigated.\n\nAll women were assessed with ARSR. After RT, the women self-reported itching (n=97), burning (n=64) and irritation (n=96). Two SNPs in X-Ray Repair Cross Complementing 2 gene (XRCC2) rs2040639 and interferon gamma (IFNG) rs2069705 genes were found to be associated with ARSR.\n\nAn association between two SNPs and ARSR was found. The possibility of using these SNPs as prognostic biomarkers for ARSR as tools to improve the care of patients needs further investigation.", "doi": "10.21873/anticanres.13047", "pmid": "30504388", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "38/12/6763"}], "notes": [], "created": "2019-01-09T07:22:14.356Z", "modified": "2021-07-07T13:42:51.249Z"}, {"entity": "publication", "iuid": "fd7be1158fed4b8099143c1223dfa9c6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/fd7be1158fed4b8099143c1223dfa9c6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/fd7be1158fed4b8099143c1223dfa9c6"}}, "title": "Genomes from uncultivated prokaryotes: a comparison of metagenome-assembled and single-amplified genomes", "authors": [{"family": "Alneberg", "given": "Johannes", "initials": "J"}, {"family": "Karlsson", "given": "Christofer M G", "initials": "CMG"}, {"family": "Divne", "given": "Anna Maria", "initials": "AM"}, {"family": "Bergin", "given": "Claudia", "initials": "C"}, {"family": "Homa", "given": "Felix", "initials": "F"}, {"family": "Lindh", "given": "Markus V", "initials": "MV"}, {"family": "Hugerth", "given": "Luisa W", "initials": "LW"}, {"family": "Ettema", "given": "Thijs J G", "initials": "TJG"}, {"family": "Bertilsson", "given": "Stefan", "initials": "S"}, {"family": "Andersson", "given": "Anders F", "initials": "AF"}, {"family": "Pinhassi", "given": "Jarone", "initials": "J"}], "type": "journal-article", "published": "2018-12-00", "journal": {"volume": "6", "issn": "2049-2618", "issue": "1", "pages": null, "title": "Microbiome", "issn-l": "2049-2618"}, "abstract": "Prokaryotes dominate the biosphere and regulate biogeochemical processes essential to all life. Yet, our knowledge about their biology is for the most part limited to the minority that has been successfully cultured. Molecular techniques now allow for obtaining genome sequences of uncultivated prokaryotic taxa, facilitating in-depth analyses that may ultimately improve our understanding of these key organisms.\n\nWe compared results from two culture-independent strategies for recovering bacterial genomes: single-amplified genomes and metagenome-assembled genomes. Single-amplified genomes were obtained from samples collected at an offshore station in the Baltic Sea Proper and compared to previously obtained metagenome-assembled genomes from a time series at the same station. Among 16 single-amplified genomes analyzed, seven were found to match metagenome-assembled genomes, affiliated with a diverse set of taxa. Notably, genome pairs between the two approaches were nearly identical (average 99.51% sequence identity; range 98.77-99.84%) across overlapping regions (30-80% of each genome). Within matching pairs, the single-amplified genomes were consistently smaller and less complete, whereas the genetic functional profiles were maintained. For the metagenome-assembled genomes, only on average 3.6% of the bases were estimated to be missing from the genomes due to wrongly binned contigs.\n\nThe strong agreement between the single-amplified and metagenome-assembled genomes emphasizes that both methods generate accurate genome information from uncultivated bacteria. Importantly, this implies that the research questions and the available resources are allowed to determine the selection of genomics approach for microbiome studies.", "doi": "10.1186/s40168-018-0550-0", "pmid": "30266101", "labels": {"Microbial Single Cell Genomics": "Collaborative", "NGI Stockholm (Genomics Production)": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "BioProject", "description": "Baltic Sea Surface Water Metagenome", "key": "PRJNA273799"}, {"db": "SRA", "description": "Baltic Sea Surface Water Metagenome", "key": "SRP058493"}], "notes": [], "created": "2018-10-19T15:07:15.693Z", "modified": "2024-01-16T13:48:45.059Z"}, {"entity": "publication", "iuid": "88bcc1f516cf4e0fa06df4f5f42b8912", "links": {"self": {"href": "https://publications.scilifelab.se/publication/88bcc1f516cf4e0fa06df4f5f42b8912.json"}, "display": {"href": "https://publications.scilifelab.se/publication/88bcc1f516cf4e0fa06df4f5f42b8912"}}, "title": "Genome sequencing and conservation genomics in the Scandinavian wolverine population", "authors": [{"family": "Ekblom", "given": "Robert", "initials": "R"}, {"family": "Brechlin", "given": "Birte", "initials": "B"}, {"family": "Persson", "given": "Jens", "initials": "J"}, {"family": "Smeds", "given": "Linn\u00e9a", "initials": "L"}, {"family": "Johansson", "given": "Malin", "initials": "M"}, {"family": "Magnusson", "given": "Jessica", "initials": "J"}, {"family": "Flagstad", "given": "\u00d8ystein", "initials": "\u00d8"}, {"family": "Ellegren", "given": "Hans", "initials": "H"}], "type": "journal-article", "published": "2018-12-00", "journal": {"volume": "32", "issn": "0888-8892", "issue": "6", "pages": "1301-1312", "title": "Conservation Biology", "issn-l": null}, "abstract": null, "doi": "10.1111/cobi.13157", "pmid": "29935028", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [], "notes": [], "created": "2018-12-10T06:29:08.862Z", "modified": "2020-01-21T13:56:12.170Z"}, {"entity": "publication", "iuid": "1395e138b69949e3b221577f74c6d32c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1395e138b69949e3b221577f74c6d32c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1395e138b69949e3b221577f74c6d32c"}}, "title": "Gene expression correlated with delay in shell formation in larval Pacific oysters (Crassostrea gigas) exposed to experimental ocean acidification provides insights into shell formation mechanisms", "authors": [{"family": "De Wit", "given": "Pierre", "initials": "P"}, {"family": "Durland", "given": "Evan", "initials": "E"}, {"family": "Ventura", "given": "Alexander", "initials": "A"}, {"family": "Langdon", "given": "Chris J", "initials": "CJ"}], "type": "journal-article", "published": "2018-12-00", "journal": {"volume": "19", "issn": "1471-2164", "issue": "1", "pages": null, "title": "BMC Genomics", "issn-l": "1471-2164"}, "abstract": null, "doi": "10.1186/s12864-018-4519-y", "pmid": "29471790", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "BioProject", "description": "Crassostrea gigas embryonic gene expression", "key": "PRJNA306408"}, {"db": "Dryad", "description": "https://datadryad.org/resource/doi:10.5061/dryad.8m5v4", "key": "10.5061/dryad.8m5v4"}], "notes": [], "created": "2018-02-27T13:44:13.067Z", "modified": "2020-01-21T13:56:12.162Z"}, {"entity": "publication", "iuid": "84a17b565be4486b99e827275a31a204", "links": {"self": {"href": "https://publications.scilifelab.se/publication/84a17b565be4486b99e827275a31a204.json"}, "display": {"href": "https://publications.scilifelab.se/publication/84a17b565be4486b99e827275a31a204"}}, "title": "GWAS and colocalization analyses implicate carotid intima-media thickness and carotid plaque loci in cardiovascular outcomes", "authors": [{"family": "Franceschini", "given": "Nora", "initials": "N"}, {"family": null, "given": "", "initials": ""}, {"family": "Giambartolomei", "given": "Claudia", "initials": "C"}, {"family": "de Vries", "given": "Paul S", "initials": "PS"}, {"family": "Finan", "given": "Chris", "initials": "C"}, {"family": "Bis", "given": "Joshua C", "initials": "JC"}, {"family": "Huntley", "given": "Rachael P", "initials": "RP"}, {"family": "Lovering", "given": "Ruth C", "initials": "RC"}, {"family": "Tajuddin", "given": "Salman M", "initials": "SM"}, {"family": "Winkler", "given": "Thomas W", "initials": "TW"}, {"family": "Graff", "given": "Misa", "initials": "M"}, {"family": "Kavousi", "given": "Maryam", "initials": "M"}, {"family": "Dale", "given": "Caroline", "initials": "C"}, {"family": "Smith", "given": "Albert V", "initials": "AV"}, {"family": "Hofer", "given": "Edith", "initials": "E"}, {"family": "van Leeuwen", "given": "Elisabeth M", "initials": "EM"}, {"family": "Nolte", "given": "Ilja M", "initials": "IM"}, {"family": "Lu", "given": "Lingyi", "initials": "L"}, {"family": "Scholz", "given": "Markus", "initials": "M"}, {"family": "Sargurupremraj", "given": "Muralidharan", "initials": "M"}, {"family": "Pitk\u00e4nen", "given": "Niina", "initials": "N"}, {"family": "Franz\u00e9n", "given": "Oscar", "initials": "O"}, {"family": "Joshi", "given": "Peter K", "initials": "PK"}, {"family": "Noordam", "given": "Raymond", "initials": "R"}, {"family": "Marioni", "given": "Riccardo E", "initials": "RE"}, {"family": "Hwang", "given": "Shih Jen", "initials": "SJ"}, {"family": "Musani", "given": "Solomon K", "initials": "SK"}, {"family": "Schminke", "given": "Ulf", "initials": "U"}, {"family": "Palmas", "given": "Walter", "initials": "W"}, {"family": "Isaacs", "given": "Aaron", "initials": "A"}, {"family": "Correa", "given": "Adolfo", "initials": "A"}, {"family": "Zonderman", "given": "Alan B", "initials": "AB"}, {"family": "Hofman", "given": "Albert", "initials": "A"}, {"family": "Teumer", "given": "Alexander", "initials": "A"}, {"family": "Cox", "given": "Amanda J", "initials": "AJ"}, {"family": "Uitterlinden", "given": "Andr\u00e9 G", "initials": "AG"}, {"family": "Wong", "given": "Andrew", "initials": "A"}, {"family": "Smit", "given": "Andries J", "initials": "AJ"}, {"family": "Newman", "given": "Anne B", "initials": "AB"}, {"family": "Britton", "given": "Annie", "initials": "A"}, {"family": "Ruusalepp", "given": "Arno", "initials": "A"}, {"family": "Sennblad", "given": "Bengt", "initials": "B"}, {"family": "Hedblad", "given": "Bo", "initials": "B"}, {"family": "Pasaniuc", "given": "Bogdan", "initials": "B"}, {"family": "Penninx", "given": "Brenda W", "initials": "BW"}, {"family": "Langefeld", "given": "Carl D", "initials": "CD"}, {"family": "Wassel", "given": "Christina L", "initials": "CL"}, {"family": "Tzourio", "given": "Christophe", "initials": "C"}, {"family": "Fava", "given": "Cristiano", "initials": "C"}, {"family": "Baldassarre", "given": "Damiano", "initials": "D"}, {"family": "O\u2019Leary", "given": "Daniel H", "initials": "DH"}, {"family": "Teupser", "given": "Daniel", "initials": "D"}, {"family": "Kuh", "given": "Diana", "initials": "D"}, {"family": "Tremoli", "given": "Elena", "initials": "E"}, {"family": "Mannarino", "given": "Elmo", "initials": "E"}, {"family": "Grossi", "given": "Enzo", "initials": "E"}, {"family": "Boerwinkle", "given": "Eric", "initials": "E"}, {"family": "Schadt", "given": "Eric E", "initials": "EE"}, {"family": "Ingelsson", "given": "Erik", "initials": "E"}, {"family": "Veglia", "given": "Fabrizio", "initials": "F"}, {"family": "Rivadeneira", "given": "Fernando", "initials": "F"}, {"family": "Beutner", "given": "Frank", "initials": "F"}, {"family": "Chauhan", "given": "Ganesh", "initials": "G"}, {"family": "Heiss", "given": "Gerardo", "initials": "G"}, {"family": "Snieder", "given": "Harold", "initials": "H"}, {"family": "Campbell", "given": "Harry", "initials": "H"}, {"family": "V\u00f6lzke", "given": "Henry", "initials": "H"}, {"family": "Markus", "given": "Hugh S", "initials": "HS"}, {"family": "Deary", "given": "Ian J", "initials": "IJ"}, {"family": "Jukema", "given": "J Wouter", "initials": "JW"}, {"family": "de Graaf", "given": "Jacqueline", "initials": "J"}, {"family": "Price", "given": "Jacqueline", "initials": "J"}, {"family": "Pott", "given": "Janne", "initials": "J"}, {"family": "Hopewell", "given": "Jemma C", "initials": "JC"}, {"family": "Liang", "given": "Jingjing", "initials": "J"}, {"family": "Thiery", "given": "Joachim", "initials": "J"}, {"family": "Engmann", "given": "Jorgen", "initials": "J"}, {"family": "Gertow", "given": "Karl", "initials": "K"}, {"family": "Rice", "given": "Kenneth", "initials": "K"}, {"family": "Taylor", "given": "Kent D", "initials": "KD"}, {"family": "Dhana", "given": "Klodian", "initials": "K"}, {"family": "Kiemeney", "given": "Lambertus A L M", "initials": "LALM"}, {"family": "Lind", "given": "Lars", "initials": "L"}, {"family": "Raffield", "given": "Laura M", "initials": "LM"}, {"family": "Launer", "given": "Lenore J", "initials": "LJ"}, {"family": "Holdt", "given": "Lesca M", "initials": "LM"}, {"family": "D\u00f6rr", "given": "Marcus", "initials": "M"}, {"family": "Dichgans", "given": "Martin", "initials": "M"}, {"family": "Traylor", "given": "Matthew", "initials": "M"}, {"family": "Sitzer", "given": "Matthias", "initials": "M"}, {"family": "Kumari", "given": "Meena", "initials": "M"}, {"family": "Kivimaki", "given": "Mika", "initials": "M"}, {"family": "Nalls", "given": "Mike A", "initials": "MA"}, {"family": "Melander", "given": "Olle", "initials": "O"}, {"family": "Raitakari", "given": "Olli", "initials": "O"}, {"family": "Franco", "given": "Oscar H", "initials": "OH"}, {"family": "Rueda-Ochoa", "given": "Oscar L", "initials": "OL"}, {"family": "Roussos", "given": "Panos", "initials": "P"}, {"family": "Whincup", "given": "Peter H", "initials": "PH"}, {"family": "Amouyel", "given": "Philippe", "initials": "P"}, {"family": "Giral", "given": "Philippe", "initials": "P"}, {"family": "Anugu", "given": "Pramod", "initials": "P"}, {"family": "Wong", "given": "Quenna", "initials": "Q"}, {"family": "Malik", "given": "Rainer", "initials": "R"}, {"family": "Rauramaa", "given": "Rainer", "initials": "R"}, {"family": "Burkhardt", "given": "Ralph", "initials": "R"}, {"family": "Hardy", "given": "Rebecca", "initials": "R"}, {"family": "Schmidt", "given": "Reinhold", "initials": "R"}, {"family": "de Mutsert", "given": "Ren\u00e9e", "initials": "R"}, {"family": "Morris", "given": "Richard W", "initials": "RW"}, {"family": "Strawbridge", "given": "Rona J", "initials": "RJ"}, {"family": "Wannamethee", "given": "S Goya", "initials": "SG"}, {"family": "H\u00e4gg", "given": "Sara", "initials": "S"}, {"family": "Shah", "given": "Sonia", "initials": "S"}, {"family": "McLachlan", "given": "Stela", "initials": "S"}, {"family": "Trompet", "given": "Stella", "initials": "S"}, {"family": "Seshadri", "given": "Sudha", "initials": "S"}, {"family": "Kurl", "given": "Sudhir", "initials": "S"}, {"family": "Heckbert", "given": "Susan R", "initials": "SR"}, {"family": "Ring", "given": "Susan", "initials": "S"}, {"family": "Harris", "given": "Tamara B", "initials": "TB"}, {"family": "Lehtim\u00e4ki", "given": "Terho", "initials": "T"}, {"family": "Galesloot", "given": "Tessel E", "initials": "TE"}, {"family": "Shah", "given": "Tina", "initials": "T"}, {"family": "de Faire", "given": "Ulf", "initials": "U"}, {"family": "Plagnol", "given": "Vincent", "initials": "V"}, {"family": "Rosamond", "given": "Wayne D", "initials": "WD"}, {"family": "Post", "given": "Wendy", "initials": "W"}, {"family": "Zhu", "given": "Xiaofeng", "initials": "X"}, {"family": "Zhang", "given": "Xiaoling", "initials": "X"}, {"family": "Guo", "given": "Xiuqing", "initials": "X"}, {"family": "Saba", "given": "Yasaman", "initials": "Y"}, {"family": "Dehghan", "given": "Abbas", "initials": "A"}, {"family": "Seldenrijk", "given": "Adrie", "initials": "A"}, {"family": "Morrison", "given": "Alanna C", "initials": "AC"}, {"family": "Hamsten", "given": "Anders", "initials": "A"}, {"family": "Psaty", "given": "Bruce M", "initials": "BM"}, {"family": "van Duijn", "given": "Cornelia M", "initials": "CM"}, {"family": "Lawlor", "given": "Deborah A", "initials": "DA"}, {"family": "Mook-Kanamori", "given": "Dennis O", "initials": "DO"}, {"family": "Bowden", "given": "Donald W", "initials": "DW"}, {"family": "Schmidt", "given": "Helena", "initials": "H"}, {"family": "Wilson", "given": "James F", "initials": "JF"}, {"family": "Wilson", "given": "James G", "initials": "JG"}, {"family": "Rotter", "given": "Jerome I", "initials": "JI"}, {"family": "Wardlaw", "given": "Joanna M", "initials": "JM"}, {"family": "Deanfield", "given": "John", "initials": "J"}, {"family": "Halcox", "given": "Julian", "initials": "J"}, {"family": "Lyytik\u00e4inen", "given": "Leo Pekka", "initials": "LP"}, {"family": "Loeffler", "given": "Markus", "initials": "M"}, {"family": "Evans", "given": "Michele K", "initials": "MK"}, {"family": "Debette", "given": "St\u00e9phanie", "initials": "S"}, {"family": "Humphries", "given": "Steve E", "initials": "SE"}, {"family": "V\u00f6lker", "given": "Uwe", "initials": "U"}, {"family": "Gudnason", "given": "Vilmundur", "initials": "V"}, {"family": "Hingorani", "given": "Aroon D", "initials": "AD"}, {"family": "Bj\u00f6rkegren", "given": "Johan L M", "initials": "JLM"}, {"family": "Casas", "given": "Juan P", "initials": "JP"}, {"family": "O\u2019Donnell", "given": "Christopher J", "initials": "CJ"}], "type": "journal-article", "published": "2018-12-00", "journal": {"volume": "9", "issn": "2041-1723", "issue": "1", "pages": null, "title": "Nat Commun", "issn-l": "2041-1723"}, "abstract": null, "doi": "10.1038/s41467-018-07340-5", "pmid": "30510157", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2018-12-06T16:14:41.258Z", "modified": "2024-01-16T13:48:45.075Z"}, {"entity": "publication", "iuid": "9258b9fa88224ef59fe19969b83c75c0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9258b9fa88224ef59fe19969b83c75c0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9258b9fa88224ef59fe19969b83c75c0"}}, "title": "Effects of predation stress and food ration on perch gut microbiota", "authors": [{"family": "Zha", "given": "Yinghua", "initials": "Y"}, {"family": "Eiler", "given": "Alexander", "initials": "A"}, {"family": "Johansson", "given": "Frank", "initials": "F"}, {"family": "Svanb\u00e4ck", "given": "Richard", "initials": "R"}], "type": "journal-article", "published": "2018-12-00", "journal": {"volume": "6", "issn": "2049-2618", "issue": "1", "pages": null, "title": "Microbiome", "issn-l": "2049-2618"}, "abstract": null, "doi": "10.1186/s40168-018-0400-0", "pmid": "29409543", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "SRA", "description": null, "key": "SRP090413"}], "notes": [], "created": "2018-02-27T14:37:36.600Z", "modified": "2024-01-16T13:48:45.109Z"}, {"entity": "publication", "iuid": "29ec285c10f54847ae79de7575c84980", "links": {"self": {"href": "https://publications.scilifelab.se/publication/29ec285c10f54847ae79de7575c84980.json"}, "display": {"href": "https://publications.scilifelab.se/publication/29ec285c10f54847ae79de7575c84980"}}, "title": "Convergent evolution of complex genomic rearrangements in two fungal meiotic drive elements", "authors": [{"family": "Svedberg", "given": "Jesper", "initials": "J"}, {"family": "Hosseini", "given": "Sara", "initials": "S"}, {"family": "Chen", "given": "Jun", "initials": "J"}, {"family": "Vogan", "given": "Aaron A", "initials": "AA"}, {"family": "Mozgova", "given": "Iva", "initials": "I"}, {"family": "Hennig", "given": "Lars", "initials": "L"}, {"family": "Manitchotpisit", "given": "Pennapa", "initials": "P"}, {"family": "Abusharekh", "given": "Anna", "initials": "A"}, {"family": "Hammond", "given": "Thomas M", "initials": "TM"}, {"family": "Lascoux", "given": "Martin", "initials": "M"}, {"family": "Johannesson", "given": "Hanna", "initials": "H"}], "type": "journal-article", "published": "2018-12-00", "journal": {"volume": "9", "issn": "2041-1723", "issue": "1", "pages": null, "title": "Nat Commun", "issn-l": "2041-1723"}, "abstract": "Meiotic drive is widespread in nature. The conflict it generates is expected to be an important motor for evolutionary change and innovation. In this study, we investigated the genomic consequences of two large multi-gene meiotic drive elements, Sk-2 and Sk-3, found in the filamentous ascomycete Neurospora intermedia. Using long-read sequencing, we generated the first complete and well-annotated genome assemblies of large, highly diverged, non-recombining regions associated with meiotic drive elements. Phylogenetic analysis shows that, even though Sk-2 and Sk-3 are located in the same chromosomal region, they do not form sister clades, suggesting independent origins or at least a long evolutionary separation. We conclude that they have in a convergent manner accumulated similar patterns of tandem inversions and dense repeat clusters, presumably in response to similar needs to create linkage between genes causing drive and resistance.", "doi": "10.1038/s41467-018-06562-x", "pmid": "30315196", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "BioProject", "description": "Genomics of spore killing in Neurospora intermedia.", "key": "PRJNA486257"}, {"db": "figshare", "description": "Follow link to download", "key": "https://doi.org/10.6084/m9.figshare.c.4202669.v1"}], "notes": [], "created": "2018-10-22T10:10:47.479Z", "modified": "2024-01-16T13:48:45.117Z"}, {"entity": "publication", "iuid": "0dc67e907cf74f1d9332d303ebc4e9f6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0dc67e907cf74f1d9332d303ebc4e9f6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0dc67e907cf74f1d9332d303ebc4e9f6"}}, "title": "Comprehensive analysis of CTNNB1 in adrenocortical carcinomas: Identification of novel mutations and correlation to survival", "authors": [{"family": "Maharjan", "given": "Rajani", "initials": "R"}, {"family": "Backman", "given": "Samuel", "initials": "S"}, {"family": "\u00c5kerstr\u00f6m", "given": "Tobias", "initials": "T"}, {"family": "Hellman", "given": "Per", "initials": "P"}, {"family": "Bj\u00f6rklund", "given": "Peyman", "initials": "P"}], "type": "journal-article", "published": "2018-12-00", "journal": {"volume": "8", "issn": "2045-2322", "issue": "1", "pages": "8610", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": null, "doi": "10.1038/s41598-018-26799-2", "pmid": "29872083", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [], "notes": [], "created": "2018-09-14T12:11:02.761Z", "modified": "2020-01-21T13:56:13.600Z"}, {"entity": "publication", "iuid": "6ffac0923e9747bf8995a9b6c804133a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6ffac0923e9747bf8995a9b6c804133a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6ffac0923e9747bf8995a9b6c804133a"}}, "title": "Comparative omics and feeding manipulations in chicken indicate a shift of the endocrine role of visceral fat towards reproduction", "authors": [{"family": "Bornel\u00f6v", "given": "Susanne", "initials": "S"}, {"family": "Seroussi", "given": "Eyal", "initials": "E"}, {"family": "Yosefi", "given": "Sara", "initials": "S"}, {"family": "Benjamini", "given": "Sharon", "initials": "S"}, {"family": "Miyara", "given": "Shoval", "initials": "S"}, {"family": "Ruzal", "given": "Mark", "initials": "M"}, {"family": "Grabherr", "given": "Manfred", "initials": "M"}, {"family": "Rafati", "given": "Nima", "initials": "N"}, {"family": "Molin", "given": "Anna Maja", "initials": "AM"}, {"family": "Pendavis", "given": "Ken", "initials": "K"}, {"family": "Burgess", "given": "Shane C", "initials": "SC"}, {"family": "Andersson", "given": "Leif", "initials": "L"}, {"family": "Friedman-Einat", "given": "Miriam", "initials": "M"}], "type": "journal-article", "published": "2018-12-00", "journal": {"volume": "19", "issn": "1471-2164", "issue": "1", "pages": null, "title": "BMC Genomics", "issn-l": "1471-2164"}, "abstract": null, "doi": "10.1186/s12864-018-4675-0", "pmid": "29695257", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "BioProject", "description": "Comparative RNA-seq in chicken reveals new reproductive adipokines", "key": "PRJEB23373"}], "notes": [], "created": "2018-05-03T11:09:55.199Z", "modified": "2024-01-16T13:48:45.125Z"}, {"entity": "publication", "iuid": "b132b31294784723bb2d008456c45f1d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b132b31294784723bb2d008456c45f1d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b132b31294784723bb2d008456c45f1d"}}, "title": "Analysis of porcine body size variation using re-sequencing data of miniature and large pigs", "authors": [{"family": "Reimer", "given": "C", "initials": "C"}, {"family": "Rubin", "given": "C J", "initials": "CJ"}, {"family": "Sharifi", "given": "A R", "initials": "AR"}, {"family": "Ha", "given": "N T", "initials": "NT"}, {"family": "Weigend", "given": "S", "initials": "S"}, {"family": "Waldmann", "given": "K H", "initials": "KH"}, {"family": "Distl", "given": "O", "initials": "O"}, {"family": "Pant", "given": "S D", "initials": "SD"}, {"family": "Fredholm", "given": "M", "initials": "M"}, {"family": "Schlather", "given": "M", "initials": "M"}, {"family": "Simianer", "given": "H", "initials": "H"}], "type": "journal-article", "published": "2018-12-00", "journal": {"volume": "19", "issn": "1471-2164", "issue": "1", "pages": null, "title": "BMC Genomics", "issn-l": "1471-2164"}, "abstract": null, "doi": "10.1186/s12864-018-5009-y", "pmid": "30231878", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "Dryad", "description": "Data from: Comparative analyses of QTLs influencing obesity and metabolic phenotypes in pigs and humans", "key": "https://doi.org/10.5061/dryad.3jj7f"}, {"db": "SRA", "description": "Data from: Strong signatures of selection in the domestic pig genome", "key": "ERP001813"}, {"db": "SRA", "description": "Data from: The sequence and analysis of a Chinese pig genome", "key": "SRA051254"}, {"db": "SRA", "description": "Data from: Minipig and beagle animal model genomes aid species selection in pharmaceutical discovery and development", "key": "SRR578029"}, {"db": "SRA", "description": "Data from: Minipig and beagle animal model genomes aid species selection in pharmaceutical discovery and development", "key": "SRR578191"}, {"db": "SRA", "description": "Data from: Minipig and beagle animal model genomes aid species selection in pharmaceutical discovery and development", "key": "SRR578192"}, {"db": "BioProject", "description": "Goettingen Miniature Pig and MiniLEWE sequencing", "key": "PRJEB27654"}], "notes": [], "created": "2018-09-24T05:40:33.940Z", "modified": "2024-01-16T13:48:45.140Z"}, {"entity": "publication", "iuid": "72b0ee883e3c42ff92513eaeee1cb366", "links": {"self": {"href": "https://publications.scilifelab.se/publication/72b0ee883e3c42ff92513eaeee1cb366.json"}, "display": {"href": "https://publications.scilifelab.se/publication/72b0ee883e3c42ff92513eaeee1cb366"}}, "title": "Out in the Cold: Identification of Genomic Regions Associated With Cold Tolerance in the Biocontrol Fungus Clonostachys rosea Through Genome-Wide Association Mapping.", "authors": [{"family": "Broberg", "given": "Martin", "initials": "M"}, {"family": "Dubey", "given": "Mukesh", "initials": "M"}, {"family": "Sun", "given": "Man-Hong", "initials": "MH"}, {"family": "Ihrmark", "given": "Katarina", "initials": "K"}, {"family": "Schroers", "given": "Hans-Josef", "initials": "HJ"}, {"family": "Li", "given": "Shi-Dong", "initials": "SD"}, {"family": "Jensen", "given": "Dan Funck", "initials": "DF"}, {"family": "Brandstr\u00f6m Durling", "given": "Mikael", "initials": "M"}, {"family": "Karlsson", "given": "Magnus", "initials": "M"}], "type": "journal article", "published": "2018-11-22", "journal": {"volume": "9", "issn": "1664-302X", "issue": null, "pages": "2844", "title": "Front Microbiol", "issn-l": "1664-302X"}, "abstract": "There is an increasing importance for using biocontrol agents in combating plant diseases sustainably and in the long term. As large scale genomic sequencing becomes economically viable, the impact of single nucleotide polymorphisms (SNPs) on biocontrol-associated phenotypes can be easily studied across entire genomes of fungal populations. Here, we improved a previously reported genome assembly of the biocontrol fungus Clonostachys rosea strain IK726 using the PacBio sequencing platform, which resulted in a total genome size of 70.7 Mbp and 21,246 predicted genes. We further performed whole-genome re-sequencing of 52 additional C. rosea strains isolated globally using Illumina sequencing technology, in order to perform genome-wide association studies in conditions relevant for biocontrol activity. One such condition is the ability to grow at lower temperatures commonly encountered in cryic or frigid soils in temperate regions, as these will be prevalent for protecting growing crops in temperate climates. Growth rates at 10\u00b0C on potato dextrose agar of the 53 sequenced strains of C. rosea were measured and ranged between 0.066 and 0.413 mm/day. Performing a genome wide association study, a total of 1,478 SNP markers were significantly associated with the trait and located in 227 scaffolds, within or close to (< 1000 bp distance) 265 different genes. The predicted gene products included several chaperone proteins, membrane transporters, lipases, and proteins involved in chitin metabolism with possible roles in cold tolerance. The data reported in this study provides a foundation for future investigations into the genetic basis for cold tolerance in fungi, with important implications for biocontrol.", "doi": "10.3389/fmicb.2018.02844", "pmid": "30524411", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC6262169"}], "notes": [], "created": "2019-01-07T20:46:44.834Z", "modified": "2021-06-21T14:00:23.124Z"}, {"entity": "publication", "iuid": "3c5e8313fb3b429da738c13f5f14ac04", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3c5e8313fb3b429da738c13f5f14ac04.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3c5e8313fb3b429da738c13f5f14ac04"}}, "title": "Genome-Wide Association Studies of Estimated Fatty Acid Desaturase Activity in Serum and Adipose Tissue in Elderly Individuals: Associations with Insulin Sensitivity", "authors": [{"family": "Marklund", "given": "Matti", "initials": "M"}, {"family": "Morris", "given": "Andrew", "initials": "A"}, {"family": "Mahajan", "given": "Anubha", "initials": "A"}, {"family": "Ingelsson", "given": "Erik", "initials": "E"}, {"family": "Lindgren", "given": "Cecilia", "initials": "C"}, {"family": "Lind", "given": "Lars", "initials": "L"}, {"family": "Ris\u00e9rus", "given": "Ulf", "initials": "U"}], "type": "journal-article", "published": "2018-11-17", "journal": {"volume": "10", "issn": "2072-6643", "issue": "11", "pages": "1791", "title": "Nutrients", "issn-l": "2072-6643"}, "abstract": null, "doi": "10.3390/nu10111791", "pmid": "30453627", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2018-11-23T07:49:09.789Z", "modified": "2024-01-16T13:48:45.185Z"}, {"entity": "publication", "iuid": "1c854d000cef41898abc281c3f96c4e3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1c854d000cef41898abc281c3f96c4e3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1c854d000cef41898abc281c3f96c4e3"}}, "title": "Diet-dependent gene expression highlights the importance of Cytochrome P450 in detoxification of algal secondary metabolites in a marine isopod.", "authors": [{"family": "De Wit", "given": "Pierre", "initials": "P"}, {"family": "Yamada", "given": "Keith", "initials": "K"}, {"family": "Panova", "given": "Marina", "initials": "M"}, {"family": "Andr\u00e9", "given": "Carl", "initials": "C"}, {"family": "Johannesson", "given": "Kerstin", "initials": "K"}], "type": "journal article", "published": "2018-11-14", "journal": {"volume": "8", "issn": "2045-2322", "issue": "1", "pages": "16824", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "Isopods of the genus Idotea have an unusual ability to feed on algae containing high amounts of chemical defense molecules, such as species of the genera Fucus and Ulva. In this study, we compared gene expression patterns of Idotea balthica individuals fed with Fucus vesiculosus to individuals fed with Ulva lactuca. We generated the first-ever transcriptome assembly for this species, and found 3,233 differentially expressed genes across feeding regimes. However, only a handful of biological functions were enriched with regard to differentially expressed genes, the most notable being \"alkaloid metabolic process\". Within this category, we found eight differentially expressed cytochrome P450 (CYP) unigenes, all of which had a higher expression in the U. lactuca diet treatment. A phylogenetic analysis showed that the differentially expressed CYP genes are closely related to a CYP gene described from the hepatopancreas of the spiny lobster Panulirus argus, and we hypothesize that these transcripts are involved in metabolite detoxification. This is a first step in the understanding of this algae-grazer interaction, and will form a basis for future work to characterize cytochrome P450 functioning in marine crustaceans.", "doi": "10.1038/s41598-018-34937-z", "pmid": "30429500", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-018-34937-z"}, {"db": "pmc", "key": "PMC6235865"}], "notes": [], "created": "2019-01-04T14:04:11.901Z", "modified": "2020-01-21T13:56:13.568Z"}, {"entity": "publication", "iuid": "b105e92bc27d4c6f92109308208147d7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b105e92bc27d4c6f92109308208147d7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b105e92bc27d4c6f92109308208147d7"}}, "title": "Integrative Analysis of Three RNA Sequencing Methods Identifies Mutually Exclusive Exons of MADS-Box Isoforms During Early Bud Development in Picea abies", "authors": [{"family": "Akhter", "given": "Shirin", "initials": "S"}, {"family": "Kretzschmar", "given": "Warren W", "initials": "WW"}, {"family": "Nordal", "given": "Veronika", "initials": "V"}, {"family": "Delhomme", "given": "Nicolas", "initials": "N"}, {"family": "Street", "given": "Nathaniel R", "initials": "NR"}, {"family": "Nilsson", "given": "Ove", "initials": "O"}, {"family": "Emanuelsson", "given": "Olof", "initials": "O"}, {"family": "Sundstr\u00f6m", "given": "Jens F", "initials": "JF"}], "type": "journal-article", "published": "2018-11-13", "journal": {"volume": "9", "issn": "1664-462X", "issue": null, "pages": null, "title": "Front Plant Sci", "issn-l": "1664-462X"}, "abstract": "Recent efforts to sequence the genomes and transcriptomes of several gymnosperm species have revealed an increased complexity in certain gene families in gymnosperms as compared to angiosperms. One example of this is the gymnosperm sister clade to angiosperm TM3-like MADS-box genes, which at least in the conifer lineage has expanded in number of genes. We have previously identified a member of this sub-clade, the conifer gene \n            DEFICIENS AGAMOUS LIKE 19 (DAL19), as being specifically upregulated in cone-setting shoots. Here, we show through Sanger sequencing of mRNA-derived cDNA and mapping to assembled conifer genomic sequences that DAL19 produces six mature mRNA splice variants in Picea abies. These splice variants use alternate first and last exons, while their four central exons constitute a core region present in all six transcripts. Thus, they are likely to be transcript isoforms. Quantitative Real-Time PCR revealed that two mutually exclusive first DAL19 exons are differentially expressed across meristems that will form either male or female cones, or vegetative shoots. Furthermore, mRNA in situ hybridization revealed that two mutually exclusive last DAL19 exons were expressed in a cell-specific pattern within bud meristems. Based on these findings in DAL19, we developed a sensitive approach to transcript isoform assembly from short-read sequencing of mRNA. We applied this method to 42 putative MADS-box core regions in P. abies, from which we assembled 1084 putative transcripts. We manually curated these transcripts to arrive at 933 assembled transcript isoforms of 38 putative MADS-box genes. 152 of these isoforms, which we assign to 28 putative MADS-box genes, were differentially expressed across eight female, male, and vegetative buds. We further provide evidence of the expression of 16 out of the 38 putative MADS-box genes by mapping PacBio Iso-Seq circular consensus reads derived from pooled sample sequencing to assembled transcripts. In summary, our analyses reveal the use of mutually exclusive exons of MADS-box gene isoforms during early bud development in P. abies, and we find that the large number of identified MADS-box transcripts in P. abies results not only from expansion of the gene family through gene duplication events but also from the generation of numerous splice variants.", "doi": "10.3389/fpls.2018.01625", "pmid": "30483285", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support and Infrastructure": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [], "notes": [], "created": "2018-12-10T06:26:27.642Z", "modified": "2020-01-21T13:56:17.461Z"}, {"entity": "publication", "iuid": "3874af5c7acd44ee826efc0f8b3c8333", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3874af5c7acd44ee826efc0f8b3c8333.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3874af5c7acd44ee826efc0f8b3c8333"}}, "title": "Computational and Statistical Analysis of Array-Based DNA Methylation Data.", "authors": [{"family": "Nordlund", "given": "Jessica", "initials": "J", "orcid": "0000-0001-8699-9959", "researcher": {"href": "https://publications.scilifelab.se/researcher/ddf48c9262134821bcc6ce1180049753.json"}}, {"family": "B\u00e4cklin", "given": "Christofer", "initials": "C"}, {"family": "Raine", "given": "Amanda", "initials": "A"}], "type": "journal article", "published": "2018-11-01", "journal": {"volume": "1878", "issn": "1940-6029", "issue": null, "pages": "173-191", "title": "Methods Mol. Biol.", "issn-l": "1064-3745"}, "abstract": "The characterization of aberrant DNA methylation is emerging as a key part of the study of cancer development and phenotype. The technical advancements and decreasing costs of methods for high-throughput profiling of DNA methylation have brought about a high interest in the use of such methods in disease association studies. Here we discuss the principles for DNA methylation analysis using data from the Infinium DNA methylation BeadChip assays and describe the computational steps and statistical considerations going from processing of the raw array data to analysis of differential methylation. Moreover, we provide detailed guidelines on how to perform tumor subtype classification based on DNA methylation signatures.", "doi": "10.1007/978-1-4939-8868-6_10", "pmid": "30378076", "labels": {"National Genomics Infrastructure": "Technology development", "NGI Uppsala (SNP&SEQ Technology Platform)": "Technology development"}, "xrefs": [], "notes": [], "created": "2019-09-26T07:44:35.122Z", "modified": "2021-07-07T14:48:21.804Z"}, {"entity": "publication", "iuid": "cb250e6a3a9a44cd9bbab1ba2f2fbb48", "links": {"self": {"href": "https://publications.scilifelab.se/publication/cb250e6a3a9a44cd9bbab1ba2f2fbb48.json"}, "display": {"href": "https://publications.scilifelab.se/publication/cb250e6a3a9a44cd9bbab1ba2f2fbb48"}}, "title": "Genomes of two archaeal endosymbionts show convergent adaptations to an intracellular lifestyle", "authors": [{"family": "Lind", "given": "Anders E", "initials": "AE"}, {"family": "Lewis", "given": "William H", "initials": "WH"}, {"family": "Spang", "given": "Anja", "initials": "A"}, {"family": "Guy", "given": "Lionel", "initials": "L"}, {"family": "Embley", "given": "T Martin", "initials": "TM"}, {"family": "Ettema", "given": "Thijs J G", "initials": "TJG"}], "type": "journal-article", "published": "2018-11-00", "journal": {"volume": "12", "issn": "1751-7370", "issue": "11", "pages": "2655-2667", "title": "ISME J", "issn-l": "1751-7362"}, "abstract": "Endosymbiosis is a widespread phenomenon in the microbial world and can be based on diverse interactions between endosymbiont and host cell. The vast majority of the known endosymbiotic interactions involve bacteria that have invaded eukaryotic host cells. However, methanogenic archaea have been found to thrive in anaerobic, hydrogenosome-containing protists and it was suggested that this symbiosis is based on the transfer of hydrogen. Here, we used culture-independent genomics approaches to sequence the genomes of two distantly related methanogenic endosymbionts that have been acquired in two independent events by closely related anaerobic ciliate hosts Nyctotherus ovalis and Metopus contortus, respectively. The sequences obtained were then validated as originating from the ciliate endosymbionts by in situ probing experiments. Comparative analyses of these genomes and their closest free-living counterparts reveal that the genomes of both endosymbionts are in an early stage of adaptation towards endosymbiosis as evidenced by the large number of genes undergoing pseudogenization. For instance, the observed loss of genes involved in amino acid biosynthesis in both endosymbiont genomes indicates that the endosymbionts rely on their hosts for obtaining several essential nutrients. Furthermore, the endosymbionts appear to have gained significant amounts of genes of potentially secreted proteins, providing targets for future studies aiming to elucidate possible mechanisms underpinning host-interactions. Altogether, our results provide the first genomic insights into prokaryotic endosymbioses from the archaeal domain of life.", "doi": "10.1038/s41396-018-0207-9", "pmid": "29991760", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "BioProject", "description": "Draft genomes of Methanobrevibacter sp. NOE and Methanocorpusculum sp. MCE", "key": "PRJNA380999"}], "notes": [], "created": "2018-10-22T10:09:04.749Z", "modified": "2024-01-16T13:48:45.243Z"}, {"entity": "publication", "iuid": "2a17afb4d4ba45369c1a7e23f91caf7e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2a17afb4d4ba45369c1a7e23f91caf7e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2a17afb4d4ba45369c1a7e23f91caf7e"}}, "title": "Genome Analyses of >200,000 Individuals Identify 58 Loci for Chronic Inflammation and Highlight Pathways that Link Inflammation and Complex Disorders", "authors": [{"family": "Ligthart", "given": "Symen", "initials": "S"}, {"family": "Vaez", "given": "Ahmad", "initials": "A"}, {"family": "V\u00f5sa", "given": "Urmo", "initials": "U"}, {"family": "Stathopoulou", "given": "Maria G", "initials": "MG"}, {"family": "de Vries", "given": "Paul S", "initials": "PS"}, {"family": "Prins", "given": "Bram P", "initials": "BP"}, {"family": "Van der Most", "given": "Peter J", "initials": "PJ"}, {"family": "Tanaka", "given": "Toshiko", "initials": "T"}, {"family": "Naderi", "given": "Elnaz", "initials": "E"}, {"family": "Rose", "given": "Lynda M", "initials": "LM"}, {"family": "Wu", "given": "Ying", "initials": "Y"}, {"family": "Karlsson", "given": "Robert", "initials": "R"}, {"family": "Barbalic", "given": "Maja", "initials": "M"}, {"family": "Lin", "given": "Honghuang", "initials": "H"}, {"family": "Pool", "given": "Ren\u00e9", "initials": "R"}, {"family": "Zhu", "given": "Gu", "initials": "G"}, {"family": "Mac\u00e9", "given": "Aur\u00e9lien", "initials": "A"}, {"family": "Sidore", "given": "Carlo", "initials": "C"}, {"family": "Trompet", "given": "Stella", "initials": "S"}, {"family": "Mangino", "given": "Massimo", "initials": "M"}, {"family": "Sabater-Lleal", "given": "Maria", "initials": "M"}, {"family": "Kemp", "given": "John P", "initials": "JP"}, {"family": "Abbasi", "given": "Ali", "initials": "A"}, {"family": "Kacprowski", "given": "Tim", "initials": "T"}, {"family": "Verweij", "given": "Niek", "initials": "N"}, {"family": "Smith", "given": "Albert V", "initials": "AV"}, {"family": "Huang", "given": "Tao", "initials": "T"}, {"family": "Marzi", "given": "Carola", "initials": "C"}, {"family": "Feitosa", "given": "Mary F", "initials": "MF"}, {"family": "Lohman", "given": "Kurt K", "initials": "KK"}, {"family": "Kleber", "given": "Marcus E", "initials": "ME"}, {"family": "Milaneschi", "given": "Yuri", "initials": "Y"}, {"family": "Mueller", "given": "Christian", "initials": "C"}, {"family": "Huq", "given": "Mahmudul", "initials": "M"}, {"family": "Vlachopoulou", "given": "Efthymia", "initials": "E"}, {"family": "Lyytik\u00e4inen", "given": "Leo Pekka", "initials": "LP"}, {"family": "Oldmeadow", "given": "Christopher", "initials": "C"}, {"family": "Deelen", "given": "Joris", "initials": "J"}, {"family": "Perola", "given": "Markus", "initials": "M"}, {"family": "Zhao", "given": "Jing Hua", "initials": "JH"}, {"family": "Feenstra", "given": "Bjarke", "initials": "B"}, {"family": "Amini", "given": "Marzyeh", "initials": "M"}, {"family": "Lahti", "given": "Jari", "initials": "J"}, {"family": "Schraut", "given": "Katharina E", "initials": "KE"}, {"family": "Fornage", "given": "Myriam", "initials": "M"}, {"family": "Suktitipat", "given": "Bhoom", "initials": "B"}, {"family": "Chen", "given": "Wei Min", "initials": "WM"}, {"family": "Li", "given": "Xiaohui", "initials": "X"}, {"family": "Nutile", "given": "Teresa", "initials": "T"}, {"family": "Malerba", "given": "Giovanni", "initials": "G"}, {"family": "Luan", "given": "Jian\u2019an", "initials": "J"}, {"family": "Bak", "given": "Tom", "initials": "T"}, {"family": "Schork", "given": "Nicholas", "initials": "N"}, {"family": "Del Greco M.", "given": "Fabiola", "initials": "F"}, {"family": "Thiering", "given": "Elisabeth", "initials": "E"}, {"family": "Mahajan", "given": "Anubha", "initials": "A"}, {"family": "Marioni", "given": "Riccardo E", "initials": "RE"}, {"family": "Mihailov", "given": "Evelin", "initials": "E"}, {"family": "Eriksson", "given": "Joel", "initials": "J"}, {"family": "Ozel", "given": "Ayse Bilge", "initials": "AB"}, {"family": "Zhang", "given": "Weihua", "initials": "W"}, {"family": "Nethander", "given": "Maria", "initials": "M"}, {"family": "Cheng", "given": "Yu Ching", "initials": "YC"}, {"family": "Aslibekyan", "given": "Stella", "initials": "S"}, {"family": "Ang", "given": "Wei", "initials": "W"}, {"family": "Gandin", "given": "Ilaria", "initials": "I"}, {"family": "Yengo", "given": "Lo\u00efc", "initials": "L"}, {"family": "Portas", "given": "Laura", "initials": "L"}, {"family": "Kooperberg", "given": "Charles", "initials": "C"}, {"family": "Hofer", "given": "Edith", "initials": "E"}, {"family": "Rajan", "given": "Kumar B", "initials": "KB"}, {"family": "Schurmann", "given": "Claudia", "initials": "C"}, {"family": "den Hollander", "given": "Wouter", "initials": "W"}, {"family": "Ahluwalia", "given": "Tarunveer S", "initials": "TS"}, {"family": "Zhao", "given": "Jing", "initials": "J"}, {"family": "Draisma", "given": "Harmen H M", "initials": "HHM"}, {"family": "Ford", "given": "Ian", "initials": "I"}, {"family": "Timpson", "given": "Nicholas", "initials": "N"}, {"family": "Teumer", "given": "Alexander", "initials": "A"}, {"family": "Huang", "given": "Hongyan", "initials": "H"}, {"family": "Wahl", "given": "Simone", "initials": "S"}, {"family": "Liu", "given": "YongMei", "initials": "Y"}, {"family": "Huang", "given": "Jie", "initials": "J"}, {"family": "Uh", "given": "Hae Won", "initials": "HW"}, {"family": "Geller", "given": "Frank", "initials": "F"}, {"family": "Joshi", "given": "Peter K", "initials": "PK"}, {"family": "Yanek", "given": "Lisa R", "initials": "LR"}, {"family": "Trabetti", "given": "Elisabetta", "initials": "E"}, {"family": "Lehne", "given": "Benjamin", "initials": "B"}, {"family": "Vozzi", "given": "Diego", "initials": "D"}, {"family": "Verbanck", "given": "Marie", "initials": "M"}, {"family": "Biino", "given": "Ginevra", "initials": "G"}, {"family": "Saba", "given": "Yasaman", "initials": "Y"}, {"family": "Meulenbelt", "given": "Ingrid", "initials": "I"}, {"family": "O\u2019Connell", "given": "Jeff R", "initials": "JR"}, {"family": "Laakso", "given": "Markku", "initials": "M"}, {"family": "Giulianini", "given": "Franco", "initials": "F"}, {"family": "Magnusson", "given": "Patrik K E", "initials": "PKE"}, {"family": "Ballantyne", "given": "Christie M", "initials": "CM"}, {"family": "Hottenga", "given": "Jouke Jan", "initials": "JJ"}, {"family": "Montgomery", "given": "Grant W", "initials": "GW"}, {"family": "Rivadineira", "given": "Fernando", "initials": "F"}, {"family": "Rueedi", "given": "Rico", "initials": "R"}, {"family": "Steri", "given": "Maristella", "initials": "M"}, {"family": "Herzig", "given": "Karl Heinz", "initials": "KH"}, {"family": "Stott", "given": "David J", "initials": "DJ"}, {"family": "Menni", "given": "Cristina", "initials": "C"}, {"family": "Fr\u00e5nberg", "given": "Mattias", "initials": "M"}, {"family": "St. Pourcain", "given": "Beate", "initials": "B"}, {"family": "Felix", "given": "Stephan B", "initials": "SB"}, {"family": "Pers", "given": "Tune H", "initials": "TH"}, {"family": "Bakker", "given": "Stephan J L", "initials": "SJL"}, {"family": "Kraft", "given": "Peter", "initials": "P"}, {"family": "Peters", "given": "Annette", "initials": "A"}, {"family": "Vaidya", "given": "Dhananjay", "initials": "D"}, {"family": "Delgado", "given": "Graciela", "initials": "G"}, {"family": "Smit", "given": "Johannes H", "initials": "JH"}, {"family": "Gro\u00dfmann", "given": "Vera", "initials": "V"}, {"family": "Sinisalo", "given": "Juha", "initials": "J"}, {"family": "Sepp\u00e4l\u00e4", "given": "Ilkka", "initials": "I"}, {"family": "Williams", "given": "Stephen R", "initials": "SR"}, {"family": "Holliday", "given": "Elizabeth G", "initials": "EG"}, {"family": "Moed", "given": "Matthijs", "initials": "M"}, {"family": "Langenberg", "given": "Claudia", "initials": "C"}, {"family": "R\u00e4ikk\u00f6nen", "given": "Katri", "initials": "K"}, {"family": "Ding", "given": "Jingzhong", "initials": "J"}, {"family": "Campbell", "given": "Harry", "initials": "H"}, {"family": "Sale", "given": "Michele M", "initials": "MM"}, {"family": "Chen", "given": "Yii Der I", "initials": "YDI"}, {"family": "James", "given": "Alan L", "initials": "AL"}, {"family": "Ruggiero", "given": "Daniela", "initials": "D"}, {"family": "Soranzo", "given": "Nicole", "initials": "N"}, {"family": "Hartman", "given": "Catharina A", "initials": "CA"}, {"family": "Smith", "given": "Erin N", "initials": "EN"}, {"family": "Berenson", "given": "Gerald S", "initials": "GS"}, {"family": "Fuchsberger", "given": "Christian", "initials": "C"}, {"family": "Hernandez", "given": "Dena", "initials": "D"}, {"family": "Tiesler", "given": "Carla M T", "initials": "CMT"}, {"family": "Giedraitis", "given": "Vilmantas", "initials": "V"}, {"family": 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{"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2018-11-13T13:46:09.532Z", "modified": "2024-01-16T13:48:45.250Z"}, {"entity": "publication", "iuid": "858a5e72e3634699aa43189f9bfa220e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/858a5e72e3634699aa43189f9bfa220e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/858a5e72e3634699aa43189f9bfa220e"}}, "title": "Fine-mapping type 2 diabetes loci to single-variant resolution using high-density imputation and islet-specific epigenome maps.", "authors": [{"family": "Mahajan", "given": "Anubha", "initials": "A"}, {"family": "Taliun", "given": "Daniel", "initials": "D"}, {"family": "Thurner", "given": "Matthias", "initials": "M"}, {"family": "Robertson", "given": "Neil R", "initials": "NR"}, {"family": "Torres", "given": "Jason M", 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"Goncalo R", "initials": "GR"}, {"family": "Meigs", "given": "James B", "initials": "JB"}, {"family": "Rotter", "given": "Jerome I", "initials": "JI"}, {"family": "Marchini", "given": "Jonathan", "initials": "J"}, {"family": "Pedersen", "given": "Oluf", "initials": "O"}, {"family": "Hansen", "given": "Torben", "initials": "T"}, {"family": "Langenberg", "given": "Claudia", "initials": "C"}, {"family": "Wareham", "given": "Nicholas J", "initials": "NJ"}, {"family": "Stefansson", "given": "Kari", "initials": "K"}, {"family": "Gloyn", "given": "Anna L", "initials": "AL"}, {"family": "Morris", "given": "Andrew P", "initials": "AP"}, {"family": "Boehnke", "given": "Michael", "initials": "M"}, {"family": "McCarthy", "given": "Mark I", "initials": "MI"}], "type": "journal article", "published": "2018-11-00", "journal": {"volume": "50", "issn": "1546-1718", "issue": "11", "pages": "1505-1513", "title": "Nat. Genet.", "issn-l": "1061-4036"}, "abstract": "We expanded GWAS discovery for type 2 diabetes (T2D) by combining data from 898,130 European-descent individuals (9% cases), after imputation to high-density reference panels. With these data, we (i) extend the inventory of T2D-risk variants (243 loci, 135 newly implicated in T2D predisposition, comprising 403 distinct association signals); (ii) enrich discovery of lower-frequency risk alleles (80 index variants with minor allele frequency <5%, 14 with estimated allelic odds ratio >2); (iii) substantially improve fine-mapping of causal variants (at 51 signals, one variant accounted for >80% posterior probability of association (PPA)); (iv) extend fine-mapping through integration of tissue-specific epigenomic information (islet regulatory annotations extend the number of variants with PPA >80% to 73); (v) highlight validated therapeutic targets (18 genes with associations attributable to coding variants); and (vi) demonstrate enhanced potential for clinical translation (genome-wide chip heritability explains 18% of T2D risk; individuals in the extremes of a T2D polygenic risk score differ more than ninefold in prevalence).", "doi": "10.1038/s41588-018-0241-6", "pmid": "30297969", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41588-018-0241-6"}, {"db": "pmc", "key": "PMC6287706"}, {"db": "mid", "key": "EMS80721"}], "notes": [], "created": "2019-01-09T07:22:15.185Z", "modified": "2020-01-21T13:56:13.660Z"}, {"entity": "publication", "iuid": "a409ff6da19044c791a2e8fa0725ec5c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a409ff6da19044c791a2e8fa0725ec5c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a409ff6da19044c791a2e8fa0725ec5c"}}, "title": "Gene-level associations in suicide attempter families show overrepresentation of synaptic genes and genes differentially expressed in brain development", "authors": [{"family": "Sokolowski", "given": "Marcus", "initials": "M"}, {"family": "Wasserman", "given": "Jerzy", "initials": "J"}, {"family": "Wasserman", "given": "Danuta", "initials": "D"}], "type": "journal-article", "published": "2018-10-31", "journal": {"volume": null, "issn": "1552-4841", "issue": null, "pages": null, "title": "Am. J. Med. Genet.", "issn-l": "1552-4841"}, "abstract": null, "doi": "10.1002/ajmg.b.32694", "pmid": "30381879", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [], "notes": [], "created": "2018-11-13T13:46:10.104Z", "modified": "2020-01-21T13:56:12.155Z"}, {"entity": "publication", "iuid": "bbfbc0a5f29846959fe3c7c2831e3f98", "links": {"self": {"href": "https://publications.scilifelab.se/publication/bbfbc0a5f29846959fe3c7c2831e3f98.json"}, "display": {"href": "https://publications.scilifelab.se/publication/bbfbc0a5f29846959fe3c7c2831e3f98"}}, "title": "Cigarette smoking affects microRNAs and inflammatory biomarkers in healthy individuals and an association to single nucleotide polymorphisms is indicated", "authors": [{"family": "Andersson", "given": "Bengt \u00c5ke", "initials": "B\u00c5"}, {"family": "Sayardoust", "given": "Shariel", "initials": "S"}, {"family": "L\u00f6fgren", "given": "Sture", "initials": "S"}, {"family": "Rutqvist", "given": "Lars Erik", "initials": "LE"}, {"family": "Laytragoon-Lewin", "given": "Nongnit", "initials": "N"}], "type": "journal-article", "published": "2018-10-30", "journal": {"volume": null, "issn": "1366-5804", "issue": null, "pages": "1-17", "title": "Biomarkers", "issn-l": "1354-750X"}, "abstract": "Cigarette smoke induces inflammation and remodels immune response. Genetic and epigenetic alterations might be involved in the pathogenesis of smoking related diseases. In this study, we investigated the effect of smoking on systemic inflammation biomarkers and epigenetic changes at microRNA (miRNA) expression level. We also examined if the levels of inflammatory biomarkers were associated with selected single nucleotide polymorphisms (SNPs).\n\nFrom 39 smokers and 101 non-smokers, levels of total white blood cells (WBCs) and its subpopulations, plasma cytokines/chemokines/proteins and miRNAs were analysed. For three biomarkers, C-reactive protein (CRP), MCP-1 and IFN-\u03b3 that were affected by smoking, the influence of SNPs was analyzed.\n\nElevated levels of total WBCs, neutrophils, monocytes, lymphocytes, CRP, MCP-1, IFN-\u03b3 and lower levels of miR-21 were detected in smokers. The elevated levels of IFN-\u03b3 in smokers was only statistically significantly associated with rs2069705 AG/GG SNP-genotype.\n\nA lower level of oncomir miRNA-21 and a higher level of immune modelling cytokine IFN-\u03b3 detected in smokers could be a protective immune response to cigarette smoke. The higher level of IFN-\u03b3 in smokers with a specific SNP genotype also suggests that a genetic interaction with smoking might predict the pathobiology of smoking related disease.", "doi": "10.1080/1354750x.2018.1539764", "pmid": "30375257", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2018-11-13T13:46:10.439Z", "modified": "2024-01-16T13:48:45.269Z"}, {"entity": "publication", "iuid": "6e3731261f1f4db5beb2ad1db2d840ab", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6e3731261f1f4db5beb2ad1db2d840ab.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6e3731261f1f4db5beb2ad1db2d840ab"}}, "title": "Dynamics of a Perturbed Microbial Community during Thermophilic Anaerobic Digestion of Chemically Defined Soluble Organic Compounds", "authors": [{"family": "\u0160afari\u010d", "given": "Luka", "initials": "L"}, {"family": "Shakeri Yekta", "given": "Sepehr", "initials": "S"}, {"family": "Liu", "given": "Tong", "initials": "T"}, {"family": "Svensson", "given": "Bo", "initials": "B"}, {"family": "Schn\u00fcrer", "given": "Anna", "initials": "A"}, {"family": "Bastviken", "given": "David", "initials": "D"}, {"family": "Bj\u00f6rn", "given": "Annika", "initials": "A"}], "type": "journal-article", "published": "2018-10-11", "journal": {"volume": "6", "issn": "2076-2607", "issue": "4", "pages": "105", "title": "Microorganisms", "issn-l": "2076-2607"}, "abstract": null, "doi": "10.3390/microorganisms6040105", "pmid": "30314333", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "SRA", "description": null, "key": "SRP149871"}], "notes": [], "created": "2018-10-22T10:11:09.695Z", "modified": "2020-01-21T13:56:12.147Z"}, {"entity": "publication", "iuid": "3f6c987638d84add91fc127d7dc6af75", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3f6c987638d84add91fc127d7dc6af75.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3f6c987638d84add91fc127d7dc6af75"}}, "title": "De Novo Assembly of Two Swedish Genomes Reveals Missing Segments from the Human GRCh38 Reference and Improves Variant Calling of Population-Scale Sequencing Data.", "authors": [{"family": "Ameur", "given": "Adam", "initials": "A", "orcid": "0000-0001-6085-6749", "researcher": {"href": "https://publications.scilifelab.se/researcher/e960811513664a78b2804a00ee70f7c3.json"}}, {"family": "Che", "given": "Huiwen", "initials": "H"}, {"family": "Martin", "given": "Marcel", "initials": "M", "orcid": "0000-0002-0680-200X", "researcher": {"href": "https://publications.scilifelab.se/researcher/132afd4fea2e4e86bdf43708c8f49907.json"}}, {"family": "Bunikis", "given": "Ignas", "initials": "I"}, {"family": "Dahlberg", "given": "Johan", "initials": "J"}, {"family": "H\u00f6ijer", "given": "Ida", "initials": "I", "orcid": "0000-0002-3915-3384", "researcher": {"href": "https://publications.scilifelab.se/researcher/4ba4ce20b1b447ada4fdc8256211436e.json"}}, {"family": "H\u00e4ggqvist", "given": "Susana", "initials": "S"}, {"family": "Vezzi", "given": "Francesco", "initials": "F"}, {"family": "Nordlund", "given": "Jessica", "initials": "J", "orcid": "0000-0001-8699-9959", "researcher": {"href": "https://publications.scilifelab.se/researcher/ddf48c9262134821bcc6ce1180049753.json"}}, {"family": "Olason", "given": "Pall", "initials": "P"}, {"family": "Feuk", "given": "Lars", "initials": "L", "orcid": "0000-0003-2355-2919", "researcher": {"href": "https://publications.scilifelab.se/researcher/3eb2f826b3554d4b9971bf0766b275c4.json"}}, {"family": "Gyllensten", "given": "Ulf", "initials": "U"}], "type": "journal article", "published": "2018-10-09", "journal": {"volume": "9", "issn": "2073-4425", "issue": "10", "pages": "486", "title": "Genes", "issn-l": "2073-4425"}, "abstract": "The current human reference sequence (GRCh38) is a foundation for large-scale sequencing projects. However, recent studies have suggested that GRCh38 may be incomplete and give a suboptimal representation of specific population groups. Here, we performed a de novo assembly of two Swedish genomes that revealed over 10 Mb of sequences absent from the human GRCh38 reference in each individual. Around 6 Mb of these novel sequences (NS) are shared with a Chinese personal genome. The NS are highly repetitive, have an elevated GC-content, and are primarily located in centromeric or telomeric regions. Up to 1 Mb of NS can be assigned to chromosome Y, and large segments are also missing from GRCh38 at chromosomes 14, 17, and 21. Inclusion of NS into the GRCh38 reference radically improves the alignment and variant calling from short-read whole-genome sequencing data at several genomic loci. A re-analysis of a Swedish population-scale sequencing project yields > 75,000 putative novel single nucleotide variants (SNVs) and removes > 10,000 false positive SNV calls per individual, some of which are located in protein coding regions. Our results highlight that the GRCh38 reference is not yet complete and demonstrate that personal genome assemblies from local populations can improve the analysis of short-read whole-genome sequencing data.", "doi": "10.3390/genes9100486", "pmid": "30304863", "labels": {"National Genomics Infrastructure": "Collaborative", "NGI Uppsala (SNP&SEQ Technology Platform)": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "genes9100486"}, {"db": "pmc", "key": "PMC6210158"}], "notes": [], "created": "2018-11-20T14:44:03.808Z", "modified": "2024-01-16T13:48:45.362Z"}, {"entity": "publication", "iuid": "d81f995be00e4d5aacf709de1fccb700", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d81f995be00e4d5aacf709de1fccb700.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d81f995be00e4d5aacf709de1fccb700"}}, "title": "Biased Inference of Selection Due to GC-Biased Gene Conversion and the Rate of Protein Evolution in Flycatchers When Accounting for It", "authors": [{"family": "Bol\u00edvar", "given": "Paulina", "initials": "P"}, {"family": "Mugal", "given": "Carina F", "initials": "CF"}, {"family": "Rossi", "given": "Matteo", "initials": "M"}, {"family": "Nater", "given": "Alexander", "initials": "A"}, {"family": "Wang", "given": "Mi", "initials": "M"}, {"family": "Dutoit", "given": "Ludovic", "initials": "L"}, {"family": "Ellegren", "given": "Hans", "initials": "H"}], "type": "journal-article", "published": "2018-10-01", "journal": {"volume": "35", "issn": "0737-4038", "issue": "10", "pages": "2475-2486", "title": "", "issn-l": null}, "abstract": null, "doi": "10.1093/molbev/msy149", "pmid": "30085180", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "SRA", "description": "Data from: Divergence in gene expression within and between two closely related flycatcher species. https://doi.org/10.1111/mec.13596", "key": "ERP001377"}], "notes": [], "created": "2018-10-22T10:07:11.593Z", "modified": "2024-01-16T13:48:45.405Z"}, {"entity": "publication", "iuid": "524aab4cca634eddbaaa020947156da9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/524aab4cca634eddbaaa020947156da9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/524aab4cca634eddbaaa020947156da9"}}, "title": "Mutation, methylation, and gene expression profiles in dup(1q)-positive pediatric B-cell precursor acute lymphoblastic leukemia.", "authors": [{"family": "Gunnarsson", "given": "Rebeqa", "initials": "R"}, {"family": "Dilorenzo", "given": "Sebastian", "initials": "S"}, {"family": "Lundin-Str\u00f6m", "given": "Kristina B", "initials": "KB"}, {"family": "Olsson", "given": "Linda", "initials": "L"}, {"family": "Biloglav", "given": "Andrea", "initials": "A"}, {"family": "Lilljebj\u00f6rn", "given": "Henrik", "initials": "H", "orcid": "0000-0001-8703-1173", "researcher": {"href": "https://publications.scilifelab.se/researcher/b3a75300e8c346858ce8dd8f64ecae85.json"}}, {"family": "Rissler", "given": "Marianne", "initials": "M"}, {"family": "Wahlberg", "given": "Per", "initials": "P"}, {"family": "Lundmark", "given": "Anders", "initials": "A"}, {"family": "Castor", "given": "Anders", "initials": "A"}, {"family": "Behrendtz", "given": "Mikael", "initials": "M"}, {"family": "Fioretos", "given": "Thoas", "initials": "T", "orcid": "0000-0002-3235-6154", "researcher": {"href": "https://publications.scilifelab.se/researcher/35a5c1b6023345c6b1317c590bf80680.json"}}, {"family": "Paulsson", "given": "Kajsa", "initials": "K", "orcid": "0000-0001-7950-222X", "researcher": {"href": "https://publications.scilifelab.se/researcher/2033b23811f1432c90ad860dd993e7a8.json"}}, {"family": "Isaksson", "given": "Anders", "initials": "A", "orcid": "0000-0001-6576-7825", "researcher": {"href": "https://publications.scilifelab.se/researcher/5d38a1f99951441399c146b96e58f9ba.json"}}, {"family": "Johansson", "given": "Bertil", "initials": "B"}], "type": "journal article", "published": "2018-10-00", "journal": {"volume": "32", "issn": "1476-5551", "issue": "10", "pages": "2117-2125", "title": "Leukemia", "issn-l": "0887-6924"}, "abstract": "High-throughput sequencing was applied to investigate the mutation/methylation patterns on 1q and gene expression profiles in pediatric B-cell precursor acute lymphoblastic leukemia (BCP ALL) with/without (w/wo) dup(1q). Sequencing of the breakpoint regions and all exons on 1q in seven dup(1q)-positive cases revealed non-synonymous somatic single nucleotide variants (SNVs) in BLZF1, FMN2, KCNT2, LCE1C, NES, and PARP1. Deep sequencing of these in a validation cohort w (n = 17)/wo (n = 94) dup(1q) revealed similar SNV frequencies in the two groups (47% vs. 35%; P = 0.42). Only 0.6% of the 36,259 CpGs on 1q were differentially methylated between cases w (n = 14)/wo (n = 13) dup(1q). RNA sequencing of high hyperdiploid (HeH) and t(1;19)(q23;p13)-positive cases w (n = 14)/wo (n = 52) dup(1q) identified 252 and 424 differentially expressed genes, respectively; only seven overlapped. Of the overexpressed genes in the HeH and t(1;19) groups, 23 and 31%, respectively, mapped to 1q; 60-80% of these encode nucleic acid/protein binding factors or proteins with catalytic activity. We conclude that the pathogenetically important consequence of dup(1q) in BCP ALL is a gene-dosage effect, with the deregulated genes differing between genetic subtypes, but involving similar molecular functions, biological processes, and protein classes.", "doi": "10.1038/s41375-018-0092-2", "pmid": "29626196", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1038/s41375-018-0092-2"}, {"db": "pmc", "key": "PMC6170391"}], "notes": [], "created": "2018-10-22T10:04:01.973Z", "modified": "2024-01-16T13:48:45.412Z"}, {"entity": "publication", "iuid": "3fb8c298d49140d092a8dc83561ec1bb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3fb8c298d49140d092a8dc83561ec1bb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3fb8c298d49140d092a8dc83561ec1bb"}}, "title": "Genetic architecture of traits associated with reproductive barriers in Silene: Coupling, sex chromosomes and variation.", "authors": [{"family": "Liu", "given": "Xiaodong", "initials": "X"}, {"family": "Karrenberg", "given": "Sophie", "initials": "S", "orcid": "0000-0002-7146-588X", "researcher": {"href": "https://publications.scilifelab.se/researcher/3a982636b44f4b93b7ec0bd64e5d6bfb.json"}}], "type": "journal article", "published": "2018-10-00", "journal": {"volume": "27", "issn": "1365-294X", "issue": "19", "pages": "3889-3904", "title": "Mol. Ecol.", "issn-l": "0962-1083"}, "abstract": "The evolution of reproductive barriers and their underlying genetic architecture is of central importance for the formation of new species. Reproductive barriers can be controlled either by few large-effect loci suggesting strong selection on key traits, or by many small-effect loci, consistent with gradual divergence or with selection on polygenic or multiple traits. Genetic coupling between reproductive barrier loci further promotes divergence, particularly divergence with ongoing gene flow. In this study, we investigated the genetic architectures of ten morphological, phenological and life history traits associated with reproductive barriers between the hybridizing sister species Silene dioica and S. latifolia; both are dioecious with XY-sex determination. We used quantitative trait locus (QTL) mapping in two reciprocal F 2 crosses. One to six QTLs per trait, including nine major QTLs (PVE > 20%), were detected on 11 of the 12 linkage groups. We found strong evidence for coupling of QTLs for uncorrelated traits and for an important role of sex chromosomes in the genetic architectures of reproductive barrier traits. Unexpectedly, QTLs detected in the two F2 crosses differed largely, despite limited phenotypic differences between them and sufficient statistical power. The widely dispersed genetic architectures of traits associated with reproductive barriers suggest gradual divergence or multifarious selection. Coupling of the underlying QTLs likely promoted divergence with gene flow in this system. The low congruence of QTLs between the two crosses further points to variable and possibly redundant genetic architectures of traits associated with reproductive barriers, with important implications for the evolutionary dynamics of divergence and speciation.", "doi": "10.1111/mec.14562", "pmid": "29577481", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "Dryad", "key": "10.5061/dryad.8dt0gd1"}], "notes": [], "created": "2019-01-07T22:26:08.993Z", "modified": "2021-06-21T14:03:55.838Z"}, {"entity": "publication", "iuid": "c18fc22d368f4c109f76e74dbc4c0d6d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c18fc22d368f4c109f76e74dbc4c0d6d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c18fc22d368f4c109f76e74dbc4c0d6d"}}, "title": "Ancient genomes suggest the eastern Pontic-Caspian steppe as the source of western Iron Age nomads.", "authors": [{"family": "Krzewi\u0144ska", "given": "Maja", "initials": "M", "orcid": "0000-0002-6702-8724", "researcher": {"href": "https://publications.scilifelab.se/researcher/c483febf380c4d9db683e5a73ba89816.json"}}, {"family": "K\u0131l\u0131n\u00e7", "given": "G\u00fcl\u015fah Merve", "initials": "GM", "orcid": "0000-0002-2024-3910", "researcher": {"href": "https://publications.scilifelab.se/researcher/1bc478401dfd4be2965d23f4af757b8e.json"}}, {"family": "Juras", "given": "Anna", "initials": "A"}, {"family": "Koptekin", "given": "Dilek", "initials": "D"}, {"family": "Chyle\u0144ski", "given": "Maciej", "initials": "M", "orcid": "0000-0003-1347-1904", "researcher": {"href": "https://publications.scilifelab.se/researcher/e211127b50ca4ed8ab6b2ae9bede0102.json"}}, {"family": "Nikitin", "given": "Alexey G", "initials": "AG", "orcid": "0000-0002-3897-4607", "researcher": {"href": "https://publications.scilifelab.se/researcher/7f103c7d36c24ac981fbd8291fea853c.json"}}, {"family": "Shcherbakov", "given": "Nikolai", "initials": "N", "orcid": "0000-0001-7731-7178", "researcher": {"href": "https://publications.scilifelab.se/researcher/61dd678e7fb441b2a2560ec728319507.json"}}, {"family": "Shuteleva", "given": "Iia", "initials": "I", "orcid": "0000-0001-7731-7178", "researcher": {"href": "https://publications.scilifelab.se/researcher/61dd678e7fb441b2a2560ec728319507.json"}}, {"family": "Leonova", "given": "Tatiana", "initials": "T"}, {"family": "Kraeva", "given": "Liudmila", "initials": "L", "orcid": "0000-0002-6524-6998", "researcher": {"href": "https://publications.scilifelab.se/researcher/f11ac245436b40a88c66740d94f27353.json"}}, {"family": "Sungatov", "given": "Flarit A", "initials": "FA", "orcid": "0000-0001-5982-9030", "researcher": {"href": "https://publications.scilifelab.se/researcher/4bbdcfb0afa84a899f1dead7ff3c5531.json"}}, {"family": "Sultanova", "given": "Alfija N", "initials": "AN", "orcid": "0000-0002-5409-8344", "researcher": {"href": "https://publications.scilifelab.se/researcher/bfc71e882ea64d408cb1d5201aae554a.json"}}, {"family": "Potekhina", "given": "Inna", "initials": "I"}, {"family": "\u0141ukasik", "given": "Sylwia", "initials": "S"}, {"family": "Krenz-Niedba\u0142a", "given": "Marta", "initials": "M"}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L", "orcid": "0000-0001-8270-7613", "researcher": {"href": "https://publications.scilifelab.se/researcher/48ecf726779249ac9d12f4f7a1cc62bf.json"}}, {"family": "Sinika", "given": "Vitaly", "initials": "V", "orcid": "0000-0002-1621-9205", "researcher": {"href": "https://publications.scilifelab.se/researcher/64dffb07a3a342d78eb91d9c02f87f83.json"}}, {"family": "Jakobsson", "given": "Mattias", "initials": "M", "orcid": "0000-0001-7840-7853", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a4abe0fcb20492d9ec849c9fbf58a71.json"}}, {"family": "Stor\u00e5", "given": "Jan", "initials": "J", "orcid": "0000-0001-6319-7857", "researcher": {"href": "https://publications.scilifelab.se/researcher/57e9174cbd2a4c39be948b88b9ab2d3a.json"}}, {"family": "G\u00f6therstr\u00f6m", "given": "Anders", "initials": "A", "orcid": "0000-0001-6307-8188", "researcher": {"href": "https://publications.scilifelab.se/researcher/2a1a0a680ab8456cbf5a941e9718fd5a.json"}}], "type": "historical article", "published": "2018-10-00", "journal": {"volume": "4", "issn": "2375-2548", "issue": "10", "pages": "eaat4457", "title": "Sci Adv", "issn-l": "2375-2548"}, "abstract": "For millennia, the Pontic-Caspian steppe was a connector between the Eurasian steppe and Europe. In this scene, multidirectional and sequential movements of different populations may have occurred, including those of the Eurasian steppe nomads. We sequenced 35 genomes (low to medium coverage) of Bronze Age individuals (Srubnaya-Alakulskaya) and Iron Age nomads (Cimmerians, Scythians, and Sarmatians) that represent four distinct cultural entities corresponding to the chronological sequence of cultural complexes in the region. Our results suggest that, despite genetic links among these peoples, no group can be considered a direct ancestor of the subsequent group. The nomadic populations were heterogeneous and carried genetic affinities with populations from several other regions including the Far East and the southern Urals. We found evidence of a stable shared genetic signature, making the eastern Pontic-Caspian steppe a likely source of western nomadic groups.", "doi": "10.1126/sciadv.aat4457", "pmid": "30417088", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "aat4457"}, {"db": "pmc", "key": "PMC6223350"}], "notes": [], "created": "2018-10-22T10:10:13.051Z", "modified": "2024-01-16T13:48:45.440Z"}, {"entity": "publication", "iuid": "0b038994cb004c3a9df400da6deade31", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0b038994cb004c3a9df400da6deade31.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0b038994cb004c3a9df400da6deade31"}}, "title": "Interferon-\u03b1 enhances the IL-12-induced STAT4 activation selectively in carriers of the STAT4 SLE risk allele rs7574865[T].", "authors": [{"family": "Hagberg", "given": "Niklas", "initials": "N"}, {"family": "R\u00f6nnblom", "given": "Lars", "initials": "L"}], "type": "journal article", "published": "2018-09-29", "journal": {"volume": null, "issn": "1468-2060", "issue": null, "pages": null, "title": "Ann. Rheum. Dis.", "issn-l": "0003-4967"}, "abstract": null, "doi": "10.1136/annrheumdis-2018-213836", "pmid": "30269051", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "annrheumdis-2018-213836"}], "notes": [], "created": "2019-01-09T07:22:15.905Z", "modified": "2020-01-21T13:56:14.807Z"}, {"entity": "publication", "iuid": "e76ed1b2f4ea42628c05f389e376f495", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e76ed1b2f4ea42628c05f389e376f495.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e76ed1b2f4ea42628c05f389e376f495"}}, "title": "Epigenetic influences on aging: a longitudinal genome-wide methylation study in old Swedish twins", "authors": [{"family": "Wang", "given": "Yunzhang", "initials": "Y"}, {"family": "Karlsson", "given": "Robert", "initials": "R"}, {"family": "Lampa", "given": "Erik", "initials": "E"}, {"family": "Zhang", "given": "Qian", "initials": "Q"}, {"family": "Hedman", "given": "\u00c5sa K", "initials": "\u00c5K"}, {"family": "Almgren", "given": "Malin", "initials": "M"}, {"family": "Almqvist", "given": "Catarina", "initials": "C"}, {"family": "McRae", "given": "Allan F", "initials": "AF"}, {"family": "Marioni", "given": "Riccardo E", "initials": "RE"}, {"family": "Ingelsson", "given": "Erik", "initials": "E"}, {"family": "Visscher", "given": "Peter M", "initials": "PM"}, {"family": "Deary", "given": "Ian J", "initials": "IJ"}, {"family": "Lind", "given": "Lars", "initials": "L"}, {"family": "Morris", "given": "Tiffany", "initials": "T"}, {"family": "Beck", "given": "Stephan", "initials": "S"}, {"family": "Pedersen", "given": "Nancy L", "initials": "NL"}, {"family": "H\u00e4gg", "given": "Sara", "initials": "S"}], "type": "journal-article", "published": "2018-09-28", "journal": {"volume": null, "issn": "1559-2308", "issue": null, "pages": null, "title": "Epigenetics", "issn-l": "1559-2294"}, "abstract": null, "doi": "10.1080/15592294.2018.1526028", "pmid": "30264654", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "EBI", "description": "https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-7309", "key": "E-MTAB-7309"}], "notes": [], "created": "2018-10-03T12:19:07.045Z", "modified": "2024-01-16T13:48:45.464Z"}, {"entity": "publication", "iuid": "1c1ee87a79fa49479cf514aa5bbb3ec2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1c1ee87a79fa49479cf514aa5bbb3ec2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1c1ee87a79fa49479cf514aa5bbb3ec2"}}, "title": "Methanogens and Iron-Reducing Bacteria: the Overlooked Members of Mercury-Methylating Microbial Communities in Boreal Lakes", "authors": [{"family": "Bravo", "given": "Andrea G", "initials": "AG"}, {"family": "Peura", "given": "Sari", "initials": "S"}, {"family": "Buck", "given": "Moritz", "initials": "M"}, {"family": "Ahmed", "given": "Omneya", "initials": "O"}, {"family": "Mateos-Rivera", "given": "Alejandro", "initials": "A"}, {"family": "Herrero Ortega", "given": "Sonia", "initials": "S"}, {"family": "Schaefer", "given": "Jeffra K", "initials": "JK"}, {"family": "Bouchet", "given": "Sylvain", "initials": "S"}, {"family": "Tolu", "given": "Julie", "initials": "J"}, {"family": "Bj\u00f6rn", "given": "Erik", "initials": "E"}, {"family": "Bertilsson", "given": "Stefan", "initials": "S"}], "type": "journal-article", "published": "2018-09-21", "journal": {"volume": "84", "issn": "0099-2240", "issue": "23", "pages": null, "title": "Appl Environ Microbiol", "issn-l": null}, "abstract": "Methylmercury is a potent human neurotoxin which biomagnifies in aquatic food webs. Although anaerobic microorganisms containing the \n                hgcA gene potentially mediate the formation of methylmercury in natural environments, the diversity of these mercury-methylating microbial communities remains largely unexplored. Previous studies have implicated sulfate-reducing bacteria as the main mercury methylators in aquatic ecosystems. In the present study, we characterized the diversity of mercury-methylating microbial communities of boreal lake sediments using high-throughput sequencing of 16S rRNA and hgcA genes. Our results show that in the lake sediments, Methanomicrobiales and Geobacteraceae also represent abundant members of the mercury-methylating communities. In fact, incubation experiments with a mercury isotopic tracer and molybdate revealed that only between 38% and 45% of mercury methylation was attributed to sulfate reduction. These results suggest that methanogens and iron-reducing bacteria may contribute to more than half of the mercury methylation in boreal lakes.IMPORTANCE Despite the global awareness that mercury, and methylmercury in particular, is a neurotoxin to which millions of people continue to be exposed, there are sizable gaps in the understanding of the processes and organisms involved in methylmercury formation in aquatic ecosystems. In the present study, we shed light on the diversity of the microorganisms responsible for methylmercury formation in boreal lake sediments. All the microorganisms identified are associated with the processing of organic matter in aquatic systems. Moreover, our results show that the well-known mercury-methylating sulfate-reducing bacteria constituted only a minor portion of the potential mercury methylators. In contrast, methanogens and iron-reducing bacteria were important contributors to methylmercury formation, highlighting their role in mercury cycling in the environment.", "doi": "10.1128/aem.01774-18", "pmid": "30242005", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [], "notes": [], "created": "2018-12-10T06:30:18.313Z", "modified": "2020-01-21T13:56:17.332Z"}, {"entity": "publication", "iuid": "f1e99712bfc64f97b38f171b84909d5e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f1e99712bfc64f97b38f171b84909d5e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f1e99712bfc64f97b38f171b84909d5e"}}, "title": "The all-intracellular order Legionellales is unexpectedly diverse, globally distributed and lowly abundant", "authors": [{"family": "Graells", "given": "Tiscar", "initials": "T"}, {"family": "Ishak", "given": "Helena", "initials": "H"}, {"family": "Larsson", "given": "Madeleine", "initials": "M"}, {"family": "Guy", "given": "Lionel", "initials": "L"}], "type": "journal-article", "published": "2018-09-10", "journal": {"volume": null, "issn": "1574-6941", "issue": null, "pages": null, "title": "FEMS Microbiol. Ecol.", "issn-l": "0168-6496"}, "abstract": null, "doi": "10.1093/femsle/fiy185", "pmid": "30203072", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [], "notes": [], "created": "2018-12-10T06:27:14.186Z", "modified": "2020-01-21T13:56:12.132Z"}, {"entity": "publication", "iuid": "8210d101bd0a4b3f8307061e9443d54a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8210d101bd0a4b3f8307061e9443d54a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8210d101bd0a4b3f8307061e9443d54a"}}, "title": "Neuronal Expression of Opioid Gene is Controlled by Dual Epigenetic and Transcriptional Mechanism in Human Brain.", "authors": [{"family": "Bazov", "given": "Igor", "initials": "I"}, {"family": "Sarkisyan", "given": "Daniil", "initials": "D"}, {"family": "Kononenko", "given": "Olga", "initials": "O"}, {"family": "Watanabe", "given": "Hiroyuki", "initials": "H"}, {"family": "Taqi", "given": "Mumtaz Malik", "initials": "MM"}, {"family": "St\u00e5lhandske", "given": "Lada", "initials": "L"}, {"family": "Verbeek", "given": "Dineke S", "initials": "DS"}, {"family": "Mulder", "given": "Jan", "initials": "J"}, {"family": "Rajkowska", "given": "Grazyna", "initials": "G"}, {"family": "Sheedy", "given": "Donna", "initials": "D"}, {"family": "Kril", "given": "Jillian", "initials": "J"}, {"family": "Sun", "given": "Xueguang", "initials": "X"}, {"family": "Syv\u00e4nen", "given": "Ann-Christine", "initials": "AC", "orcid": "0000-0002-9681-9146", "researcher": {"href": "https://publications.scilifelab.se/researcher/f7012e35025543379380cb90efd71243.json"}}, {"family": "Yakovleva", "given": "Tatiana", "initials": "T"}, {"family": "Bakalkin", "given": "Georgy", "initials": "G"}], "type": "journal article", "published": "2018-09-01", "journal": {"volume": "28", "issn": "1460-2199", "issue": "9", "pages": "3129-3142", "title": "Cereb. Cortex", "issn-l": "1047-3211"}, "abstract": "Molecular mechanisms that define patterns of neuropeptide expression are essential for the formation and rewiring of neural circuits. The prodynorphin gene (PDYN) gives rise to dynorphin opioid peptides mediating depression and substance dependence. We here demonstrated that PDYN is expressed in neurons in human dorsolateral prefrontal cortex (dlPFC), and identified neuronal differentially methylated region in PDYN locus framed by CCCTC-binding factor binding sites. A short, nucleosome size human-specific promoter CpG island (CGI), a core of this region may serve as a regulatory module, which is hypomethylated in neurons, enriched in 5-hydroxymethylcytosine, and targeted by USF2, a methylation-sensitive E-box transcription factor (TF). USF2 activates PDYN transcription in model systems, and binds to nonmethylated CGI in dlPFC. USF2 and PDYN expression is correlated, and USF2 and PDYN proteins are co-localized in dlPFC. Segregation of activatory TF and repressive CGI methylation may ensure contrasting PDYN expression in neurons and glia in human brain.", "doi": "10.1093/cercor/bhx181", "pmid": "28968778", "labels": {"Fluorescence Tissue Profiling": "Collaborative", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "4049562"}], "notes": [], "created": "2017-10-30T14:56:20.881Z", "modified": "2024-01-16T13:48:45.553Z"}, {"entity": "publication", "iuid": "64721e82902c46b0826f678881b284b5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/64721e82902c46b0826f678881b284b5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/64721e82902c46b0826f678881b284b5"}}, "title": "Complex Evolutionary History of Translation Elongation Factor 2 and Diphthamide Biosynthesis in Archaea and Parabasalids", "authors": [{"family": "Narrowe", "given": "Adrienne B", "initials": "AB"}, {"family": "Spang", "given": "Anja", "initials": "A"}, {"family": "Stairs", "given": "Courtney W", "initials": "CW"}, {"family": "Caceres", "given": "Eva F", "initials": "EF"}, {"family": "Baker", "given": "Brett J", "initials": "BJ"}, {"family": "Miller", "given": "Christopher S", "initials": "CS"}, {"family": "Ettema", "given": "Thijs J G", "initials": "TJG"}], "type": "journal-article", "published": "2018-09-01", "journal": {"volume": "10", "issn": "1759-6653", "issue": "9", "pages": "2380-2393", "title": "Genome Biol Evol", "issn-l": "1759-6653"}, "abstract": null, "doi": "10.1093/gbe/evy154", "pmid": "30060184", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [], "notes": [], "created": "2018-12-10T06:26:59.627Z", "modified": "2020-01-21T13:56:12.125Z"}, {"entity": "publication", "iuid": "7627ac20899545c99ff75d47554bfbd0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7627ac20899545c99ff75d47554bfbd0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7627ac20899545c99ff75d47554bfbd0"}}, "title": "Sex-biased gene expression, sexual antagonism and levels of genetic diversity in the collared flycatcher (Ficedula albicollis) genome", "authors": [{"family": "Dutoit", "given": "Ludovic", "initials": "L"}, {"family": "Mugal", "given": "Carina F", "initials": "CF"}, {"family": "Bol\u00edvar", "given": "Paulina", "initials": "P"}, {"family": "Wang", "given": "Mi", "initials": "M"}, {"family": "Nadachowska-Brzyska", "given": "Krystyna", "initials": "K"}, {"family": "Smeds", "given": "Linn\u00e9a", "initials": "L"}, {"family": "Yazdi", "given": "Homa P", "initials": "HP"}, {"family": "Gustafsson", "given": "Lars", "initials": "L"}, {"family": "Ellegren", "given": "Hans", "initials": "H"}], "type": "journal-article", "published": "2018-09-00", "journal": {"volume": "27", "issn": "0962-1083", "issue": "18", "pages": "3572-3581", "title": "Mol Ecol", "issn-l": "0962-1083"}, "abstract": null, "doi": "10.1111/mec.14789", "pmid": "30055065", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "BioProject", "description": "Whole genome sequencing and de novo assembly of the collared flycatcher.", "key": "PRJEB2984"}, {"db": "SRA", "description": "Flycatcher genome sequencing and population resequencing", "key": "ERP001377"}], "notes": [], "created": "2018-10-22T10:08:16.189Z", "modified": "2024-01-16T13:48:45.582Z"}, {"entity": "publication", "iuid": "ac65bcde708c467a89a3c3d866344ce9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ac65bcde708c467a89a3c3d866344ce9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ac65bcde708c467a89a3c3d866344ce9"}}, "title": "Sequentially acting SOX proteins orchestrate astrocyte\u2010 and oligodendrocyte\u2010specific gene expression", "authors": [{"family": "Klum", "given": "Susanne", "initials": "S"}, {"family": "Zaouter", "given": "C\u00e9cile", "initials": "C"}, {"family": "Alekseenko", "given": "Zhanna", "initials": "Z"}, {"family": "Bj\u00f6rklund", "given": "\u00c5sa K", "initials": "\u00c5K"}, {"family": "Hagey", "given": "Daniel W", "initials": "DW"}, {"family": "Ericson", "given": "Johan", "initials": "J"}, {"family": "Muhr", "given": "Jonas", "initials": "J"}, {"family": "Bergsland", "given": "Maria", "initials": "M"}], "type": "journal-article", "published": "2018-08-30", "journal": {"volume": null, "issn": "1469-3178", "issue": null, "pages": "e46635", "title": "EMBO Rep.", "issn-l": "1469-221X"}, "abstract": "SOX transcription factors have important roles during astrocyte and oligodendrocyte development, but how glial genes are specified and activated in a sub-lineage-specific fashion remains unknown. Here, we define glial-specific gene expression in the developing spinal cord using single-cell RNA-sequencing. Moreover, by ChIP-seq analyses we show that these glial gene sets are extensively preselected already in multipotent neural precursor cells through prebinding by SOX3. In the subsequent lineage-restricted glial precursor cells, astrocyte genes become additionally targeted by SOX9 at DNA regions strongly enriched for Nfi binding motifs. Oligodendrocyte genes instead are prebound by SOX9 only, at sites which during oligodendrocyte maturation are targeted by SOX10. Interestingly, reporter gene assays and functional studies in the spinal cord reveal that SOX3 binding represses the synergistic activation of astrocyte genes by SOX9 and NFIA, whereas oligodendrocyte genes are activated in a combinatorial manner by SOX9 and SOX10. These genome-wide studies demonstrate how sequentially expressed SOX proteins act on lineage-specific regulatory DNA elements to coordinate glial gene expression both in a temporal and in a sub-lineage-specific fashion.", "doi": "10.15252/embr.201846635", "pmid": "30166336", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [], "notes": [], "created": "2018-09-28T16:05:21.577Z", "modified": "2024-01-16T13:48:45.697Z"}, {"entity": "publication", "iuid": "f68a54ce39ff44abba37badf71d54fdf", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f68a54ce39ff44abba37badf71d54fdf.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f68a54ce39ff44abba37badf71d54fdf"}}, "title": "Novel Autotrophic Organisms Contribute Significantly to the Internal Carbon Cycling Potential of a Boreal Lake", "authors": [{"family": "Peura", "given": "Sari", "initials": "S"}, {"family": "Buck", "given": "Moritz", "initials": "M"}, {"family": "Aalto", "given": "Sanni L", "initials": "SL"}, {"family": "Morales", "given": "Sergio E", "initials": "SE"}, {"family": "Nyk\u00e4nen", "given": "Hannu", "initials": "H"}, {"family": "Eiler", "given": "Alexander", "initials": "A"}], "type": "journal-article", "published": "2018-08-14", "journal": {"volume": "9", "issn": "2150-7511", "issue": "4", "pages": null, "title": "MBio", "issn-l": null}, "abstract": "Oxygen-stratified lakes are typical for the boreal zone and also a major source of greenhouse gas emissions in the region. Due to shallow light penetration, restricting the growth of phototrophic organisms, and large allochthonous organic carbon inputs from the catchment area, the lake metabolism is expected to be dominated by heterotrophic organisms. In this study, we test this assumption and show that the potential for autotrophic carbon fixation and internal carbon cycling is high throughout the water column. Further, we show that during the summer stratification carbon fixation can exceed respiration in a boreal lake even below the euphotic zone. Metagenome-assembled genomes and 16S profiling of a vertical transect of the lake revealed multiple organisms in an oxygen-depleted compartment belonging to novel or poorly characterized phyla. Many of these organisms were chemolithotrophic, potentially deriving their energy from reactions related to sulfur, iron, and nitrogen transformations. The community, as well as the functions, was stratified along the redox gradient. The autotrophic potential in the lake metagenome below the oxygenic zone was high, pointing toward a need for revising our concepts of internal carbon cycling in boreal lakes. Further, the importance of chemolithoautotrophy for the internal carbon cycling suggests that many predicted climate change-associated fluctuations in the physical properties of the lake, such as altered mixing patterns, likely have consequences for the whole-lake metabolism even beyond the impact to the phototrophic community.\n                IMPORTANCE Autotrophic organisms at the base of the food web are the only life form capable of turning inorganic carbon into the organic form, facilitating the survival of all other organisms. In certain environments, the autotrophic production is limited by environmental conditions and the food web is supported by external carbon inputs. One such environment is stratified boreal lakes, which are one of the biggest natural sources of greenhouse gas emissions in the boreal region. Thus, carbon cycling in these habitats is of utmost importance for the future climate. Here, we demonstrate a high potential for internal carbon cycling via phototrophic and novel chemolithotrophic organisms in the anoxic, poorly illuminated layers of a boreal lake. Our results significantly increase our knowledge on the microbial communities and their metabolic potential in oxygen-depleted freshwaters and help to understand and predict how climate change-induced alterations could impact the lake carbon dynamics.", "doi": "10.1128/mbio.00916-18", "pmid": "30108167", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "SRA", "description": null, "key": "SRP076290"}], "notes": [], "created": "2018-09-14T12:11:54.432Z", "modified": "2024-01-16T13:48:45.735Z"}, {"entity": "publication", "iuid": "eda563d110614789bbab92cb01dd72d2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/eda563d110614789bbab92cb01dd72d2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/eda563d110614789bbab92cb01dd72d2"}}, "title": "Extensive genomic diversity among Mycobacterium marinum strains revealed by whole genome sequencing", "authors": [{"family": "Das", "given": "Sarbashis", "initials": "S"}, {"family": "Pettersson", "given": "Fredrik", "initials": "F"}, {"family": "Behra", "given": "Phani Rama Krishna", "initials": "PRK"}, {"family": "Mallick", "given": "Amrita", "initials": "A"}, {"family": "Cheramie", "given": "Martin", "initials": "M"}, {"family": "Shirreff", "given": "Lisa", "initials": "L"}, {"family": "Tanner DuCote", "given": "Tanner", "initials": "T"}, {"family": "Dasgupta", "given": "Santanu", "initials": "S"}, {"family": "Ennis", "given": "Don G", "initials": "DG"}, {"family": "Kirsebom", "given": "Leif", "initials": "L", "orcid": "0000-0002-5092-512X", "researcher": {"href": "https://publications.scilifelab.se/researcher/e80849a89d0043b0b4daff9804c67332.json"}}], "type": "posted-content", "published": "2018-08-13", "journal": {"title": "Sci. Rep.", "issn": "2045-2322", "issn-l": "2045-2322", "volume": "8", "issue": "1", "pages": null}, "abstract": "Mycobacterium marinum is the causative agent for the tuberculosis-like disease mycobacteriosis in fish and skin lesions in humans. Ubiquitous in its geographical distribution, M. marinum is known to occupy diverse fish as hosts. However, information about its genomic diversity is limited. Here, we provide the genome sequences for 15 M. marinum strains isolated from infected humans and fish. Comparative genomic analysis of these and four available genomes of the M. marinum strains M, E11, MB2 and Europe reveal high genomic diversity among the strains, leading to the conclusion that M. marinum should be divided into two different clusters, the \"M\"- and the \"Aronson\"-type. We suggest that these two clusters should be considered to represent two M. marinum subspecies. Our data also show that the M. marinum pan-genome for both groups is open and expanding and we provide data showing high number of mutational hotspots in M. marinum relative to other mycobacteria such as Mycobacterium tuberculosis. This high genomic diversity might be related to the ability of M. marinum to occupy different ecological niches.", "doi": "10.1038/s41598-018-30152-y", "pmid": "30104693", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2018-02-09T10:51:10.898Z", "modified": "2024-01-16T13:48:45.750Z"}, {"entity": "publication", "iuid": "c96afccb586a4170b645b616dc18405c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c96afccb586a4170b645b616dc18405c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c96afccb586a4170b645b616dc18405c"}}, "title": "Clonal relatedness in tumour pairs of breast cancer patients.", "authors": [{"family": "Biermann", "given": "Jana", "initials": "J"}, {"family": "Parris", "given": "Toshima Z", "initials": "TZ"}, {"family": "Nemes", "given": "Szil\u00e1rd", "initials": "S"}, {"family": "Danielsson", "given": "Anna", "initials": "A"}, {"family": "Engqvist", "given": "Hanna", "initials": "H"}, {"family": "Werner R\u00f6nnerman", "given": "Elisabeth", "initials": "E"}, {"family": "Forssell-Aronsson", "given": "Eva", "initials": "E"}, {"family": "Kov\u00e1cs", "given": "Anik\u00f3", "initials": "A"}, {"family": "Karlsson", "given": "Per", "initials": "P"}, {"family": "Helou", "given": "Khalil", "initials": "K"}], "type": "journal article", "published": "2018-08-09", "journal": {"volume": "20", "issn": "1465-542X", "issue": "1", "pages": "96", "title": "Breast Cancer Res.", "issn-l": "1465-5411"}, "abstract": "Molecular classification of tumour clonality is currently not evaluated in multiple invasive breast carcinomas, despite evidence suggesting common clonal origins. There is no consensus about which type of data (e.g. copy number, mutation, histology) and especially which statistical method is most suitable to distinguish clonal recurrences from independent primary tumours.\r\n\r\nThirty-seven invasive breast tumour pairs were stratified according to laterality and time interval between the diagnoses of the two tumours. In a multi-omics approach, tumour clonality was analysed by integrating clinical characteristics (n\u00a0=\u200937), DNA copy number (n\u2009=\u200937), DNA methylation (n\u00a0=\u20098), gene expression microarray (n\u00a0=\u20097), RNA sequencing (n\u2009=\u20093), and SNP genotyping data (n\u2009=\u20093). Different statistical methods, e.g. the diagnostic similarity index (SI), were used to classify the tumours as clonally related recurrences or independent primary tumours.\r\n\r\nThe SI and hierarchical clustering showed similar tendencies and the highest concordance with the other methods. Concordant evidence for tumour clonality was found in 46% (17/37) of patients. Notably, no association was found between the current clinical guidelines and molecular tumour features.\r\n\r\nA more accurate classification of clonal relatedness between multiple breast tumours may help to mitigate treatment failure and relapse by integrating tumour-associated molecular features, clinical parameters, and statistical methods. Guidelines need to be defined with exact thresholds to standardise clonality testing in a routine diagnostic setting.", "doi": "10.1186/s13058-018-1022-y", "pmid": "30092821", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support and Infrastructure": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1186/s13058-018-1022-y"}, {"db": "GEO", "description": "Genome-wide multi-omics profiling reveals extensive genetic complexity in 8p11-p12 amplified breast carcinomas", "key": "GSE97293"}, {"db": "GEO", "description": "Genome-wide multi-omics profiling reveals extensive genetic complexity in 8p11-p12 amplified breast carcinomas [expression]", "key": "GSE97177"}], "notes": [], "created": "2018-08-16T15:30:10.983Z", "modified": "2024-01-16T13:48:45.779Z"}, {"entity": "publication", "iuid": "77bb5a125912473b99cbdc00c8121a2d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/77bb5a125912473b99cbdc00c8121a2d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/77bb5a125912473b99cbdc00c8121a2d"}}, "title": "A genetic map of ostrich Z chromosome and the role of inversions in avian sex chromosome evolution.", "authors": [{"family": "Papoli Yazdi", "given": "Homa", "initials": "H"}, {"family": "Ellegren", "given": "Hans", "initials": "H"}], "type": "journal article", "published": "2018-08-07", "journal": {"volume": null, "issn": "1759-6653", "issue": null, "title": "Genome Biol Evol", "issn-l": "1759-6653"}, "abstract": "Recombination arrest is a necessary step for the evolution of distinct sex chromosomes. Structural changes, such as inversions, may represent the mechanistic basis for recombination suppression and comparisons of the structural organization of chromosomes as given by chromosome-level assemblies offer the possibility to infer inversions across species at some detail. In birds, deduction of the process of sex chromosome evolution has been hampered by the lack of a validated chromosome-level assembly from a representative of one of the two basal clades of modern birds, Paleognathae. We therefore developed a high-density genetic linkage map of the ostrich Z chromosome and used this to correct an existing assembly, including correction of a large chimeric superscaffold and the order and orientation of other superscaffolds. We identified the pseudoautosomal region (PAR) as a 52\u2009Mb segment (\u224860% of the Z chromosome) where recombination occurred in both sexes. By comparing the order and location of genes on the ostrich Z chromosome with that of six bird species from the other major clade of birds (Neognathae), and of reptilian outgroup species, 25 Z-linked inversions were inferred in the avian lineages. We defined Z chromosome organization in an early avian ancestor and identified inversions spanning the candidate sex-determining DMRT1 gene in this ancestor, which could potentially have triggered the onset of avian sex chromosome evolution. We conclude that avian sex chromosome evolution has been characterized by a complex process of probably both Z-linked and W-linked inversions (and/or other processes). This study illustrates the need for validated chromosome-level assemblies for inference of genome evolution.", "doi": "10.1093/gbe/evy163", "pmid": "30099482", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "5067707"}], "notes": [], "created": "2018-08-16T15:30:10.251Z", "modified": "2024-01-16T13:48:45.796Z"}, {"entity": "publication", "iuid": "334c0f55fee64de19dd15c3914ee2fdd", "links": {"self": {"href": "https://publications.scilifelab.se/publication/334c0f55fee64de19dd15c3914ee2fdd.json"}, "display": {"href": "https://publications.scilifelab.se/publication/334c0f55fee64de19dd15c3914ee2fdd"}}, "title": "Substrate-Induced Response in Biogas Process Performance and Microbial Community Relates Back to Inoculum Source", "authors": [{"family": "Liu", "given": "Tong", "initials": "T"}, {"family": "Sun", "given": "Li", "initials": "L"}, {"family": "Nordberg", "given": "\u00c5ke", "initials": "\u00c5"}, {"family": "Schn\u00fcrer", "given": "Anna", "initials": "A"}], "type": "journal-article", "published": "2018-08-05", "journal": {"volume": "6", "issn": "2076-2607", "issue": "3", "pages": "80", "title": "Microorganisms", "issn-l": "2076-2607"}, "abstract": null, "doi": "10.3390/microorganisms6030080", "pmid": "30081593", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [], "notes": [], "created": "2018-09-14T11:56:27.428Z", "modified": "2020-01-21T13:56:12.110Z"}, {"entity": "publication", "iuid": "74b25d02bcc9431e857482349c2c97ea", "links": {"self": {"href": "https://publications.scilifelab.se/publication/74b25d02bcc9431e857482349c2c97ea.json"}, "display": {"href": "https://publications.scilifelab.se/publication/74b25d02bcc9431e857482349c2c97ea"}}, "title": "Investigation of viable taxa in the deep terrestrial biosphere suggests high rates of nutrient recycling", "authors": [{"family": "Lopez-Fernandez", "given": "Margarita", "initials": "M"}, {"family": "Broman", "given": "Elias", "initials": "E"}, {"family": "Turner", "given": "Stephanie", "initials": "S"}, {"family": "Wu", "given": "Xiaofen", "initials": "X"}, {"family": "Bertilsson", "given": "Stefan", "initials": "S"}, {"family": "Dopson", "given": "Mark", "initials": "M"}], "type": "journal-article", "published": "2018-08-01", "journal": {"volume": "94", "issn": "1574-6941", "issue": "8", "pages": null, "title": "FEMS Microbiol. Ecol.", "issn-l": "0168-6496"}, "abstract": null, "doi": "10.1093/femsec/fiy121", "pmid": "29931252", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "BioProject", "description": "16S rRNA gene sequences obtained from the deep terrestrial biosphere", "key": "PRJNA431355"}, {"db": "SRA", "description": null, "key": "SRP131350"}], "notes": [], "created": "2018-09-14T11:55:42.051Z", "modified": "2024-01-16T13:48:45.817Z"}, {"entity": "publication", "iuid": "6534c95240554009b2d09a446c42afca", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6534c95240554009b2d09a446c42afca.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6534c95240554009b2d09a446c42afca"}}, "title": "Sex-specific manifestation of genetic risk for attention deficit hyperactivity disorder in the general population.", "authors": [{"family": "Martin", "given": "Joanna", "initials": "J"}, {"family": "Taylor", "given": "Mark J", "initials": "MJ"}, {"family": "Rydell", "given": "Mina", "initials": "M"}, {"family": "Riglin", "given": "Lucy", "initials": "L"}, {"family": "Eyre", "given": "Olga", "initials": "O"}, {"family": "Lu", "given": "Yi", "initials": "Y"}, {"family": "Lundstr\u00f6m", "given": "Sebastian", "initials": "S"}, {"family": "Larsson", "given": "Henrik", "initials": "H"}, {"family": "Thapar", "given": "Anita", "initials": "A"}, {"family": "Lichtenstein", "given": "Paul", "initials": "P"}], "type": "journal article", "published": "2018-08-00", "journal": {"volume": "59", "issn": "1469-7610", "issue": "8", "pages": "908-916", "title": "J Child Psychol Psychiatry", "issn-l": "0021-9630"}, "abstract": "Attention deficit hyperactivity disorder (ADHD) is more commonly diagnosed in males than in females. A growing body of research suggests that females with ADHD might be underdiagnosed or receive alternative diagnoses, such as anxiety or depression. Other lines of reasoning suggest that females might be protected from developing ADHD, requiring a higher burden of genetic risk to manifest the disorder.\n\nWe tested these two hypotheses, using common variant genetic data from two population-based cohorts. First, we tested whether females and males diagnosed with anxiety or depression differ in terms of their genetic risk for ADHD, assessed as polygenic risk scores (PRS). Second, we tested whether females and males with ADHD differed in ADHD genetic risk burden. We used three different diagnostic definitions: registry-based clinical diagnoses, screening-based research diagnoses and algorithm-based research diagnoses, to investigate possible referral biases.\n\nIn individuals with a registry-based clinical diagnosis of anxiety or depression, females had higher ADHD PRS than males [OR(CI)\u00a0=\u00a01.39 (1.12-1.73)] but there was no sex difference for screening-based [OR(CI)\u00a0=\u00a01.15 (0.94-1.42)] or algorithm-based [OR(CI)\u00a0=\u00a01.04 (0.89-1.21)] diagnoses. There was also no sex difference in ADHD PRS in individuals with ADHD diagnoses that were registry-based [OR(CI)\u00a0=\u00a01.04 (0.84-1.30)], screening-based [OR(CI)\u00a0=\u00a00.96 (0.85-1.08)] or algorithm-based [OR(CI)\u00a0=\u00a01.15 (0.78-1.68)].\n\nThis study provides genetic evidence that ADHD risk may be more likely to manifest or be diagnosed as anxiety or depression in females than in males. Contrary to some earlier studies, the results do not support increased ADHD genetic risk in females with ADHD as compared to affected males.", "doi": "10.1111/jcpp.12874", "pmid": "29451303", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC6055636"}], "notes": [], "created": "2018-08-16T15:30:16.600Z", "modified": "2020-01-21T13:56:10.940Z"}, {"entity": "publication", "iuid": "defa169f656c4c1ca249656bd3207190", "links": {"self": {"href": "https://publications.scilifelab.se/publication/defa169f656c4c1ca249656bd3207190.json"}, "display": {"href": "https://publications.scilifelab.se/publication/defa169f656c4c1ca249656bd3207190"}}, "title": "Proteome\u2010wide analysis of phospho\u2010regulated PDZ domain interactions", "authors": [{"family": "Sundell", "given": "Gustav N", "initials": "GN"}, {"family": "Arnold", "given": "Roland", "initials": "R"}, {"family": "Ali", "given": "Muhammad", "initials": "M"}, {"family": "Naksukpaiboon", "given": "Piangfan", "initials": "P"}, {"family": "Orts", "given": "Julien", "initials": "J"}, {"family": "G\u00fcntert", "given": "Peter", "initials": "P"}, {"family": "Chi", "given": "Celestine N", "initials": "CN"}, {"family": "Ivarsson", "given": "Ylva", "initials": "Y"}], "type": "journal-article", "published": "2018-08-00", "journal": {"volume": "14", "issn": "1744-4292", "issue": "8", "pages": "e8129", "title": "Mol. Syst. Biol.", "issn-l": "1744-4292"}, "abstract": "A key function of reversible protein phosphorylation is to regulate protein-protein interactions, many of which involve short linear motifs (3-12 amino acids). Motif-based interactions are difficult to capture because of their often low-to-moderate affinities. Here, we describe phosphomimetic proteomic peptide-phage display, a powerful method for simultaneously finding motif-based interaction and pinpointing phosphorylation switches. We computationally designed an oligonucleotide library encoding human C-terminal peptides containing known or predicted Ser/Thr phosphosites and phosphomimetic variants thereof. We incorporated these oligonucleotides into a phage library and screened the PDZ (PSD-95/Dlg/ZO-1) domains of Scribble and DLG1 for interactions potentially enabled or disabled by ligand phosphorylation. We identified known and novel binders and characterized selected interactions through microscale thermophoresis, isothermal titration calorimetry, and NMR We uncover site-specific phospho-regulation of PDZ domain interactions, provide a structural framework for how PDZ domains accomplish phosphopeptide binding, and discuss ligand phosphorylation as a switching mechanism of PDZ domain interactions. The approach is readily scalable and can be used to explore the potential phospho-regulation of motif-based interactions on a large scale.", "doi": "10.15252/msb.20178129", "pmid": "30126976", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Drug Discovery and Development": "Service"}, "xrefs": [], "notes": [], "created": "2018-10-31T10:38:56.704Z", "modified": "2025-10-17T13:05:08.396Z"}, {"entity": "publication", "iuid": "ebf16e5efd5441d2a032e3b5cc30a27e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ebf16e5efd5441d2a032e3b5cc30a27e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ebf16e5efd5441d2a032e3b5cc30a27e"}}, "title": "Prenatal arsenic exposure is associated with increased plasma IGFBP3 concentrations in 9-year-old children partly via changes in DNA methylation.", "authors": [{"family": "Gliga", "given": "Anda R", "initials": "AR"}, {"family": "Engstr\u00f6m", "given": "Karin", "initials": "K"}, {"family": "Kippler", "given": "Maria", "initials": "M"}, {"family": "Skr\u00f6der", "given": "Helena", "initials": "H"}, {"family": "Ahmed", "given": "Sultan", "initials": "S"}, {"family": "Vahter", "given": "Marie", "initials": "M"}, {"family": "Raqib", "given": "Rubhana", "initials": "R"}, {"family": "Broberg", "given": "Karin", "initials": "K"}], "type": "journal article", "published": "2018-08-00", "journal": {"volume": "92", "issn": "1432-0738", "issue": "8", "pages": "2487-2500", "title": "Arch. Toxicol.", "issn-l": "0340-5761"}, "abstract": "Exposure to inorganic arsenic (As), a carcinogen and epigenetic toxicant, has been associated with lower circulating levels of insulin-like growth factor 1 (IGF1) and impaired growth in children of pre-school age. The aim of this study was to assess the potential impact of exposure to As on IGF1 and insulin-like growth factor-binding protein 3 (IGFBP3) as well as DNA methylation changes in 9-year-old children. To this end, we studied 9-year-old children from a longitudinal mother-child cohort in rural Bangladesh (n\u2009=\u2009551). Prenatal and concurrent exposure to As was assessed via concentrations in maternal urine at gestational week 8 and in child urine at 9 years, measured by HPLC-HG-ICPMS. Plasma IGF1 and IGFBP3 concentrations were quantified with immunoassays. DNA methylation was measured in blood mononuclear cells at 9\u00a0years in a sub-sample (n\u2009=\u2009113) using the Infinium HumanMethylation450K BeadChip. In multivariable-adjusted linear regression models, prenatal As (natural log-transformed), but not children's concurrent urinary As, was positively associated with IGFBP3 concentrations (\u03b2\u2009=\u200976, 95% CI 19, 133). As concentrations were not associated with IGF1. DNA methylation analysis revealed CpGs associated with both prenatal As and IGFBP3. Mediation analysis suggested that methylation of 12 CpG sites for all children was mediator of effect for the association between prenatal As and IGFBP3. We also found differentially methylated regions, generally hypermethylated, that were associated with both prenatal As and IGFBP3. In all, our study revealed that prenatal exposure to As was positively associated with IGFBP3 concentrations in children at 9\u00a0years, independent of IGF1, and this association may, at least in part, be epigenetically mediated.", "doi": "10.1007/s00204-018-2239-3", "pmid": "29947889", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1007/s00204-018-2239-3"}, {"db": "pmc", "key": "PMC6063321"}], "notes": [], "created": "2018-08-16T15:30:14.115Z", "modified": "2024-01-16T13:48:45.846Z"}, {"entity": "publication", "iuid": "e265f217f2b7496c8c857ad8f66226b7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e265f217f2b7496c8c857ad8f66226b7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e265f217f2b7496c8c857ad8f66226b7"}}, "title": "Gene discovery and polygenic prediction from a genome-wide association study of educational attainment in 1.1 million individuals.", "authors": [{"family": "Lee", "given": "James J", "initials": "JJ"}, {"family": "Wedow", "given": "Robbee", "initials": "R"}, {"family": "Okbay", "given": "Aysu", "initials": "A"}, {"family": "Kong", "given": "Edward", "initials": "E"}, {"family": "Maghzian", "given": "Omeed", "initials": "O"}, {"family": "Zacher", "given": "Meghan", "initials": "M"}, {"family": "Nguyen-Viet", "given": "Tuan Anh", "initials": "TA"}, {"family": "Bowers", "given": "Peter", "initials": "P"}, {"family": "Sidorenko", "given": "Julia", "initials": "J"}, {"family": "Karlsson Linn\u00e9r", "given": "Richard", "initials": "R"}, {"family": "Fontana", "given": "Mark Alan", "initials": "MA"}, {"family": "Kundu", "given": "Tushar", "initials": "T"}, {"family": "Lee", "given": "Chanwook", "initials": "C"}, {"family": "Li", "given": "Hui", "initials": "H"}, {"family": "Li", "given": "Ruoxi", "initials": "R"}, {"family": "Royer", "given": "Rebecca", "initials": "R"}, {"family": "Timshel", "given": "Pascal N", "initials": "PN"}, {"family": "Walters", "given": "Raymond K", "initials": "RK"}, {"family": "Willoughby", "given": "Emily A", "initials": "EA"}, {"family": "Yengo", "given": "Lo\u00efc", "initials": "L"}, {"family": "23andMe Research Team", "given": "", "initials": ""}, {"family": "COGENT (Cognitive Genomics Consortium)", "given": "", "initials": ""}, {"family": "Social Science Genetic Association Consortium", "given": "", "initials": ""}, {"family": "Alver", "given": "Maris", "initials": "M"}, {"family": "Bao", "given": "Yanchun", "initials": "Y"}, {"family": "Clark", "given": "David W", "initials": "DW"}, {"family": "Day", "given": "Felix R", "initials": "FR"}, {"family": "Furlotte", "given": "Nicholas A", "initials": "NA"}, {"family": "Joshi", "given": "Peter K", "initials": "PK"}, {"family": "Kemper", "given": "Kathryn E", "initials": "KE"}, {"family": "Kleinman", "given": "Aaron", "initials": "A"}, {"family": "Langenberg", "given": "Claudia", "initials": "C"}, {"family": "M\u00e4gi", "given": "Reedik", "initials": "R"}, {"family": "Trampush", "given": "Joey W", "initials": "JW"}, {"family": "Verma", "given": "Shefali Setia", "initials": "SS"}, {"family": "Wu", "given": "Yang", "initials": "Y"}, {"family": "Lam", "given": "Max", "initials": "M"}, {"family": "Zhao", "given": "Jing Hua", "initials": "JH"}, {"family": "Zheng", "given": "Zhili", "initials": "Z"}, {"family": "Boardman", "given": "Jason D", "initials": "JD"}, {"family": "Campbell", "given": "Harry", "initials": "H"}, {"family": "Freese", "given": "Jeremy", "initials": "J"}, {"family": "Harris", "given": "Kathleen Mullan", "initials": "KM"}, {"family": "Hayward", "given": "Caroline", "initials": "C"}, {"family": "Herd", "given": "Pamela", "initials": "P"}, {"family": "Kumari", "given": "Meena", "initials": "M"}, {"family": "Lencz", "given": "Todd", "initials": "T"}, {"family": "Luan", "given": "Jian'an", "initials": "J"}, {"family": "Malhotra", "given": "Anil K", "initials": "AK"}, {"family": "Metspalu", "given": "Andres", "initials": "A"}, {"family": "Milani", "given": "Lili", "initials": "L"}, {"family": "Ong", "given": "Ken K", "initials": "KK"}, {"family": "Perry", "given": "John R B", "initials": "JRB"}, {"family": "Porteous", "given": "David J", "initials": "DJ"}, {"family": "Ritchie", "given": "Marylyn D", "initials": "MD"}, {"family": "Smart", "given": "Melissa C", "initials": "MC"}, {"family": "Smith", "given": "Blair H", "initials": "BH"}, {"family": "Tung", "given": "Joyce Y", "initials": "JY"}, {"family": "Wareham", "given": "Nicholas J", "initials": "NJ"}, {"family": "Wilson", "given": "James F", "initials": "JF"}, {"family": "Beauchamp", "given": "Jonathan P", "initials": "JP"}, {"family": "Conley", "given": "Dalton C", "initials": "DC"}, {"family": "Esko", "given": "T\u00f5nu", "initials": "T"}, {"family": "Lehrer", "given": "Steven F", "initials": "SF"}, {"family": "Magnusson", "given": "Patrik K E", "initials": "PKE"}, {"family": "Oskarsson", "given": "Sven", "initials": "S"}, {"family": "Pers", "given": "Tune H", "initials": "TH"}, {"family": "Robinson", "given": "Matthew R", "initials": "MR"}, {"family": "Thom", "given": "Kevin", "initials": "K"}, {"family": "Watson", "given": "Chelsea", "initials": "C"}, {"family": "Chabris", "given": "Christopher F", "initials": "CF"}, {"family": "Meyer", "given": "Michelle N", "initials": "MN"}, {"family": "Laibson", "given": "David I", "initials": "DI"}, {"family": "Yang", "given": "Jian", "initials": "J"}, {"family": "Johannesson", "given": "Magnus", "initials": "M"}, {"family": "Koellinger", "given": "Philipp D", "initials": "PD"}, {"family": "Turley", "given": "Patrick", "initials": "P"}, {"family": "Visscher", "given": "Peter M", "initials": "PM"}, {"family": "Benjamin", "given": "Daniel J", "initials": "DJ"}, {"family": "Cesarini", "given": "David", "initials": "D"}], "type": "journal article", "published": "2018-08-00", "journal": {"volume": "50", "issn": "1546-1718", "issue": "8", "pages": "1112-1121", "title": "Nat. Genet.", "issn-l": "1061-4036"}, "abstract": "Here we conducted a large-scale genetic association analysis of educational attainment in a sample of approximately 1.1\u2009million individuals and identify 1,271\u2009independent genome-wide-significant SNPs. For the SNPs taken together, we found evidence of heterogeneous effects across environments. The SNPs implicate genes involved in brain-development processes and neuron-to-neuron communication. In a separate analysis of the X chromosome, we identify 10\u2009independent genome-wide-significant SNPs and estimate a SNP heritability of around 0.3% in both men and women, consistent with partial dosage compensation. A joint (multi-phenotype) analysis of educational attainment and three related cognitive phenotypes generates polygenic scores that explain 11-13% of the variance in educational attainment and 7-10% of the variance in cognitive performance. This prediction accuracy substantially increases the utility of polygenic scores as tools in research.", "doi": "10.1038/s41588-018-0147-3", "pmid": "30038396", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41588-018-0147-3"}], "notes": [], "created": "2018-08-16T15:30:11.963Z", "modified": "2024-01-16T13:48:45.868Z"}, {"entity": "publication", "iuid": "599d9f62c7cd43bf93af368f46b08c88", "links": {"self": {"href": "https://publications.scilifelab.se/publication/599d9f62c7cd43bf93af368f46b08c88.json"}, "display": {"href": "https://publications.scilifelab.se/publication/599d9f62c7cd43bf93af368f46b08c88"}}, "title": "Epigenetics in pediatric acute lymphoblastic leukemia.", "authors": [{"family": "Nordlund", "given": "Jessica", "initials": "J", "orcid": "0000-0001-8699-9959", "researcher": {"href": "https://publications.scilifelab.se/researcher/ddf48c9262134821bcc6ce1180049753.json"}}, {"family": "Syv\u00e4nen", "given": "Ann-Christine", "initials": "AC", "orcid": "0000-0002-9681-9146", "researcher": {"href": "https://publications.scilifelab.se/researcher/f7012e35025543379380cb90efd71243.json"}}], "type": "journal article", "published": "2018-08-00", "journal": {"volume": "51", "issn": "1096-3650", "issue": null, "pages": "129-138", "title": "Semin. Cancer Biol.", "issn-l": "1044-579X"}, "abstract": "Acute lymphoblastic leukemia (ALL) is the most common malignancy in children. ALL arises from the malignant transformation of progenitor B- and T-cells in the bone marrow into leukemic cells, but the mechanisms underlying this transformation are not well understood. Recent technical advances and decreasing costs of methods for high-throughput DNA sequencing and SNP genotyping have stimulated systematic studies of the epigenetic changes in leukemic cells from pediatric ALL patients. The results emerging from these studies are increasing our understanding of the epigenetic component of leukemogenesis and have demonstrated the potential of DNA methylation as a biomarker for lineage and subtype classification, prognostication, and disease progression in ALL. In this review, we provide a concise examination of the epigenetic studies in ALL, with a focus on DNA methylation and mutations perturbing genes involved in chromatin modification, and discuss the future role of epigenetic analyses in research and clinical management of ALL.", "doi": "10.1016/j.semcancer.2017.09.001", "pmid": "28887175", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "S1044-579X(17)30091-3"}], "notes": [], "created": "2017-12-05T12:37:19.501Z", "modified": "2024-01-16T13:48:45.876Z"}, {"entity": "publication", "iuid": "ab6f9bb6fde644719766160c28d9a3b5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ab6f9bb6fde644719766160c28d9a3b5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ab6f9bb6fde644719766160c28d9a3b5"}}, "title": "Acute sleep loss results in tissue-specific alterations in genome-wide DNA methylation state and metabolic fuel utilization in humans", "authors": [{"family": "Cedernaes", "given": "Jonathan", "initials": "J"}, {"family": "Sch\u00f6nke", "given": "Milena", "initials": "M"}, {"family": "Westholm", "given": "Jakub Orzechowski", "initials": "JO"}, {"family": "Mi", "given": "Jia", "initials": "J"}, {"family": "Chibalin", "given": "Alexander", "initials": "A"}, {"family": "Voisin", "given": "Sarah", "initials": "S"}, {"family": "Osler", "given": "Megan", "initials": "M"}, {"family": "Vogel", "given": "Heike", "initials": "H"}, {"family": "H\u00f6rnaeus", "given": "Katarina", "initials": "K"}, {"family": "Dickson", "given": "Suzanne L", "initials": "SL"}, {"family": "Lind", "given": "Sara Bergstr\u00f6m", "initials": "SB"}, {"family": "Bergquist", "given": "Jonas", "initials": "J"}, {"family": "Schi\u00f6th", "given": "Helgi B", "initials": "HB"}, {"family": "Zierath", "given": "Juleen R", "initials": "JR"}, {"family": "Benedict", "given": "Christian", "initials": "C"}], "type": "journal-article", "published": "2018-08-00", "journal": {"volume": "4", "issn": "2375-2548", "issue": "8", "pages": "eaar8590", "title": "Sci Adv", "issn-l": "2375-2548"}, "abstract": null, "doi": "10.1126/sciadv.aar8590", "pmid": "30140739", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative", "Swedish Metabolomics Centre": "Service"}, "xrefs": [], "notes": [], "created": "2018-08-23T08:30:20.679Z", "modified": "2025-10-17T13:03:17.992Z"}, {"entity": "publication", "iuid": "dac35e84534a43a0933f1f769c8cd016", "links": {"self": {"href": "https://publications.scilifelab.se/publication/dac35e84534a43a0933f1f769c8cd016.json"}, "display": {"href": "https://publications.scilifelab.se/publication/dac35e84534a43a0933f1f769c8cd016"}}, "title": "Insights into Avian Incomplete Dosage Compensation: Sex-Biased Gene Expression Coevolves with Sex Chromosome Degeneration in the Common Whitethroat.", "authors": [{"family": "Sigeman", "given": "Hanna", "initials": "H", "orcid": "0000-0002-1457-4174", "researcher": {"href": "https://publications.scilifelab.se/researcher/f75fea472d1d495a92228c50bd63891e.json"}}, {"family": "Ponnikas", "given": "Suvi", "initials": "S"}, {"family": "Videvall", "given": "Elin", "initials": "E"}, {"family": "Zhang", "given": "Hongkai", "initials": "H"}, {"family": "Chauhan", "given": "Pallavi", "initials": "P"}, {"family": "Naurin", "given": "Sara", "initials": "S"}, {"family": "Hansson", "given": "Bengt", "initials": "B", "orcid": "0000-0001-6694-8169", "researcher": {"href": "https://publications.scilifelab.se/researcher/01f0144e207c41dcbc4d5aec68690e4b.json"}}], "type": "journal article", "published": "2018-07-26", "journal": {"volume": "9", "issn": "2073-4425", "issue": "8", "pages": "373", "title": "Genes", "issn-l": "2073-4425"}, "abstract": "Non-recombining sex chromosomes (Y and W) accumulate deleterious mutations and degenerate. This poses a problem for the heterogametic sex (XY males; ZW females) because a single functional gene copy often implies less gene expression and a potential imbalance of crucial expression networks. Mammals counteract this by dosage compensation, resulting in equal sex chromosome expression in males and females, whereas birds show incomplete dosage compensation with significantly lower expression in females (ZW). Here, we study the evolution of Z and W sequence divergence and sex-specific gene expression in the common whitethroat ( Sylvia communis), a species within the Sylvioidea clade where a neo-sex chromosome has been formed by a fusion between an autosome and the ancestral sex chromosome. In line with data from other birds, females had lower expression than males at the majority of sex-linked genes. Results from the neo-sex chromosome region showed that W gametologs have diverged functionally to a higher extent than their Z counterparts, and that the female-to-male expression ratio correlated negatively with the degree of functional divergence of these gametologs. We find it most likely that sex-linked genes are being suppressed in females as a response to W chromosome degradation, rather than that these genes experience relaxed selection, and thus diverge more, by having low female expression. Overall, our data of this unique avian neo-sex chromosome system suggest that incomplete dosage compensation evolves, at least partly, through gradual accumulation of deleterious mutations at the W chromosome and declining female gene expression.", "doi": "10.3390/genes9080373", "pmid": "30049999", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "genes9080373"}, {"db": "pmc", "key": "PMC6116046"}], "notes": [], "created": "2019-01-07T18:04:28.926Z", "modified": "2021-06-21T14:14:10.621Z"}, {"entity": "publication", "iuid": "6446fb0c0b9a4a8195f8004fa44e9bbe", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6446fb0c0b9a4a8195f8004fa44e9bbe.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6446fb0c0b9a4a8195f8004fa44e9bbe"}}, "title": "The psoriasis risk allele HLA-Cw0602 shows evidence of association with chronic or recurrent streptococcal tonsillitis.", "authors": [{"family": "Haapasalo", "given": "Karita", "initials": "K"}, {"family": "Koskinen", "given": "Lotta L E", "initials": "LLE"}, {"family": "Suvilehto", "given": "Jari", "initials": "J"}, {"family": "Jousilahti", "given": "Pekka", "initials": "P"}, {"family": "Wolin", "given": "Annika", "initials": "A"}, {"family": "Suomela", "given": "Sari", "initials": "S"}, {"family": "Trembath", "given": "Richard", "initials": "R"}, {"family": "Barker", "given": "Jonathan", "initials": "J"}, {"family": "Vuopio", "given": "Jaana", "initials": "J"}, {"family": "Kere", "given": "Juha", "initials": "J"}, {"family": "Jokiranta", "given": "T Sakari", "initials": "TS"}, {"family": "Saavalainen", "given": "P\u00e4ivi", "initials": "P"}], "type": "journal article", "published": "2018-07-23", "journal": {"volume": null, "issn": "1098-5522", "issue": null, "title": "Infect. Immun.", "issn-l": "0019-9567"}, "abstract": "Pharyngeal tonsillitis is one of the most common upper respiratory tract infections and Group A streptococcus is the most important bacterial pathogen causing it. While most patients experience tonsillitis only rarely, a subset of patients suffer from recurrent or chronic tonsillitis or pharyngitis. The predisposing factors for recurring or chronic form of this disease are not yet fully understood but genetic predisposition has been suggested. A genetic association study using Illumina's Immunochip SNP array was performed to search for new genetic biomarkers in pharyngeal tonsillitis. Over 100,000 SNPs relevant to immune-mediated diseases were analyzed in a cohort of 95 patients subjected to tonsillectomy due to recurrent/chronic tonsillitis and 504 controls. Genetic association between the cases and controls showed strongest association with two peaks in the HLA locus (OR 3.7-4.7, p=4.9-5.7x10", "doi": "10.1128/IAI.00304-18", "pmid": "30037793", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "IAI.00304-18"}], "notes": [], "created": "2018-08-16T15:30:12.685Z", "modified": "2024-01-16T13:48:45.963Z"}, {"entity": "publication", "iuid": "b0695922d8e0440cb8ba1f5ebf6b25a4", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b0695922d8e0440cb8ba1f5ebf6b25a4.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b0695922d8e0440cb8ba1f5ebf6b25a4"}}, "title": "Microdeletion of 7p12.1p13, including IKZF1, causes intellectual impairment, overgrowth, and susceptibility to leukaemia.", "authors": [{"family": "J\u00e4rviaho", "given": "Tekla", "initials": "T"}, {"family": "Zachariadis", "given": "Vasilios", "initials": "V"}, {"family": "Tesi", "given": "Bianca", "initials": "B"}, {"family": "Chiang", "given": "Samuel", "initials": "S"}, {"family": "Bryceson", "given": "Yenan T", "initials": "YT"}, {"family": "M\u00f6tt\u00f6nen", "given": "Merja", "initials": "M"}, {"family": "Niinim\u00e4ki", "given": "Riitta", "initials": "R"}, {"family": "Bang", "given": "Benedicte", "initials": "B"}, {"family": "Rahikkala", "given": "Elisa", "initials": "E"}, {"family": "Taylan", "given": "Fulya", "initials": "F"}, {"family": "Uusimaa", "given": "Johanna", "initials": "J"}, {"family": "Harila-Saari", "given": "Arja", "initials": "A"}, {"family": "Nordgren", "given": "Ann", "initials": "A"}], "type": "letter", "published": "2018-07-13", "journal": {"volume": null, "issn": "1365-2141", "issue": null, "title": "Br. J. Haematol.", "issn-l": "0007-1048"}, "abstract": null, "doi": "10.1111/bjh.15494", "pmid": "30004112", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2018-08-16T15:30:13.429Z", "modified": "2024-01-16T13:48:45.999Z"}, {"entity": "publication", "iuid": "42a1e90686e64d3283edb58f0af1ec60", "links": {"self": {"href": "https://publications.scilifelab.se/publication/42a1e90686e64d3283edb58f0af1ec60.json"}, "display": {"href": "https://publications.scilifelab.se/publication/42a1e90686e64d3283edb58f0af1ec60"}}, "title": "Primary glioblastoma cells for precision medicine: a quantitative portrait of genomic (in)stability during the first 30 passages.", "authors": [{"family": "Baskaran", "given": "Sathishkumar", "initials": "S"}, {"family": "Mayrhofer", "given": "Markus", "initials": "M"}, {"family": "Kultima", "given": "Hanna G\u00f6ransson", "initials": "HG"}, {"family": "Bergstr\u00f6m", "given": "Tobias", "initials": "T"}, {"family": "Elfineh", "given": "Lioudmila", "initials": "L"}, {"family": "Cavelier", "given": "Lucia", "initials": "L", "orcid": "0009-0003-8195-370X", "researcher": {"href": "https://publications.scilifelab.se/researcher/f01226edb140436da0c9d166c1f5fe51.json"}}, {"family": "Isaksson", "given": "Anders", "initials": "A"}, {"family": "Nelander", "given": "Sven", "initials": "S"}], "type": "journal article", "published": "2018-07-05", "journal": {"volume": "20", "issn": "1523-5866", "issue": "8", "pages": "1080-1091", "title": "Neuro-oncology", "issn-l": "1522-8517"}, "abstract": "Primary glioblastoma cell (GC) cultures have emerged as a key model in brain tumor research, with the potential to uncover patient-specific differences in therapy response. However, there is limited quantitative information about the stability of such cells during the initial 20-30 passages of culture.\n\nWe interrogated 3 patient-derived GC cultures at dense time intervals during the first 30 passages of culture. Combining state-of-the-art signal processing methods with a mathematical model of growth, we estimated clonal composition, rates of change, affected pathways, and correlations between altered gene dosage and transcription.\n\nWe demonstrate that GC cultures undergo sequential clonal takeovers, observed through variable proportions of specific subchromosomal lesions, variations in aneuploid cell content, and variations in subpopulation cell cycling times. The GC cultures also show significant transcriptional drift in several metabolic and signaling pathways, including ribosomal synthesis, telomere packaging and signaling via the mammalian target of rapamycin, Wnt, and interferon pathways, to a high degree explained by changes in gene dosage. In addition to these adaptations, the cultured GCs showed signs of shifting transcriptional subtype. Compared with chromosomal aberrations and gene expression, DNA methylations remained comparatively stable during passaging, and may be favorable as a biomarker.\n\nTaken together, GC cultures undergo significant genomic and transcriptional changes that need to be considered in functional experiments and biomarker studies that involve primary glioblastoma cells.", "doi": "10.1093/neuonc/noy024", "pmid": "29462414", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Clinical Genomics Uppsala": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Clinical Genomics": "Collaborative"}, "xrefs": [{"db": "pii", "key": "4860173"}, {"db": "pmc", "key": "PMC6280139"}], "notes": [], "created": "2018-10-25T08:50:53.954Z", "modified": "2024-01-16T13:48:46.006Z"}, {"entity": "publication", "iuid": "dd944194e0184f4296000d038a6b45bd", "links": {"self": {"href": "https://publications.scilifelab.se/publication/dd944194e0184f4296000d038a6b45bd.json"}, "display": {"href": "https://publications.scilifelab.se/publication/dd944194e0184f4296000d038a6b45bd"}}, "title": "The mycoparasitic fungus Clonostachys rosea responds with both common and specific gene expression during interspecific interactions with fungal prey", "authors": [{"family": "Nygren", "given": "Kristiina", "initials": "K"}, {"family": "Dubey", "given": "Mukesh", "initials": "M"}, {"family": "Zapparata", "given": "Antonio", "initials": "A"}, {"family": "Iqbal", "given": "Mudassir", "initials": "M"}, {"family": "Tzelepis", "given": "Georgios D", "initials": "GD"}, {"family": "Durling", "given": "Mikael Brandstr\u00f6m", "initials": "MB"}, {"family": "Jensen", "given": "Dan Funck", "initials": "DF"}, {"family": "Karlsson", "given": "Magnus", "initials": "M"}], "type": "journal-article", "published": "2018-07-00", "journal": {"volume": "11", "issn": "1752-4571", "issue": "6", "pages": "931-949", "title": "Evol Appl", "issn-l": "1752-4571"}, "abstract": null, "doi": "10.1111/eva.12609", "pmid": "29928301", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "SRA", "description": null, "key": "SRX3389264"}, {"db": "SRA", "description": null, "key": "SRX3389265"}, {"db": "SRA", "description": null, "key": "SRX3389266"}, {"db": "SRA", "description": null, "key": "SRX3389267"}, {"db": "SRA", "description": null, "key": "SRX3389268"}, {"db": "SRA", "description": null, "key": "SRX3389269"}], "notes": [], "created": "2018-09-14T12:11:41.309Z", "modified": "2024-01-16T13:48:46.020Z"}, {"entity": "publication", "iuid": "c44045d9e91c41a98a3649722fd11337", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c44045d9e91c41a98a3649722fd11337.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c44045d9e91c41a98a3649722fd11337"}}, "title": "The STAT4 SLE risk allele rs7574865[T] is associated with increased IL-12-induced IFN-\u03b3 production in T cells from patients with SLE.", "authors": [{"family": "Hagberg", "given": "Niklas", "initials": "N", "orcid": "0000-0003-2064-2716", "researcher": {"href": "https://publications.scilifelab.se/researcher/0d0998bb419c424083b0978ebdbe8629.json"}}, {"family": "Joelsson", "given": "Martin", "initials": "M"}, {"family": "Leonard", "given": "Dag", "initials": "D"}, {"family": "Reid", "given": "Sarah", "initials": "S"}, {"family": "Eloranta", "given": "Maija-Leena", "initials": "ML"}, {"family": "Mo", "given": "John", "initials": "J"}, {"family": "Nilsson", "given": "Magnus K", "initials": "MK"}, {"family": "Syv\u00e4nen", "given": "Ann-Christine", "initials": "AC", "orcid": "0000-0002-9681-9146", "researcher": {"href": "https://publications.scilifelab.se/researcher/f7012e35025543379380cb90efd71243.json"}}, {"family": "Bryceson", "given": "Yenan T", "initials": "YT"}, {"family": "R\u00f6nnblom", "given": "Lars", "initials": "L"}], "type": "journal article", "published": "2018-07-00", "journal": {"volume": "77", "issn": "1468-2060", "issue": "7", "pages": "1070-1077", "title": "Ann. Rheum. Dis.", "issn-l": "0003-4967"}, "abstract": "Genetic variants in the transcription factor STAT4 are associated with increased susceptibility to systemic lupus erythematosus (SLE) and a more severe disease phenotype. This study aimed to clarify how the SLE-associated intronic STAT4 risk allele rs7574865[T] affects the function of immune cells in SLE.\n\nPeripheral blood mononuclear cells (PBMCs) were isolated from 52 genotyped patients with SLE. Phosphorylation of STAT4 (pSTAT4) and STAT1 (pSTAT1) in response to interferon (IFN)-\u03b1, IFN-\u03b3 or interleukin (IL)-12, total levels of STAT4, STAT1 and T-bet, and frequency of IFN-\u03b3+ cells on IL-12 stimulation were determined by flow cytometry in subsets of immune cells before and after preactivation of cells with phytohaemagglutinin (PHA) and IL-2. Cellular responses and phenotypes were correlated to STAT4 risk allele carriership. Janus kinase inhibitors (JAKi) selective for TYK2 (TYK2i) or JAK2 (JAK2i) were evaluated for inhibition of IL-12 or IFN-\u03b3-induced activation of SLE PBMCs.\n\nIn resting PBMCs, the STAT4 risk allele was neither associated with total levels of STAT4 or STAT1, nor cytokine-induced pSTAT4 or pSTAT1. Following PHA/IL-2 activation, CD8+ T cells from STAT4 risk allele carriers displayed increased levels of STAT4 resulting in increased pSTAT4 in response to IL-12 and IFN-\u03b1, and an augmented IL-12-induced IFN-\u03b3 production in CD8+ and CD4+ T cells. The TYK2i and the JAK2i efficiently blocked IL-12 and IFN-\u03b3-induced activation of PBMCs from STAT4 risk patients, respectively.\n\nT cells from patients with SLE carrying the STAT4 risk allele rs7574865[T] display an augmented response to IL-12 and IFN-\u03b1. This subset of patients may benefit from JAKi treatment.", "doi": "10.1136/annrheumdis-2017-212794", "pmid": "29475858", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "annrheumdis-2017-212794"}, {"db": "pmc", "key": "PMC6029643"}], "notes": [], "created": "2018-05-25T13:36:29.406Z", "modified": "2024-01-16T13:48:46.027Z"}, {"entity": "publication", "iuid": "cdaa993318d2467fb7c208faa4cf604b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/cdaa993318d2467fb7c208faa4cf604b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/cdaa993318d2467fb7c208faa4cf604b"}}, "title": "Novel gene variants associated with cardiovascular disease in systemic lupus erythematosus and rheumatoid arthritis.", "authors": [{"family": "Leonard", "given": "Dag", "initials": "D"}, {"family": "Svenungsson", "given": "Elisabet", "initials": "E"}, {"family": "Dahlqvist", "given": "Johanna", "initials": "J"}, {"family": "Alexsson", "given": "Andrei", "initials": "A"}, {"family": "\u00c4rlestig", "given": "Lisbeth", "initials": "L"}, {"family": "Taylor", "given": "Kimberly E", "initials": "KE"}, {"family": "Sandling", "given": "Johanna K", "initials": "JK"}, {"family": "Bengtsson", "given": "Christine", "initials": "C"}, {"family": "Frodlund", "given": "Martina", "initials": "M"}, {"family": "J\u00f6nsen", "given": "Andreas", "initials": "A"}, {"family": "Eketj\u00e4ll", "given": "Susanna", "initials": "S"}, {"family": "Jensen-Urstad", "given": "Kerstin", "initials": "K"}, {"family": "Gunnarsson", "given": "Iva", "initials": "I"}, {"family": "Sj\u00f6wall", "given": "Christopher", "initials": "C", "orcid": "0000-0003-0900-2048", "researcher": {"href": "https://publications.scilifelab.se/researcher/fe4dd47b8ca1436e8a26fdea33f5e7f6.json"}}, {"family": "Bengtsson", "given": "Anders A", "initials": "AA"}, {"family": "Eloranta", "given": "Maija-Leena", "initials": "ML"}, {"family": "Syv\u00e4nen", "given": "Ann-Christine", "initials": "AC", "orcid": "0000-0002-9681-9146", "researcher": {"href": "https://publications.scilifelab.se/researcher/f7012e35025543379380cb90efd71243.json"}}, {"family": "Rantap\u00e4\u00e4-Dahlqvist", "given": "Solbritt", "initials": "S"}, {"family": "Criswell", "given": "Lindsey A", "initials": "LA"}, {"family": "R\u00f6nnblom", "given": "Lars", "initials": "L"}], "type": "comparative study", "published": "2018-07-00", "journal": {"volume": "77", "issn": "1468-2060", "issue": "7", "title": "Ann. Rheum. Dis.", "pages": "1063-1069", "issn-l": "0003-4967"}, "abstract": "Patients with systemic lupus erythematosus (SLE) and rheumatoid arthritis (RA) have increased risk of cardiovascular disease (CVD). We investigated whether single nucleotide polymorphisms (SNPs) at autoimmunity risk loci were associated with CVD in SLE and RA.\n\nPatients with SLE (n=1045) were genotyped using the 200K Immunochip SNP array (Illumina). The allele frequency was compared between patients with and without different manifestations of CVD. Results were replicated in a second SLE cohort (n=1043) and in an RA cohort (n=824). We analysed publicly available genetic data from general population, performed electrophoretic mobility shift assays and measured cytokine levels and occurrence of antiphospholipid antibodies (aPLs).\n\nWe identified two new putative risk loci associated with increased risk for CVD in two SLE populations, which remained after adjustment for traditional CVD risk factors. An IL19 risk allele, rs17581834(T) was associated with stroke/myocardial infarction (MI) in SLE (OR 2.3 (1.5 to 3.4), P=8.5\u00d710-5) and RA (OR 2.8 (1.4 to 5.6), P=3.8\u00d710-3), meta-analysis (OR 2.5 (2.0 to 2.9), P=3.5\u00d710-7), but not in population controls. The IL19 risk allele affected protein binding, and SLE patients with the risk allele had increased levels of plasma-IL10 (P=0.004) and aPL (P=0.01). An SRP54-AS1 risk allele, rs799454(G) was associated with stroke/transient ischaemic attack in SLE (OR 1.7 (1.3 to 2.2), P=2.5\u00d710-5) but not in RA. The SRP54-AS1 risk allele is an expression quantitative trait locus for four genes.\n\nThe IL19 risk allele was associated with stroke/MI in SLE and RA, but not in the general population, indicating that shared immune pathways may be involved in the CVD pathogenesis in inflammatory rheumatic diseases.", "doi": "10.1136/annrheumdis-2017-212614", "pmid": "29514802", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "annrheumdis-2017-212614"}, {"db": "pmc", "key": "PMC6029634"}], "notes": [], "created": "2018-05-25T13:37:05.316Z", "modified": "2024-01-16T13:48:46.041Z"}, {"entity": "publication", "iuid": "a505fac240f04a6db82466c755afc9c4", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a505fac240f04a6db82466c755afc9c4.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a505fac240f04a6db82466c755afc9c4"}}, "title": "Genome-wide association meta-analysis in 269,867 individuals identifies new genetic and functional links to intelligence.", "authors": [{"family": "Savage", "given": "Jeanne E", "initials": "JE"}, {"family": "Jansen", "given": "Philip R", "initials": "PR"}, {"family": "Stringer", "given": "Sven", "initials": "S"}, {"family": "Watanabe", "given": "Kyoko", "initials": "K"}, {"family": "Bryois", "given": "Julien", "initials": "J"}, {"family": "de Leeuw", "given": "Christiaan A", "initials": "CA"}, {"family": "Nagel", "given": "Mats", "initials": "M"}, {"family": "Awasthi", "given": "Swapnil", "initials": "S"}, {"family": "Barr", "given": "Peter B", "initials": "PB"}, {"family": "Coleman", "given": "Jonathan R I", "initials": "JRI"}, {"family": "Grasby", "given": "Katrina L", "initials": "KL"}, {"family": "Hammerschlag", "given": "Anke R", "initials": "AR"}, {"family": "Kaminski", "given": "Jakob A", "initials": "JA"}, {"family": "Karlsson", "given": "Robert", "initials": "R"}, {"family": "Krapohl", "given": "Eva", "initials": "E"}, {"family": "Lam", "given": "Max", "initials": "M"}, {"family": "Nygaard", "given": "Marianne", "initials": "M"}, {"family": "Reynolds", "given": "Chandra A", "initials": "CA"}, {"family": "Trampush", "given": "Joey W", "initials": "JW"}, {"family": "Young", "given": "Hannah", "initials": "H"}, {"family": "Zabaneh", "given": "Delilah", "initials": "D"}, {"family": "H\u00e4gg", "given": "Sara", "initials": "S"}, {"family": "Hansell", "given": "Narelle K", "initials": "NK"}, {"family": "Karlsson", "given": "Ida K", "initials": "IK"}, {"family": "Linnarsson", "given": "Sten", "initials": "S"}, {"family": "Montgomery", "given": "Grant W", "initials": "GW"}, {"family": "Mu\u00f1oz-Manchado", "given": "Ana B", "initials": "AB"}, {"family": "Quinlan", "given": "Erin B", "initials": "EB"}, {"family": "Schumann", "given": "Gunter", "initials": "G"}, {"family": "Skene", "given": "Nathan G", "initials": "NG"}, {"family": "Webb", "given": "Bradley T", "initials": "BT"}, {"family": "White", "given": "Tonya", "initials": "T"}, {"family": "Arking", "given": "Dan E", "initials": "DE"}, {"family": "Avramopoulos", "given": "Dimitrios", "initials": "D"}, {"family": "Bilder", "given": "Robert M", "initials": "RM"}, {"family": "Bitsios", "given": "Panos", "initials": "P"}, {"family": "Burdick", "given": "Katherine E", "initials": "KE"}, {"family": "Cannon", "given": "Tyrone D", "initials": "TD"}, {"family": "Chiba-Falek", "given": "Ornit", "initials": "O"}, {"family": "Christoforou", "given": "Andrea", "initials": "A"}, {"family": "Cirulli", "given": "Elizabeth T", "initials": "ET"}, {"family": "Congdon", "given": "Eliza", "initials": "E"}, {"family": "Corvin", "given": "Aiden", "initials": "A"}, {"family": "Davies", "given": "Gail", "initials": "G"}, {"family": "Deary", "given": "Ian J", "initials": "IJ"}, {"family": "DeRosse", "given": "Pamela", "initials": "P"}, {"family": "Dickinson", "given": "Dwight", "initials": "D"}, {"family": "Djurovic", "given": "Srdjan", "initials": "S"}, {"family": "Donohoe", "given": "Gary", "initials": "G"}, {"family": "Conley", "given": "Emily Drabant", "initials": "ED"}, {"family": "Eriksson", "given": "Johan G", "initials": "JG"}, {"family": "Espeseth", "given": "Thomas", "initials": "T"}, {"family": "Freimer", "given": "Nelson A", "initials": "NA"}, {"family": "Giakoumaki", "given": "Stella", "initials": "S"}, {"family": "Giegling", "given": "Ina", "initials": "I"}, {"family": "Gill", "given": "Michael", "initials": "M"}, {"family": "Glahn", "given": "David C", "initials": "DC"}, {"family": "Hariri", "given": "Ahmad R", "initials": "AR"}, {"family": "Hatzimanolis", "given": "Alex", "initials": "A"}, {"family": "Keller", "given": "Matthew C", "initials": "MC"}, {"family": "Knowles", "given": "Emma", "initials": "E"}, {"family": "Koltai", "given": "Deborah", "initials": "D"}, {"family": "Konte", "given": "Bettina", "initials": "B"}, {"family": "Lahti", "given": "Jari", "initials": "J"}, {"family": "Le Hellard", "given": "Stephanie", "initials": "S"}, {"family": "Lencz", "given": "Todd", "initials": "T"}, {"family": "Liewald", "given": "David C", "initials": "DC"}, {"family": "London", "given": "Edythe", "initials": "E"}, {"family": "Lundervold", "given": "Astri J", "initials": "AJ"}, {"family": "Malhotra", "given": "Anil K", "initials": "AK"}, {"family": "Melle", "given": "Ingrid", "initials": "I"}, {"family": "Morris", "given": "Derek", "initials": "D"}, {"family": "Need", "given": "Anna C", "initials": "AC"}, {"family": "Ollier", "given": "William", "initials": "W"}, {"family": "Palotie", "given": "Aarno", "initials": "A"}, {"family": "Payton", "given": "Antony", "initials": "A"}, {"family": "Pendleton", "given": "Neil", "initials": "N"}, {"family": "Poldrack", "given": "Russell A", "initials": "RA"}, {"family": "R\u00e4ikk\u00f6nen", "given": "Katri", 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"initials": "S"}, {"family": "van der Sluis", "given": "Sophie", "initials": "S"}, {"family": "Sullivan", "given": "Patrick F", "initials": "PF"}, {"family": "Vrieze", "given": "Scott I", "initials": "SI"}, {"family": "Wright", "given": "Margaret J", "initials": "MJ"}, {"family": "Posthuma", "given": "Danielle", "initials": "D"}], "type": "journal article", "published": "2018-07-00", "journal": {"volume": "50", "issn": "1546-1718", "issue": "7", "pages": "912-919", "title": "Nat. Genet.", "issn-l": "1061-4036"}, "abstract": "Intelligence is highly heritable", "doi": "10.1038/s41588-018-0152-6", "pmid": "29942086", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41588-018-0152-6"}], "notes": [], "created": "2018-08-16T15:30:14.990Z", "modified": "2024-01-16T13:48:46.064Z"}, {"entity": "publication", "iuid": "063c889fe9784694a611e1bdb721d8cf", "links": {"self": {"href": "https://publications.scilifelab.se/publication/063c889fe9784694a611e1bdb721d8cf.json"}, "display": {"href": "https://publications.scilifelab.se/publication/063c889fe9784694a611e1bdb721d8cf"}}, "title": "The contribution of common genetic risk variants for ADHD to a general factor of childhood psychopathology.", "authors": [{"family": "Brikell", "given": "Isabell", "initials": "I"}, {"family": "Larsson", "given": "Henrik", "initials": "H"}, {"family": "Lu", "given": "Yi", "initials": "Y"}, {"family": "Pettersson", "given": "Erik", "initials": "E"}, {"family": "Chen", "given": "Qi", "initials": "Q"}, {"family": "Kuja-Halkola", "given": "Ralf", "initials": "R"}, {"family": "Karlsson", "given": "Robert", "initials": "R"}, {"family": "Lahey", "given": "Benjamin B", "initials": "BB"}, {"family": "Lichtenstein", "given": "Paul", "initials": "P"}, {"family": "Martin", "given": "Joanna", "initials": "J"}], "type": "journal article", "published": "2018-06-22", "journal": {"volume": null, "issn": "1476-5578", "issue": null, "title": "Mol. Psychiatry", "issn-l": "1359-4184"}, "abstract": "Common genetic risk variants have been implicated in the etiology of clinical attention-deficit/hyperactivity disorder (ADHD) diagnoses and symptoms in the general population. However, given the extensive comorbidity across ADHD and other psychiatric conditions, the extent to which genetic variants associated with ADHD also influence broader psychopathology dimensions remains unclear. The aim of this study was to evaluate the associations between ADHD polygenic risk scores (PRS) and a broad range of childhood psychiatric symptoms, and to quantify the extent to which such associations can be attributed to a general factor of childhood psychopathology. We derived ADHD PRS for 13,457 children aged 9 or 12 from the Child and Adolescent Twin Study in Sweden, using results from an independent meta-analysis of genome-wide association studies of ADHD diagnosis and symptoms. We estimated associations between ADHD PRS, a general psychopathology factor, and several dimensions of neurodevelopmental, externalizing, and internalizing symptoms, using structural equation modeling. Higher ADHD PRS were statistically significantly associated with elevated neurodevelopmental, externalizing, and depressive symptoms (R ", "doi": "10.1038/s41380-018-0109-2", "pmid": "29934545", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41380-018-0109-2"}], "notes": [], "created": "2018-08-16T15:30:15.839Z", "modified": "2020-08-04T14:50:05.680Z"}, {"entity": "publication", "iuid": "bf6a05225afc4d75b05e3c0c53c77044", "links": {"self": {"href": "https://publications.scilifelab.se/publication/bf6a05225afc4d75b05e3c0c53c77044.json"}, "display": {"href": "https://publications.scilifelab.se/publication/bf6a05225afc4d75b05e3c0c53c77044"}}, "title": "Novel genetic associations for blood pressure identified via gene-alcohol interaction in up to 570K individuals across multiple ancestries.", "authors": [{"family": "Feitosa", "given": "Mary F", "initials": "MF"}, {"family": "Kraja", 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"initials": "P"}, {"family": "Wagenknecht", "given": "Lynne E", "initials": "LE"}, {"family": "Wareham", "given": "Nicholas J", "initials": "NJ"}, {"family": "Watkins", "given": "Hugh", "initials": "H"}, {"family": "Weir", "given": "David R", "initials": "DR"}, {"family": "Wickremasinghe", "given": "Ananda R", "initials": "AR"}, {"family": "Wu", "given": "Tangchun", "initials": "T"}, {"family": "Zheng", "given": "Wei", "initials": "W"}, {"family": "Bouchard", "given": "Claude", "initials": "C"}, {"family": "Christensen", "given": "Kaare", "initials": "K"}, {"family": "Evans", "given": "Michele K", "initials": "MK"}, {"family": "Gudnason", "given": "Vilmundur", "initials": "V"}, {"family": "Horta", "given": "Bernardo L", "initials": "BL"}, {"family": "Kardia", "given": "Sharon L R", "initials": "SLR"}, {"family": "Liu", "given": "Yongmei", "initials": "Y"}, {"family": "Pereira", "given": "Alexandre C", "initials": "AC"}, {"family": "Psaty", "given": "Bruce M", "initials": "BM"}, {"family": "Ridker", "given": "Paul M", "initials": "PM"}, {"family": "van Dam", "given": "Rob M", "initials": "RM"}, {"family": "Gauderman", "given": "W James", "initials": "WJ"}, {"family": "Zhu", "given": "Xiaofeng", "initials": "X"}, {"family": "Mook-Kanamori", "given": "Dennis O", "initials": "DO"}, {"family": "Fornage", "given": "Myriam", "initials": "M"}, {"family": "Rotimi", "given": "Charles N", "initials": "CN"}, {"family": "Cupples", "given": "L Adrienne", "initials": "LA"}, {"family": "Kelly", "given": "Tanika N", "initials": "TN"}, {"family": "Fox", "given": "Ervin R", "initials": "ER"}, {"family": "Hayward", "given": "Caroline", "initials": "C"}, {"family": "van Duijn", "given": "Cornelia M", "initials": "CM"}, {"family": "Tai", "given": "E Shyong", "initials": "ES"}, {"family": "Wong", "given": "Tien Yin", "initials": "TY"}, {"family": "Kooperberg", "given": "Charles", "initials": "C"}, {"family": "Palmas", "given": "Walter", "initials": "W"}, {"family": "Rice", "given": "Kenneth", "initials": "K"}, {"family": "Morrison", "given": "Alanna C", "initials": "AC"}, {"family": "Elliott", "given": "Paul", "initials": "P"}, {"family": "Caulfield", "given": "Mark J", "initials": "MJ"}, {"family": "Munroe", "given": "Patricia B", "initials": "PB"}, {"family": "Rao", "given": "Dabeeru C", "initials": "DC"}, {"family": "Province", "given": "Michael A", "initials": "MA"}, {"family": "Levy", "given": "Daniel", "initials": "D"}], "type": "journal article", "published": "2018-06-18", "journal": {"volume": "13", "issn": "1932-6203", "issue": "6", "pages": "e0198166", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "Heavy alcohol consumption is an established risk factor for hypertension; the mechanism by which alcohol consumption impact blood pressure (BP) regulation remains unknown. We hypothesized that a genome-wide association study accounting for gene-alcohol consumption interaction for BP might identify additional BP loci and contribute to the understanding of alcohol-related BP regulation. We conducted a large two-stage investigation incorporating joint testing of main genetic effects and single nucleotide variant (SNV)-alcohol consumption interactions. In Stage 1, genome-wide discovery meta-analyses in \u2248131K individuals across several ancestry groups yielded 3,514 SNVs (245 loci) with suggestive evidence of association (P < 1.0 x 10-5). In Stage 2, these SNVs were tested for independent external replication in \u2248440K individuals across multiple ancestries. We identified and replicated (at Bonferroni correction threshold) five novel BP loci (380 SNVs in 21 genes) and 49 previously reported BP loci (2,159 SNVs in 109 genes) in European ancestry, and in multi-ancestry meta-analyses (P < 5.0 x 10-8). For African ancestry samples, we detected 18 potentially novel BP loci (P < 5.0 x 10-8) in Stage 1 that warrant further replication. Additionally, correlated meta-analysis identified eight novel BP loci (11 genes). Several genes in these loci (e.g., PINX1, GATA4, BLK, FTO and GABBR2) have been previously reported to be associated with alcohol consumption. These findings provide insights into the role of alcohol consumption in the genetic architecture of hypertension.", "doi": "10.1371/journal.pone.0198166", "pmid": "29912962", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "PONE-D-18-04838"}, {"db": "dbGaP", "description": null, "key": "phs000930"}], "notes": [], "created": "2018-06-19T08:24:15.756Z", "modified": "2024-01-16T13:48:46.111Z"}, {"entity": "publication", "iuid": "0b7149b563544ff390db27e0229d0286", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0b7149b563544ff390db27e0229d0286.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0b7149b563544ff390db27e0229d0286"}}, "title": "Multi-ethnic genome-wide association study for atrial fibrillation.", "authors": [{"family": "Roselli", "given": "Carolina", "initials": "C", 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{"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}, {"family": "Noordam", "given": "Raymond", "initials": "R"}, {"family": "Oellers", "given": "Heidi", "initials": "H"}, {"family": "Olesen", "given": "Morten S", "initials": "MS"}, {"family": "Orho-Melander", "given": "Marju", "initials": "M"}, {"family": "Padmanabhan", "given": "Sandosh", "initials": "S"}, {"family": "Pak", "given": "Hui-Nam", "initials": "HN"}, {"family": "Par\u00e9", "given": "Guillaume", "initials": "G"}, {"family": "Pedersen", "given": "Nancy L", "initials": "NL"}, {"family": "Pera", "given": "Joanna", "initials": "J"}, {"family": "Pereira", "given": "Alexandre", "initials": "A"}, {"family": "Porteous", "given": "David", "initials": "D"}, {"family": "Psaty", "given": "Bruce M", "initials": "BM"}, {"family": "Pulit", "given": "Sara L", "initials": "SL", "orcid": "0000-0002-2502-3669", "researcher": {"href": "https://publications.scilifelab.se/researcher/58262d1f682844fa9c5ac03cc66c98bd.json"}}, {"family": "Pullinger", "given": "Clive R", "initials": "CR"}, {"family": "Rader", "given": "Daniel J", "initials": "DJ"}, {"family": "Refsgaard", "given": "Lena", "initials": "L"}, {"family": "Ribas\u00e9s", "given": "Marta", "initials": "M", "orcid": "0000-0003-1039-1116", "researcher": {"href": "https://publications.scilifelab.se/researcher/643ddd67f10547c3a68ab3c5cd9ee627.json"}}, {"family": "Ridker", "given": "Paul M", "initials": "PM"}, {"family": "Rienstra", "given": "Michiel", "initials": "M", "orcid": "0000-0002-2581-070X", "researcher": {"href": "https://publications.scilifelab.se/researcher/59631fa00f1341c69ff195433b9558bc.json"}}, {"family": "Risch", "given": "Lorenz", "initials": "L"}, {"family": "Roden", "given": "Dan M", "initials": "DM"}, {"family": "Rosand", "given": "Jonathan", "initials": "J"}, {"family": "Rosenberg", "given": "Michael A", "initials": "MA"}, {"family": "Rost", "given": "Natalia", "initials": "N"}, {"family": "Rotter", "given": "Jerome I", "initials": "JI"}, {"family": "Saba", "given": "Samir", "initials": "S"}, {"family": "Sandhu", "given": "Roopinder K", "initials": "RK"}, {"family": "Schnabel", "given": "Renate B", "initials": "RB"}, {"family": "Schramm", "given": "Katharina", "initials": "K"}, {"family": "Schunkert", "given": "Heribert", "initials": "H"}, {"family": "Schurman", "given": "Claudia", "initials": "C"}, {"family": "Scott", "given": "Stuart A", "initials": "SA", "orcid": "0000-0001-5720-1864", "researcher": {"href": "https://publications.scilifelab.se/researcher/2cb1efe5da074b6885f59ba4d80cbcd5.json"}}, {"family": "Sepp\u00e4l\u00e4", "given": "Ilkka", "initials": "I", "orcid": "0000-0002-5595-2573", "researcher": {"href": "https://publications.scilifelab.se/researcher/002e1ad9cce74565b24a9d69186abdbe.json"}}, {"family": "Shaffer", "given": "Christian", "initials": "C"}, {"family": "Shah", "given": "Svati", "initials": "S"}, {"family": "Shalaby", "given": "Alaa A", "initials": "AA"}, {"family": "Shim", "given": "Jaemin", "initials": "J"}, {"family": "Shoemaker", "given": "M Benjamin", "initials": "MB"}, {"family": "Siland", "given": "Joylene E", "initials": "JE", "orcid": "0000-0003-4404-1245", "researcher": {"href": "https://publications.scilifelab.se/researcher/1bde79f9f39d43e78b477b2f34662fd6.json"}}, {"family": "Sinisalo", "given": "Juha", "initials": "J", "orcid": "0000-0002-0169-5137", "researcher": {"href": "https://publications.scilifelab.se/researcher/6fde24cdfda24aed83d888da0d9b6811.json"}}, {"family": "Sinner", "given": "Moritz F", "initials": "MF"}, {"family": "Slowik", "given": "Agnieszka", "initials": "A"}, {"family": "Smith", "given": "Albert V", "initials": "AV", "orcid": "0000-0003-1942-5845", "researcher": {"href": "https://publications.scilifelab.se/researcher/7b28739aa7d746718d670363d7c18a40.json"}}, {"family": "Smith", "given": "Blair H", "initials": "BH", "orcid": "0000-0002-5362-9430", "researcher": {"href": "https://publications.scilifelab.se/researcher/ed343544e1324911931517689ad9ba6b.json"}}, {"family": "Smith", "given": "J Gustav", "initials": "JG"}, {"family": "Smith", "given": "Jonathan D", "initials": "JD", "orcid": "0000-0002-0415-386X", "researcher": {"href": "https://publications.scilifelab.se/researcher/bff6aa4d1bef4ec597a324b3f5f08f6b.json"}}, {"family": "Smith", "given": "Nicholas L", "initials": "NL"}, {"family": "Soliman", "given": "Elsayed Z", "initials": "EZ", "orcid": "0000-0001-5632-8150", "researcher": {"href": "https://publications.scilifelab.se/researcher/96e79156ff664c509217e8834a728c79.json"}}, {"family": "Sotoodehnia", "given": "Nona", "initials": "N"}, {"family": "Stricker", "given": "Bruno H", "initials": "BH"}, {"family": "Sun", "given": "Albert", "initials": "A"}, {"family": "Sun", "given": "Han", "initials": "H"}, {"family": "Svendsen", "given": "Jesper H", "initials": "JH", "orcid": "0000-0001-8466-8515", "researcher": {"href": "https://publications.scilifelab.se/researcher/a99cc6393d014fd9b0f98df016f5854c.json"}}, {"family": "Tanaka", "given": "Toshihiro", "initials": "T", "orcid": "0000-0001-6201-9784", "researcher": {"href": "https://publications.scilifelab.se/researcher/021685ef890444bbb2870298ca2399d1.json"}}, {"family": "Tanriverdi", "given": "Kahraman", "initials": "K"}, {"family": "Taylor", "given": "Kent D", "initials": "KD"}, {"family": "Teder-Laving", "given": "Maris", "initials": "M"}, {"family": "Teumer", "given": "Alexander", "initials": "A", "orcid": "0000-0002-8309-094X", "researcher": {"href": "https://publications.scilifelab.se/researcher/dc9c2667a55b47a6a08aea764fab0946.json"}}, {"family": "Th\u00e9riault", "given": "S\u00e9bastien", "initials": "S"}, {"family": "Trompet", "given": "Stella", "initials": "S"}, {"family": "Tucker", "given": "Nathan R", "initials": "NR", "orcid": "0000-0002-5071-4218", "researcher": {"href": "https://publications.scilifelab.se/researcher/f89b1366ff014dc6a9cc5fe4bd37becf.json"}}, {"family": "Tveit", "given": "Arnljot", "initials": "A"}, {"family": "Uitterlinden", "given": "Andre G", "initials": "AG"}, {"family": "Van Der Harst", "given": "Pim", "initials": "P", "orcid": "0000-0002-2713-686X", "researcher": {"href": "https://publications.scilifelab.se/researcher/a710eb0e12344e8fb5083599c95a1b2e.json"}}, {"family": "Van Gelder", "given": "Isabelle C", "initials": "IC"}, {"family": "Van Wagoner", "given": "David R", "initials": "DR", "orcid": "0000-0001-8250-9828", "researcher": {"href": "https://publications.scilifelab.se/researcher/f0472987e8c34f3284810916d6396afa.json"}}, {"family": "Verweij", "given": "Niek", "initials": "N", "orcid": "0000-0002-4303-7685", "researcher": {"href": "https://publications.scilifelab.se/researcher/7306319d42a640a483b937de588a17a4.json"}}, {"family": "Vlachopoulou", "given": "Efthymia", "initials": "E"}, {"family": "V\u00f6lker", "given": "Uwe", "initials": "U"}, {"family": "Wang", "given": "Biqi", "initials": "B"}, {"family": "Weeke", "given": "Peter E", "initials": "PE"}, {"family": "Weijs", "given": "Bob", "initials": "B", "orcid": "0000-0003-3202-4931", "researcher": {"href": "https://publications.scilifelab.se/researcher/a5f4a2e7a32d45a1843f130d3dd2cbfa.json"}}, {"family": "Weiss", "given": "Raul", "initials": "R"}, {"family": "Weiss", "given": "Stefan", "initials": "S", "orcid": "0000-0002-3553-4315", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a7c021b692c4fc1b2468c63fd0b2c43.json"}}, {"family": "Wells", "given": "Quinn S", "initials": "QS"}, {"family": "Wiggins", "given": "Kerri L", "initials": "KL", "orcid": "0000-0003-2749-1279", "researcher": {"href": "https://publications.scilifelab.se/researcher/a9d1f9cb10ef4038abb10fb6ee289504.json"}}, {"family": "Wong", "given": "Jorge A", "initials": "JA"}, {"family": "Woo", "given": "Daniel", "initials": "D"}, {"family": "Worrall", "given": "Bradford B", "initials": "BB"}, {"family": "Yang", "given": "Pil-Sung", "initials": "PS"}, {"family": "Yao", "given": "Jie", "initials": "J"}, {"family": "Yoneda", "given": "Zachary T", "initials": "ZT"}, {"family": "Zeller", "given": "Tanja", "initials": "T"}, {"family": "Zeng", "given": "Lingyao", "initials": "L"}, {"family": "Lubitz", "given": "Steven A", "initials": "SA", "orcid": "0000-0002-9599-4866", "researcher": {"href": "https://publications.scilifelab.se/researcher/25bb007311104c92983dbcce80f72260.json"}}, {"family": "Lunetta", "given": "Kathryn L", "initials": "KL"}, {"family": "Ellinor", "given": "Patrick T", "initials": "PT", "orcid": "0000-0002-2067-0533", "researcher": {"href": "https://publications.scilifelab.se/researcher/dd513dc49e0945bc8298f72d1244648d.json"}}], "type": "journal article", "published": "2018-06-11", "journal": {"volume": "50", "issn": "1546-1718", "issue": "9", "pages": "1225-1233", "title": "Nat. Genet.", "issn-l": "1061-4036"}, "abstract": "Atrial fibrillation (AF) affects more than 33 million individuals worldwide1 and has a complex heritability2. We conducted the largest meta-analysis of genome-wide association studies (GWAS) for AF to date, consisting of more than half a million individuals, including 65,446 with AF. In total, we identified 97 loci significantly associated with AF, including 67 that were novel in a combined-ancestry analysis, and 3 that were novel in a European-specific analysis. We sought to identify AF-associated genes at the GWAS loci by performing RNA-sequencing and expression quantitative trait locus analyses in 101 left atrial samples, the most relevant tissue for AF. We also performed transcriptome-wide analyses that identified 57 AF-associated genes, 42 of which overlap with GWAS loci. The identified loci implicate genes enriched within cardiac developmental, electrophysiological, contractile and structural pathways. These results extend our understanding of the biological pathways underlying AF and may facilitate the development of therapeutics for AF.", "doi": "10.1038/s41588-018-0133-9", "pmid": "29892015", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41588-018-0133-9"}, {"db": "pmc", "key": "PMC6136836"}, {"db": "mid", "key": "NIHMS986675"}], "notes": [], "created": "2019-01-09T07:22:19.148Z", "modified": "2021-07-07T15:50:02.934Z"}, {"entity": "publication", "iuid": "937bc08ab3ab4db49e117c514bd26f7d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/937bc08ab3ab4db49e117c514bd26f7d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/937bc08ab3ab4db49e117c514bd26f7d"}}, "title": "Presence of Aedes and Anopheles mosquito larvae is correlated to bacteria found in domestic water-storage containers", "authors": [{"family": "Nilsson", "given": "Louise K J", "initials": "LKJ"}, {"family": "Sharma", "given": "Anil", "initials": "A"}, {"family": "Bhatnagar", "given": "Raj K", "initials": "RK"}, {"family": "Bertilsson", "given": "Stefan", "initials": "S"}, {"family": "Terenius", "given": "Olle", "initials": "O"}], "type": "journal-article", "published": "2018-06-01", "journal": {"volume": "94", "issn": "1574-6941", "issue": "6", "pages": null, "title": "FEMS Microbiol. Ecol.", "issn-l": "0168-6496"}, "abstract": null, "doi": "10.1093/femsec/fiy058", "pmid": "29617987", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "BioProject", "description": "Bacteria in domestic water-storage containers with or without mosquito larvae", "key": "PRJEB23603"}], "notes": [], "created": "2018-09-14T11:53:12.563Z", "modified": "2024-01-16T13:48:46.154Z"}, {"entity": "publication", "iuid": "9e64fa647d38400ba492319e0a977640", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9e64fa647d38400ba492319e0a977640.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9e64fa647d38400ba492319e0a977640"}}, "title": "Paternally expressed imprinted genes associate with hybridization barriers in Capsella", "authors": [{"family": "Lafon-Placette", "given": "Cl\u00e9ment", "initials": "C"}, {"family": "Hatorangan", "given": "Marcelinus R", "initials": "MR"}, {"family": "Steige", "given": "Kim A", "initials": "KA"}, {"family": "Cornille", "given": "Amandine", "initials": "A"}, {"family": "Lascoux", "given": "Martin", "initials": "M"}, {"family": "Slotte", "given": "Tanja", "initials": "T"}, {"family": "K\u00f6hler", "given": "Claudia", "initials": "C"}], "type": "journal-article", "published": "2018-06-00", "journal": {"volume": "4", "issn": "2055-0278", "issue": "6", "pages": "352-357", "title": "NPLANTS", "issn-l": "2055-0278"}, "abstract": null, "doi": "10.1038/s41477-018-0161-6", "pmid": "29808019", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "GEO", "description": null, "key": "GSE103209"}], "notes": [], "created": "2018-09-14T11:54:00.459Z", "modified": "2024-01-16T13:48:46.176Z"}, {"entity": "publication", "iuid": "a29bd4ef267a4b778f2f943952323440", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a29bd4ef267a4b778f2f943952323440.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a29bd4ef267a4b778f2f943952323440"}}, "title": "A genome scan for quantitative trait loci affecting average daily gain and Kleiber ratio in Baluchi Sheep.", "authors": [{"family": "Pasandideh", "given": "Majid", "initials": "M", "orcid": "0000-0001-5340-7072", "researcher": {"href": "https://publications.scilifelab.se/researcher/431b9c421917406c8d4f3769bfde17ed.json"}}, {"family": "Rahimi-Mianji", "given": "Ghodrat", "initials": "G"}, {"family": "Gholizadeh", "given": "Mohsen", "initials": "M"}], "type": "journal article", "published": "2018-06-00", "journal": {"volume": "97", "issn": "0973-7731", "issue": "2", "pages": "493-503", "title": "J. Genet.", "issn-l": "0022-1333"}, "abstract": "Genomewide association study (GWAS) is an efficient tool for the detection of SNPs and candidate genes in quantitative traits. Growth rate is an important trait for increasing the meat production in sheep. A total of 96 Baluchi sheep were genotyped using Illumina Ovine SNP50 BeadChip to run a GWAS for an average daily gain (ADG) and Kleiber ratio (KR) traits in different periods of age in sheep. Traits included were average daily gain from birth to three months (ADG 0-3), from three months to six months (ADG3-6), from six months to nine months (ADG6-9), from nine months to yearling (ADG9-12), from birth to six months (ADG0-6), from three months to nine months (ADG3-9), from three months to yearling (ADG3-12) and corresponding Kleiber ratios (KR0-3, KR3-6, KR6-9, KR9-12, KR0-6, KR3-9 and KR3-12, respectively). A total of 42,243 SNPs passed the quality-control filters and were analysed by PLINK software in a linear mixed model. Two SNPs were identified on two chromosomes at the 5% genomewide significance level for KR(3-9) and KR(6-9). Two candidate genes, namely MAGI1 and ZNF770, were identified correspondingly harbouring and close to these QTL. Also, a total of 21 SNPs were found on chromosomes 2, 3, 5, 6, 7, 10, 17, 19, 20 and 25 at the 5% chromosomewide significance level for ADG and KR traits. Thus, we suggest more studies to discover the causative variants for growth traits in sheep.", "doi": null, "pmid": "29932070", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [], "notes": [], "created": "2019-01-09T07:22:18.276Z", "modified": "2025-11-17T09:37:20.445Z"}, {"entity": "publication", "iuid": "2432b8319537478db9d2c886bdae3627", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2432b8319537478db9d2c886bdae3627.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2432b8319537478db9d2c886bdae3627"}}, "title": "Equilibrative nucleoside transporter 1 gene polymorphisms and clinical outcomes following acute coronary syndromes: findings from the PLATelet inhibition and patient Outcomes (PLATO) study.", "authors": [{"family": "Parker", "given": "William A E", "initials": "WAE"}, {"family": "Eriksson", "given": "Niclas", "initials": "N"}, {"family": "Becker", "given": "Richard C", "initials": "RC"}, {"family": "Voora", "given": "Deepak", "initials": "D"}, {"family": "\u00c5kerblom", "given": "Axel", "initials": "A"}, {"family": "Himmelmann", "given": "Anders", "initials": "A"}, {"family": "James", "given": "Stefan K", "initials": "SK"}, {"family": "Wallentin", "given": "Lars", "initials": "L"}, {"family": "Storey", "given": "Robert F", "initials": "RF"}, {"family": "PLATO Investigators", "given": "", "initials": ""}], "type": "journal article", "published": "2018-05-31", "journal": {"volume": null, "issn": "1369-1635", "issue": null, "pages": "1-10", "title": "Platelets", "issn-l": "0953-7104"}, "abstract": "In the PLATelet inhibition and patient Outcomes (PLATO) study, the P2Y", "doi": "10.1080/09537104.2018.1478404", "pmid": "29851527", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2018-06-15T07:31:29.862Z", "modified": "2024-01-16T13:48:46.258Z"}, {"entity": "publication", "iuid": "363baf22ded848369cab003f044d527c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/363baf22ded848369cab003f044d527c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/363baf22ded848369cab003f044d527c"}}, "title": "Common genetic variation in the autoimmune regulator (AIRE) locus is associated with autoimmune Addison's disease in Sweden.", "authors": [{"family": "Eriksson", "given": "Daniel", "initials": "D", "orcid": "0000-0001-5473-3312", "researcher": {"href": "https://publications.scilifelab.se/researcher/f9c26578a5e548f783b9465e04fb0bfc.json"}}, {"family": "Bianchi", "given": "Matteo", "initials": "M"}, {"family": "Landegren", "given": "Nils", "initials": "N"}, {"family": "Dalin", "given": "Frida", "initials": "F"}, {"family": "Skov", "given": "Jakob", "initials": "J"}, {"family": "Hultin-Rosenberg", "given": "Lina", "initials": "L"}, {"family": "Mathioudaki", "given": "Argyri", "initials": "A"}, {"family": "Nordin", "given": "Jessika", "initials": "J"}, {"family": "Hallgren", "given": "\u00c5sa", "initials": "\u00c5"}, {"family": "Andersson", "given": "G\u00f6ran", "initials": "G"}, {"family": "Tandre", "given": "Karolina", "initials": "K"}, {"family": "Rantap\u00e4\u00e4 Dahlqvist", "given": "Solbritt", "initials": "S"}, {"family": "S\u00f6derkvist", "given": "Peter", "initials": "P", "orcid": "0000-0001-9867-8706", "researcher": {"href": "https://publications.scilifelab.se/researcher/c1fc163b9a08421180f7f235af3897f4.json"}}, {"family": "R\u00f6nnblom", "given": "Lars", "initials": "L"}, {"family": "Hulting", "given": "Anna-Lena", "initials": "AL"}, {"family": "Wahlberg", "given": "Jeanette", "initials": "J"}, {"family": "Dahlqvist", "given": "Per", "initials": "P"}, {"family": "Ekwall", "given": "Olov", "initials": "O"}, {"family": "Meadows", "given": "Jennifer R S", "initials": "JRS"}, {"family": "Lindblad-Toh", "given": "Kerstin", "initials": "K", "orcid": "0000-0001-8338-0253", "researcher": {"href": "https://publications.scilifelab.se/researcher/e0063145f7d6476f80ab42f94833f4cf.json"}}, {"family": "Bensing", "given": "Sophie", "initials": "S"}, {"family": "Rosengren Pielberg", "given": "Gerli", "initials": "G"}, {"family": "K\u00e4mpe", "given": "Olle", "initials": "O", "orcid": "0000-0001-6091-9914", "researcher": {"href": "https://publications.scilifelab.se/researcher/2c547dc809a14cdaa47b623cf638162b.json"}}], "type": "journal article", "published": "2018-05-30", "journal": {"volume": "8", "issn": "2045-2322", "issue": "1", "pages": "8395", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "Autoimmune Addison's disease (AAD) is the predominating cause of primary adrenal failure. Despite its high heritability, the rarity of disease has long made candidate-gene studies the only feasible methodology for genetic studies. Here we conducted a comprehensive reinvestigation of suggested AAD risk loci and more than 1800 candidate genes with associated regulatory elements in 479 patients with AAD and 2394 controls. Our analysis enabled us to replicate many risk variants, but several other previously suggested risk variants failed confirmation. By exploring the full set of 1800 candidate genes, we further identified common variation in the autoimmune regulator (AIRE) as a novel risk locus associated to sporadic AAD in our study. Our findings not only confirm that multiple loci are associated with disease risk, but also show to what extent the multiple risk loci jointly associate to AAD. In total, risk loci discovered to date only explain about 7% of variance in liability to AAD in our study population.", "doi": "10.1038/s41598-018-26842-2", "pmid": "29849176", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-018-26842-2"}, {"db": "pmc", "key": "PMC5976627"}], "notes": [], "created": "2018-06-15T07:31:30.585Z", "modified": "2024-01-16T13:48:46.273Z"}, {"entity": "publication", "iuid": "f6c63ebca6b24dbdb0c965a6353ac836", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f6c63ebca6b24dbdb0c965a6353ac836.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f6c63ebca6b24dbdb0c965a6353ac836"}}, "title": "Study of 300,486 individuals identifies 148 independent genetic loci influencing general cognitive function.", "authors": [{"family": "Davies", "given": "Gail", "initials": "G"}, {"family": "Lam", "given": "Max", "initials": "M"}, {"family": "Harris", "given": "Sarah E", "initials": "SE"}, {"family": "Trampush", "given": "Joey W", "initials": "JW"}, {"family": "Luciano", "given": "Michelle", "initials": "M"}, {"family": "Hill", "given": "W David", "initials": "WD"}, {"family": "Hagenaars", "given": "Saskia P", "initials": "SP"}, {"family": "Ritchie", "given": "Stuart J", "initials": "SJ"}, {"family": "Marioni", "given": "Riccardo E", "initials": "RE"}, {"family": "Fawns-Ritchie", "given": "Chloe", "initials": "C"}, {"family": "Liewald", "given": "David C M", "initials": "DCM"}, {"family": "Okely", "given": "Judith A", "initials": "JA"}, {"family": "Ahola-Olli", "given": "Ari V", "initials": "AV"}, {"family": "Barnes", "given": "Catriona L K", "initials": "CLK"}, {"family": "Bertram", "given": "Lars", "initials": "L"}, {"family": "Bis", "given": "Joshua C", "initials": "JC"}, {"family": "Burdick", "given": "Katherine E", "initials": "KE"}, {"family": "Christoforou", "given": "Andrea", "initials": "A"}, {"family": "DeRosse", "given": "Pamela", "initials": "P"}, {"family": "Djurovic", "given": "Srdjan", "initials": "S"}, {"family": "Espeseth", "given": "Thomas", "initials": "T"}, {"family": "Giakoumaki", "given": "Stella", "initials": "S"}, {"family": "Giddaluru", "given": "Sudheer", "initials": "S"}, {"family": "Gustavson", "given": "Daniel E", "initials": "DE"}, {"family": "Hayward", "given": "Caroline", "initials": "C"}, {"family": "Hofer", "given": "Edith", "initials": "E"}, {"family": "Ikram", "given": "M Arfan", "initials": "MA"}, {"family": "Karlsson", "given": "Robert", "initials": "R"}, {"family": "Knowles", "given": "Emma", "initials": "E"}, {"family": "Lahti", "given": "Jari", "initials": "J"}, {"family": "Leber", "given": "Markus", "initials": "M"}, {"family": "Li", "given": "Shuo", "initials": "S"}, {"family": "Mather", "given": "Karen A", "initials": "KA"}, {"family": "Melle", "given": "Ingrid", "initials": "I"}, {"family": "Morris", "given": "Derek", "initials": "D"}, {"family": "Oldmeadow", "given": "Christopher", "initials": "C"}, {"family": "Palviainen", "given": "Teemu", "initials": "T"}, {"family": "Payton", "given": "Antony", "initials": "A"}, {"family": "Pazoki", "given": "Raha", "initials": "R"}, {"family": "Petrovic", "given": "Katja", "initials": "K"}, {"family": "Reynolds", "given": "Chandra A", "initials": "CA"}, {"family": "Sargurupremraj", "given": "Muralidharan", "initials": "M"}, {"family": "Scholz", "given": "Markus", "initials": "M"}, {"family": "Smith", "given": "Jennifer A", "initials": "JA"}, {"family": "Smith", "given": "Albert V", "initials": "AV"}, {"family": "Terzikhan", "given": "Natalie", "initials": "N"}, {"family": "Thalamuthu", "given": "Anbupalam", "initials": "A"}, {"family": "Trompet", "given": "Stella", "initials": "S"}, {"family": "van der Lee", "given": "Sven J", "initials": "SJ"}, {"family": "Ware", "given": "Erin B", "initials": "EB"}, {"family": "Windham", "given": "B Gwen", "initials": "BG"}, {"family": "Wright", "given": "Margaret J", "initials": "MJ"}, {"family": "Yang", "given": "Jingyun", "initials": "J"}, {"family": "Yu", "given": "Jin", "initials": "J"}, {"family": "Ames", "given": "David", "initials": "D"}, {"family": "Amin", "given": "Najaf", "initials": "N"}, {"family": "Amouyel", "given": "Philippe", "initials": "P"}, {"family": "Andreassen", "given": "Ole A", "initials": "OA"}, {"family": "Armstrong", "given": "Nicola J", "initials": "NJ"}, {"family": "Assareh", "given": "Amelia A", "initials": "AA"}, {"family": "Attia", "given": "John R", "initials": "JR"}, {"family": "Attix", "given": "Deborah", "initials": "D"}, {"family": "Avramopoulos", "given": "Dimitrios", "initials": "D"}, {"family": "Bennett", "given": "David A", "initials": "DA"}, {"family": "B\u00f6hmer", "given": "Anne C", "initials": "AC"}, {"family": "Boyle", "given": "Patricia A", "initials": "PA"}, {"family": "Brodaty", "given": "Henry", "initials": "H"}, {"family": "Campbell", "given": "Harry", "initials": "H"}, {"family": "Cannon", "given": "Tyrone D", "initials": "TD"}, {"family": "Cirulli", "given": "Elizabeth T", "initials": "ET"}, {"family": "Congdon", "given": "Eliza", "initials": "E"}, {"family": "Conley", "given": "Emily Drabant", "initials": "ED"}, {"family": "Corley", "given": "Janie", "initials": "J"}, {"family": "Cox", "given": "Simon R", "initials": "SR"}, {"family": "Dale", "given": "Anders M", "initials": "AM"}, {"family": "Dehghan", "given": "Abbas", "initials": "A"}, {"family": "Dick", "given": "Danielle", "initials": "D"}, {"family": "Dickinson", "given": "Dwight", "initials": "D"}, {"family": "Eriksson", "given": "Johan G", "initials": "JG"}, {"family": "Evangelou", "given": "Evangelos", "initials": "E"}, {"family": "Faul", "given": "Jessica D", "initials": "JD"}, {"family": "Ford", "given": "Ian", "initials": "I"}, {"family": "Freimer", "given": "Nelson A", "initials": "NA"}, {"family": "Gao", "given": "He", "initials": "H"}, {"family": "Giegling", "given": "Ina", "initials": "I"}, {"family": "Gillespie", "given": "Nathan A", "initials": "NA"}, {"family": "Gordon", "given": "Scott D", "initials": "SD"}, {"family": "Gottesman", "given": "Rebecca F", "initials": "RF"}, {"family": "Griswold", "given": "Michael E", "initials": "ME"}, {"family": "Gudnason", "given": "Vilmundur", "initials": "V"}, {"family": "Harris", "given": "Tamara B", "initials": "TB"}, {"family": "Hartmann", "given": "Annette M", "initials": "AM"}, {"family": "Hatzimanolis", "given": "Alex", "initials": "A"}, {"family": "Heiss", "given": "Gerardo", "initials": "G"}, {"family": "Holliday", "given": "Elizabeth G", "initials": "EG"}, {"family": "Joshi", "given": "Peter K", "initials": "PK"}, {"family": "K\u00e4h\u00f6nen", "given": "Mika", "initials": "M"}, {"family": "Kardia", "given": "Sharon L R", "initials": "SLR"}, {"family": "Karlsson", "given": "Ida", "initials": "I"}, {"family": "Kleineidam", "given": "Luca", "initials": "L"}, {"family": "Knopman", "given": "David S", "initials": "DS"}, {"family": "Kochan", "given": "Nicole A", "initials": "NA"}, {"family": "Konte", "given": "Bettina", "initials": "B"}, {"family": "Kwok", "given": "John B", "initials": "JB"}, {"family": "Le Hellard", "given": "Stephanie", "initials": "S"}, {"family": "Lee", "given": "Teresa", "initials": "T"}, {"family": "Lehtim\u00e4ki", "given": "Terho", "initials": "T"}, {"family": "Li", "given": "Shu-Chen", "initials": "SC"}, {"family": "Liu", "given": "Tian", "initials": "T"}, {"family": "Koini", "given": "Marisa", "initials": "M"}, {"family": "London", "given": "Edythe", "initials": "E"}, {"family": "Longstreth", "given": "Will T", "initials": "WT"}, {"family": "Lopez", "given": "Oscar L", "initials": "OL"}, {"family": "Loukola", "given": "Anu", "initials": "A"}, {"family": "Luck", "given": "Tobias", "initials": "T"}, {"family": "Lundervold", "given": "Astri J", "initials": "AJ"}, {"family": "Lundquist", "given": "Anders", "initials": "A"}, {"family": "Lyytik\u00e4inen", "given": "Leo-Pekka", "initials": "LP"}, {"family": "Martin", "given": "Nicholas G", "initials": "NG"}, {"family": "Montgomery", "given": "Grant W", "initials": "GW"}, {"family": "Murray", "given": "Alison D", "initials": "AD"}, {"family": "Need", "given": "Anna C", "initials": "AC"}, {"family": "Noordam", "given": "Raymond", "initials": "R"}, {"family": "Nyberg", "given": "Lars", "initials": "L"}, {"family": "Ollier", "given": "William", "initials": "W"}, {"family": "Papenberg", "given": "Goran", "initials": "G"}, {"family": "Pattie", "given": "Alison", "initials": "A"}, {"family": "Polasek", "given": "Ozren", "initials": "O"}, {"family": "Poldrack", "given": "Russell A", "initials": "RA"}, {"family": "Psaty", "given": "Bruce M", "initials": "BM"}, {"family": "Reppermund", "given": "Simone", "initials": "S"}, {"family": "Riedel-Heller", "given": "Steffi G", "initials": "SG"}, {"family": "Rose", "given": "Richard J", "initials": "RJ"}, {"family": "Rotter", "given": "Jerome I", "initials": "JI"}, {"family": "Roussos", "given": "Panos", "initials": "P"}, {"family": "Rovio", "given": "Suvi P", "initials": "SP"}, {"family": "Saba", "given": "Yasaman", "initials": "Y"}, {"family": "Sabb", "given": "Fred W", "initials": "FW"}, {"family": "Sachdev", "given": "Perminder S", "initials": "PS"}, {"family": "Satizabal", "given": "Claudia L", "initials": "CL"}, {"family": "Schmid", "given": "Matthias", "initials": "M"}, {"family": "Scott", "given": "Rodney J", "initials": "RJ"}, {"family": "Scult", "given": "Matthew A", "initials": "MA"}, {"family": "Simino", "given": "Jeannette", "initials": "J"}, {"family": "Slagboom", "given": "P Eline", "initials": "PE"}, {"family": "Smyrnis", "given": "Nikolaos", "initials": "N"}, {"family": "Soumar\u00e9", "given": "A\u00efcha", "initials": "A"}, {"family": "Stefanis", "given": "Nikos C", "initials": "NC"}, {"family": "Stott", "given": "David J", "initials": "DJ"}, {"family": "Straub", "given": "Richard E", "initials": "RE"}, {"family": "Sundet", "given": "Kjetil", "initials": "K"}, {"family": "Taylor", "given": "Adele M", "initials": "AM"}, {"family": "Taylor", "given": "Kent D", "initials": "KD"}, {"family": "Tzoulaki", "given": "Ioanna", "initials": "I"}, {"family": "Tzourio", "given": "Christophe", "initials": "C"}, {"family": "Uitterlinden", "given": "Andr\u00e9", "initials": "A"}, {"family": "Vitart", "given": "Veronique", "initials": "V"}, {"family": "Voineskos", "given": "Aristotle N", "initials": "AN"}, {"family": "Kaprio", "given": "Jaakko", "initials": "J"}, {"family": "Wagner", "given": "Michael", "initials": "M"}, {"family": "Wagner", "given": "Holger", "initials": "H"}, {"family": "Weinhold", "given": "Leonie", "initials": "L"}, {"family": "Wen", "given": "K Hoyan", "initials": "KH"}, {"family": "Widen", "given": "Elisabeth", "initials": "E"}, {"family": "Yang", "given": "Qiong", "initials": "Q"}, {"family": "Zhao", "given": "Wei", "initials": "W"}, {"family": "Adams", "given": "Hieab H H", "initials": "HHH"}, {"family": "Arking", "given": "Dan E", "initials": "DE"}, {"family": "Bilder", "given": "Robert M", "initials": "RM"}, {"family": "Bitsios", "given": "Panos", "initials": "P"}, {"family": "Boerwinkle", "given": "Eric", "initials": "E"}, {"family": "Chiba-Falek", "given": "Ornit", "initials": "O"}, {"family": "Corvin", "given": "Aiden", "initials": "A"}, {"family": "De Jager", "given": "Philip L", "initials": "PL"}, {"family": "Debette", "given": "St\u00e9phanie", "initials": "S"}, {"family": "Donohoe", "given": "Gary", "initials": "G"}, {"family": "Elliott", "given": "Paul", "initials": "P"}, {"family": "Fitzpatrick", "given": "Annette L", "initials": "AL"}, {"family": "Gill", "given": "Michael", "initials": "M"}, {"family": "Glahn", "given": "David C", "initials": "DC"}, {"family": "H\u00e4gg", "given": "Sara", "initials": "S"}, {"family": "Hansell", "given": "Narelle K", "initials": "NK"}, {"family": "Hariri", "given": "Ahmad R", "initials": "AR"}, {"family": "Ikram", "given": "M Kamran", "initials": "MK"}, {"family": "Jukema", "given": "J Wouter", "initials": "JW"}, {"family": "Vuoksimaa", "given": "Eero", "initials": "E"}, {"family": "Keller", "given": "Matthew C", "initials": "MC"}, {"family": "Kremen", "given": "William S", "initials": "WS"}, {"family": "Launer", "given": "Lenore", "initials": "L"}, {"family": "Lindenberger", "given": "Ulman", "initials": "U"}, {"family": "Palotie", "given": "Aarno", "initials": "A"}, {"family": "Pedersen", "given": "Nancy L", "initials": "NL"}, {"family": "Pendleton", "given": "Neil", "initials": "N"}, {"family": "Porteous", "given": "David J", "initials": "DJ"}, {"family": "R\u00e4ikk\u00f6nen", "given": "Katri", "initials": "K"}, {"family": "Raitakari", "given": "Olli T", "initials": "OT"}, {"family": "Ramirez", "given": "Alfredo", "initials": "A"}, {"family": "Reinvang", "given": "Ivar", "initials": "I"}, {"family": "Rudan", "given": "Igor", "initials": "I"}, {"family": "Schmidt", "given": "Reinhold", "initials": "R"}, {"family": "Schmidt", "given": "Helena", "initials": "H"}, {"family": "Schofield", "given": "Peter W", "initials": "PW"}, {"family": "Schofield", "given": "Peter R", "initials": "PR"}, {"family": "Starr", "given": "John M", "initials": "JM"}, {"family": "Steen", "given": "Vidar M", "initials": "VM"}, {"family": "Trollor", "given": "Julian N", "initials": "JN"}, {"family": "Turner", "given": "Steven T", "initials": "ST"}, {"family": "Van Duijn", "given": "Cornelia M", "initials": "CM"}, {"family": "Villringer", "given": "Arno", "initials": "A"}, {"family": "Weinberger", "given": "Daniel R", "initials": "DR"}, {"family": "Weir", "given": "David R", "initials": "DR"}, {"family": "Wilson", "given": "James F", "initials": "JF"}, {"family": "Malhotra", "given": "Anil", "initials": "A"}, {"family": "McIntosh", "given": "Andrew M", "initials": "AM"}, {"family": "Gale", "given": "Catharine R", "initials": "CR"}, {"family": "Seshadri", "given": "Sudha", "initials": "S"}, {"family": "Mosley", "given": "Thomas H", "initials": "TH"}, {"family": "Bressler", "given": "Jan", "initials": "J"}, {"family": "Lencz", "given": "Todd", "initials": "T"}, {"family": "Deary", "given": "Ian J", "initials": "IJ"}], "type": "journal article", "published": "2018-05-29", "journal": {"volume": "9", "issn": "2041-1723", "issue": "1", "pages": "2098", "title": "Nat Commun", "issn-l": "2041-1723"}, "abstract": "General cognitive function is a prominent and relatively stable human trait that is associated with many important life outcomes. We combine cognitive and genetic data from the CHARGE and COGENT consortia, and UK Biobank (total N\u2009=\u2009300,486; age 16-102) and find 148 genome-wide significant independent loci (P\u2009<\u20095\u2009\u00d7\u200910", "doi": "10.1038/s41467-018-04362-x", "pmid": "29844566", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-018-04362-x"}, {"db": "pmc", "key": "PMC5974083"}], "notes": [], "created": "2018-06-15T07:31:31.488Z", "modified": "2024-01-16T13:48:46.281Z"}, {"entity": "publication", "iuid": "23ed7542420348a2ad0dc84ea88454d3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/23ed7542420348a2ad0dc84ea88454d3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/23ed7542420348a2ad0dc84ea88454d3"}}, "title": "A genome-wide association study of IgM antibody against phosphorylcholine: shared genetics and phenotypic relationship to chronic lymphocytic leukemia.", "authors": [{"family": "Chen", "given": "Xu", "initials": "X"}, {"family": "Gustafsson", "given": "Stefan", "initials": "S"}, {"family": "Whitington", "given": "Thomas", "initials": "T"}, {"family": "Born\u00e9", "given": "Yan", "initials": "Y"}, {"family": "Lorentzen", "given": "Erik", "initials": "E"}, {"family": "Sun", "given": "Jitong", "initials": "J"}, {"family": "Almgren", "given": "Peter", "initials": "P"}, {"family": "Su", "given": "Jun", "initials": "J"}, {"family": "Karlsson", "given": "Robert", "initials": "R"}, {"family": "Song", "given": "Jie", "initials": "J"}, {"family": "Lu", "given": "Yi", "initials": "Y"}, {"family": "Zhan", "given": "Yiqiang", "initials": "Y"}, {"family": "H\u00e4gg", "given": "Sara", "initials": "S"}, {"family": "Svensson", "given": "Per", "initials": "P"}, {"family": "Smedby", "given": "Karin E", "initials": "KE"}, {"family": "Slager", "given": "Susan L", "initials": "SL"}, {"family": "Ingelsson", "given": "Erik", "initials": "E"}, {"family": "Lindgren", "given": "Cecilia M", "initials": "CM"}, {"family": "Morris", "given": "Andrew P", "initials": "AP"}, {"family": "Melander", "given": "Olle", "initials": "O"}, {"family": "Karlsson", "given": "Thomas", "initials": "T"}, {"family": "de Faire", "given": "Ulf", "initials": "U"}, {"family": "Caidahl", "given": "Kenneth", "initials": "K"}, {"family": "Engstr\u00f6m", "given": "Gunnar", "initials": "G"}, {"family": "Lind", "given": "Lars", "initials": "L"}, {"family": "Karlsson", "given": "Mikael C I", "initials": "MCI"}, {"family": "Pedersen", "given": "Nancy L", "initials": "NL"}, {"family": "Frosteg\u00e5rd", "given": "Johan", "initials": "J"}, {"family": "Magnusson", "given": "Patrik K E", "initials": "PKE"}], "type": "journal article", "published": "2018-05-15", "journal": {"volume": "27", "issn": "1460-2083", "issue": "10", "pages": "1809-1818", "title": "Hum. Mol. Genet.", "issn-l": "0964-6906"}, "abstract": "Phosphorylcholine (PC) is an epitope on oxidized low-density lipoprotein (oxLDL), apoptotic cells and several pathogens like Streptococcus pneumoniae. Immunoglobulin M against PC (IgM anti-PC) has the ability to inhibit uptake of oxLDL by macrophages and increase clearance of apoptotic cells. From our genome-wide association studies (GWASs) in four European-ancestry cohorts, six single nucleotide polymorphisms (SNPs) in 11q24.1 were discovered (in 3002 individuals) and replicated (in 646 individuals) to be associated with serum level of IgM anti-PC (the leading SNP rs35923643-G, combined \u03b2\u2009=\u20090.19, 95% confidence interval 0.13-0.24, P\u2009=\u20094.3\u2009\u00d7\u200910-11). The haplotype tagged by rs35923643-G (or its proxy SNP rs735665-A) is also known as the top risk allele for chronic lymphocytic leukemia (CLL), and a main increasing allele for general IgM. By using summary GWAS results of IgM anti-PC and CLL in the polygenic risk score (PRS) analysis, PRS on the basis of IgM anti-PC risk alleles positively associated with CLL risk (explained 0.6% of CLL variance, P\u2009=\u20091.2\u2009\u00d7\u200910-15). Functional prediction suggested that rs35923643-G might impede the binding of Runt-related transcription factor 3, a tumor suppressor playing a central role in the immune regulation of cancers. Contrary to the expectations from the shared genetics between IgM anti-PC and CLL, an inverse relationship at the phenotypic level was found in a nested case-control study (30 CLL cases with 90 age- and sex-matched controls), potentially reflecting reverse causation. The suggested function of the top variant as well as the phenotypic association between IgM anti-PC and CLL risk needs replication and motivates further studies.", "doi": "10.1093/hmg/ddy094", "pmid": "29547969", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "4935077"}], "notes": [], "created": "2018-05-25T13:25:50.026Z", "modified": "2024-01-16T13:48:46.299Z"}, {"entity": "publication", "iuid": "9fbcd3915ba44ca9ae17976d8120258a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9fbcd3915ba44ca9ae17976d8120258a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9fbcd3915ba44ca9ae17976d8120258a"}}, "title": "Habitual coffee consumption and cognitive function: a Mendelian randomization meta-analysis in up to 415,530 participants.", "authors": [{"family": "Zhou", "given": "Ang", "initials": "A"}, {"family": "Taylor", "given": "Amy E", "initials": "AE"}, {"family": "Karhunen", "given": "Ville", "initials": "V"}, {"family": "Zhan", "given": "Yiqiang", "initials": "Y"}, {"family": "Rovio", "given": "Suvi P", "initials": "SP"}, {"family": "Lahti", "given": "Jari", "initials": "J"}, {"family": "Sj\u00f6gren", "given": "Per", "initials": "P"}, {"family": "Byberg", "given": "Liisa", "initials": "L"}, {"family": "Lyall", "given": "Donald M", "initials": "DM"}, {"family": "Auvinen", "given": "Juha", "initials": "J"}, {"family": "Lehtim\u00e4ki", "given": "Terho", "initials": "T"}, {"family": "K\u00e4h\u00f6nen", "given": "Mika", "initials": "M"}, {"family": "Hutri-K\u00e4h\u00f6nen", "given": "Nina", "initials": "N"}, {"family": "Per\u00e4l\u00e4", "given": "Mia Maria", "initials": "MM"}, {"family": "Micha\u00eblsson", "given": "Karl", "initials": "K"}, {"family": "Mahajan", "given": "Anubha", "initials": "A"}, {"family": "Lind", "given": "Lars", "initials": "L"}, {"family": "Power", "given": "Chris", "initials": "C"}, {"family": "Eriksson", "given": "Johan G", "initials": "JG"}, {"family": "Raitakari", "given": "Olli T", "initials": "OT"}, {"family": "H\u00e4gg", "given": "Sara", "initials": "S"}, {"family": "Pedersen", "given": "Nancy L", "initials": "NL"}, {"family": "Veijola", "given": "Juha", "initials": "J"}, {"family": "J\u00e4rvelin", "given": "Marjo-Riitta", "initials": "MR"}, {"family": "Munaf\u00f2", "given": "Marcus R", "initials": "MR"}, {"family": "Ingelsson", "given": "Erik", "initials": "E"}, {"family": "Llewellyn", "given": "David J", "initials": "DJ"}, {"family": "Hypp\u00f6nen", "given": "Elina", "initials": "E"}], "type": "journal article", "published": "2018-05-14", "journal": {"volume": "8", "issn": "2045-2322", "issue": "1", "pages": "7526", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "Coffee's long-term effect on cognitive function remains unclear with studies suggesting both benefits and adverse effects. We used Mendelian randomization to investigate the causal relationship between habitual coffee consumption and cognitive function in mid- to later life. This included up to 415,530 participants and 300,760 coffee drinkers from 10 meta-analysed European ancestry cohorts. In each cohort, composite cognitive scores that capture global cognition and memory were computed using available tests. A genetic score derived using CYP1A1/2 (rs2472297) and AHR (rs6968865) was chosen as a proxy for habitual coffee consumption. Null associations were observed when examining the associations of the genetic score with global and memory cognition (\u03b2\u2009=\u2009-0.0007, 95% C.I. -0.009 to 0.008, P\u2009=\u20090.87; \u03b2\u2009=\u2009-0.001, 95% C.I. -0.005 to 0.002, P\u2009=\u20090.51, respectively), with high consistency between studies (P", "doi": "10.1038/s41598-018-25919-2", "pmid": "29760501", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-018-25919-2"}, {"db": "pmc", "key": "PMC5951917"}], "notes": [], "created": "2018-05-25T13:25:46.689Z", "modified": "2024-01-16T13:48:46.323Z"}, {"entity": "publication", "iuid": "6906d97c439e481b8f58469e6a267c86", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6906d97c439e481b8f58469e6a267c86.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6906d97c439e481b8f58469e6a267c86"}}, "title": "Genome-wide association meta-analysis of circulating odd-numbered chain saturated fatty acids: Results from the CHARGE Consortium.", "authors": [{"family": "de Oliveira Otto", "given": "Marcia C", "initials": "MC"}, {"family": "Lemaitre", "given": "Rozenn N", "initials": "RN"}, {"family": "Sun", "given": "Qi", "initials": "Q"}, {"family": "King", "given": "Irena B", "initials": "IB"}, {"family": "Wu", "given": "Jason H Y", "initials": "JHY"}, {"family": "Manichaikul", "given": "Ani", "initials": "A"}, {"family": "Rich", "given": "Stephen S", "initials": "SS"}, {"family": "Tsai", "given": "Michael Y", "initials": "MY"}, {"family": "Chen", "given": "Y D", "initials": "YD"}, {"family": "Fornage", "given": "Myriam", "initials": "M"}, {"family": "Weihua", "given": "Guan", "initials": "G"}, {"family": "Aslibekyan", "given": "Stella", "initials": "S"}, {"family": "Irvin", "given": "Marguerite R", "initials": "MR"}, {"family": "Kabagambe", "given": "Edmond K", "initials": "EK"}, {"family": "Arnett", "given": "Donna K", "initials": "DK"}, {"family": "Jensen", "given": "Majken K", "initials": "MK"}, {"family": "McKnight", "given": "Barbara", "initials": "B"}, {"family": "Psaty", "given": "Bruce M", "initials": "BM"}, {"family": "Steffen", "given": "Lyn M", "initials": "LM"}, {"family": "Smith", "given": "Caren E", "initials": "CE"}, {"family": "Ris\u00e9rus", "given": "Ulf", "initials": "U"}, {"family": "Lind", "given": "Lars", "initials": "L"}, {"family": "Hu", "given": "Frank B", "initials": "FB"}, {"family": "Rimm", "given": "Eric B", "initials": "EB"}, {"family": "Siscovick", "given": "David S", "initials": "DS"}, {"family": "Mozaffarian", "given": "Dariush", "initials": "D"}], "type": "journal article", "published": "2018-05-08", "journal": {"volume": "13", "issn": "1932-6203", "issue": "5", "pages": "e0196951", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "Odd-numbered chain saturated fatty acids (OCSFA) have been associated with potential health benefits. Although some OCSFA (e.g., C15:0 and C17:0) are found in meats and dairy products, sources and metabolism of C19:0 and C23:0 are relatively unknown, and the influence of non-dietary determinants, including genetic factors, on circulating levels of OCSFA is not established.\n\nTo elucidate the biological processes that influence circulating levels of OCSFA by investigating associations between genetic variation and OCSFA.\n\nWe performed a meta-analysis of genome-wide association studies (GWAS) of plasma phospholipid/erythrocyte levels of C15:0, C17:0, C19:0, and C23:0 among 11,494 individuals of European descent. We also investigated relationships between specific single nucleotide polymorphisms (SNPs) in the lactase (LCT) gene, associated with adult-onset lactase intolerance, with circulating levels of dairy-derived OCSFA, and evaluated associations of candidate sphingolipid genes with C23:0 levels.\n\nWe found no genome-wide significant evidence that common genetic variation is associated with circulating levels of C15:0 or C23:0. In two cohorts with available data, we identified one intronic SNP (rs13361131) in myosin X gene (MYO10) associated with C17:0 level (P = 1.37\u00d710-8), and two intronic SNP (rs12874278 and rs17363566) in deleted in lymphocytic leukemia 1 (DLEU1) region associated with C19:0 level (P = 7.07\u00d710-9). In contrast, when using a candidate-gene approach, we found evidence that three SNPs in LCT (rs11884924, rs16832067, and rs3816088) are associated with circulating C17:0 level (adjusted P = 4\u00d710-2). In addition, nine SNPs in the ceramide synthase 4 (CERS4) region were associated with circulating C23:0 levels (adjusted P<5\u00d710-2).\n\nOur findings suggest that circulating levels of OCSFA may be predominantly influenced by non-genetic factors. SNPs associated with C17:0 level in the LCT gene may reflect genetic influence in dairy consumption or in metabolism of dairy foods. SNPs associated with C23:0 may reflect a role of genetic factors in the synthesis of sphingomyelin.", "doi": "10.1371/journal.pone.0196951", "pmid": "29738550", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "PONE-D-18-05019"}, {"db": "pmc", "key": "PMC5940220"}], "notes": [], "created": "2018-05-25T13:25:47.618Z", "modified": "2024-01-16T13:48:46.337Z"}, {"entity": "publication", "iuid": "c3dcf2e9bf1d4382866d6a7c7b6018f7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c3dcf2e9bf1d4382866d6a7c7b6018f7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c3dcf2e9bf1d4382866d6a7c7b6018f7"}}, "title": "The GTPase domain of gamma-tubulin is required for normal mitochondrial function and spatial organization.", "authors": [{"family": "Lindstr\u00f6m", "given": "Lisa", "initials": "L"}, {"family": "Li", "given": "Tongbin", "initials": "T"}, {"family": "Malycheva", "given": "Darina", "initials": "D"}, {"family": "Kancharla", "given": "Arun", "initials": "A"}, {"family": "Nilsson", "given": "Hel\u00e9n", "initials": "H"}, {"family": "Vishnu", "given": "Neelanjan", "initials": "N"}, {"family": "Mulder", "given": "Hindrik", "initials": "H"}, {"family": "Johansson", "given": "Martin", "initials": "M"}, {"family": "Rossell\u00f3", "given": "Catalina Ana", "initials": "CA"}, {"family": "Alvarado-Kristensson", "given": "Maria", "initials": "M", "orcid": "0000-0003-0598-7986", "researcher": {"href": "https://publications.scilifelab.se/researcher/70ee81797eff452fa037821f293d8673.json"}}], "type": "journal article", "published": "2018-05-03", "journal": {"title": "Commun Biol", "issn": "2399-3642", "volume": "1", "issue": "1", "pages": "37", "issn-l": "2399-3642"}, "abstract": "In the cell, \u03b3-tubulin establishes a cellular network of threads named the \u03b3-string meshwork. However, the functions of this meshwork remain to be determined. We investigated the traits of the meshwork and show that \u03b3-strings have the ability to connect the cytoplasm and the mitochondrial DNA together. We also show that \u03b3-tubulin has a role in the maintenance of the mitochondrial network and functions as reduced levels of \u03b3-tubulin or impairment of its GTPase domain disrupts the mitochondrial network and alters both their respiratory capacity and the expression of mitochondrial-related genes. By contrast, reduced mitochondrial number or increased protein levels of \u03b3-tubulin DNA-binding domain enhanced the association of \u03b3-tubulin with mitochondria. Our results demonstrate that \u03b3-tubulin is an important mitochondrial structural component that maintains the mitochondrial network, providing mitochondria with a cellular infrastructure. We propose that \u03b3-tubulin provides a cytoskeletal element that gives form to the mitochondrial network.", "doi": "10.1038/s42003-018-0037-3", "pmid": "30271923", "labels": {"Integrated Microscopy Technologies Gothenburg": "Service", "National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s42003-018-0037-3"}, {"db": "pmc", "key": "PMC6123723"}], "notes": [], "created": "2020-01-23T16:26:11.434Z", "modified": "2021-11-03T15:41:13.583Z"}, {"entity": "publication", "iuid": "f25799db31874a55adf3d174418bff26", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f25799db31874a55adf3d174418bff26.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f25799db31874a55adf3d174418bff26"}}, "title": "Transcription profiling of peripheral B cells in antibody-positive primary Sj\u00f6gren's syndrome reveals upregulated expression of CX3CR1 and a type I and type II interferon signature.", "authors": [{"family": "Imgenberg-Kreuz", "given": "J", "initials": "J", "orcid": "0000-0002-7230-8990", "researcher": {"href": "https://publications.scilifelab.se/researcher/5d4c2f630d484ee780c2c12aaabdb939.json"}}, {"family": "Sandling", "given": "J K", "initials": "JK"}, {"family": "Bj\u00f6rk", "given": "A", "initials": "A"}, {"family": "Nordlund", "given": "J", "initials": "J", "orcid": "0000-0001-8699-9959", "researcher": {"href": "https://publications.scilifelab.se/researcher/ddf48c9262134821bcc6ce1180049753.json"}}, {"family": "Kvarnstr\u00f6m", "given": "M", "initials": "M"}, {"family": "Eloranta", "given": "M-L", "initials": "ML"}, {"family": "R\u00f6nnblom", "given": "L", "initials": "L"}, {"family": "Wahren-Herlenius", "given": "M", "initials": "M", "orcid": "0000-0002-0915-7245", "researcher": {"href": "https://publications.scilifelab.se/researcher/a8451e7f5e6e4e4da0bace3dfafaeb38.json"}}, {"family": "Syv\u00e4nen", "given": "A-C", "initials": "AC", "orcid": "0000-0002-9681-9146", "researcher": {"href": "https://publications.scilifelab.se/researcher/f7012e35025543379380cb90efd71243.json"}}, {"family": "Nordmark", "given": "G", "initials": "G", "orcid": "0000-0002-3829-7431", "researcher": {"href": "https://publications.scilifelab.se/researcher/188fda53498740dbb007441cc94bb1ad.json"}}], "type": "journal article", "published": "2018-05-00", "journal": {"volume": "87", "issn": "1365-3083", "issue": "5", "pages": "e12662", "title": "Scand. J. Immunol.", "issn-l": "0300-9475"}, "abstract": "B cells play a key role in the pathogenesis of primary Sj\u00f6gren's syndrome (pSS). The aim of this study was to analyse the transcriptome of CD19+ B cells from patients with pSS and healthy controls to decipher the B cell-specific contribution to pSS. RNA from purified CD19+ B cells from 12 anti-SSA antibody-positive untreated female patients with pSS and 20 healthy blood donors was subjected to whole transcriptome sequencing. A false discovery rate corrected significance threshold of \u03b1 < 0.05 was applied to define differential gene expression. As validation, gene expression in B cells from 17 patients with pSS and 16 healthy controls was analysed using a targeted gene panel. RNA-sequencing identified 4047 differentially expressed autosomal genes in pSS B cells. Upregulated expression of type I and type II interferon (IFN)-induced genes was observed, establishing an IFN signature in pSS B cells. Among the top upregulated and validated genes were CX3CR1, encoding the fractalkine receptor involved in regulation of B-cell malignancies, CCL5/RANTES and CCR1. Increased expression of several members of the TNF superfamily was also identified; TNFSF4/Ox40L, TNFSF10/TRAIL, TNFSF13B/BAFF, TNFRSF17/BCMA as well as S100A8 and -A9/calprotectin, TLR7, STAT1 and STAT2. Among genes with downregulated expression in pSS B cells were SOCS1 and SOCS3, CD70 and TNFAIP3/A20. We conclude that B cells from patients with anti-SSA antibody-positive pSS display immune activation with upregulated expression of chemokines, chemokine receptors and a prominent type I and type II IFN signature, while suppressors of cytokine signalling are downregulated. This adds insight into the autoimmune process and suggests potential targets for future functional studies.", "doi": "10.1111/sji.12662", "pmid": "29655283", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2018-05-03T11:10:51.391Z", "modified": "2024-01-16T13:48:46.360Z"}, {"entity": "publication", "iuid": "3463715dd7664c96bd06baa4e0719f09", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3463715dd7664c96bd06baa4e0719f09.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3463715dd7664c96bd06baa4e0719f09"}}, "title": "Sulfasalazine-Induced Agranulocytosis Is Associated With the Human Leukocyte Antigen Locus.", "authors": [{"family": "Wadelius", "given": "Mia", "initials": "M"}, {"family": "Eriksson", "given": "Niclas", "initials": "N"}, {"family": "Kreutz", "given": "Reinhold", "initials": "R"}, {"family": "Bondon-Guitton", "given": "Emmanuelle", "initials": "E"}, {"family": "Iba\u00f1ez", "given": "Luisa", "initials": "L"}, {"family": "Carvajal", "given": "Alfonso", "initials": "A"}, {"family": "Lucena", "given": "M Isabel", "initials": "MI"}, {"family": "Sancho Ponce", "given": "Esther", "initials": "E"}, {"family": "Molokhia", "given": "Mariam", "initials": "M"}, {"family": "Martin", "given": "Javier", "initials": "J"}, {"family": "Axelsson", "given": "Tomas", "initials": "T"}, {"family": "Kohnke", "given": "Hugo", "initials": "H"}, {"family": "Yue", "given": "Qun-Ying", "initials": "QY"}, {"family": "Magnusson", "given": "Patrik K E", "initials": "PKE"}, {"family": "Bengtsson", "given": "Mats", "initials": "M"}, {"family": "Hallberg", "given": "P\u00e4r", "initials": "P"}, {"family": "EuDAC", "given": "", "initials": ""}], "type": "journal article", "published": "2018-05-00", "journal": {"volume": "103", "issn": "1532-6535", "issue": "5", "pages": "843-853", "title": "Clin. Pharmacol. Ther.", "issn-l": "0009-9236"}, "abstract": "Agranulocytosis is a serious, although rare, adverse reaction to sulfasalazine, which is used to treat inflammatory joint and bowel disease. We performed a genome-wide association study comprising 9,380,034 polymorphisms and 180 HLA alleles in 36 cases of sulfasalazine-induced agranulocytosis and 5,170 population controls. Sulfasalazine-induced agranulocytosis was significantly associated with the HLA region on chromosome 6. The top hit (rs9266634) was located close to HLA-B, odds ratio (OR) 5.36 (95% confidence interval (CI) (2.97, 9.69) P = 2.55 \u00d7 10 -8 ). We HLA-sequenced a second cohort consisting of 40 cases and 142 treated controls, and confirmed significant associations with HLA-B*08:01, OR = 2.25 (95% CI (1.02, 4.97) P = 0.0439), in particular the HLA-B*08:01 haplotype HLA-DQB1*02:01-DRB1*03:01-B*08:01-C*07:01, OR = 3.79 (95% CI (1.63, 8.80) P = 0.0019), and with HLA-A*31:01, OR = 4.81 (95% CI (1.52, 15.26) P = 0.0077). The number needed to test for HLA-B*08:01 and HLA-A*31:01 to avoid one case was estimated to be 1,500. We suggest that intensified monitoring or alternative treatment should be considered for known carriers of HLA-B*08:01 or HLA-A*31:01.", "doi": "10.1002/cpt.805", "pmid": "28762467", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC5947520"}], "notes": [], "created": "2019-01-04T09:53:05.174Z", "modified": "2021-06-21T14:28:06.039Z"}, {"entity": "publication", "iuid": "898ddd65d58643969e6d9dba00dc324d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/898ddd65d58643969e6d9dba00dc324d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/898ddd65d58643969e6d9dba00dc324d"}}, "title": "Host genetic variation strongly influences the microbiome structure and function in fungal fruiting-bodies", "authors": [{"family": "Pent", "given": "Mari", "initials": "M"}, {"family": "Hiltunen", "given": "Markus", "initials": "M"}, {"family": "P\u00f5ldmaa", "given": "Kadri", "initials": "K"}, {"family": "Furneaux", "given": "Brendan", "initials": "B"}, {"family": "Hildebrand", "given": "Falk", "initials": "F"}, {"family": "Johannesson", "given": "Hanna", "initials": "H"}, {"family": "Ryberg", "given": "Martin", "initials": "M"}, {"family": "Bahram", "given": "Mohammad", "initials": "M"}], "type": "journal-article", "published": "2018-05-00", "journal": {"volume": "20", "issn": "1462-2912", "issue": "5", "pages": "1641-1650", "title": "Environ Microbiol", "issn-l": "1462-2912"}, "abstract": null, "doi": "10.1111/1462-2920.14069", "pmid": "29441658", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "www.mg-rast.org", "description": "raw sequences", "key": "mgp20495"}], "notes": [], "created": "2018-09-14T12:11:21.339Z", "modified": "2024-01-16T13:48:46.410Z"}, {"entity": "publication", "iuid": "2f07d186b7424c66a07a9fbe4dd1de20", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2f07d186b7424c66a07a9fbe4dd1de20.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2f07d186b7424c66a07a9fbe4dd1de20"}}, "title": "Genome-wide association analyses identify 44 risk variants and refine the genetic architecture of major depression.", "authors": [{"family": "Wray", "given": "Naomi R", "initials": "NR"}, {"family": "Ripke", "given": "Stephan", "initials": "S"}, {"family": "Mattheisen", "given": "Manuel", "initials": "M"}, {"family": "Trzaskowski", "given": "Maciej", "initials": "M"}, {"family": "Byrne", "given": "Enda M", "initials": "EM"}, {"family": "Abdellaoui", "given": "Abdel", "initials": "A"}, {"family": "Adams", "given": "Mark J", "initials": "MJ"}, {"family": "Agerbo", "given": "Esben", "initials": "E"}, {"family": "Air", "given": "Tracy M", "initials": "TM"}, {"family": "Andlauer", "given": "Till M F", "initials": "TMF"}, {"family": "Bacanu", "given": "Silviu-Alin", "initials": "SA"}, {"family": "B\u00e6kvad-Hansen", "given": "Marie", "initials": "M"}, {"family": "Beekman", "given": "Aartjan F T", "initials": "AFT"}, {"family": "Bigdeli", "given": "Tim B", "initials": "TB"}, {"family": "Binder", "given": "Elisabeth B", "initials": "EB"}, {"family": "Blackwood", "given": "Douglas R H", "initials": "DRH"}, {"family": "Bryois", "given": "Julien", "initials": "J"}, {"family": "Buttensch\u00f8n", "given": "Henriette N", "initials": "HN"}, {"family": "Bybjerg-Grauholm", "given": "Jonas", "initials": "J"}, {"family": "Cai", "given": "Na", "initials": "N"}, {"family": "Castelao", "given": "Enrique", "initials": "E"}, {"family": "Christensen", "given": "Jane Hvarregaard", "initials": "JH"}, {"family": "Clarke", "given": "Toni-Kim", "initials": "TK"}, {"family": "Coleman", "given": "Jonathan I R", "initials": "JIR"}, {"family": "Colodro-Conde", "given": "Luc\u00eda", "initials": "L"}, {"family": "Couvy-Duchesne", "given": "Baptiste", "initials": "B"}, {"family": "Craddock", "given": "Nick", "initials": "N"}, {"family": "Crawford", "given": "Gregory E", "initials": "GE"}, {"family": "Crowley", "given": "Cheynna A", "initials": "CA"}, {"family": "Dashti", "given": "Hassan S", "initials": "HS"}, {"family": "Davies", "given": "Gail", "initials": "G"}, {"family": "Deary", "given": "Ian J", "initials": "IJ"}, {"family": "Degenhardt", "given": "Franziska", "initials": "F"}, {"family": "Derks", "given": "Eske M", "initials": "EM"}, {"family": "Direk", "given": "Nese", "initials": "N"}, {"family": "Dolan", "given": "Conor V", "initials": "CV"}, {"family": "Dunn", "given": "Erin C", "initials": "EC"}, {"family": "Eley", "given": "Thalia C", "initials": "TC"}, {"family": "Eriksson", "given": "Nicholas", "initials": "N"}, {"family": "Escott-Price", "given": "Valentina", "initials": "V"}, {"family": "Kiadeh", "given": "Farnush Hassan Farhadi", "initials": "FHF"}, {"family": "Finucane", "given": "Hilary K", "initials": "HK"}, {"family": "Forstner", "given": "Andreas J", "initials": "AJ"}, {"family": "Frank", "given": "Josef", "initials": "J"}, {"family": "Gaspar", "given": "H\u00e9l\u00e9na A", "initials": "HA"}, {"family": "Gill", "given": "Michael", "initials": "M"}, {"family": "Giusti-Rodr\u00edguez", "given": "Paola", "initials": "P"}, {"family": "Goes", "given": "Fernando S", "initials": "FS"}, {"family": "Gordon", "given": "Scott D", "initials": "SD"}, {"family": "Grove", "given": "Jakob", "initials": "J"}, {"family": "Hall", "given": "Lynsey S", "initials": "LS"}, {"family": "Hannon", "given": "Eilis", "initials": "E"}, {"family": "Hansen", "given": "Christine S\u00f8holm", "initials": "CS"}, {"family": "Hansen", "given": "Thomas F", "initials": "TF"}, {"family": "Herms", "given": "Stefan", "initials": "S"}, {"family": "Hickie", "given": "Ian B", "initials": "IB"}, {"family": "Hoffmann", "given": "Per", "initials": "P"}, {"family": "Homuth", "given": "Georg", "initials": "G"}, 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"initials": "Y"}, {"family": "Milani", "given": "Lili", "initials": "L"}, {"family": "Mill", "given": "Jonathan", "initials": "J"}, {"family": "Mondimore", "given": "Francis M", "initials": "FM"}, {"family": "Montgomery", "given": "Grant W", "initials": "GW"}, {"family": "Mostafavi", "given": "Sara", "initials": "S"}, {"family": "Mullins", "given": "Niamh", "initials": "N"}, {"family": "Nauck", "given": "Matthias", "initials": "M"}, {"family": "Ng", "given": "Bernard", "initials": "B"}, {"family": "Nivard", "given": "Michel G", "initials": "MG"}, {"family": "Nyholt", "given": "Dale R", "initials": "DR"}, {"family": "O'Reilly", "given": "Paul F", "initials": "PF"}, {"family": "Oskarsson", "given": "Hogni", "initials": "H"}, {"family": "Owen", "given": "Michael J", "initials": "MJ"}, {"family": "Painter", "given": "Jodie N", "initials": "JN"}, {"family": "Pedersen", "given": "Carsten B\u00f8cker", "initials": "CB"}, {"family": "Pedersen", "given": "Marianne Gi\u00f8rtz", "initials": "MG"}, {"family": "Peterson", "given": "Roseann E", "initials": "RE"}, {"family": "Pettersson", "given": "Erik", "initials": "E"}, {"family": "Peyrot", "given": "Wouter J", "initials": "WJ"}, {"family": "Pistis", "given": "Giorgio", "initials": "G"}, {"family": "Posthuma", "given": "Danielle", "initials": "D"}, {"family": "Purcell", "given": "Shaun M", "initials": "SM"}, {"family": "Quiroz", "given": "Jorge A", "initials": "JA"}, {"family": "Qvist", "given": "Per", "initials": "P"}, {"family": "Rice", "given": "John P", "initials": "JP"}, {"family": "Riley", "given": "Brien P", "initials": "BP"}, {"family": "Rivera", "given": "Margarita", "initials": "M"}, {"family": "Saeed Mirza", "given": "Saira", "initials": "S"}, {"family": "Saxena", "given": "Richa", "initials": "R"}, {"family": "Schoevers", "given": "Robert", "initials": "R"}, {"family": "Schulte", "given": "Eva C", "initials": "EC"}, {"family": "Shen", "given": "Ling", "initials": "L"}, {"family": "Shi", "given": "Jianxin", "initials": "J"}, {"family": "Shyn", "given": "Stanley I", "initials": "SI"}, {"family": "Sigurdsson", "given": "Engilbert", "initials": "E"}, {"family": "Sinnamon", "given": "Grant B C", "initials": "GBC"}, {"family": "Smit", "given": "Johannes H", "initials": "JH"}, {"family": "Smith", "given": "Daniel J", "initials": "DJ"}, {"family": "Stefansson", "given": "Hreinn", "initials": "H"}, {"family": "Steinberg", "given": "Stacy", "initials": "S"}, {"family": "Stockmeier", "given": "Craig A", "initials": "CA"}, {"family": "Streit", "given": "Fabian", "initials": "F"}, {"family": "Strohmaier", "given": "Jana", "initials": "J"}, {"family": "Tansey", "given": "Katherine E", "initials": "KE"}, {"family": "Teismann", "given": "Henning", "initials": "H"}, {"family": "Teumer", "given": "Alexander", "initials": "A"}, {"family": "Thompson", "given": "Wesley", "initials": "W"}, {"family": "Thomson", "given": "Pippa A", "initials": "PA"}, {"family": "Thorgeirsson", "given": "Thorgeir E", "initials": "TE"}, {"family": "Tian", "given": "Chao", "initials": "C"}, {"family": "Traylor", "given": "Matthew", "initials": "M"}, {"family": "Treutlein", "given": "Jens", "initials": "J"}, {"family": "Trubetskoy", "given": "Vassily", "initials": "V"}, {"family": "Uitterlinden", "given": "Andr\u00e9 G", "initials": "AG"}, {"family": "Umbricht", "given": "Daniel", "initials": "D"}, {"family": "Van der Auwera", "given": "Sandra", "initials": "S"}, {"family": "van Hemert", "given": "Albert M", "initials": "AM"}, {"family": "Viktorin", "given": "Alexander", "initials": "A"}, {"family": "Visscher", "given": "Peter M", "initials": "PM"}, {"family": "Wang", "given": "Yunpeng", "initials": "Y"}, {"family": "Webb", "given": "Bradley T", "initials": "BT"}, {"family": "Weinsheimer", "given": "Shantel Marie", "initials": "SM"}, {"family": "Wellmann", "given": "J\u00fcrgen", "initials": "J"}, {"family": "Willemsen", "given": "Gonneke", "initials": "G"}, {"family": "Witt", "given": "Stephanie H", "initials": "SH"}, {"family": "Wu", "given": "Yang", "initials": "Y"}, {"family": "Xi", "given": "Hualin S", "initials": "HS"}, {"family": "Yang", "given": "Jian", "initials": "J"}, {"family": "Zhang", "given": "Futao", "initials": "F"}, {"family": "eQTLGen", "given": "", "initials": ""}, {"family": "23andMe", "given": "", "initials": ""}, {"family": "Arolt", "given": "Volker", "initials": "V"}, {"family": "Baune", "given": "Bernhard T", "initials": "BT"}, {"family": "Berger", "given": "Klaus", "initials": "K"}, {"family": "Boomsma", "given": "Dorret I", "initials": "DI"}, {"family": "Cichon", "given": "Sven", "initials": "S"}, {"family": "Dannlowski", "given": "Udo", "initials": "U"}, {"family": "de Geus", "given": "E C J", "initials": "ECJ"}, {"family": "DePaulo", "given": "J Raymond", "initials": "JR"}, {"family": "Domenici", "given": "Enrico", "initials": "E"}, {"family": "Domschke", "given": "Katharina", "initials": "K"}, {"family": "Esko", "given": "T\u00f5nu", "initials": "T"}, {"family": "Grabe", "given": "Hans J", "initials": "HJ"}, {"family": "Hamilton", "given": "Steven P", "initials": "SP"}, {"family": "Hayward", "given": "Caroline", "initials": "C"}, {"family": "Heath", "given": "Andrew C", "initials": "AC"}, {"family": "Hinds", "given": "David A", "initials": "DA"}, {"family": "Kendler", "given": "Kenneth S", "initials": "KS"}, {"family": "Kloiber", "given": "Stefan", "initials": "S"}, {"family": "Lewis", "given": "Glyn", "initials": "G"}, {"family": "Li", "given": "Qingqin S", "initials": "QS"}, {"family": "Lucae", "given": "Susanne", "initials": "S"}, {"family": "Madden", "given": "Pamela F A", "initials": "PFA"}, {"family": "Magnusson", "given": "Patrik K", "initials": "PK"}, {"family": "Martin", "given": "Nicholas G", "initials": "NG"}, {"family": "McIntosh", "given": "Andrew M", "initials": "AM"}, {"family": "Metspalu", "given": "Andres", "initials": "A"}, {"family": "Mors", "given": "Ole", "initials": "O"}, {"family": "Mortensen", "given": "Preben Bo", "initials": "PB"}, {"family": "M\u00fcller-Myhsok", "given": "Bertram", "initials": "B"}, {"family": "Nordentoft", "given": "Merete", "initials": "M"}, {"family": "N\u00f6then", "given": "Markus M", "initials": "MM"}, {"family": "O'Donovan", "given": "Michael C", "initials": "MC"}, {"family": "Paciga", "given": "Sara A", "initials": "SA"}, {"family": "Pedersen", "given": "Nancy L", "initials": "NL"}, {"family": "Penninx", "given": "Brenda W J H", "initials": "BWJH"}, {"family": "Perlis", "given": "Roy H", "initials": "RH"}, {"family": "Porteous", "given": "David J", "initials": "DJ"}, {"family": "Potash", "given": "James B", "initials": "JB"}, {"family": "Preisig", "given": "Martin", "initials": "M"}, {"family": "Rietschel", "given": "Marcella", "initials": "M"}, {"family": "Schaefer", "given": "Catherine", "initials": "C"}, {"family": "Schulze", "given": "Thomas G", "initials": "TG"}, {"family": "Smoller", "given": "Jordan W", "initials": "JW"}, {"family": "Stefansson", "given": "Kari", "initials": "K"}, {"family": "Tiemeier", "given": "Henning", "initials": "H"}, {"family": "Uher", "given": "Rudolf", "initials": "R"}, {"family": "V\u00f6lzke", "given": "Henry", "initials": "H"}, {"family": "Weissman", "given": "Myrna M", "initials": "MM"}, {"family": "Werge", "given": "Thomas", "initials": "T"}, {"family": "Winslow", "given": "Ashley R", "initials": "AR"}, {"family": "Lewis", "given": "Cathryn M", "initials": "CM"}, {"family": "Levinson", "given": "Douglas F", "initials": "DF"}, {"family": "Breen", "given": "Gerome", "initials": "G"}, {"family": "B\u00f8rglum", "given": "Anders D", "initials": "AD"}, {"family": "Sullivan", "given": "Patrick F", "initials": "PF"}, {"family": "Major Depressive Disorder Working Group of the Psychiatric Genomics Consortium", "given": "", "initials": ""}], "type": "journal article", "published": "2018-05-00", "journal": {"volume": "50", "issn": "1546-1718", "issue": "5", "pages": "668-681", "title": "Nat. Genet.", "issn-l": "1061-4036"}, "abstract": "Major depressive disorder (MDD) is a common illness accompanied by considerable morbidity, mortality, costs, and heightened risk of suicide. We conducted a genome-wide association meta-analysis based in 135,458 cases and 344,901 controls and identified 44 independent and significant loci. The genetic findings were associated with clinical features of major depression and implicated brain regions exhibiting anatomical differences in cases. Targets of antidepressant medications and genes involved in gene splicing were enriched for smaller association signal. We found important relationships of genetic risk for major depression with educational attainment, body mass, and schizophrenia: lower educational attainment and higher body mass were putatively causal, whereas major depression and schizophrenia reflected a partly shared biological etiology. All humans carry lesser or greater numbers of genetic risk factors for major depression. These findings help refine the basis of major depression and imply that a continuous measure of risk underlies the clinical phenotype.", "doi": "10.1038/s41588-018-0090-3", "pmid": "29700475", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41588-018-0090-3"}, {"db": "pmc", "key": "PMC5934326"}, {"db": "mid", "key": "NIHMS943355"}], "notes": [], "created": "2018-05-25T13:25:53.611Z", "modified": "2024-01-16T13:48:46.418Z"}, {"entity": "publication", "iuid": "f912fc1a59804c958694b9e1bd792580", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f912fc1a59804c958694b9e1bd792580.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f912fc1a59804c958694b9e1bd792580"}}, "title": "DNA methylation mapping identifies gene regulatory effects in patients with systemic lupus erythematosus.", "authors": [{"family": "Imgenberg-Kreuz", "given": "Juliana", "initials": "J"}, {"family": "Carlsson Alml\u00f6f", "given": "Jonas", "initials": "J"}, {"family": "Leonard", "given": "Dag", "initials": "D"}, {"family": "Alexsson", "given": "Andrei", "initials": "A"}, {"family": "Nordmark", "given": "Gunnel", "initials": "G"}, {"family": "Eloranta", "given": "Maija-Leena", "initials": "ML"}, {"family": "Rantap\u00e4\u00e4-Dahlqvist", "given": "Solbritt", "initials": "S"}, {"family": "Bengtsson", "given": "Anders A", "initials": "AA"}, {"family": "J\u00f6nsen", "given": "Andreas", "initials": "A"}, {"family": "Padyukov", "given": "Leonid", "initials": "L"}, {"family": "Gunnarsson", "given": "Iva", "initials": "I"}, {"family": "Svenungsson", "given": "Elisabet", "initials": "E"}, {"family": "Sj\u00f6wall", "given": "Christopher", "initials": "C", "orcid": "0000-0003-0900-2048", "researcher": {"href": "https://publications.scilifelab.se/researcher/fe4dd47b8ca1436e8a26fdea33f5e7f6.json"}}, {"family": "R\u00f6nnblom", "given": "Lars", "initials": "L"}, {"family": "Syv\u00e4nen", "given": "Ann-Christine", "initials": "AC", "orcid": "0000-0002-9681-9146", "researcher": {"href": "https://publications.scilifelab.se/researcher/f7012e35025543379380cb90efd71243.json"}}, {"family": "Sandling", "given": "Johanna K", "initials": "JK"}], "type": "journal article", "published": "2018-05-00", "journal": {"volume": "77", "issn": "1468-2060", "issue": "5", "pages": "736-743", "title": "Ann. Rheum. Dis.", "issn-l": "0003-4967"}, "abstract": "Systemic lupus erythematosus (SLE) is a chronic autoimmune condition with heterogeneous presentation and complex aetiology where DNA methylation changes are emerging as a contributing factor. In order to discover novel epigenetic associations and investigate their relationship to genetic risk for SLE, we analysed DNA methylation profiles in a large collection of patients with SLE and healthy individuals.\n\nDNA extracted from blood from 548 patients with SLE and 587 healthy controls were analysed on the Illumina HumanMethylation 450 k BeadChip, which targets 485 000 CpG sites across the genome. Single nucleotide polymorphism (SNP) genotype data for 196 524 SNPs on the Illumina ImmunoChip from the same individuals were utilised for methylation quantitative trait loci (cis-meQTLs) analyses.\n\nWe identified and replicated differentially methylated CpGs (DMCs) in SLE at 7245 CpG sites in the genome. The largest methylation differences were observed at type I interferon-regulated genes which exhibited decreased methylation in SLE. We mapped cis-meQTLs and identified genetic regulation of methylation levels at 466 of the DMCs in SLE. The meQTLs for DMCs in SLE were enriched for genetic association to SLE, and included seven SLE genome-wide association study (GWAS) loci: PTPRC (CD45), MHC-class III, UHRF1BP1, IRF5, IRF7, IKZF3 and UBE2L3. In addition, we observed association between genotype and variance of methylation at 20 DMCs in SLE, including at the HLA-DQB2 locus.\n\nOur results suggest that several of the genetic risk variants for SLE may exert their influence on the phenotype through alteration of DNA methylation levels at regulatory regions of target genes.", "doi": "10.1136/annrheumdis-2017-212379", "pmid": "29437559", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "annrheumdis-2017-212379"}, {"db": "pmc", "key": "PMC5909746"}], "notes": [], "created": "2018-05-25T13:31:01.394Z", "modified": "2024-01-16T13:48:46.436Z"}, {"entity": "publication", "iuid": "2fbe656ef4894b12b0e51cf2485d8978", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2fbe656ef4894b12b0e51cf2485d8978.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2fbe656ef4894b12b0e51cf2485d8978"}}, "title": "Significant loss of mitochondrial diversity within the last century due to extinction of peripheral populations in eastern gorillas.", "authors": [{"family": "van der Valk", "given": "Tom", "initials": "T", "orcid": "0000-0001-6582-3452", "researcher": {"href": "https://publications.scilifelab.se/researcher/f56ca19cfa4f4909be996b2c99ec24f1.json"}}, {"family": "Sandoval-Castellanos", "given": "Edson", "initials": "E", "orcid": "0000-0002-0840-8225", "researcher": {"href": "https://publications.scilifelab.se/researcher/40a78dc09c8441438303e4cf539d8832.json"}}, {"family": "Caillaud", "given": "Damien", "initials": "D"}, {"family": "Ngobobo", "given": "Urbain", "initials": "U"}, {"family": "Binyinyi", "given": "Escobar", "initials": "E"}, {"family": "Nishuli", "given": "Radar", "initials": "R"}, {"family": "Stoinski", "given": "Tara", "initials": "T"}, {"family": "Gilissen", "given": "Emmanuel", "initials": "E"}, {"family": "Sonet", "given": "Gontran", "initials": "G"}, {"family": "Semal", "given": "Patrick", "initials": "P"}, {"family": "Kalthoff", "given": "Daniela C", "initials": "DC"}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L", "orcid": "0000-0001-8270-7613", "researcher": {"href": "https://publications.scilifelab.se/researcher/48ecf726779249ac9d12f4f7a1cc62bf.json"}}, {"family": "Guschanski", "given": "Katerina", "initials": "K", "orcid": "0000-0002-8493-5457", "researcher": {"href": "https://publications.scilifelab.se/researcher/84b8b0757f02429b9bd419acb42ab6a3.json"}}], "type": "journal article", "published": "2018-04-25", "journal": {"volume": "8", "issn": "2045-2322", "issue": "1", "pages": "6551", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "Species and populations are disappearing at an alarming rate as a direct result of human activities. Loss of genetic diversity associated with population decline directly impacts species' long-term survival. Therefore, preserving genetic diversity is of considerable conservation importance. However, to assist in conservation efforts, it is important to understand how genetic diversity is spatially distributed and how it changes due to anthropogenic pressures. In this study, we use historical museum and modern faecal samples of two critically endangered eastern gorilla taxa, Grauer's (Gorilla beringei graueri) and mountain gorillas (Gorilla beringei beringei), to directly infer temporal changes in genetic diversity within the last century. Using over 100 complete mitochondrial genomes, we observe a significant decline in haplotype and nucleotide diversity in Grauer's gorillas. By including historical samples from now extinct populations we show that this decline can be attributed to the loss of peripheral populations rather than a decrease in genetic diversity within the core range of the species. By directly quantifying genetic changes in the recent past, our study shows that human activities have severely impacted eastern gorilla genetic diversity within only four to five generations. This rapid loss calls for dedicated conservation actions, which should include preservation of the remaining peripheral populations.", "doi": "10.1038/s41598-018-24497-7", "pmid": "29695730", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-018-24497-7"}, {"db": "pmc", "key": "PMC5917027"}], "notes": [], "created": "2018-09-14T12:10:20.876Z", "modified": "2024-01-16T13:48:46.451Z"}, {"entity": "publication", "iuid": "a10e2aa7b8904098803eae744c48c5aa", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a10e2aa7b8904098803eae744c48c5aa.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a10e2aa7b8904098803eae744c48c5aa"}}, "title": "A GWAS meta-analysis from 5 population-based cohorts implicates ion channel genes in the pathogenesis of irritable bowel syndrome.", "authors": [{"family": "Bonfiglio", "given": "F", "initials": "F"}, {"family": "Henstr\u00f6m", "given": "M", "initials": "M"}, {"family": "Nag", "given": "A", "initials": "A"}, {"family": "Hadizadeh", "given": "F", "initials": "F"}, {"family": "Zheng", "given": "T", "initials": "T"}, {"family": "Cenit", "given": "M C", "initials": "MC"}, {"family": "Tigchelaar", "given": "E", "initials": "E"}, {"family": "Williams", "given": "F", "initials": "F"}, {"family": "Reznichenko", "given": "A", "initials": "A"}, {"family": "Ek", "given": "W E", "initials": "WE"}, {"family": "Rivera", "given": "N V", "initials": "NV"}, {"family": "Homuth", "given": "G", "initials": "G"}, {"family": "Aghdassi", "given": "A A", "initials": "AA"}, {"family": "Kacprowski", "given": "T", "initials": "T"}, {"family": "M\u00e4nnikk\u00f6", "given": "M", "initials": "M"}, {"family": "Karhunen", "given": "V", "initials": "V"}, {"family": "Bujanda", "given": "L", "initials": "L"}, {"family": "Rafter", "given": "J", "initials": "J"}, {"family": "Wijmenga", "given": "C", "initials": "C"}, {"family": "Ronkainen", "given": "J", "initials": "J"}, {"family": "Hysi", "given": "P", "initials": "P"}, {"family": "Zhernakova", "given": "A", "initials": "A"}, {"family": "D'Amato", "given": "M", "initials": "M"}], "type": "journal article", "published": "2018-04-19", "journal": {"volume": null, "issn": "1365-2982", "issue": null, "pages": "e13358", "title": "Neurogastroenterol. Motil.", "issn-l": "1350-1925"}, "abstract": "Irritable bowel syndrome (IBS) shows genetic predisposition, however, large-scale, powered gene mapping studies are lacking. We sought to exploit existing genetic (genotype) and epidemiological (questionnaire) data from a series of population-based cohorts for IBS genome-wide association studies (GWAS) and their meta-analysis.\n\nBased on questionnaire data compatible with Rome III Criteria, we identified a total of 1335 IBS cases and 9768 asymptomatic individuals from 5 independent European genotyped cohorts. Individual GWAS were carried out with sex-adjusted logistic regression under an additive model, followed by meta-analysis using the inverse variance method. Functional annotation of significant results was obtained via a computational pipeline exploiting ontology and interaction networks, and tissue-specific and gene set enrichment analyses.\n\nSuggestive GWAS signals (P\u00a0\u2264\u00a05.0\u00a0\u00d7\u00a010\n\nOur results confirm the feasibility of population-based studies for gene-discovery efforts in IBS, identify risk genes and loci to be prioritized in independent follow-ups, and pinpoint ion channels as important players and potential therapeutic targets warranting further investigation.", "doi": "10.1111/nmo.13358", "pmid": "29673008", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "GENBANK", "key": "rs17112758"}], "notes": [], "created": "2018-05-25T13:37:49.819Z", "modified": "2024-01-16T13:48:46.487Z"}, {"entity": "publication", "iuid": "f4929533142f424c823e32270df6618f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f4929533142f424c823e32270df6618f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f4929533142f424c823e32270df6618f"}}, "title": "Genetic and Environmental Contributions to the Covariation Between Cardiometabolic Traits.", "authors": [{"family": "Chen", "given": "Xu", "initials": "X"}, {"family": "Kuja-Halkola", "given": "Ralf", "initials": "R"}, {"family": "Chang", "given": "Zheng", "initials": "Z"}, {"family": "Karlsson", "given": "Robert", "initials": "R"}, {"family": "H\u00e4gg", "given": "Sara", "initials": "S"}, {"family": "Svensson", "given": "Per", "initials": "P"}, {"family": "Pedersen", "given": "Nancy L", "initials": "NL"}, {"family": "Magnusson", "given": "Patrik K E", "initials": "PKE"}], "type": "journal article", "published": "2018-04-18", "journal": {"volume": "7", "issn": "2047-9980", "issue": "9", "title": "J Am Heart Assoc", "issn-l": "2047-9980"}, "abstract": "The variation and covariation for many cardiometabolic traits have been decomposed into genetic and environmental fractions, by using twin or single-nucleotide polymorphism (SNP) models. However, differences in population, age, sex, and other factors hamper the comparison between twin- and SNP-based estimates.\n\nTwenty-four cardiometabolic traits and 700,000 genotyped SNPs were available in the study base of 10\u00a0682 twins from TwinGene cohort. For the 27 highly correlated pairs (absolute phenotypic correlation coefficient \u22650.40), twin-based bivariate structural equation\u00a0models were performed in 3870 complete twin pairs, and SNP-based bivariate genomic relatedness matrix restricted maximum likelihood methods were performed in 5779 unrelated individuals. In twin models, the model including additive genetic variance and unique/nonshared environmental variance was the best-fitted model for 7 pairs (5 of them were between blood pressure traits); the model including additive genetic variance, common/shared environmental variance, and unique/nonshared environmental variance components was best fitted for 4 pairs, but estimates of shared environment were close to zero; and the model including additive genetic variance, dominant genetic variance, and unique/nonshared environmental variance was best fitted for 16 pairs, in which significant dominant genetic effects were identified for 13 pairs (including all 9 obesity-related pairs). However, SNP models did not identify significant estimates of dominant genetic effects for any pairs. In the paired \n\nBeside additive genetic effects and nonshared environment, nonadditive genetic effects (dominance) also contribute to the covariation between certain cardiometabolic traits (especially for obesity-related pairs); contributions from the shared environment seem to be weak for their covariation in TwinGene samples.", "doi": "10.1161/JAHA.117.007806", "pmid": "29669715", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "JAHA.117.007806"}], "notes": [], "created": "2018-05-25T13:25:48.502Z", "modified": "2024-01-16T13:48:46.495Z"}, {"entity": "publication", "iuid": "bb48704f814e4d59bc438c99232c9264", "links": {"self": {"href": "https://publications.scilifelab.se/publication/bb48704f814e4d59bc438c99232c9264.json"}, "display": {"href": "https://publications.scilifelab.se/publication/bb48704f814e4d59bc438c99232c9264"}}, "title": "Data quality of whole genome bisulfite sequencing on Illumina platforms.", "authors": [{"family": "Raine", "given": "Amanda", "initials": "A", "orcid": "0000-0002-2775-6516", "researcher": {"href": "https://publications.scilifelab.se/researcher/a97b7df8379f42f0a412fb7c234a6c70.json"}}, {"family": "Liljedahl", "given": "Ulrika", "initials": "U", "orcid": "0000-0002-1250-392X", "researcher": {"href": "https://publications.scilifelab.se/researcher/241618974ae142b38e5fe84236819f2b.json"}}, {"family": "Nordlund", "given": "Jessica", "initials": "J", "orcid": "0000-0001-8699-9959", "researcher": {"href": "https://publications.scilifelab.se/researcher/ddf48c9262134821bcc6ce1180049753.json"}}], "type": "journal article", "published": "2018-04-18", "journal": {"volume": "13", "issn": "1932-6203", "issue": "4", "pages": "e0195972", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "The powerful HiSeq X sequencers with their patterned flowcell technology and fast turnaround times are instrumental for many large-scale genomic and epigenomic studies. However, assessment of DNA methylation by sodium bisulfite treatment results in sequencing libraries of low diversity, which may impact data quality and yield. In this report we assess the quality of WGBS data generated on the HiSeq X system in comparison with data generated on the HiSeq 2500 system and the newly released NovaSeq system. We report a systematic issue with low basecall quality scores assigned to guanines in the second read of WGBS when using certain Real Time Analysis (RTA) software versions on the HiSeq X sequencer, reminiscent of an issue that was previously reported with certain HiSeq 2500 software versions. However, with the HD.3.4.0 /RTA 2.7.7 software upgrade for the HiSeq X system, we observed an overall improved quality and yield of the WGBS data generated, which in turn empowers cost-effective and high quality DNA methylation studies.", "doi": "10.1371/journal.pone.0195972", "pmid": "29668744", "labels": {"National Genomics Infrastructure": "Technology development", "NGI Uppsala (SNP&SEQ Technology Platform)": "Technology development", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "PONE-D-17-37428"}, {"db": "pmc", "key": "PMC5905984"}], "notes": [], "created": "2018-05-14T05:44:07.600Z", "modified": "2024-01-16T13:48:46.511Z"}, {"entity": "publication", "iuid": "96f77819b96e402899d9104cf571a35d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/96f77819b96e402899d9104cf571a35d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/96f77819b96e402899d9104cf571a35d"}}, "title": "Female-specific Association Between Variants on Chromosome 9 and Self-reported Diagnosis of Irritable Bowel Syndrome.", "authors": [{"family": "Bonfiglio", "given": "Ferdinando", "initials": "F"}, {"family": "Zheng", "given": "Tenghao", "initials": "T"}, {"family": "Garcia-Etxebarria", "given": "Koldo", "initials": "K"}, {"family": "Hadizadeh", "given": "Fatemeh", "initials": "F"}, {"family": "Bujanda", "given": "Luis", "initials": "L"}, {"family": "Bresso", "given": "Francesca", "initials": "F"}, {"family": "Agreus", "given": "Lars", "initials": "L"}, {"family": "Andreasson", "given": "Anna", "initials": "A"}, {"family": "Dlugosz", "given": "Aldona", "initials": "A"}, {"family": "Lindberg", "given": "Greger", "initials": "G"}, {"family": "Schmidt", "given": "Peter T", "initials": "PT"}, {"family": "Karling", "given": "Pontus", "initials": "P"}, {"family": "Ohlsson", "given": "Bodil", "initials": "B"}, {"family": "Simren", "given": "Magnus", "initials": "M"}, {"family": "Walter", "given": "Susanna", "initials": "S"}, {"family": "Nardone", "given": "Gerardo", "initials": "G"}, {"family": "Cuomo", "given": "Rosario", "initials": "R"}, {"family": "Usai-Satta", "given": "Paolo", "initials": "P"}, {"family": "Galeazzi", "given": "Francesca", "initials": "F"}, {"family": "Neri", "given": "Matteo", "initials": "M"}, {"family": "Portincasa", "given": "Piero", "initials": "P"}, {"family": "Bellini", "given": "Massimo", "initials": "M"}, {"family": "Barbara", "given": "Giovanni", "initials": "G"}, {"family": "Latiano", "given": "Anna", "initials": "A"}, {"family": "H\u00fcbenthal", "given": "Matthias", "initials": "M"}, {"family": "Thijs", "given": "Vincent", "initials": "V"}, {"family": "Netea", "given": "Mihai G", "initials": "MG"}, {"family": "Jonkers", "given": "Daisy", "initials": "D"}, {"family": "Chang", "given": "Lin", "initials": "L"}, {"family": "Mayer", "given": "Emeran A", "initials": "EA"}, {"family": "Wouters", "given": "Mira M", "initials": "MM"}, {"family": "Boeckxstaens", "given": "Guy", "initials": "G"}, {"family": "Camilleri", "given": "Michael", "initials": "M"}, {"family": "Franke", "given": "Andre", "initials": "A"}, {"family": "Zhernakova", "given": "Alexandra", "initials": "A"}, {"family": "D'Amato", "given": "Mauro", "initials": "M"}], "type": "journal article", "published": "2018-04-04", "journal": {"volume": null, "issn": "1528-0012", "issue": null, "title": "Gastroenterology", "issn-l": "0016-5085"}, "abstract": "Genetic factors are believed to affect risk for irritable bowel syndrome (IBS), but there have been no sufficiently powered and adequately sized studies. To identify DNA variants associated with IBS risk, we performed a genome-wide association study (GWAS) of the large UK Biobank population-based cohort, which includes genotype and health data from 500,000 participants.\n\nWe studied 7,287,191 high-quality single-nucleotide polymorphisms in individuals who self-reported a doctor's diagnosis of IBS (cases; m=9576) compared to the remainder of the cohort (controls; n=336,499) (mean age of study subjects, 40-69 years). Genome-wide significant findings were further investigated in 2045 patients with IBS from tertiary centers and 7955 population controls from Europe and the United States, and a small general population sample from Sweden (n=249). Functional annotation of GWAS results was carried out by integrating data from multiple biorepositories, to obtain biological insights from the observed associations.\n\nWe identified a genome-wide significant association on chromosome 9q31.2 (SNP rs10512344; P=3.57\u00d710\n\nIn a sufficiently powered GWAS of IBS, we associated variants at the locus 9q32.1 with risk of IBS in women. This observation may provide additional rationale for investigating the role of sex hormones and autonomic dysfunction in IBS.", "doi": "10.1053/j.gastro.2018.03.064", "pmid": "29626450", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "S0016-5085(18)30407-4"}], "notes": [], "created": "2018-05-25T13:37:47.262Z", "modified": "2024-01-16T13:48:46.558Z"}, {"entity": "publication", "iuid": "d3b23e22ff0f40558f8a329b86c8f633", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d3b23e22ff0f40558f8a329b86c8f633.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d3b23e22ff0f40558f8a329b86c8f633"}}, "title": "Refining the accuracy of validated target identification through coding variant fine-mapping in type 2 diabetes.", "authors": [{"family": "Mahajan", "given": "Anubha", "initials": "A"}, {"family": "Wessel", "given": "Jennifer", "initials": "J"}, {"family": "Willems", "given": "Sara M", "initials": "SM"}, {"family": "Zhao", "given": "Wei", "initials": "W"}, {"family": "Robertson", "given": "Neil R", "initials": "NR"}, {"family": "Chu", "given": "Audrey Y", "initials": "AY"}, {"family": "Gan", "given": "Wei", "initials": "W"}, {"family": "Kitajima", "given": "Hidetoshi", "initials": "H"}, {"family": "Taliun", "given": "Daniel", "initials": "D"}, {"family": "Rayner", "given": "N William", "initials": "NW"}, {"family": "Guo", "given": "Xiuqing", "initials": "X"}, {"family": "Lu", "given": "Yingchang", "initials": "Y"}, {"family": "Li", "given": "Man", "initials": "M"}, {"family": "Jensen", "given": "Richard A", "initials": "RA"}, {"family": "Hu", "given": "Yao", "initials": "Y"}, {"family": "Huo", "given": "Shaofeng", "initials": "S"}, {"family": "Lohman", "given": "Kurt K", "initials": "KK"}, {"family": "Zhang", "given": "Weihua", "initials": "W"}, {"family": "Cook", "given": "James P", "initials": "JP"}, {"family": "Prins", "given": "Bram Peter", "initials": "BP"}, {"family": "Flannick", "given": "Jason", "initials": "J"}, {"family": "Grarup", "given": "Niels", "initials": "N"}, {"family": "Trubetskoy", "given": "Vassily Vladimirovich", "initials": "VV"}, {"family": "Kravic", "given": "Jasmina", "initials": "J"}, {"family": "Kim", "given": "Young Jin", "initials": "YJ"}, {"family": "Rybin", "given": "Denis V", "initials": "DV"}, {"family": "Yaghootkar", "given": "Hanieh", "initials": "H"}, {"family": "M\u00fcller-Nurasyid", "given": "Martina", "initials": "M"}, {"family": "Meidtner", "given": "Karina", "initials": "K"}, {"family": "Li-Gao", "given": "Ruifang", "initials": "R"}, {"family": "Varga", "given": "Tibor V", "initials": "TV"}, {"family": "Marten", "given": "Jonathan", "initials": "J"}, {"family": "Li", "given": "Jin", "initials": "J"}, {"family": "Smith", "given": "Albert Vernon", "initials": "AV"}, {"family": "An", "given": "Ping", "initials": "P"}, {"family": "Ligthart", "given": "Symen", "initials": "S"}, {"family": "Gustafsson", "given": "Stefan", "initials": "S"}, {"family": "Malerba", "given": "Giovanni", "initials": "G"}, {"family": "Demirkan", "given": "Ayse", "initials": "A"}, {"family": "Tajes", "given": "Juan Fernandez", "initials": "JF"}, {"family": "Steinthorsdottir", "given": "Valgerdur", "initials": "V"}, {"family": "Wuttke", "given": "Matthias", "initials": "M"}, {"family": "Lecoeur", "given": "C\u00e9cile", "initials": "C"}, {"family": "Preuss", "given": "Michael", "initials": "M"}, {"family": "Bielak", "given": "Lawrence F", "initials": "LF"}, {"family": "Graff", "given": "Marielisa", "initials": "M"}, {"family": "Highland", "given": "Heather M", "initials": "HM"}, {"family": "Justice", "given": "Anne E", "initials": "AE"}, {"family": "Liu", "given": "Dajiang J", "initials": "DJ"}, {"family": "Marouli", "given": "Eirini", "initials": "E"}, {"family": "Peloso", "given": "Gina Marie", "initials": "GM"}, {"family": "Warren", "given": "Helen R", "initials": "HR"}, {"family": "ExomeBP Consortium", "given": "", "initials": ""}, {"family": "MAGIC Consortium", "given": "", "initials": ""}, {"family": "GIANT Consortium", "given": "", "initials": ""}, {"family": "Afaq", "given": "Saima", "initials": "S"}, {"family": "Afzal", "given": "Shoaib", "initials": "S"}, {"family": "Ahlqvist", "given": "Emma", "initials": "E"}, {"family": "Almgren", "given": "Peter", "initials": "P"}, {"family": "Amin", "given": "Najaf", "initials": "N"}, {"family": "Bang", "given": "Lia B", "initials": "LB"}, {"family": "Bertoni", "given": "Alain G", "initials": "AG"}, {"family": "Bombieri", "given": "Cristina", "initials": "C"}, {"family": "Bork-Jensen", "given": "Jette", "initials": "J"}, {"family": "Brandslund", "given": "Ivan", "initials": "I"}, {"family": "Brody", "given": "Jennifer A", "initials": "JA"}, {"family": "Burtt", "given": "No\u00ebl P", "initials": "NP"}, {"family": "Canouil", "given": "Micka\u00ebl", "initials": "M"}, {"family": "Chen", "given": "Yii-Der Ida", "initials": "YI"}, {"family": "Cho", "given": "Yoon Shin", "initials": "YS"}, {"family": "Christensen", "given": "Cramer", "initials": "C"}, {"family": "Eastwood", "given": "Sophie V", "initials": "SV"}, {"family": "Eckardt", "given": "Kai-Uwe", "initials": "KU"}, {"family": "Fischer", "given": "Krista", "initials": "K"}, {"family": "Gambaro", "given": "Giovanni", "initials": "G"}, {"family": "Giedraitis", "given": "Vilmantas", "initials": "V"}, {"family": "Grove", "given": "Megan L", "initials": "ML"}, {"family": "de Haan", "given": "Hugoline G", "initials": "HG"}, {"family": "Hackinger", "given": "Sophie", "initials": "S"}, {"family": "Hai", "given": "Yang", "initials": "Y"}, {"family": "Han", "given": "Sohee", "initials": "S"}, {"family": "Tybj\u00e6rg-Hansen", "given": "Anne", "initials": "A"}, {"family": "Hivert", "given": "Marie-France", "initials": "MF"}, {"family": "Isomaa", "given": "Bo", "initials": "B"}, {"family": "J\u00e4ger", "given": "Susanne", "initials": "S"}, {"family": "J\u00f8rgensen", "given": "Marit E", "initials": "ME"}, {"family": "J\u00f8rgensen", "given": "Torben", "initials": "T"}, {"family": "K\u00e4r\u00e4j\u00e4m\u00e4ki", "given": "Annemari", "initials": "A"}, {"family": "Kim", "given": "Bong-Jo", "initials": "BJ"}, {"family": "Kim", "given": "Sung Soo", "initials": "SS"}, {"family": "Koistinen", "given": "Heikki A", "initials": "HA"}, {"family": "Kovacs", "given": "Peter", "initials": "P"}, {"family": "Kriebel", "given": "Jennifer", "initials": "J"}, {"family": "Kronenberg", "given": "Florian", "initials": "F"}, {"family": "L\u00e4ll", "given": "Kristi", "initials": "K"}, {"family": "Lange", "given": "Leslie A", "initials": "LA"}, {"family": "Lee", "given": "Jung-Jin", "initials": "JJ"}, {"family": "Lehne", "given": "Benjamin", "initials": "B"}, {"family": "Li", "given": "Huaixing", "initials": "H"}, {"family": "Lin", "given": "Keng-Hung", "initials": "KH"}, {"family": "Linneberg", "given": "Allan", "initials": "A"}, {"family": "Liu", "given": "Ching-Ti", "initials": "CT"}, {"family": "Liu", "given": "Jun", "initials": "J"}, {"family": "Loh", "given": "Marie", "initials": "M"}, {"family": "M\u00e4gi", "given": "Reedik", "initials": "R"}, {"family": "Mamakou", "given": "Vasiliki", "initials": "V"}, {"family": "McKean-Cowdin", "given": "Roberta", "initials": "R"}, {"family": "Nadkarni", "given": "Girish", "initials": "G"}, {"family": "Neville", "given": "Matt", "initials": "M"}, {"family": "Nielsen", "given": "Sune F", "initials": "SF"}, {"family": "Ntalla", "given": "Ioanna", "initials": "I"}, {"family": "Peyser", "given": "Patricia A", "initials": "PA"}, {"family": "Rathmann", "given": "Wolfgang", "initials": "W"}, {"family": "Rice", "given": "Kenneth", "initials": "K"}, {"family": "Rich", "given": "Stephen S", "initials": "SS"}, {"family": "Rode", "given": "Line", "initials": "L"}, {"family": "Rolandsson", "given": "Olov", "initials": "O"}, {"family": "Sch\u00f6nherr", "given": "Sebastian", "initials": "S"}, {"family": "Selvin", "given": "Elizabeth", "initials": "E"}, {"family": "Small", "given": "Kerrin S", "initials": "KS"}, {"family": "Stan\u010d\u00e1kov\u00e1", "given": "Alena", "initials": "A"}, {"family": "Surendran", "given": "Praveen", "initials": "P"}, {"family": "Taylor", "given": "Kent D", "initials": "KD"}, {"family": "Teslovich", "given": "Tanya M", "initials": "TM"}, {"family": "Thorand", "given": "Barbara", "initials": "B"}, {"family": "Thorleifsson", "given": "Gudmar", "initials": "G"}, {"family": "Tin", "given": "Adrienne", "initials": "A"}, {"family": "T\u00f6njes", "given": "Anke", "initials": "A"}, {"family": "Varbo", "given": "Anette", "initials": "A"}, {"family": "Witte", "given": "Daniel R", "initials": "DR"}, {"family": "Wood", "given": "Andrew R", "initials": "AR"}, {"family": "Yajnik", "given": "Pranav", "initials": "P"}, {"family": "Yao", "given": "Jie", "initials": 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"D"}, {"family": "Nordestgaard", "given": "B\u00f8rge G", "initials": "BG"}, {"family": "Palmer", "given": "Colin N A", "initials": "CNA"}, {"family": "Pankow", "given": "James S", "initials": "JS"}, {"family": "Pedersen", "given": "Oluf", "initials": "O"}, {"family": "Psaty", "given": "Bruce M", "initials": "BM"}, {"family": "Rauramaa", "given": "Rainer", "initials": "R"}, {"family": "Sattar", "given": "Naveed", "initials": "N"}, {"family": "Schulze", "given": "Matthias B", "initials": "MB"}, {"family": "Soranzo", "given": "Nicole", "initials": "N"}, {"family": "Spector", "given": "Timothy D", "initials": "TD"}, {"family": "Stefansson", "given": "Kari", "initials": "K"}, {"family": "Stumvoll", "given": "Michael", "initials": "M"}, {"family": "Thorsteinsdottir", "given": "Unnur", "initials": "U"}, {"family": "Tuomi", "given": "Tiinamaija", "initials": "T"}, {"family": "Tuomilehto", "given": "Jaakko", "initials": "J"}, {"family": "Wareham", "given": "Nicholas J", "initials": "NJ"}, {"family": "Wilson", "given": "James G", "initials": "JG"}, {"family": "Zeggini", "given": "Eleftheria", "initials": "E"}, {"family": "Scott", "given": "Robert A", "initials": "RA"}, {"family": "Barroso", "given": "In\u00eas", "initials": "I"}, {"family": "Frayling", "given": "Timothy M", "initials": "TM"}, {"family": "Goodarzi", "given": "Mark O", "initials": "MO"}, {"family": "Meigs", "given": "James B", "initials": "JB"}, {"family": "Boehnke", "given": "Michael", "initials": "M"}, {"family": "Saleheen", "given": "Danish", "initials": "D"}, {"family": "Morris", "given": "Andrew P", "initials": "AP"}, {"family": "Rotter", "given": "Jerome I", "initials": "JI"}, {"family": "McCarthy", "given": "Mark I", "initials": "MI"}], "type": "journal article", "published": "2018-04-00", "journal": {"volume": "50", "issn": "1546-1718", "issue": "4", "pages": "559-571", "title": "Nat. Genet.", "issn-l": "1061-4036"}, "abstract": "We aggregated coding variant data for 81,412 type 2 diabetes cases and 370,832 controls of diverse ancestry, identifying 40 coding variant association signals (P\u2009<\u20092.2\u2009\u00d7\u200910\n            -7); of these, 16 map outside known risk-associated loci. We make two important observations. First, only five of these signals are driven by low-frequency variants: even for these, effect sizes are modest (odds ratio \u22641.29). Second, when we used large-scale genome-wide association data to fine-map the associated variants in their regional context, accounting for the global enrichment of complex trait associations in coding sequence, compelling evidence for coding variant causality was obtained for only 16 signals. At 13 others, the associated coding variants clearly represent 'false leads' with potential to generate erroneous mechanistic inference. Coding variant associations offer a direct route to biological insight for complex diseases and identification of validated therapeutic targets; however, appropriate mechanistic inference requires careful specification of their causal contribution to disease predisposition.", "doi": "10.1038/s41588-018-0084-1", "pmid": "29632382", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41588-018-0084-1"}, {"db": "pmc", "key": "PMC5898373"}, {"db": "mid", "key": "NIHMS938867"}], "notes": [], "created": "2019-01-09T07:22:20.125Z", "modified": "2020-01-21T13:56:13.737Z"}, {"entity": "publication", "iuid": "3d83cbfecc514236942cec0c1cebfe69", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3d83cbfecc514236942cec0c1cebfe69.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3d83cbfecc514236942cec0c1cebfe69"}}, "title": "RNA Sequencing of Stentor Cell Fragments Reveals Transcriptional Changes during Cellular Regeneration", "authors": [{"family": "Onsbring", "given": "Henning", "initials": "H"}, {"family": "Jamy", "given": "Mahwash", "initials": "M"}, {"family": "Ettema", "given": "Thijs J G", "initials": "TJG"}], "type": "journal-article", "published": "2018-04-00", "journal": {"volume": "28", "issn": "0960-9822", "issue": "8", "pages": "1281-1288.e3", "title": "Current Biology", "issn-l": "0960-9822"}, "abstract": null, "doi": "10.1016/j.cub.2018.02.055", "pmid": "29628369", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "GENBANK", "description": "TSA: Stentor polymorphus, transcriptome shotgun assembly", "key": "GGGV00000000"}, {"db": "SRA", "description": null, "key": "SRP132767"}, {"db": "data.mendeley.com", "description": "https://data.mendeley.com/datasets/nmgz3m3ptn/1", "key": "https://doi.org/10.17632/nmgz3m3ptn.1"}], "notes": [], "created": "2018-10-22T10:02:47.460Z", "modified": "2024-01-16T13:48:46.581Z"}, {"entity": "publication", "iuid": "f86c0d25946743a0b41428c43f098abb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f86c0d25946743a0b41428c43f098abb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f86c0d25946743a0b41428c43f098abb"}}, "title": "Multiancestry genome-wide association study of 520,000 subjects identifies 32 loci associated with stroke and stroke subtypes.", "authors": [{"family": "Malik", "given": "Rainer", "initials": "R"}, {"family": "Chauhan", "given": "Ganesh", "initials": "G"}, {"family": "Traylor", "given": "Matthew", "initials": "M", "orcid": "0000-0001-6624-8621", "researcher": {"href": "https://publications.scilifelab.se/researcher/09da34e6de524815b381ce009719c70e.json"}}, {"family": "Sargurupremraj", "given": 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"Patrick F", "initials": "PF"}, {"family": "Meschia", "given": "James F", "initials": "JF"}, {"family": "Mitchell", "given": "Braxton D", "initials": "BD"}, {"family": "Mosley", "given": "Thomas H", "initials": "TH"}, {"family": "Nalls", "given": "Michael A", "initials": "MA"}, {"family": "Ninomiya", "given": "Toshiharu", "initials": "T"}, {"family": "O'Donnell", "given": "Martin J", "initials": "MJ"}, {"family": "Psaty", "given": "Bruce M", "initials": "BM"}, {"family": "Pulit", "given": "Sara L", "initials": "SL", "orcid": "0000-0002-2502-3669", "researcher": {"href": "https://publications.scilifelab.se/researcher/58262d1f682844fa9c5ac03cc66c98bd.json"}}, {"family": "Rannikm\u00e4e", "given": "Kristiina", "initials": "K"}, {"family": "Reiner", "given": "Alexander P", "initials": "AP"}, {"family": "Rexrode", "given": "Kathryn M", "initials": "KM"}, {"family": "Rice", "given": "Kenneth", "initials": "K"}, {"family": "Rich", "given": "Stephen S", "initials": "SS"}, {"family": "Ridker", "given": "Paul M", "initials": "PM"}, {"family": "Rost", "given": "Natalia S", "initials": "NS"}, {"family": "Rothwell", "given": "Peter M", "initials": "PM"}, {"family": "Rotter", "given": "Jerome I", "initials": "JI"}, {"family": "Rundek", "given": "Tatjana", "initials": "T"}, {"family": "Sacco", "given": "Ralph L", "initials": "RL"}, {"family": "Sakaue", "given": "Saori", "initials": "S"}, {"family": "Sale", "given": "Michele M", "initials": "MM"}, {"family": "Salomaa", "given": "Veikko", "initials": "V"}, {"family": "Sapkota", "given": "Bishwa R", "initials": "BR"}, {"family": "Schmidt", "given": "Reinhold", "initials": "R"}, {"family": "Schmidt", "given": "Carsten O", "initials": "CO"}, {"family": "Schminke", "given": "Ulf", "initials": "U"}, {"family": "Sharma", "given": "Pankaj", "initials": "P"}, {"family": "Slowik", "given": "Agnieszka", "initials": "A"}, {"family": "Sudlow", "given": "Cathie L M", "initials": "CLM"}, {"family": "Tanislav", "given": "Christian", "initials": "C"}, {"family": "Tatlisumak", "given": "Turgut", "initials": "T"}, {"family": "Taylor", "given": "Kent D", "initials": "KD"}, {"family": "Thijs", "given": "Vincent N S", "initials": "VNS"}, {"family": "Thorleifsson", "given": "Gudmar", "initials": "G"}, {"family": "Thorsteinsdottir", "given": "Unnur", "initials": "U"}, {"family": "Tiedt", "given": "Steffen", "initials": "S"}, {"family": "Trompet", "given": "Stella", "initials": "S"}, {"family": "Tzourio", "given": "Christophe", "initials": "C"}, {"family": "van Duijn", "given": "Cornelia M", "initials": "CM"}, {"family": "Walters", "given": "Matthew", "initials": "M"}, {"family": "Wareham", "given": "Nicholas J", "initials": "NJ"}, {"family": "Wassertheil-Smoller", "given": "Sylvia", "initials": "S"}, {"family": "Wilson", "given": "James G", "initials": "JG"}, {"family": "Wiggins", "given": "Kerri L", "initials": "KL", "orcid": "0000-0003-2749-1279", "researcher": {"href": "https://publications.scilifelab.se/researcher/a9d1f9cb10ef4038abb10fb6ee289504.json"}}, {"family": "Yang", "given": "Qiong", "initials": "Q", "orcid": "0000-0002-3658-1375", "researcher": {"href": "https://publications.scilifelab.se/researcher/430f81a2a8334a0e887346376b2f530e.json"}}, {"family": "Yusuf", "given": "Salim", "initials": "S"}, {"family": "AFGen Consortium", "given": "", "initials": ""}, {"family": "Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) Consortium", "given": "", "initials": ""}, {"family": "International Genomics of Blood Pressure (iGEN-BP) Consortium", "given": "", "initials": ""}, {"family": "INVENT Consortium", "given": "", "initials": ""}, {"family": "STARNET", "given": "", "initials": ""}, {"family": "Bis", "given": "Joshua C", "initials": "JC"}, {"family": "Pastinen", "given": "Tomi", "initials": "T"}, {"family": "Ruusalepp", "given": "Arno", "initials": "A"}, {"family": "Schadt", "given": "Eric E", "initials": "EE", "orcid": "0000-0002-7892-8808", "researcher": {"href": "https://publications.scilifelab.se/researcher/74c9874617f94eec8f58d6febf75786f.json"}}, {"family": "Koplev", "given": "Simon", "initials": "S", "orcid": "0000-0002-8586-5614", "researcher": {"href": "https://publications.scilifelab.se/researcher/1b98325250b04317914e8895b3cefb35.json"}}, {"family": "Bj\u00f6rkegren", "given": "Johan L M", "initials": "JLM"}, {"family": "Codoni", "given": "Veronica", "initials": "V"}, {"family": "Civelek", "given": "Mete", "initials": "M", "orcid": "0000-0002-8141-0284", "researcher": {"href": "https://publications.scilifelab.se/researcher/647c7636e87f43ec960627d299d4cc2b.json"}}, {"family": "Smith", "given": "Nicholas L", "initials": "NL"}, {"family": "Tr\u00e9gou\u00ebt", "given": "David A", "initials": "DA", "orcid": "0000-0001-9084-7800", "researcher": {"href": "https://publications.scilifelab.se/researcher/adb3fe1a732b41d79a4a165a64c322d1.json"}}, {"family": "Christophersen", "given": "Ingrid E", "initials": "IE", "orcid": "0000-0002-6141-4712", "researcher": {"href": "https://publications.scilifelab.se/researcher/6430b9a129c1433a8e883a16a174b7a1.json"}}, {"family": "Roselli", "given": "Carolina", "initials": "C", "orcid": "0000-0001-5267-6756", "researcher": {"href": "https://publications.scilifelab.se/researcher/1dd28aad250f42719d505c21ed76013b.json"}}, {"family": "Lubitz", "given": "Steven A", "initials": "SA"}, {"family": "Ellinor", "given": "Patrick T", "initials": "PT", "orcid": "0000-0002-2067-0533", "researcher": {"href": "https://publications.scilifelab.se/researcher/dd513dc49e0945bc8298f72d1244648d.json"}}, {"family": "Tai", "given": "E Shyong", "initials": "ES"}, {"family": "Kooner", "given": "Jaspal S", "initials": "JS"}, {"family": "Kato", "given": "Norihiro", "initials": "N"}, {"family": "He", "given": "Jiang", "initials": "J"}, {"family": "van der Harst", "given": "Pim", "initials": "P", "orcid": "0000-0002-2713-686X", "researcher": {"href": "https://publications.scilifelab.se/researcher/a710eb0e12344e8fb5083599c95a1b2e.json"}}, {"family": "Elliott", "given": "Paul", "initials": "P", "orcid": "0000-0002-7511-5684", "researcher": {"href": "https://publications.scilifelab.se/researcher/cd5be37d90db471f8ffe1a8908f30441.json"}}, {"family": "Chambers", "given": "John C", "initials": "JC"}, {"family": "Takeuchi", "given": "Fumihiko", "initials": "F", "orcid": "0000-0003-3185-5661", "researcher": {"href": "https://publications.scilifelab.se/researcher/3f76d5798d144915b7d63f64917ec1e3.json"}}, {"family": "Johnson", "given": "Andrew D", "initials": "AD"}, {"family": "BioBank Japan Cooperative Hospital Group", "given": "", "initials": ""}, {"family": "COMPASS Consortium", "given": "", "initials": ""}, {"family": "EPIC-CVD Consortium", "given": "", "initials": ""}, {"family": "EPIC-InterAct Consortium", "given": "", "initials": ""}, {"family": "International Stroke Genetics Consortium (ISGC)", "given": "", "initials": ""}, {"family": "METASTROKE Consortium", "given": "", "initials": ""}, {"family": "Neurology Working Group of the CHARGE Consortium", "given": "", "initials": ""}, {"family": "NINDS Stroke Genetics Network (SiGN)", "given": "", "initials": ""}, {"family": "UK Young Lacunar DNA Study", "given": "", "initials": ""}, {"family": "MEGASTROKE Consortium", "given": "", "initials": ""}, {"family": "Sanghera", "given": "Dharambir K", "initials": "DK"}, {"family": "Melander", "given": "Olle", "initials": "O"}, {"family": "Jern", "given": "Christina", "initials": "C", "orcid": "0000-0002-7531-2354", "researcher": {"href": "https://publications.scilifelab.se/researcher/13e58d6c4a2e44cd9067f38a2ff2ea32.json"}}, {"family": "Strbian", "given": "Daniel", "initials": "D"}, {"family": "Fernandez-Cadenas", "given": "Israel", "initials": "I"}, {"family": "Longstreth", "given": "W T", "initials": "WT"}, {"family": "Rolfs", "given": "Arndt", "initials": "A"}, {"family": "Hata", "given": "Jun", "initials": "J"}, {"family": "Woo", "given": "Daniel", "initials": "D"}, {"family": "Rosand", "given": "Jonathan", "initials": "J"}, {"family": "Pare", "given": "Guillaume", "initials": "G"}, {"family": "Hopewell", "given": "Jemma C", "initials": "JC"}, {"family": "Saleheen", "given": "Danish", "initials": "D", "orcid": "0000-0001-6193-020X", "researcher": {"href": "https://publications.scilifelab.se/researcher/bbd250d7c853482084f2e8e221341790.json"}}, {"family": "Stefansson", "given": "Kari", "initials": "K"}, {"family": "Worrall", "given": "Bradford B", "initials": "BB"}, {"family": "Kittner", "given": "Steven J", "initials": "SJ"}, {"family": "Seshadri", "given": "Sudha", "initials": "S"}, {"family": "Fornage", "given": "Myriam", "initials": "M"}, {"family": "Markus", "given": "Hugh S", "initials": "HS"}, {"family": "Howson", "given": "Joanna M M", "initials": "JMM"}, {"family": "Kamatani", "given": "Yoichiro", "initials": "Y", "orcid": "0000-0001-8748-5597", "researcher": {"href": "https://publications.scilifelab.se/researcher/6cf00b09991c4b40bd77a4f2c5bfad97.json"}}, {"family": "Debette", "given": "Stephanie", "initials": "S"}, {"family": "Dichgans", "given": "Martin", "initials": "M", "orcid": "0000-0002-0654-387X", "researcher": {"href": "https://publications.scilifelab.se/researcher/f41f224e973440f6a78a49b54ca35e3a.json"}}], "type": "journal article", "published": "2018-04-00", "journal": {"volume": "50", "issn": "1546-1718", "issue": "4", "pages": "524-537", "title": "Nat. Genet.", "issn-l": "1061-4036"}, "abstract": "Stroke has multiple etiologies, but the underlying genes and pathways are largely unknown. We conducted a multiancestry genome-wide-association meta-analysis in 521,612 individuals (67,162 cases and 454,450 controls) and discovered 22 new stroke risk loci, bringing the total to 32. We further found shared genetic variation with related vascular traits, including blood pressure, cardiac traits, and venous thromboembolism, at individual loci (n = 18), and using genetic risk scores and linkage-disequilibrium-score regression. Several loci exhibited distinct association and pleiotropy patterns for etiological stroke subtypes. Eleven new susceptibility loci indicate mechanisms not previously implicated in stroke pathophysiology, with prioritization of risk variants and genes accomplished through bioinformatics analyses using extensive functional datasets. Stroke risk loci were significantly enriched in drug targets for antithrombotic therapy.", "doi": "10.1038/s41588-018-0058-3", "pmid": "29531354", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "mid", "key": "NIHMS959658"}, {"db": "pmc", "key": "PMC5968830"}, {"db": "pii", "key": "10.1038/s41588-018-0058-3"}], "notes": [], "created": "2018-05-25T13:25:52.583Z", "modified": "2024-01-16T13:48:46.589Z"}, {"entity": "publication", "iuid": "d205bac97d41475f912f6b0f5e039ed6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d205bac97d41475f912f6b0f5e039ed6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d205bac97d41475f912f6b0f5e039ed6"}}, "title": "An in vitro evaluation of browser and grazer fermentation efficiency and microbiota using European moose spring and summer foods", "authors": [{"family": "Krizsan", "given": "Sophie J", "initials": "SJ"}, {"family": "Mateos-Rivera", "given": "Alejandro", "initials": "A"}, {"family": "Bertilsson", "given": "Stefan", "initials": "S"}, {"family": "Felton", "given": "Annika", "initials": "A"}, {"family": "Anttila", "given": "Anne", "initials": "A"}, {"family": "Ramin", "given": "Mohammad", "initials": "M"}, {"family": "Vaga", "given": "Merko", "initials": "M"}, {"family": "Gidlund", "given": "Helena", "initials": "H"}, {"family": "Huhtanen", "given": "Pekka", "initials": "P"}], "type": "journal-article", "published": "2018-04-00", "journal": {"volume": "8", "issn": "2045-7758", "issue": "8", "pages": "4183-4196", "title": "Ecol Evol", "issn-l": "2045-7758"}, "abstract": null, "doi": "10.1002/ece3.3920", "pmid": "29721290", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2018-09-14T12:07:08.239Z", "modified": "2024-01-16T13:48:46.635Z"}, {"entity": "publication", "iuid": "5550cc23aeed489b8afc6a667e6dfe6c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5550cc23aeed489b8afc6a667e6dfe6c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5550cc23aeed489b8afc6a667e6dfe6c"}}, "title": "Four millennia of Iberian biomolecular prehistory illustrate the impact of prehistoric migrations at the far end of Eurasia.", "authors": [{"family": "Valdiosera", "given": "Cristina", "initials": "C", "orcid": "0000-0003-4948-2226", "researcher": {"href": "https://publications.scilifelab.se/researcher/113ef0dde1dd48e388f75c43bd672005.json"}}, {"family": "G\u00fcnther", "given": "Torsten", "initials": "T", "orcid": "0000-0001-9460-390X", "researcher": {"href": "https://publications.scilifelab.se/researcher/84159bff82a64a938bcff107f550c901.json"}}, {"family": "Vera-Rodr\u00edguez", "given": "Juan Carlos", "initials": "JC"}, {"family": "Ure\u00f1a", "given": "Irene", "initials": "I"}, {"family": "Iriarte", "given": "Eneko", "initials": "E"}, {"family": "Rodr\u00edguez-Varela", "given": "Ricardo", "initials": "R"}, {"family": "Sim\u00f5es", "given": "Luciana G", "initials": "LG"}, {"family": "Mart\u00ednez-S\u00e1nchez", "given": "Rafael M", "initials": "RM"}, {"family": "Svensson", "given": "Emma M", "initials": "EM"}, {"family": "Malmstr\u00f6m", "given": "Helena", "initials": "H"}, {"family": "Rodr\u00edguez", "given": "Laura", "initials": "L"}, {"family": "Berm\u00fadez de Castro", "given": "Jos\u00e9-Mar\u00eda", "initials": "JM"}, {"family": "Carbonell", "given": "Eudald", "initials": "E"}, {"family": "Alday", "given": "Alfonso", "initials": "A"}, {"family": "Hern\u00e1ndez Vera", "given": "Jos\u00e9 Antonio", "initials": "JA"}, {"family": "G\u00f6therstr\u00f6m", "given": "Anders", "initials": "A", "orcid": "0000-0001-6307-8188", "researcher": {"href": "https://publications.scilifelab.se/researcher/2a1a0a680ab8456cbf5a941e9718fd5a.json"}}, {"family": "Carretero", "given": "Jos\u00e9-Miguel", "initials": "JM"}, {"family": "Arsuaga", "given": "Juan Luis", "initials": "JL"}, {"family": "Smith", "given": "Colin I", "initials": "CI"}, {"family": "Jakobsson", "given": "Mattias", "initials": "M", "orcid": "0000-0001-7840-7853", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a4abe0fcb20492d9ec849c9fbf58a71.json"}}], "type": "historical article", "published": "2018-03-27", "journal": {"volume": "115", "issn": "1091-6490", "issue": "13", "pages": "3428-3433", "title": "Proc. Natl. Acad. Sci. U.S.A.", "issn-l": "0027-8424"}, "abstract": "Population genomic studies of ancient human remains have shown how modern-day European population structure has been shaped by a number of prehistoric migrations. The Neolithization of Europe has been associated with large-scale migrations from Anatolia, which was followed by migrations of herders from the Pontic steppe at the onset of the Bronze Age. Southwestern Europe was one of the last parts of the continent reached by these migrations, and modern-day populations from this region show intriguing similarities to the initial Neolithic migrants. Partly due to climatic conditions that are unfavorable for DNA preservation, regional studies on the Mediterranean remain challenging. Here, we present genome-wide sequence data from 13 individuals combined with stable isotope analysis from the north and south of Iberia covering a four-millennial temporal transect (7,500-3,500 BP). Early Iberian farmers and Early Central European farmers exhibit significant genetic differences, suggesting two independent fronts of the Neolithic expansion. The first Neolithic migrants that arrived in Iberia had low levels of genetic diversity, potentially reflecting a small number of individuals; this diversity gradually increased over time from mixing with local hunter-gatherers and potential population expansion. The impact of post-Neolithic migrations on Iberia was much smaller than for the rest of the continent, showing little external influence from the Neolithic to the Bronze Age. Paleodietary reconstruction shows that these populations have a remarkable degree of dietary homogeneity across space and time, suggesting a strong reliance on terrestrial food resources despite changing culture and genetic make-up.", "doi": "10.1073/pnas.1717762115", "pmid": "29531053", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC5879675"}, {"db": "pii", "key": "1717762115"}], "notes": [], "created": "2018-09-14T12:12:32.794Z", "modified": "2024-01-16T13:48:46.649Z"}, {"entity": "publication", "iuid": "06db42c21e214df7b355d3fddb234a6d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/06db42c21e214df7b355d3fddb234a6d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/06db42c21e214df7b355d3fddb234a6d"}}, "title": "Changes in methylation within the STK32B promoter are associated with an increased risk for generalized anxiety disorder in adolescents.", "authors": [{"family": "Ciuculete", "given": "Diana M", "initials": "DM"}, {"family": "Bostr\u00f6m", "given": "Adrian E", "initials": "AE"}, {"family": "Tuunainen", "given": "Anna-Kaisa", "initials": "AK"}, {"family": "Sohrabi", "given": "Farah", "initials": "F"}, {"family": "Kular", "given": "Lara", "initials": "L"}, {"family": "Jagodic", "given": "Maja", "initials": "M"}, {"family": "Voisin", "given": "Sarah", "initials": "S"}, {"family": "Mwinyi", "given": "Jessica", "initials": "J"}, {"family": "Schi\u00f6th", "given": "Helgi B", "initials": "HB"}], "type": "journal article", "published": "2018-03-26", "journal": {"volume": "102", "issn": "1879-1379", "issue": null, "pages": "44-51", "title": "J Psychiatr Res", "issn-l": "0022-3956"}, "abstract": "Generalized anxiety disorder (GAD) is highly prevalent among adolescents. An early detection of individuals at risk may prevent later psychiatric condition. Genome-wide studies investigating single nucleotide polymorphisms (SNPs) concluded that a focus on epigenetic mechanisms, which mediate the impact of environmental factors, could more efficiently help the understanding of GAD pathogenesis. We investigated the relationship between epigenetic shifts in blood and the risk to develop GAD, evaluated by the Development and Well-Being Assessment (DAWBA) score, in 221 otherwise healthy adolescents. Our analysis focused specifically on methylation sites showing high inter-individual variation but low tissue-specific variation, in order to infer a potential correlation between results obtained in blood and brain. Two statistical methods were applied, 1) a linear model with limma and 2) a likelihood test followed by Bonferroni correction. Methylation findings were validated in a cohort of 160 adults applying logistic models against the outcome variable \"anxiety treatment obtained in the past\" and studied in a third cohort with regards to associated expression changes measured in monocytes. One CpG site showed 1% increased methylation in adolescents at high risk of GAD (cg16333992, p", "doi": "10.1016/j.jpsychires.2018.03.008", "pmid": "29604450", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "S0022-3956(17)31054-3"}], "notes": [], "created": "2018-05-25T13:37:48.424Z", "modified": "2024-01-16T13:48:46.657Z"}, {"entity": "publication", "iuid": "ab14422dd35047cf94364e0dbbe147e2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ab14422dd35047cf94364e0dbbe147e2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ab14422dd35047cf94364e0dbbe147e2"}}, "title": "A Meta-Analysis of Genome-Wide Association Studies of Growth Differentiation Factor-15 Concentration in Blood.", "authors": [{"family": "Jiang", "given": "Jiyang", "initials": "J"}, {"family": "Thalamuthu", "given": "Anbupalam", "initials": "A"}, {"family": "Ho", "given": "Jennifer E", "initials": "JE"}, {"family": "Mahajan", "given": "Anubha", "initials": "A"}, {"family": "Ek", "given": "Weronica E", "initials": "WE"}, {"family": "Brown", "given": "David A", "initials": "DA"}, {"family": "Breit", "given": "Samuel N", "initials": "SN"}, {"family": "Wang", "given": "Thomas J", "initials": "TJ"}, {"family": "Gyllensten", "given": "Ulf", "initials": "U"}, {"family": "Chen", "given": "Ming-Huei", "initials": "MH"}, {"family": "Enroth", "given": "Stefan", "initials": "S"}, {"family": "Januzzi", "given": "James L", "initials": "JL"}, {"family": "Lind", "given": "Lars", "initials": "L"}, {"family": "Armstrong", "given": "Nicola J", "initials": "NJ"}, {"family": "Kwok", "given": "John B", "initials": "JB"}, {"family": "Schofield", "given": "Peter R", "initials": "PR"}, {"family": "Wen", "given": "Wei", "initials": "W"}, {"family": "Trollor", "given": "Julian N", "initials": "JN"}, {"family": "Johansson", "given": "\u00c5sa", "initials": "\u00c5"}, {"family": "Morris", "given": "Andrew P", "initials": "AP"}, {"family": "Vasan", "given": "Ramachandran S", "initials": "RS"}, {"family": "Sachdev", "given": "Perminder S", "initials": "PS"}, {"family": "Mather", "given": "Karen A", "initials": "KA"}], "type": "journal article", "published": "2018-03-23", "journal": {"volume": "9", "issn": "1664-8021", "issue": null, "pages": "97", "title": "Front Genet", "issn-l": "1664-8021"}, "abstract": "Blood levels of growth differentiation factor-15 (GDF-15), also known as macrophage inhibitory cytokine-1 (MIC-1), have been associated with various pathological processes and diseases, including cardiovascular disease and cancer. Prior studies suggest genetic factors play a role in regulating blood MIC-1/GDF-15 concentration. In the current study, we conducted the largest genome-wide association study (GWAS) to date using a sample of \u223c5,400 community-based Caucasian participants, to determine the genetic variants associated with MIC-1/GDF-15 blood concentration. Conditional and joint (COJO), gene-based association, and gene-set enrichment analyses were also carried out to identify novel loci, genes, and pathways. Consistent with prior results, a locus on chromosome 19, which includes nine single nucleotide polymorphisms (SNPs) (top SNP, rs888663, ", "doi": "10.3389/fgene.2018.00097", "pmid": "29628937", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC5876753"}], "notes": [], "created": "2018-05-25T13:25:49.259Z", "modified": "2024-01-16T13:48:46.707Z"}, {"entity": "publication", "iuid": "b07f8946f3fe4f8b93fca6ce59484cd3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b07f8946f3fe4f8b93fca6ce59484cd3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b07f8946f3fe4f8b93fca6ce59484cd3"}}, "title": "Recurrent, low-frequency coding variants contributing to colorectal cancer in the Swedish population.", "authors": [{"family": "Jiao", "given": "Xiang", "initials": "X"}, {"family": "Liu", "given": "Wen", "initials": "W"}, {"family": "Mahdessian", "given": "Hovsep", "initials": "H"}, {"family": "Bryant", "given": "Patrick", "initials": "P"}, {"family": "Ringdahl", "given": "Jenny", "initials": "J"}, {"family": "Timofeeva", "given": "Maria", "initials": "M"}, {"family": "Farrington", "given": "Susan M", "initials": "SM"}, {"family": "Dunlop", "given": "Malcolm", "initials": "M"}, {"family": "Lindblom", "given": "Annika", "initials": "A"}], "type": "journal article", "published": "2018-03-16", "journal": {"volume": "13", "issn": "1932-6203", "issue": "3", "pages": "e0193547", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "Genome-wide association studies (GWAS) have identified dozens of common genetic variants associated with risk of colorectal cancer (CRC). However, the majority of CRC heritability remains unclear. In order to discover low-frequency, high-risk CRC susceptibility variants in Swedish population, we genotyped 1 515 CRC patients enriched for familial cases, and 12 108 controls. Case/control association analysis suggested eight novel variants associated with CRC risk (OR 2.0-17.6, p-value < 2.0E-07), comprised of seven coding variants in genes RAB11FIP5, POTEA, COL27A1, MUC5B, PSMA8, MYH7B, and PABPC1L as well as one variant downstream of NEU1 gene. We also confirmed 27 out of 30 risk variants previously reported from GWAS in CRC with a mixed European population background. This study identified rare, coding sequence variants associated with CRC risk through analysis in a relatively homogeneous population. The segregation data suggest a complex mode of inheritance in seemingly dominant pedigrees.", "doi": "10.1371/journal.pone.0193547", "pmid": "29547645", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "PONE-D-17-41609"}, {"db": "pmc", "key": "PMC5856271"}], "notes": [], "created": "2018-05-25T13:25:50.820Z", "modified": "2024-01-16T13:48:46.739Z"}, {"entity": "publication", "iuid": "fdd3b6eb7f1d42aba91c4f2a1ff74300", "links": {"self": {"href": "https://publications.scilifelab.se/publication/fdd3b6eb7f1d42aba91c4f2a1ff74300.json"}, "display": {"href": "https://publications.scilifelab.se/publication/fdd3b6eb7f1d42aba91c4f2a1ff74300"}}, "title": "Biological annotation of genetic loci associated with intelligence in a meta-analysis of 87,740 individuals.", "authors": [{"family": "Coleman", "given": "Jonathan R I", "initials": "JRI"}, {"family": "Bryois", "given": "Julien", "initials": "J"}, {"family": "Gaspar", "given": "H\u00e9l\u00e9na A", "initials": "HA"}, {"family": "Jansen", "given": "Philip R", "initials": "PR"}, {"family": "Savage", "given": "Jeanne E", "initials": "JE"}, {"family": "Skene", "given": "Nathan", "initials": "N"}, {"family": "Plomin", "given": "Robert", "initials": "R"}, {"family": "Mu\u00f1oz-Manchado", "given": "Ana B", "initials": "AB"}, {"family": "Linnarsson", "given": "Sten", "initials": "S"}, {"family": "Crawford", "given": "Greg", "initials": "G"}, {"family": "Hjerling-Leffler", "given": "Jens", "initials": "J"}, {"family": "Sullivan", "given": "Patrick F", "initials": "PF"}, {"family": "Posthuma", "given": "Danielle", "initials": "D"}, {"family": "Breen", "given": "Gerome", "initials": "G"}], "type": "journal article", "published": "2018-03-08", "journal": {"volume": null, "issn": "1476-5578", "issue": null, "title": "Mol. Psychiatry", "issn-l": "1359-4184"}, "abstract": "Variance in IQ is associated with a wide range of health outcomes, and 1% of the population are affected by intellectual disability. Despite a century of research, the fundamental neural underpinnings of intelligence remain unclear. We integrate results from genome-wide association studies (GWAS) of intelligence with brain tissue and single cell gene expression data to identify tissues and cell types associated with intelligence. GWAS data for IQ (N\u2009=\u200978,308) were meta-analyzed with a study comparing 1247 individuals with mean IQ ~170 to 8185 controls. Genes associated with intelligence implicate pyramidal neurons of the somatosensory cortex and CA1 region of the hippocampus, and midbrain embryonic GABAergic neurons. Tissue-specific analyses find the most significant enrichment for frontal cortex brain expressed genes. These results suggest specific neuronal cell types and genes may be involved in intelligence and provide new hypotheses for neuroscience experiments using model systems.", "doi": "10.1038/s41380-018-0040-6", "pmid": "29520040", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41380-018-0040-6"}], "notes": [], "created": "2018-05-25T13:36:28.690Z", "modified": "2024-01-16T13:48:46.778Z"}, {"entity": "publication", "iuid": "45cc3396e39641618b4e80f82db3a99c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/45cc3396e39641618b4e80f82db3a99c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/45cc3396e39641618b4e80f82db3a99c"}}, "title": "Genome-wide analysis yields new loci associating with aortic valve stenosis.", "authors": [{"family": "Helgadottir", "given": "Anna", "initials": "A"}, {"family": "Thorleifsson", "given": "Gudmar", "initials": "G"}, {"family": "Gretarsdottir", "given": "Solveig", "initials": "S"}, {"family": "Stefansson", "given": "Olafur A", "initials": "OA"}, {"family": "Tragante", "given": "Vinicius", "initials": "V"}, {"family": "Thorolfsdottir", "given": "Rosa B", "initials": "RB"}, {"family": "Jonsdottir", "given": "Ingileif", "initials": "I"}, {"family": "Bjornsson", "given": "Thorsteinn", "initials": "T"}, {"family": "Steinthorsdottir", "given": "Valgerdur", "initials": "V"}, {"family": "Verweij", "given": "Niek", "initials": "N"}, {"family": "Nielsen", "given": "Jonas B", "initials": "JB"}, {"family": "Zhou", "given": "Wei", "initials": "W"}, {"family": "Folkersen", "given": "Lasse", "initials": "L"}, {"family": "Martinsson", "given": "Andreas", "initials": "A"}, {"family": "Heydarpour", "given": "Mahyar", "initials": "M"}, {"family": "Prakash", "given": "Siddharth", "initials": "S"}, {"family": "Oskarsson", "given": "Gylfi", "initials": "G"}, {"family": "Gudbjartsson", "given": "Tomas", "initials": "T"}, {"family": "Geirsson", "given": "Arnar", "initials": "A"}, {"family": "Olafsson", "given": "Isleifur", "initials": "I"}, {"family": "Sigurdsson", "given": "Emil L", "initials": "EL"}, {"family": "Almgren", "given": "Peter", "initials": "P"}, {"family": "Melander", "given": "Olle", "initials": "O"}, {"family": "Franco-Cereceda", "given": "Anders", "initials": "A"}, {"family": "Hamsten", "given": "Anders", "initials": "A"}, {"family": "Fritsche", "given": "Lars", "initials": "L"}, {"family": "Lin", "given": "Maoxuan", "initials": "M"}, {"family": "Yang", "given": "Bo", "initials": "B"}, {"family": "Hornsby", "given": "Whitney", "initials": "W"}, {"family": "Guo", "given": "Dongchuan", "initials": "D"}, {"family": "Brummett", "given": "Chad M", "initials": "CM"}, {"family": "Abecasis", "given": "Gon\u00e7alo", "initials": "G"}, {"family": "Mathis", "given": "Michael", "initials": "M"}, {"family": "Milewicz", "given": "Dianna", "initials": "D"}, {"family": "Body", "given": "Simon C", "initials": "SC"}, {"family": "Eriksson", "given": "Per", "initials": "P"}, {"family": "Willer", "given": "Cristen J", "initials": "CJ"}, {"family": "Hveem", "given": "Kristian", "initials": "K"}, {"family": "Newton-Cheh", "given": "Christopher", "initials": "C"}, {"family": "Smith", "given": "J Gustav", "initials": "JG"}, {"family": "Danielsen", "given": "Ragnar", "initials": "R"}, {"family": "Thorgeirsson", "given": "Gudmundur", "initials": "G"}, {"family": "Thorsteinsdottir", "given": "Unnur", "initials": "U"}, {"family": "Gudbjartsson", "given": "Daniel F", "initials": "DF"}, {"family": "Holm", "given": "Hilma", "initials": "H"}, {"family": "Stefansson", "given": "Kari", "initials": "K"}], "type": "journal article", "published": "2018-03-07", "journal": {"volume": "9", "issn": "2041-1723", "issue": "1", "pages": "987", "title": "Nat Commun", "issn-l": "2041-1723"}, "abstract": "Aortic valve stenosis (AS) is the most common valvular heart disease, and valve replacement is the only definitive treatment. Here we report a large genome-wide association (GWA) study of 2,457 Icelandic AS cases and 349,342 controls with a follow-up in up to 4,850 cases and 451,731 controls of European ancestry. We identify two new AS loci, on chromosome 1p21 near PALMD (rs7543130; odds ratio (OR)\u2009=\u20091.20, P\u2009=\u20091.2\u2009\u00d7\u200910\n            -22) and on chromosome 2q22 in TEX41 (rs1830321; OR\u2009=\u20091.15, P\u2009=\u20091.8\u2009\u00d7\u200910-13). Rs7543130 also associates with bicuspid aortic valve (BAV) (OR\u2009=\u20091.28, P\u2009=\u20096.6\u2009\u00d7\u200910-10) and aortic root diameter (P\u2009=\u20091.30\u2009\u00d7\u200910-8), and rs1830321 associates with BAV (OR\u2009=\u20091.12, P\u2009=\u20095.3\u2009\u00d7\u200910-3) and coronary artery disease (OR\u2009=\u20091.05, P\u2009=\u20099.3\u2009\u00d7\u200910-5). The results implicate both cardiac developmental abnormalities and atherosclerosis-like processes in the pathogenesis of AS. We show that several pathways are shared by CAD and AS. Causal analysis suggests that the shared risk factors of Lp(a) and non-high-density lipoprotein cholesterol contribute substantially to the frequent co-occurence of these diseases.", "doi": "10.1038/s41467-018-03252-6", "pmid": "29511194", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-018-03252-6"}, {"db": "pmc", "key": "PMC5840367"}], "notes": [], "created": "2019-01-09T07:22:21.037Z", "modified": "2020-01-21T13:56:13.753Z"}, {"entity": "publication", "iuid": "a569320043c3473aa82310813a5d97e3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a569320043c3473aa82310813a5d97e3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a569320043c3473aa82310813a5d97e3"}}, "title": "Global analysis of A-to-I RNA editing reveals association with common disease variants", "authors": [{"family": "Franz\u00e9n", "given": "Oscar", "initials": "O"}, {"family": "Ermel", "given": "Raili", "initials": "R"}, {"family": "Sukhavasi", "given": "Katyayani", "initials": "K"}, {"family": "Jain", "given": "Rajeev", "initials": "R"}, {"family": "Jain", "given": "Anamika", "initials": "A"}, {"family": "Betsholtz", "given": "Christer", "initials": "C"}, {"family": "Giannarelli", "given": "Chiara", "initials": "C"}, {"family": "Kovacic", "given": "Jason C", "initials": "JC"}, {"family": "Ruusalepp", "given": "Arno", "initials": "A"}, {"family": "Skogsberg", "given": "Josefin", "initials": "J"}, {"family": "Hao", "given": "Ke", "initials": "K"}, {"family": "Schadt", "given": "Eric E", "initials": "EE"}, {"family": "Bj\u00f6rkegren", "given": "Johan L M", "initials": "JLM"}], "type": "journal-article", "published": "2018-03-06", "journal": {"volume": "6", "issn": "2167-8359", "issue": null, "pages": "e4466", "title": "PeerJ", "issn-l": "2167-8359"}, "abstract": "RNA editing modifies transcripts and may alter their regulation or function. In humans, the most common modification is adenosine to inosine (A-to-I). We examined the global characteristics of RNA editing in 4,301 human tissue samples. More than 1.6 million A-to-I edits were identified in 62% of all protein-coding transcripts. mRNA recoding was extremely rare; only 11 novel recoding sites were uncovered. Thirty single nucleotide polymorphisms from genome-wide association studies were associated with RNA editing; one that influences type 2 diabetes (rs2028299) was associated with editing in ", "doi": "10.7717/peerj.4466", "pmid": "29527417", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [], "notes": [], "created": "2018-10-26T05:48:37.219Z", "modified": "2020-01-21T13:56:10.968Z"}, {"entity": "publication", "iuid": "8246f70d04c0430eb80630fc2bbe370a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8246f70d04c0430eb80630fc2bbe370a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8246f70d04c0430eb80630fc2bbe370a"}}, "title": "DNA methylation holds prognostic information in relapsed precursor B-cell acute lymphoblastic leukemia.", "authors": [{"family": "Borss\u00e9n", "given": "Magnus", "initials": "M"}, {"family": "Nordlund", "given": "Jessica", "initials": "J", "orcid": "0000-0001-8699-9959", "researcher": {"href": "https://publications.scilifelab.se/researcher/ddf48c9262134821bcc6ce1180049753.json"}}, {"family": "Haider", "given": "Zahra", "initials": "Z"}, {"family": "Landfors", "given": "Mattias", "initials": "M"}, {"family": "Larsson", "given": "P\u00e4r", "initials": "P", "orcid": "0000-0001-9054-5191", "researcher": {"href": "https://publications.scilifelab.se/researcher/573c6350305a49cba2ac0798dea21ae0.json"}}, {"family": "Kanerva", "given": "Jukka", "initials": "J"}, {"family": "Schmiegelow", "given": "Kjeld", "initials": "K"}, {"family": "Flaegstad", "given": "Trond", "initials": "T"}, {"family": "J\u00f3nsson", "given": "\u00d3lafur G\u00edsli", "initials": "\u00d3G"}, {"family": "Frost", "given": "Britt-Marie", "initials": "BM"}, {"family": "Palle", "given": "Josefine", "initials": "J"}, {"family": "Forestier", "given": "Erik", "initials": "E"}, {"family": "Heyman", "given": "Mats", "initials": "M"}, {"family": "Hultdin", "given": "Magnus", "initials": "M"}, {"family": "L\u00f6nnerholm", "given": "Gudmar", "initials": "G"}, {"family": "Degerman", "given": "Sofie", "initials": "S", "orcid": "0000-0002-2783-0712", "researcher": {"href": "https://publications.scilifelab.se/researcher/8611162e883645f59195c4221199967f.json"}}], "type": "journal article", "published": "2018-03-05", "journal": {"volume": "10", "issn": "1868-7083", "issue": null, "pages": "31", "title": "Clin Epigenetics", "issn-l": "1868-7075"}, "abstract": "Few biological markers are associated with survival after relapse of B-cell precursor acute lymphoblastic leukemia (BCP-ALL). In pediatric T-cell ALL, we have identified promoter-associated methylation alterations that correlate with prognosis. Here, the prognostic relevance of CpG island methylation phenotype (CIMP) classification was investigated in pediatric BCP-ALL patients.\n\nSix hundred and one BCP-ALL samples from Nordic pediatric patients (age 1-18) were CIMP classified at initial diagnosis and analyzed in relation to clinical data.\n\nAmong the 137 patients that later relapsed, patients with a CIMP- profile (n = 42) at initial diagnosis had an inferior overall survival (pOS5years 33%) compared to CIMP+ patients (n = 95, pOS5years 65%) (p = 0.001), which remained significant in a Cox proportional hazards model including previously defined risk factors.\n\nCIMP classification is a strong candidate for improved risk stratification of relapsed BCP-ALL.", "doi": "10.1186/s13148-018-0466-3", "pmid": "29515676", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "466"}, {"db": "pmc", "key": "PMC5836434"}], "notes": [], "created": "2018-12-12T12:15:09.166Z", "modified": "2021-07-08T12:43:38.657Z"}, {"entity": "publication", "iuid": "666349a59ae34dc093f819c8e460a356", "links": {"self": {"href": "https://publications.scilifelab.se/publication/666349a59ae34dc093f819c8e460a356.json"}, "display": {"href": "https://publications.scilifelab.se/publication/666349a59ae34dc093f819c8e460a356"}}, "title": "Genomic signatures of 60 years of bidirectional selection for 8-week body weight in chickens", "authors": [{"family": "Lillie", "given": "M", "initials": "M"}, {"family": "Sheng", "given": "Z Y", "initials": "ZY"}, {"family": "Honaker", "given": "C F", "initials": "CF"}, {"family": "Andersson", "given": "L", "initials": "L"}, {"family": "Siegel", "given": "P B", "initials": "PB"}, {"family": "Carlborg", "given": "\u00d6", "initials": "\u00d6"}], "type": "journal-article", "published": "2018-03-01", "journal": {"volume": "97", "issn": "0032-5791", "issue": "3", "pages": "781-790", "title": "Poult. Sci.", "issn-l": null}, "abstract": null, "doi": "10.3382/ps/pex383", "pmid": "29272516", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2018-09-14T12:10:33.347Z", "modified": "2024-01-16T13:48:46.807Z"}, {"entity": "publication", "iuid": "609a07a4161646f1b19b82b935aab511", "links": {"self": {"href": "https://publications.scilifelab.se/publication/609a07a4161646f1b19b82b935aab511.json"}, "display": {"href": "https://publications.scilifelab.se/publication/609a07a4161646f1b19b82b935aab511"}}, "title": "Genetic variants influencing phenotypic variance heterogeneity.", "authors": [{"family": "Ek", "given": "Weronica E", "initials": "WE"}, {"family": "Rask-Andersen", "given": "Mathias", "initials": "M"}, {"family": "Karlsson", "given": "Torgny", "initials": "T"}, {"family": "Enroth", "given": "Stefan", "initials": "S"}, {"family": "Gyllensten", "given": "Ulf", "initials": "U"}, {"family": "Johansson", "given": "\u00c5sa", "initials": "\u00c5"}], "type": "journal article", "published": "2018-03-01", "journal": {"volume": "27", "issn": "1460-2083", "issue": "5", "pages": "799-810", "title": "Hum. Mol. Genet.", "issn-l": "0964-6906"}, "abstract": "Most genetic studies identify genetic variants associated with disease risk or with the mean value of a quantitative trait. More rarely, genetic variants associated with variance heterogeneity are considered. In this study, we have identified such variance single-nucleotide polymorphisms (vSNPs) and examined if these represent biological gene \u00d7 gene or gene \u00d7 environment interactions or statistical artifacts caused by multiple linked genetic variants influencing the same phenotype. We have performed a genome-wide study, to identify vSNPs associated with variance heterogeneity in DNA methylation levels. Genotype data from over 10 million single-nucleotide polymorphisms (SNPs), and DNA methylation levels at over 430\u00a0000 CpG sites, were analyzed in 729 individuals. We identified vSNPs for 7195 CpG sites (P\u2009<\u20099.4 \u00d7 10-11). This is a relatively low number compared to 52 335 CpG sites for which SNPs were associated with mean DNA methylation levels. We further showed that variance heterogeneity between genotypes mainly represents additional, often rare, SNPs in linkage disequilibrium (LD) with the respective vSNP and for some vSNPs, multiple low frequency variants co-segregating with one of the vSNP alleles. Therefore, our results suggest that variance heterogeneity of DNA methylation mainly represents phenotypic effects by multiple SNPs, rather than biological interactions. Such effects may also be important for interpreting variance heterogeneity of more complex clinical phenotypes.", "doi": "10.1093/hmg/ddx441", "pmid": "29325024", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "4792998"}], "notes": [], "created": "2018-05-25T13:31:04.563Z", "modified": "2024-01-16T13:48:46.815Z"}, {"entity": "publication", "iuid": "1dd273f849134fb5844f129cd7b822d9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1dd273f849134fb5844f129cd7b822d9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1dd273f849134fb5844f129cd7b822d9"}}, "title": "A Large-Scale Multi-ancestry Genome-wide Study Accounting for Smoking Behavior Identifies Multiple Significant Loci for Blood Pressure.", "authors": [{"family": "Sung", "given": "Yun J", "initials": "YJ"}, {"family": "Winkler", "given": "Thomas W", "initials": "TW"}, {"family": "de Las Fuentes", "given": "Lisa", "initials": "L"}, {"family": "Bentley", "given": "Amy R", "initials": "AR"}, {"family": "Brown", "given": "Michael R", "initials": "MR"}, {"family": "Kraja", "given": "Aldi T", "initials": "AT"}, {"family": "Schwander", "given": "Karen", "initials": "K"}, {"family": "Ntalla", "given": "Ioanna", "initials": "I"}, {"family": "Guo", "given": "Xiuqing", "initials": "X"}, {"family": "Franceschini", "given": "Nora", "initials": "N"}, {"family": "Lu", "given": "Yingchang", "initials": "Y"}, {"family": "Cheng", "given": "Ching-Yu", "initials": "CY"}, {"family": "Sim", "given": "Xueling", "initials": "X"}, {"family": "Vojinovic", "given": "Dina", "initials": "D"}, {"family": "Marten", "given": "Jonathan", "initials": "J"}, {"family": "Musani", "given": "Solomon K", "initials": "SK"}, {"family": "Li", "given": "Changwei", "initials": "C"}, {"family": "Feitosa", "given": "Mary F", "initials": "MF"}, 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"RS"}, {"family": "Evans", "given": "Michele K", "initials": "MK"}, {"family": "Gudnason", "given": "Vilmundur", "initials": "V"}, {"family": "Kardia", "given": "Sharon L R", "initials": "SLR"}, {"family": "Kritchevsky", "given": "Stephen B", "initials": "SB"}, {"family": "Levy", "given": "Daniel", "initials": "D"}, {"family": "O'Connell", "given": "Jeff R", "initials": "JR"}, {"family": "Psaty", "given": "Bruce M", "initials": "BM"}, {"family": "van Dam", "given": "Rob M", "initials": "RM"}, {"family": "Sims", "given": "Mario", "initials": "M"}, {"family": "Arnett", "given": "Donna K", "initials": "DK"}, {"family": "Mook-Kanamori", "given": "Dennis O", "initials": "DO"}, {"family": "Kelly", "given": "Tanika N", "initials": "TN"}, {"family": "Fox", "given": "Ervin R", "initials": "ER"}, {"family": "Hayward", "given": "Caroline", "initials": "C"}, {"family": "Fornage", "given": "Myriam", "initials": "M"}, {"family": "Rotimi", "given": "Charles N", "initials": "CN"}, {"family": "Province", "given": "Michael A", "initials": "MA"}, {"family": "van Duijn", "given": "Cornelia M", "initials": "CM"}, {"family": "Tai", "given": "E Shyong", "initials": "ES"}, {"family": "Wong", "given": "Tien Yin", "initials": "TY"}, {"family": "Loos", "given": "Ruth J F", "initials": "RJF"}, {"family": "Reiner", "given": "Alex P", "initials": "AP"}, {"family": "Rotter", "given": "Jerome I", "initials": "JI"}, {"family": "Zhu", "given": "Xiaofeng", "initials": "X"}, {"family": "Bierut", "given": "Laura J", "initials": "LJ"}, {"family": "Gauderman", "given": "W James", "initials": "WJ"}, {"family": "Caulfield", "given": "Mark J", "initials": "MJ"}, {"family": "Elliott", "given": "Paul", "initials": "P"}, {"family": "Rice", "given": "Kenneth", "initials": "K"}, {"family": "Munroe", "given": "Patricia B", "initials": "PB"}, {"family": "Morrison", "given": "Alanna C", "initials": "AC"}, {"family": "Cupples", "given": "L Adrienne", "initials": "LA"}, {"family": "Rao", "given": "Dabeeru C", "initials": "DC"}, {"family": "Chasman", "given": "Daniel I", "initials": "DI"}], "type": "journal article", "published": "2018-03-01", "journal": {"volume": "102", "issn": "1537-6605", "issue": "3", "pages": "375-400", "title": "Am. J. Hum. Genet.", "issn-l": "0002-9297"}, "abstract": "Genome-wide association analysis advanced understanding of blood pressure (BP), a major risk factor for vascular conditions such as coronary heart disease and stroke. Accounting for smoking behavior may help identify BP loci and extend our knowledge of its genetic architecture. We performed genome-wide association meta-analyses of systolic and diastolic BP incorporating gene-smoking interactions in 610,091 individuals. Stage 1 analysis examined \u223c18.8 million SNPs and small insertion/deletion variants in 129,913 individuals from four ancestries (European, African, Asian, and Hispanic) with follow-up analysis of promising variants in 480,178 additional individuals from five ancestries. We identified 15 loci that were genome-wide significant (p < 5\u00a0\u00d7 10", "doi": "10.1016/j.ajhg.2018.01.015", "pmid": "29455858", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "S0002-9297(18)30017-X"}], "notes": [], "created": "2018-05-25T13:25:54.630Z", "modified": "2024-01-16T13:48:46.822Z"}, {"entity": "publication", "iuid": "0a018d851bd84f3fa5dd3d5c9ba9f97c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0a018d851bd84f3fa5dd3d5c9ba9f97c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0a018d851bd84f3fa5dd3d5c9ba9f97c"}}, "title": "The fungus that came in from the cold: dry rot\u2019s pre-adapted ability to invade buildings", "authors": [{"family": "Balasundaram", "given": "S V", "initials": "SV"}, {"family": "Hess", "given": "J", "initials": "J"}, {"family": "Durling", "given": "M B", "initials": "MB"}, {"family": "Moody", "given": "S C", "initials": "SC"}, {"family": "Thorbek", "given": "L", "initials": "L"}, {"family": "Progida", "given": "C", "initials": "C"}, {"family": "LaButti", "given": "K", "initials": "K"}, {"family": "Aerts", "given": "A", "initials": "A"}, {"family": "Barry", "given": "K", "initials": "K"}, {"family": "Grigoriev", "given": "I V", "initials": "IV"}, {"family": "Boddy", "given": "L", "initials": "L"}, {"family": "H\u00f6gberg", "given": "N", "initials": "N"}, {"family": "Kauserud", "given": "H", "initials": "H"}, {"family": "Eastwood", "given": "D C", "initials": "DC"}, {"family": "Skrede", "given": "I", "initials": "I"}], "type": "journal-article", "published": "2018-03-00", "journal": {"volume": "12", "issn": "1751-7370", "issue": "3", "pages": "791-801", "title": "ISME J", "issn-l": "1751-7362"}, "abstract": null, "doi": "10.1038/s41396-017-0006-8", "pmid": "29305577", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "BioProject", "description": "Genome sequencing and assembly of Serpula lacrymans var. lacrymans and Serpula lacrymans var. shastensis", "key": "PRJNA412961"}, {"db": "Dryad", "description": null, "key": "https://doi.org/10.5061/dryad.28sb6"}], "notes": [], "created": "2018-04-04T11:30:03.648Z", "modified": "2024-01-16T13:48:46.833Z"}, {"entity": "publication", "iuid": "510dfd6804e8495085ecfb30ff4970b7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/510dfd6804e8495085ecfb30ff4970b7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/510dfd6804e8495085ecfb30ff4970b7"}}, "title": "Geobacteraceae are important members of mercury-methylating microbial communities of sediments impacted by waste water releases", "authors": [{"family": "Bravo", "given": "Andrea G", "initials": "AG"}, {"family": "Zopfi", "given": "Jakob", "initials": "J"}, {"family": "Buck", "given": "Moritz", "initials": "M"}, {"family": "Xu", "given": "Jingying", "initials": "J"}, {"family": "Bertilsson", "given": "Stefan", "initials": "S"}, {"family": "Schaefer", "given": "Jeffra K", "initials": "JK"}, {"family": "Pot\u00e9", "given": "John", "initials": "J"}, {"family": "Cosio", "given": "Claudia", "initials": "C"}], "type": "journal-article", "published": "2018-03-00", "journal": {"volume": "12", "issn": "1751-7370", "issue": "3", "pages": "802-812", "title": "ISME J", "issn-l": "1751-7362"}, "abstract": "Microbial mercury (Hg) methylation in sediments can result in bioaccumulation of the neurotoxin methylmercury\u00a0(MMHg) in aquatic food webs. Recently, the discovery of the gene hgcA, required for Hg methylation, revealed that the diversity of Hg methylators is much broader than previously thought. However, little is known about the identity of Hg-methylating microbial organisms and the environmental factors controlling their activity and distribution in lakes. Here, we combined high-throughput sequencing of 16S rRNA and hgcA genes with the\u00a0chemical characterization of sediments impacted by a waste water treatment plant that releases significant amounts of organic matter and iron. Our results highlight that the ferruginous geochemical conditions prevailing at 1-2\u2009cm depth\u00a0are conducive to MMHg formation and that the Hg-methylating guild\u00a0is\u00a0composed of iron and sulfur-transforming bacteria, syntrophs, and methanogens. Deltaproteobacteria, notably Geobacteraceae, dominated the hgcA carrying communities, while sulfate reducers constituted only a minor component, despite being considered the main Hg methylators in many anoxic aquatic environments. Because iron is widely applied in waste water treatment, the importance of Geobacteraceae for Hg methylation and the complexity of Hg-methylating communities reported here are likely to occur worldwide in sediments impacted by waste water treatment plant discharges and in\u00a0iron-rich sediments in general.", "doi": "10.1038/s41396-017-0007-7", "pmid": "29321692", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "BioProject", "description": "Mercury methylation in the bay of Vidy", "key": "PRJEB20838"}], "notes": [], "created": "2018-09-14T12:07:23.512Z", "modified": "2024-01-16T13:48:46.847Z"}, {"entity": "publication", "iuid": "55550624f1574f6096f0a3b68925bf26", "links": {"self": {"href": "https://publications.scilifelab.se/publication/55550624f1574f6096f0a3b68925bf26.json"}, "display": {"href": "https://publications.scilifelab.se/publication/55550624f1574f6096f0a3b68925bf26"}}, "title": "Cleaner fish escape salmon farms and hybridize with local wrasse populations", "authors": [{"family": "Faust", "given": "Ellika", "initials": "E"}, {"family": "Halvorsen", "given": "Kim Tallaksen", "initials": "KT"}, {"family": "Andersen", "given": "Per", "initials": "P"}, {"family": "Knutsen", "given": "Halvor", "initials": "H"}, {"family": "Andr\u00e9", "given": "Carl", "initials": "C"}], "type": "journal-article", "published": "2018-03-00", "journal": {"volume": "5", "issn": "2054-5703", "issue": "3", "pages": "171752", "title": "R. Soc. open sci.", "issn-l": "2054-5703"}, "abstract": null, "doi": "10.1098/rsos.171752", "pmid": "29657779", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "BioProject", "description": "Symphodus melops Raw sequence reads", "key": "PRJNA415388"}, {"db": "Dryad", "description": null, "key": "https://doi.org/10.5061/dryad.tv553"}], "notes": [], "created": "2018-04-17T11:47:00.876Z", "modified": "2024-01-16T13:48:46.868Z"}, {"entity": "publication", "iuid": "d293ef3dac5449d5933f54ff50b164bb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d293ef3dac5449d5933f54ff50b164bb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d293ef3dac5449d5933f54ff50b164bb"}}, "title": "The ZBED6\u2013IGF2 axis has a major effect on growth of skeletal muscle and internal organs in placental mammals", "authors": [{"family": "Younis", "given": "Shady", "initials": "S"}, {"family": "Sch\u00f6nke", "given": "Milena", "initials": "M"}, {"family": "Massart", "given": "Julie", "initials": "J"}, {"family": "Hjortebjerg", "given": "Rikke", "initials": "R"}, {"family": "Sundstr\u00f6m", "given": "Elisabeth", "initials": "E"}, {"family": "Gustafson", "given": "Ulla", "initials": "U"}, {"family": "Bj\u00f6rnholm", "given": "Marie", "initials": "M"}, {"family": "Krook", "given": "Anna", "initials": "A"}, {"family": "Frystyk", "given": "Jan", "initials": "J"}, {"family": "Zierath", "given": "Juleen R", "initials": "JR"}, {"family": "Andersson", "given": "Leif", "initials": "L"}], "type": "journal-article", "published": "2018-02-27", "journal": {"volume": "115", "issn": "0027-8424", "issue": "9", "pages": "E2048-E2057", "title": "Proc Natl Acad Sci USA", "issn-l": "0027-8424"}, "abstract": "A single nucleotide substitution in the third intron of insulin-like growth factor 2 (\n                IGF2) is associated with increased muscle mass and reduced subcutaneous fat in domestic pigs. This mutation disrupts the binding of the ZBED6 transcription factor and leads to a threefold up-regulation of IGF2 expression in pig skeletal muscle. Here, we investigated the biological significance of ZBED6-IGF2 interaction in the growth of placental mammals using two mouse models, ZBED6 knock-out (Zbed6-/-) and Igf2 knock-in mice that carry the pig IGF2 mutation. These transgenic mice exhibit markedly higher serum IGF2 concentrations, higher growth rate, increased lean mass, and larger heart, kidney, and liver; no significant changes were observed for white adipose tissues. The changes in body and lean mass were most pronounced in female mice. The phenotypic changes were concomitant with a remarkable up-regulation of Igf2 expression in adult tissues. Transcriptome analysis of skeletal muscle identified differential expression of genes belonging to the extracellular region category. Expression analysis using fetal muscles indicated a minor role of ZBED6 in regulating Igf2 expression prenatally. Furthermore, transcriptome analysis of the adult skeletal muscle revealed that this elevated expression of Igf2 was derived from the P1 and P2 promoters. The results revealed very similar phenotypic effects in the Zbed6 knock-out mouse and in the Igf2 knock-in mouse, showing that the effect of ZBED6 on growth of muscle and internal organs is mediated through the binding site in the Igf2 gene. The results explain why this ZBED6 binding site is extremely well conserved among placental mammals.", "doi": "10.1073/pnas.1719278115", "pmid": "29440408", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "SRA", "description": null, "key": "SRP128271"}], "notes": [], "created": "2018-04-04T11:30:57.231Z", "modified": "2024-01-16T13:48:46.876Z"}, {"entity": "publication", "iuid": "f246cc69585043a4b9a6882404c1918f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f246cc69585043a4b9a6882404c1918f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f246cc69585043a4b9a6882404c1918f"}}, "title": "Targeted Long-Read Sequencing of a Locus Under Long-Term Balancing Selection in Capsella", "authors": [{"family": "Bachmann", "given": "J\u00f6rg A", "initials": "JA"}, {"family": "Tedder", "given": "Andrew", "initials": "A"}, {"family": "Laenen", "given": "Benjamin", "initials": "B"}, {"family": "Steige", "given": "Kim A", "initials": "KA"}, {"family": "Slotte", "given": "Tanja", "initials": "T"}], "type": "journal-article", "published": "2018-02-23", "journal": {"volume": "8", "issn": "2160-1836", "issue": "4", "pages": "1327-1333", "title": "G3 (Bethesda)", "issn-l": "2160-1836"}, "abstract": "Rapid advances in short-read DNA sequencing technologies have revolutionized population genomic studies, but there are genomic regions where this technology reaches its limits. Limitations mostly arise due to the difficulties in assembly or alignment to genomic regions of high sequence divergence and high repeat content, which are typical characteristics for loci under strong long-term balancing selection. Studying genetic diversity at such loci therefore remains challenging. Here, we investigate the feasibility and error rates associated with targeted long-read sequencing of a locus under balancing selection. For this purpose, we generated bacterial artificial chromosomes (BACs) containing the Brassicaceae", "doi": "10.1534/g3.117.300467", "pmid": "29476024", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "BioProject", "description": "Targeted long-read sequencing of a locus under long-term balancing selection in Capsella", "key": "PRJEB24927"}], "notes": [], "created": "2018-04-04T11:30:41.758Z", "modified": "2024-01-16T13:48:46.883Z"}, {"entity": "publication", "iuid": "6d7d236d2daf4544ad99f50b40d94d09", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6d7d236d2daf4544ad99f50b40d94d09.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6d7d236d2daf4544ad99f50b40d94d09"}}, "title": "Disruption of Accumbens and Thalamic White Matter Connectivity Revealed by Diffusion Tensor Tractography in Young Men with Genetic Risk for Obesity", "authors": [{"family": "Olivo", "given": "Gaia", "initials": "G"}, {"family": "Latini", "given": "Francesco", "initials": "F"}, {"family": "Wiemerslage", "given": "Lyle", "initials": "L"}, {"family": "Larsson", "given": "Elna Marie", "initials": "EM"}, {"family": "Schi\u00f6th", "given": "Helgi B", "initials": "HB"}], "type": "journal-article", "published": "2018-02-22", "journal": {"volume": "12", "issn": "1662-5161", "issue": null, "pages": null, "title": "Front Hum Neurosci", "issn-l": "1662-5161"}, "abstract": null, "doi": "10.3389/fnhum.2018.00075", "pmid": "29520227", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2018-06-25T14:17:35.487Z", "modified": "2024-01-16T13:48:46.891Z"}, {"entity": "publication", "iuid": "01739e0a1e9745c29fbe89c5454acc58", "links": {"self": {"href": "https://publications.scilifelab.se/publication/01739e0a1e9745c29fbe89c5454acc58.json"}, "display": {"href": "https://publications.scilifelab.se/publication/01739e0a1e9745c29fbe89c5454acc58"}}, "title": "Two novel colorectal cancer risk loci in the region on chromosome 9q22.32", "authors": [{"family": "Thutkawkorapin", "given": "Jessada", "initials": "J"}, {"family": "Mahdessian", "given": "Hovsep", "initials": "H"}, {"family": "Barber", "given": "Tom", "initials": "T"}, {"family": "Picelli", "given": "Simone", "initials": "S"}, {"family": "von Holst", "given": "Susanna", "initials": "S"}, {"family": "Lundin", "given": "Johanna", "initials": "J"}, {"family": "Valle", "given": "Laura", "initials": "L"}, {"family": "Kontham", "given": "Vinaykumar", "initials": "V"}, {"family": "Liu", "given": "Tao", "initials": "T"}, {"family": "Nilsson", "given": "Daniel", "initials": "D"}, {"family": "Jiao", "given": "Xiang", "initials": "X"}, {"family": "Lindblom", "given": "Annika", "initials": "A"}], "type": "journal-article", "published": "2018-02-16", "journal": {"volume": "9", "issn": "1949-2553", "issue": "13", "pages": null, "title": "Oncotarget", "issn-l": "1949-2553"}, "abstract": null, "doi": "10.18632/oncotarget.24340", "pmid": "29541405", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2018-03-16T11:20:00.575Z", "modified": "2024-01-16T13:48:46.922Z"}, {"entity": "publication", "iuid": "aa1d01ad2ac64ae2bb82bc5aa006ae83", "links": {"self": {"href": "https://publications.scilifelab.se/publication/aa1d01ad2ac64ae2bb82bc5aa006ae83.json"}, "display": {"href": "https://publications.scilifelab.se/publication/aa1d01ad2ac64ae2bb82bc5aa006ae83"}}, "title": "CheckQC: Quick quality control of Illumina sequencing runs", "authors": [{"family": "\u00c5slin", "given": "Matilda", "initials": "M", "orcid": "0000-0002-2450-6415", "researcher": {"href": "https://publications.scilifelab.se/researcher/f3f0bf2483a543d689fb6e95804066dd.json"}}, {"family": "Brandt", "given": "Monika", "initials": "M", "orcid": "0000-0002-8184-9465", "researcher": {"href": "https://publications.scilifelab.se/researcher/ea8ed75ea33e4d69a20c986792d4db73.json"}}, {"family": "Dahlberg", "given": "Johan", "initials": "J", "orcid": "0000-0001-6962-1460", "researcher": {"href": "https://publications.scilifelab.se/researcher/81a007757a554ab487f4939e38aa44ee.json"}}], "type": "journal-article", "published": "2018-02-05", "journal": {"volume": "3", "issn": "2475-9066", "issue": "22", "pages": "556", "title": "JOSS", "issn-l": "2475-9066"}, "abstract": null, "doi": "10.21105/joss.00556", "pmid": null, "labels": {"National Genomics Infrastructure": "Technology development", "NGI Uppsala (SNP&SEQ Technology Platform)": "Technology development"}, "xrefs": [], "notes": [], "created": "2018-12-10T05:17:55.556Z", "modified": "2021-06-21T14:33:10.160Z"}, {"entity": "publication", "iuid": "b7147919cc1242938cb80d7dce70bdc1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b7147919cc1242938cb80d7dce70bdc1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b7147919cc1242938cb80d7dce70bdc1"}}, "title": "De novo mutations implicate novel genes in systemic lupus erythematosus.", "authors": [{"family": "Pullabhatla", "given": "Venu", "initials": "V"}, {"family": "Roberts", "given": "Amy L", "initials": "AL", "orcid": "0000-0002-5704-9249", "researcher": {"href": "https://publications.scilifelab.se/researcher/05b1416da7b84ac592fe45d2daf9f707.json"}}, {"family": "Lewis", "given": "Myles J", "initials": "MJ"}, {"family": "Mauro", "given": "Daniele", "initials": "D"}, {"family": "Morris", "given": "David L", "initials": "DL"}, {"family": "Odhams", "given": "Christopher A", "initials": "CA", "orcid": "0000-0003-2396-6150", "researcher": {"href": "https://publications.scilifelab.se/researcher/5abb99e204ba4f219586c75f166fa453.json"}}, {"family": "Tombleson", "given": "Philip", "initials": "P"}, {"family": "Liljedahl", "given": "Ulrika", "initials": "U", "orcid": "0000-0002-1250-392X", "researcher": {"href": "https://publications.scilifelab.se/researcher/241618974ae142b38e5fe84236819f2b.json"}}, {"family": "Vyse", "given": "Simon", "initials": "S"}, {"family": "Simpson", "given": "Michael A", "initials": "MA"}, {"family": "Sauer", "given": "Sascha", "initials": "S"}, {"family": "de Rinaldis", "given": "Emanuele", "initials": "E"}, {"family": "Syv\u00e4nen", "given": "Ann-Christine", "initials": "AC", "orcid": "0000-0002-9681-9146", "researcher": {"href": "https://publications.scilifelab.se/researcher/f7012e35025543379380cb90efd71243.json"}}, {"family": "Vyse", "given": "Timothy J", "initials": "TJ", "orcid": "0000-0003-1123-1464", "researcher": {"href": "https://publications.scilifelab.se/researcher/2fd687fcd3964ce5ba4fefb7e5c5de6e.json"}}], "type": "journal article", "published": "2018-02-01", "journal": {"volume": "27", "issn": "1460-2083", "issue": "3", "pages": "421-429", "title": "Hum. Mol. Genet.", "issn-l": "0964-6906"}, "abstract": "The omnigenic model of complex disease stipulates that the majority of the heritability will be explained by the effects of common variation on genes in the periphery of core disease pathways. Rare variant associations, expected to explain far less of the heritability, may be enriched in core disease genes and thus will be instrumental in the understanding of complex disease pathogenesis and their potential therapeutic targets. Here, using complementary whole-exome sequencing, high-density imputation, and in vitro cellular assays, we identify candidate core genes in the pathogenesis of systemic lupus erythematosus (SLE). Using extreme-phenotype sampling, we sequenced the exomes of 30 SLE parent-affected-offspring trios and identified 14 genes with missense de novo mutations (DNM), none of which are within the >80 SLE susceptibility loci implicated through genome-wide association studies. In a follow-up cohort of 10, 995 individuals of matched European ancestry, we imputed genotype data to the density of the combined UK10K-1000 genomes Phase III reference panel across the 14 candidate genes. Gene-level analyses indicate three functional candidates: DNMT3A, PRKCD, and C1QTNF4. We identify a burden of rare variants across PRKCD associated with SLE risk (P = 0.0028), and across DNMT3A associated with two severe disease prognosis sub-phenotypes (P = 0.0005 and P = 0.0033). We further characterise the TNF-dependent functions of the third candidate gene C1QTNF4 on NF-\u03baB activation and apoptosis, which are inhibited by the p.His198Gln DNM. Our results identify three novel genes in SLE susceptibility and support extreme-phenotype sampling and DNM gene discovery to aid the search for core disease genes implicated through rare variation.", "doi": "10.1093/hmg/ddx407", "pmid": "29177435", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "4644524"}, {"db": "pmc", "key": "PMC5886157"}], "notes": [], "created": "2019-01-08T08:27:18.217Z", "modified": "2021-07-07T15:18:01.652Z"}, {"entity": "publication", "iuid": "76b7f768e6704bf29190db16a9687d93", "links": {"self": {"href": "https://publications.scilifelab.se/publication/76b7f768e6704bf29190db16a9687d93.json"}, "display": {"href": "https://publications.scilifelab.se/publication/76b7f768e6704bf29190db16a9687d93"}}, "title": "Transposon-derived small RNAs triggered by miR845 mediate genome dosage response in Arabidopsis", "authors": [{"family": "Borges", "given": "Filipe", "initials": "F"}, {"family": "Parent", "given": "Jean S\u00e9bastien", "initials": "JS"}, {"family": "van Ex", "given": "Fr\u00e9d\u00e9ric", "initials": "F"}, {"family": "Wolff", "given": "Philip", "initials": "P"}, {"family": "Mart\u00ednez", "given": "German", "initials": "G"}, {"family": "K\u00f6hler", "given": "Claudia", "initials": "C"}, {"family": "Martienssen", "given": "Robert A", "initials": "RA"}], "type": "journal-article", "published": "2018-02-00", "journal": {"volume": "50", "issn": "1061-4036", "issue": "2", "pages": "186-192", "title": "Nat Genet", "issn-l": "1061-4036"}, "abstract": null, "doi": "10.1038/s41588-017-0032-5", "pmid": "29335544", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "GEO", "description": "microRNA-triggered transposon small RNAs mediate genome dosage response", "key": "GSE106117"}, {"db": "GEO", "description": "microRNA-triggered transposon small RNAs mediate genome dosage response (Bisulfite-Seq)", "key": "GSE106112"}, {"db": "GEO", "description": "microRNA-triggered transposon small RNAs mediate genome dosage response (RNA-Seq)", "key": "GSE106113"}, {"db": "GEO", "description": "microRNA-triggered transposon small RNAs mediate genome dosage response (sRNA-Seq)", "key": "GSE106114"}, {"db": "GEO", "description": "microRNA-triggered transposon small RNAs mediate genome dosage response (mir845 sRNA-Seq)", "key": "GSE106115"}, {"db": "SRA", "description": null, "key": "SRP121332"}, {"db": "BioProject", "description": "microRNA-triggered transposon small RNAs mediate genome dosage response (Bisulfite-Seq) (thale cress)", "key": "PRJNA415632"}], "notes": [], "created": "2018-09-14T12:08:07.340Z", "modified": "2020-01-21T13:56:12.071Z"}, {"entity": "publication", "iuid": "da4544017fa94bc88722701573cf2617", "links": {"self": {"href": "https://publications.scilifelab.se/publication/da4544017fa94bc88722701573cf2617.json"}, "display": {"href": "https://publications.scilifelab.se/publication/da4544017fa94bc88722701573cf2617"}}, "title": "T cells are influenced by a long non-coding RNA in the autoimmune associated  PTPN2  locus", "authors": [{"family": "Houtman", "given": "Miranda", "initials": "M"}, {"family": "Shchetynsky", "given": "Klementy", "initials": "K"}, {"family": "Chemin", "given": "Karine", "initials": "K"}, {"family": "Hensvold", "given": "Aase Haj", "initials": "AH"}, {"family": "Ramsk\u00f6ld", "given": "Daniel", "initials": "D"}, {"family": "Tandre", "given": "Karolina", "initials": "K"}, {"family": "Eloranta", "given": "Maija Leena", "initials": "ML"}, {"family": "R\u00f6nnblom", "given": "Lars", "initials": "L"}, {"family": "Uebe", "given": "Steffen", "initials": "S"}, {"family": "Catrina", "given": "Anca Irinel", "initials": "AI"}, {"family": "Malmstr\u00f6m", "given": "Vivianne", "initials": "V"}, {"family": "Padyukov", "given": "Leonid", "initials": "L"}], "type": "journal-article", "published": "2018-02-00", "journal": {"volume": "90", "issn": "0896-8411", "issue": null, "pages": "28-38", "title": "Journal of Autoimmunity", "issn-l": "0896-8411"}, "abstract": "Non-coding SNPs in the protein tyrosine phosphatase non-receptor type 2 (PTPN2) locus have been linked with several autoimmune diseases, including rheumatoid arthritis, type I diabetes, and inflammatory bowel disease. However, the functional consequences of these SNPs are poorly characterized. Herein, we show in blood cells that SNPs in the PTPN2 locus are highly correlated with DNA methylation levels at four CpG sites downstream of PTPN2 and expression levels of the long non-coding RNA (lncRNA) LINC01882 downstream of these CpG sites. We observed that LINC01882 is mainly expressed in T cells and that anti-CD3/CD28 activated na\u00efve CD4", "doi": "10.1016/j.jaut.2018.01.003", "pmid": "29398253", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2018-04-04T11:31:11.341Z", "modified": "2024-01-16T13:48:46.962Z"}, {"entity": "publication", "iuid": "03e75ccf95384d2eb4c47d150176f3d6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/03e75ccf95384d2eb4c47d150176f3d6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/03e75ccf95384d2eb4c47d150176f3d6"}}, "title": "Slow evolution of sex-biased genes in the reproductive tissue of the dioecious plant Salix viminalis", "authors": [{"family": "Darolti", "given": "Iulia", "initials": "I"}, {"family": "Wright", "given": "Alison E", "initials": "AE"}, {"family": "Pucholt", "given": "Pascal", "initials": "P"}, {"family": "Berlin", "given": "Sofia", "initials": "S"}, {"family": "Mank", "given": "Judith E", "initials": "JE"}], "type": "journal-article", "published": "2018-02-00", "journal": {"volume": "27", "issn": "0962-1083", "issue": "3", "pages": "694-708", "title": "Mol Ecol", "issn-l": "0962-1083"}, "abstract": null, "doi": "10.1111/mec.14466", "pmid": "29274186", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "BioProject", "description": "Salix viminalis RNA sequencing of 6 genotypes and 2 tissues", "key": "PRJEB15050"}], "notes": [], "created": "2018-09-14T12:12:17.599Z", "modified": "2024-01-16T13:48:46.976Z"}, {"entity": "publication", "iuid": "7b6ff8fd475b4a788c0a744863a0a6a7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7b6ff8fd475b4a788c0a744863a0a6a7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7b6ff8fd475b4a788c0a744863a0a6a7"}}, "title": "Paternal easiRNAs regulate parental genome dosage in Arabidopsis", "authors": [{"family": "Martinez", "given": "German", "initials": "G"}, {"family": "Wolff", "given": "Philip", "initials": "P"}, {"family": "Wang", "given": "Zhenxing", "initials": "Z"}, {"family": "Moreno-Romero", "given": "Jordi", "initials": "J"}, {"family": "Santos-Gonz\u00e1lez", "given": "Juan", "initials": "J"}, {"family": "Conze", "given": "Lei Liu", "initials": "LL"}, {"family": "DeFraia", "given": "Christopher", "initials": "C"}, {"family": "Slotkin", "given": "R Keith", "initials": "RK"}, {"family": "K\u00f6hler", "given": "Claudia", "initials": "C"}], "type": "journal-article", "published": "2018-02-00", "journal": {"volume": "50", "issn": "1061-4036", "issue": "2", "pages": "193-198", "title": "Nat Genet", "issn-l": "1061-4036"}, "abstract": null, "doi": "10.1038/s41588-017-0033-4", "pmid": "29335548", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "GEO", "description": "Stump-harvested forest soil microbiome and mercury methylation", "key": "GSE84122"}], "notes": [], "created": "2018-09-14T12:07:52.193Z", "modified": "2020-01-21T13:56:12.081Z"}, {"entity": "publication", "iuid": "c9af84ed6e2e41d4830e9f77a67c002f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c9af84ed6e2e41d4830e9f77a67c002f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c9af84ed6e2e41d4830e9f77a67c002f"}}, "title": "Gene expression profiling across ontogenetic stages in the wood white (Leptidea sinapis) reveals pathways linked to butterfly diapause regulation.", "authors": [{"family": "Leal", "given": "Luis", "initials": "L"}, {"family": "Talla", "given": "Venkat", "initials": "V"}, {"family": "K\u00e4llman", "given": "Thomas", "initials": "T"}, {"family": "Friberg", "given": "Magne", "initials": "M"}, {"family": "Wiklund", "given": "Christer", "initials": "C"}, {"family": "Dinc\u0103", "given": "Vlad", "initials": "V"}, {"family": "Vila", "given": "Roger", "initials": "R"}, {"family": "Backstr\u00f6m", "given": "Niclas", "initials": "N"}], "type": "journal article", "published": "2018-02-00", "journal": {"volume": "27", "issn": "1365-294X", "issue": "4", "pages": "935-948", "title": "Mol. Ecol.", "issn-l": "0962-1083"}, "abstract": "In temperate latitudes, many insects enter diapause (dormancy) during the cold season, a period during which developmental processes come to a standstill. The wood white (Leptidea sinapis) is a butterfly species distributed across western Eurasia that shows photoperiod-induced diapause with variation in critical day-length across populations at different latitudes. We assembled transcriptomes and estimated gene expression levels at different developmental stages in experimentally induced directly developing and diapausing cohorts of a single Swedish population of L.\u00a0sinapis to investigate the regulatory mechanisms underpinning diapause initiation. Different day lengths resulted in expression changes of developmental genes and affected the rate of accumulation of signal molecules, suggesting that diapause induction might be controlled by increased activity of monoamine neurotransmitters in larvae reared under short-day light conditions. Expression differences between light treatment groups of two monoamine regulator genes (DDC and ST) were observed already in instar III larvae. Once developmental pathways were irreversibly set at instar V, a handful of genes related to dopamine production were differentially expressed leading to a significant decrease in expression of global metabolic genes and increase in expression of genes related to fatty acid synthesis and sequestration. This is in line with a time-dependent (hour-glass) model of diapause regulation where a gradual shift in the concentration of monoamine neurotransmitters and their metabolites during development of larvae under short-day conditions leads to increased storage of fat, decreased energy expenditures, and ultimately developmental stasis at the pupal stage.", "doi": "10.1111/mec.14501", "pmid": "29411442", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "NGI Stockholm (Genomics Production)": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "BioProject", "description": "SRA experiments", "key": "PRJEB24745"}, {"db": "ArrayExpress", "description": "RNA-seq data", "key": "E\u2010MTAB\u20106454"}], "notes": [], "created": "2018-10-31T19:46:48.334Z", "modified": "2020-01-21T13:56:17.397Z"}, {"entity": "publication", "iuid": "0f64522256044b27a5fdfa915c82d881", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0f64522256044b27a5fdfa915c82d881.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0f64522256044b27a5fdfa915c82d881"}}, "title": "Formation of mercury methylation hotspots as a consequence of forestry operations", "authors": [{"family": "Ekl\u00f6f", "given": "Karin", "initials": "K"}, {"family": "Bishop", "given": "Kevin", "initials": "K"}, {"family": "Bertilsson", "given": "Stefan", "initials": "S"}, {"family": "Bj\u00f6rn", "given": "Erik", "initials": "E"}, {"family": "Buck", "given": "Moritz", "initials": "M"}, {"family": "Skyllberg", "given": "Ulf", "initials": "U"}, {"family": "Osman", "given": "Omneya A", "initials": "OA"}, {"family": "Kronberg", "given": "Rose Marie", "initials": "RM"}, {"family": "Bravo", "given": "Andrea G", "initials": "AG"}], "type": "journal-article", "published": "2018-02-00", "journal": {"volume": "613-614", "issn": "0048-9697", "issue": null, "pages": "1069-1078", "title": "Science of The Total Environment", "issn-l": "0048-9697"}, "abstract": "Earlier studies have shown that boreal forest logging can increase the concentration and export of methylmercury (MeHg) in stream runoff. Here we test whether forestry operations create soil environments of high MeHg net formation associated with distinct microbial communities. Furthermore, we test the hypothesis that Hg methylation hotspots are more prone to form after stump harvest than stem-only harvest, because of more severe soil compaction and soil disturbance. Concentrations of MeHg, percent MeHg of total Hg (THg), and bacterial community composition were determined at 200 soil sampling positions distributed across eight catchments. Each catchment was either stem-only harvested (n=3), stem- and stump-harvested (n=2) or left undisturbed (n=3). In support of our hypothesis, higher MeHg to THg ratios was observed in one of the stump-harvested catchments. While the effects of natural variation could not be ruled out, we noted that most of the highest % MeHg was observed in water-filled cavities created by stump removal or driving damage. This catchment also featured the highest bacterial diversity and highest relative abundance of bacterial families known to include Hg methylators. We propose that water-logged and disturbed soil environments associated with stump harvest can favor methylating microorganisms, which also enhance MeHg formation.", "doi": "10.1016/j.scitotenv.2017.09.151", "pmid": "28950669", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [], "notes": [], "created": "2018-09-14T12:07:36.259Z", "modified": "2024-01-16T13:48:46.998Z"}, {"entity": "publication", "iuid": "cbe64baa060341b19572a802b579cb37", "links": {"self": {"href": "https://publications.scilifelab.se/publication/cbe64baa060341b19572a802b579cb37.json"}, "display": {"href": "https://publications.scilifelab.se/publication/cbe64baa060341b19572a802b579cb37"}}, "title": "Dispersal timing determines the importance of priority effects in bacterial communities", "authors": [{"family": "Svoboda", "given": "Pavel", "initials": "P"}, {"family": "Lindstr\u00f6m", "given": "Eva S", "initials": "ES"}, {"family": "Ahmed Osman", "given": "Omneya", "initials": "O"}, {"family": "Langenheder", "given": "Silke", "initials": "S"}], "type": "journal-article", "published": "2018-02-00", "journal": {"volume": "12", "issn": "1751-7370", "issue": "2", "pages": "644-646", "title": "ISME J", "issn-l": "1751-7362"}, "abstract": null, "doi": "10.1038/ismej.2017.180", "pmid": "29053147", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2018-09-14T12:10:44.660Z", "modified": "2024-01-16T13:48:47.006Z"}, {"entity": "publication", "iuid": "1bfae6637d204721b3b70e933a093325", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1bfae6637d204721b3b70e933a093325.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1bfae6637d204721b3b70e933a093325"}}, "title": "Copy Number Variation Analysis of 100 Twin Pairs Enriched for Neurodevelopmental Disorders.", "authors": [{"family": "Stamouli", "given": "Sofia", "initials": "S"}, {"family": "Anderlid", "given": "Britt-Marie", "initials": "BM"}, {"family": "Willfors", "given": "Charlotte", "initials": "C"}, {"family": "Thiruvahindrapuram", "given": "Bhooma", "initials": "B"}, {"family": "Wei", "given": "John", "initials": "J"}, {"family": "Berggren", "given": "Steve", "initials": "S"}, {"family": "Nordgren", "given": "Ann", "initials": "A"}, {"family": "Scherer", "given": "Stephen W", "initials": "SW"}, {"family": "Lichtenstein", "given": "Paul", "initials": "P"}, {"family": "Tammimies", "given": "Kristiina", "initials": "K"}, {"family": "B\u00f6lte", "given": "Sven", "initials": "S"}], "type": "journal article", "published": "2018-02-00", "journal": {"volume": "21", "issn": "1832-4274", "issue": "1", "pages": "1-11", "title": "Twin Res Hum Genet", "issn-l": null}, "abstract": "Hundreds of penetrant risk loci have been identified across different neurodevelopmental disorders (NDDs), and these often involve rare (<1% frequency) copy number variations (CNVs), which can involve one or more genes. Monozygotic (MZ) twin pairs are long thought to share 100% of their genomic information. However, genetic differences in the form of postzygotic somatic variants have been reported recently both in typically developing (TD) and in clinically discordant MZ pairs. We sought to investigate the contribution of rare CNVs in 100 twin pairs enriched for NDD phenotypes with a particular focus on postzygotic CNVs in MZ pairs discordant for autism spectrum disorder (ASD) using the Illumina Infinium PsychArray. In our sample, no postzygotic de novo CNVs were found in 55 MZ twin pairs, including the 13 pairs discordant for ASD. We did detect a higher rate of CNVs overlapping genes involved in disorders of the nervous system, such as a rare deletion affecting HNRNPU, in MZ pairs discordant and concordant for ASD in comparison with TD pairs (p = .02). Our results are in concordance with earlier findings that postzygotic de novo CNV events are typically rare in genomic DNA derived from saliva or blood, and suggests that the discordance of NDDs in our sample of twins is not explained by discordant CNVs. Still, studies investigating postzygotic variation in MZ discordant twins using DNA from different tissues and single cells and higher resolution genomics are needed in the future.", "doi": "10.1017/thg.2017.69", "pmid": "29307321", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "S183242741700069X"}], "notes": [], "created": "2018-05-25T13:31:05.221Z", "modified": "2024-01-16T13:48:47.013Z"}, {"entity": "publication", "iuid": "775f25e7409f4ccdacd52bc658116f4f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/775f25e7409f4ccdacd52bc658116f4f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/775f25e7409f4ccdacd52bc658116f4f"}}, "title": "A DNA methylation biomarker of alcohol consumption.", "authors": [{"family": "Liu", "given": "C", "initials": "C"}, {"family": "Marioni", "given": "R E", "initials": "RE"}, {"family": "Hedman", "given": "\u00c5 K", "initials": "\u00c5K"}, {"family": "Pfeiffer", "given": "L", "initials": "L"}, {"family": "Tsai", "given": "P-C", "initials": "PC"}, {"family": "Reynolds", "given": "L M", "initials": "LM"}, {"family": "Just", "given": "A C", "initials": "AC"}, {"family": "Duan", "given": "Q", "initials": "Q"}, {"family": "Boer", "given": "C G", "initials": "CG"}, {"family": "Tanaka", "given": "T", "initials": "T"}, {"family": "Elks", "given": "C E", "initials": "CE"}, {"family": "Aslibekyan", "given": "S", "initials": "S"}, {"family": "Brody", "given": "J A", "initials": "JA"}, {"family": "K\u00fchnel", "given": "B", "initials": "B"}, {"family": "Herder", "given": "C", "initials": "C"}, {"family": "Almli", "given": "L M", "initials": "LM"}, {"family": "Zhi", "given": "D", "initials": "D"}, {"family": "Wang", "given": "Y", "initials": "Y"}, {"family": "Huan", "given": "T", "initials": "T"}, {"family": "Yao", "given": "C", "initials": "C"}, {"family": "Mendelson", "given": "M M", "initials": "MM"}, {"family": "Joehanes", "given": "R", "initials": "R"}, {"family": "Liang", "given": "L", "initials": "L"}, {"family": "Love", "given": "S-A", "initials": "SA"}, {"family": "Guan", "given": "W", "initials": "W"}, {"family": "Shah", "given": "S", "initials": "S"}, {"family": "McRae", "given": "A F", "initials": "AF"}, {"family": "Kretschmer", "given": "A", "initials": "A"}, {"family": "Prokisch", "given": "H", "initials": "H"}, {"family": "Strauch", "given": "K", "initials": "K"}, {"family": "Peters", "given": "A", "initials": "A"}, {"family": "Visscher", "given": "P M", "initials": "PM"}, {"family": "Wray", "given": "N R", "initials": "NR"}, {"family": "Guo", "given": "X", "initials": "X"}, {"family": "Wiggins", "given": "K L", "initials": "KL"}, {"family": "Smith", "given": "A K", "initials": "AK"}, {"family": "Binder", "given": "E B", "initials": "EB"}, {"family": "Ressler", "given": "K J", "initials": "KJ"}, {"family": "Irvin", "given": "M R", "initials": "MR"}, {"family": "Absher", "given": "D M", "initials": "DM"}, {"family": "Hernandez", "given": "D", "initials": "D"}, {"family": "Ferrucci", "given": "L", "initials": "L"}, {"family": "Bandinelli", "given": "S", "initials": "S"}, {"family": "Lohman", "given": "K", "initials": "K"}, {"family": "Ding", "given": "J", "initials": "J"}, {"family": "Trevisi", "given": "L", "initials": "L"}, {"family": "Gustafsson", "given": "S", "initials": "S"}, {"family": "Sandling", "given": "J H", "initials": "JH"}, {"family": "Stolk", "given": "L", "initials": "L"}, {"family": "Uitterlinden", "given": "A G", "initials": "AG"}, {"family": "Yet", "given": "I", "initials": "I"}, {"family": "Castillo-Fernandez", "given": "J E", "initials": "JE"}, {"family": "Spector", "given": "T D", "initials": "TD"}, {"family": "Schwartz", "given": "J D", "initials": "JD"}, {"family": "Vokonas", "given": "P", "initials": "P"}, {"family": "Lind", "given": "L", "initials": "L"}, {"family": "Li", "given": "Y", "initials": "Y"}, {"family": "Fornage", "given": "M", "initials": "M"}, {"family": "Arnett", "given": "D K", "initials": "DK"}, {"family": "Wareham", "given": "N J", "initials": "NJ"}, {"family": "Sotoodehnia", "given": "N", "initials": "N"}, {"family": "Ong", "given": "K K", "initials": "KK"}, {"family": "van Meurs", "given": "J B J", "initials": "JBJ"}, {"family": "Conneely", "given": "K N", "initials": "KN"}, {"family": "Baccarelli", "given": "A A", "initials": "AA"}, {"family": "Deary", "given": "I J", "initials": "IJ"}, {"family": "Bell", "given": "J T", "initials": "JT"}, {"family": "North", "given": "K E", "initials": "KE"}, {"family": "Liu", "given": "Y", "initials": "Y"}, {"family": "Waldenberger", "given": "M", "initials": "M"}, {"family": "London", "given": "S J", "initials": "SJ"}, {"family": "Ingelsson", "given": "E", "initials": "E"}, {"family": "Levy", "given": "D", "initials": "D"}], "type": "journal article", "published": "2018-02-00", "journal": {"volume": "23", "issn": "1476-5578", "issue": "2", "pages": "422-433", "title": "Mol. Psychiatry", "issn-l": "1359-4184"}, "abstract": "The lack of reliable measures of alcohol intake is a major obstacle to the diagnosis and treatment of alcohol-related diseases. Epigenetic modifications such as DNA methylation may provide novel biomarkers of alcohol use. To examine this possibility, we performed an epigenome-wide association study of methylation of cytosine-phosphate-guanine dinucleotide (CpG) sites in relation to alcohol intake in 13 population-based cohorts (n", "doi": "10.1038/mp.2016.192", "pmid": "27843151", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "mp2016192"}, {"db": "pmc", "key": "PMC5575985"}, {"db": "mid", "key": "NIHMS855941"}, {"db": "dbGaP", "description": "CHARGE (Cohorts for Heart and Aging Research in Genomic Epidemiology) Consortium Summary Results from Genomic Studies", "key": "phs000930"}], "notes": [], "created": "2017-05-03T12:59:55.799Z", "modified": "2024-01-16T13:48:47.037Z"}, {"entity": "publication", "iuid": "8feeddbbec5040e4a4d84314710c2608", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8feeddbbec5040e4a4d84314710c2608.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8feeddbbec5040e4a4d84314710c2608"}}, "title": "Genetical genomics of growth in a chicken model.", "authors": [{"family": "Johnsson", "given": "Martin", "initials": "M"}, {"family": "Henriksen", "given": "Rie", "initials": "R"}, {"family": "H\u00f6glund", "given": "Andrey", "initials": "A"}, {"family": "Fogelholm", "given": "Jesper", "initials": "J"}, {"family": "Jensen", "given": "Per", "initials": "P"}, {"family": "Wright", "given": "Dominic", "initials": "D"}], "type": "journal article", "published": "2018-01-23", "journal": {"volume": "19", "issn": "1471-2164", "issue": "1", "pages": "72", "title": "BMC Genomics", "issn-l": "1471-2164"}, "abstract": "The genetics underlying body mass and growth are key to understanding a wide range of topics in biology, both evolutionary and developmental. Body mass and growth traits are affected by many genetic variants of small effect. This complicates genetic mapping of growth and body mass. Experimental intercrosses between individuals from divergent populations allows us to map naturally occurring genetic variants for selected traits, such as body mass by linkage mapping. By simultaneously measuring traits and intermediary molecular phenotypes, such as gene expression, one can use integrative genomics to search for potential causative genes.\n\nIn this study, we use linkage mapping approach to map growth traits (N\u2009=\u2009471) and liver gene expression (N\u2009=\u2009130) in an advanced intercross of wild Red Junglefowl and domestic White Leghorn layer chickens. We find 16 loci for growth traits, and 1463 loci for liver gene expression, as measured by microarrays. Of these, the genes TRAK1, OSBPL8, YEATS4, CEP55, and PIP4K2B are identified as strong candidates for growth loci in the chicken. We also show a high degree of sex-specific gene-regulation, with almost every gene expression locus exhibiting sex-interactions. Finally, several trans-regulatory hotspots were found, one of which coincides with a major growth locus.\n\nThese findings not only serve to identify several strong candidates affecting growth, but also show how sex-specificity and local gene-regulation affect growth regulation in the chicken.", "doi": "10.1186/s12864-018-4441-3", "pmid": "29361907", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1186/s12864-018-4441-3"}, {"db": "pmc", "key": "PMC5782384"}, {"db": "ArrayExpress", "description": "https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-5572/", "key": "E-MTAB-5572"}], "notes": [], "created": "2018-05-25T13:31:02.222Z", "modified": "2024-01-16T13:48:47.054Z"}, {"entity": "publication", "iuid": "1c039b8df777464b9dabb5e4dc900c99", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1c039b8df777464b9dabb5e4dc900c99.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1c039b8df777464b9dabb5e4dc900c99"}}, "title": "Demography and mating system shape the genome-wide impact of purifying selection in Arabis alpina.", "authors": [{"family": "Laenen", "given": "Benjamin", "initials": "B"}, {"family": "Tedder", "given": "Andrew", "initials": "A"}, {"family": "Nowak", "given": "Michael D", "initials": "MD"}, {"family": "Tor\u00e4ng", "given": "Per", "initials": "P"}, {"family": "Wunder", "given": "J\u00f6rg", "initials": "J"}, {"family": "W\u00f6tzel", "given": "Stefan", "initials": "S"}, {"family": "Steige", "given": "Kim A", "initials": "KA"}, {"family": "Kourmpetis", "given": "Yiannis", "initials": "Y"}, {"family": "Odong", "given": "Thomas", "initials": "T"}, {"family": "Drouzas", "given": "Andreas D", "initials": "AD"}, {"family": "Bink", "given": "Marco C A M", "initials": "MCAM"}, {"family": "\u00c5gren", "given": "Jon", "initials": "J"}, {"family": "Coupland", "given": "George", "initials": "G"}, {"family": "Slotte", "given": "Tanja", "initials": "T", "orcid": "0000-0001-6020-5102", "researcher": {"href": "https://publications.scilifelab.se/researcher/67c69ee78bae41478465a7e5fa63b946.json"}}], "type": "journal article", "published": "2018-01-23", "journal": {"volume": "115", "issn": "1091-6490", "issue": "4", "pages": "816-821", "title": "Proc. Natl. Acad. Sci. U.S.A.", "issn-l": "0027-8424"}, "abstract": "Plant mating systems have profound effects on levels and structuring of genetic variation and can affect the impact of natural selection. Although theory predicts that intermediate outcrossing rates may allow plants to prevent accumulation of deleterious alleles, few studies have empirically tested this prediction using genomic data. Here, we study the effect of mating system on purifying selection by conducting population-genomic analyses on whole-genome resequencing data from 38 European individuals of the arctic-alpine crucifer Arabis alpina We find that outcrossing and mixed-mating populations maintain genetic diversity at similar levels, whereas highly self-fertilizing Scandinavian A. alpina show a strong reduction in genetic diversity, most likely as a result of a postglacial colonization bottleneck. We further find evidence for accumulation of genetic load in highly self-fertilizing populations, whereas the genome-wide impact of purifying selection does not differ greatly between mixed-mating and outcrossing populations. Our results demonstrate that intermediate levels of outcrossing may allow efficient selection against harmful alleles, whereas demographic effects can be important for relaxed purifying selection in highly selfing populations. Thus, mating system and demography shape the impact of purifying selection on genomic variation in A. alpina These results are important for an improved understanding of the evolutionary consequences of mating system variation and the maintenance of mixed-mating strategies.", "doi": "10.1073/pnas.1707492115", "pmid": "29301967", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "1707492115"}, {"db": "pmc", "key": "PMC5789905"}], "notes": [], "created": "2019-01-07T22:21:08.774Z", "modified": "2021-06-21T14:35:07.593Z"}, {"entity": "publication", "iuid": "bebd428b1dba4d089a4570a609b57d25", "links": {"self": {"href": "https://publications.scilifelab.se/publication/bebd428b1dba4d089a4570a609b57d25.json"}, "display": {"href": "https://publications.scilifelab.se/publication/bebd428b1dba4d089a4570a609b57d25"}}, "title": "Genome-wide association study in 79,366 European-ancestry individuals informs the genetic architecture of 25-hydroxyvitamin D levels.", "authors": [{"family": "Jiang", "given": "Xia", "initials": "X"}, {"family": "O'Reilly", "given": "Paul F", "initials": "PF"}, {"family": "Aschard", "given": "Hugues", "initials": "H"}, {"family": "Hsu", "given": "Yi-Hsiang", "initials": "YH"}, {"family": "Richards", "given": "J Brent", "initials": "JB"}, {"family": "Dupuis", "given": "Jos\u00e9e", "initials": "J"}, {"family": "Ingelsson", "given": "Erik", "initials": "E"}, {"family": "Karasik", "given": "David", "initials": "D"}, {"family": "Pilz", "given": "Stefan", "initials": "S"}, {"family": "Berry", "given": "Diane", "initials": "D"}, {"family": "Kestenbaum", "given": "Bryan", "initials": "B"}, {"family": "Zheng", "given": "Jusheng", "initials": "J"}, {"family": "Luan", "given": "Jianan", "initials": "J"}, {"family": "Sofianopoulou", "given": "Eleni", "initials": "E"}, {"family": "Streeten", "given": "Elizabeth A", "initials": "EA"}, {"family": "Albanes", "given": "Demetrius", "initials": "D"}, {"family": "Lutsey", "given": "Pamela L", "initials": "PL"}, {"family": "Yao", "given": "Lu", "initials": "L"}, {"family": "Tang", "given": "Weihong", "initials": "W"}, {"family": "Econs", "given": "Michael J", "initials": "MJ"}, {"family": "Wallaschofski", "given": "Henri", "initials": "H"}, {"family": "V\u00f6lzke", "given": "Henry", "initials": "H"}, {"family": "Zhou", "given": "Ang", "initials": "A"}, {"family": "Power", "given": "Chris", "initials": "C"}, {"family": "McCarthy", "given": "Mark I", "initials": "MI"}, {"family": "Michos", "given": "Erin D", "initials": "ED"}, {"family": "Boerwinkle", "given": "Eric", "initials": "E"}, {"family": "Weinstein", "given": "Stephanie J", "initials": "SJ"}, {"family": "Freedman", "given": "Neal D", "initials": "ND"}, {"family": "Huang", "given": "Wen-Yi", "initials": "WY"}, {"family": "Van Schoor", "given": "Natasja M", "initials": "NM"}, {"family": "van der Velde", "given": "Nathalie", "initials": "N"}, {"family": "Groot", "given": "Lisette C P G M de", "initials": "LCPGM"}, {"family": "Enneman", "given": "Anke", "initials": "A"}, {"family": "Cupples", "given": "L Adrienne", "initials": "LA"}, {"family": "Booth", "given": "Sarah L", "initials": "SL"}, {"family": "Vasan", "given": "Ramachandran S", "initials": "RS"}, {"family": "Liu", "given": "Ching-Ti", "initials": "CT"}, {"family": "Zhou", "given": "Yanhua", "initials": "Y"}, {"family": "Ripatti", "given": "Samuli", "initials": "S"}, {"family": "Ohlsson", "given": "Claes", "initials": "C"}, {"family": "Vandenput", "given": "Liesbeth", "initials": "L"}, {"family": "Lorentzon", "given": "Mattias", "initials": "M"}, {"family": "Eriksson", "given": "Johan G", "initials": "JG"}, {"family": "Shea", "given": "M Kyla", "initials": "MK"}, {"family": "Houston", "given": "Denise K", "initials": "DK"}, {"family": "Kritchevsky", "given": "Stephen B", "initials": "SB"}, {"family": "Liu", "given": "Yongmei", "initials": "Y"}, {"family": "Lohman", "given": "Kurt K", "initials": "KK"}, {"family": "Ferrucci", "given": "Luigi", "initials": "L"}, {"family": "Peacock", "given": "Munro", "initials": "M"}, {"family": "Gieger", "given": "Christian", "initials": "C"}, {"family": "Beekman", "given": "Marian", "initials": "M"}, {"family": "Slagboom", "given": "Eline", "initials": "E"}, {"family": "Deelen", "given": "Joris", "initials": "J"}, {"family": "Heemst", "given": "Diana van", "initials": "DV"}, {"family": "Kleber", "given": "Marcus E", "initials": "ME"}, {"family": "M\u00e4rz", "given": "Winfried", "initials": "W"}, {"family": "de Boer", "given": "Ian H", "initials": "IH"}, {"family": "Wood", "given": "Alexis C", "initials": "AC"}, {"family": "Rotter", "given": "Jerome I", "initials": "JI"}, {"family": "Rich", "given": "Stephen S", "initials": "SS"}, {"family": "Robinson-Cohen", "given": "Cassianne", "initials": "C"}, {"family": "den Heijer", "given": "Martin", "initials": "M"}, {"family": "Jarvelin", "given": "Marjo-Riitta", "initials": "MR"}, {"family": "Cavadino", "given": "Alana", "initials": "A"}, {"family": "Joshi", "given": "Peter K", "initials": "PK"}, {"family": "Wilson", "given": "James F", "initials": "JF"}, {"family": "Hayward", "given": "Caroline", "initials": "C"}, {"family": "Lind", "given": "Lars", "initials": "L"}, {"family": "Micha\u00eblsson", "given": "Karl", "initials": "K"}, {"family": "Trompet", "given": "Stella", "initials": "S"}, {"family": "Zillikens", "given": "M Carola", "initials": "MC"}, {"family": "Uitterlinden", "given": "Andre G", "initials": "AG"}, {"family": "Rivadeneira", "given": "Fernando", "initials": "F"}, {"family": "Broer", "given": "Linda", "initials": "L"}, {"family": "Zgaga", "given": "Lina", "initials": "L"}, {"family": "Campbell", "given": "Harry", "initials": "H"}, {"family": "Theodoratou", "given": "Evropi", "initials": "E"}, {"family": "Farrington", "given": "Susan M", "initials": "SM"}, {"family": "Timofeeva", "given": "Maria", "initials": "M"}, {"family": "Dunlop", "given": "Malcolm G", "initials": "MG"}, {"family": "Valdes", "given": "Ana M", "initials": "AM"}, {"family": "Tikkanen", "given": "Emmi", "initials": "E"}, {"family": "Lehtim\u00e4ki", "given": "Terho", "initials": "T"}, {"family": "Lyytik\u00e4inen", "given": "Leo-Pekka", "initials": "LP"}, {"family": "K\u00e4h\u00f6nen", "given": "Mika", "initials": "M"}, {"family": "Raitakari", "given": "Olli T", "initials": "OT"}, {"family": "Mikkil\u00e4", "given": "Vera", "initials": "V"}, {"family": "Ikram", "given": "M Arfan", "initials": "MA"}, {"family": "Sattar", "given": "Naveed", "initials": "N"}, {"family": "Jukema", "given": "J Wouter", "initials": "JW"}, {"family": "Wareham", "given": "Nicholas J", "initials": "NJ"}, {"family": "Langenberg", "given": "Claudia", "initials": "C"}, {"family": "Forouhi", "given": "Nita G", "initials": "NG"}, {"family": "Gundersen", "given": "Thomas E", "initials": "TE"}, {"family": "Khaw", "given": "Kay-Tee", "initials": "KT"}, {"family": "Butterworth", "given": "Adam S", "initials": "AS"}, {"family": "Danesh", "given": "John", "initials": "J"}, {"family": "Spector", "given": "Timothy", "initials": "T"}, {"family": "Wang", "given": "Thomas J", "initials": "TJ"}, {"family": "Hypp\u00f6nen", "given": "Elina", "initials": "E"}, {"family": "Kraft", "given": "Peter", "initials": "P"}, {"family": "Kiel", "given": "Douglas P", "initials": "DP"}], "type": "journal article", "published": "2018-01-17", "journal": {"volume": "9", "issn": "2041-1723", "issue": "1", "pages": "260", "title": "Nat Commun", "issn-l": "2041-1723"}, "abstract": "Vitamin D is a steroid hormone precursor that is associated with a range of human traits and diseases. Previous GWAS of serum 25-hydroxyvitamin D concentrations have identified four genome-wide significant loci (GC, NADSYN1/DHCR7, CYP2R1, CYP24A1). In this study, we expand the previous SUNLIGHT Consortium GWAS discovery sample size from 16,125 to 79,366 (all European descent). This larger GWAS yields two additional loci harboring genome-wide significant variants (P\u2009=\u20094.7\u00d710", "doi": "10.1038/s41467-017-02662-2", "pmid": "29343764", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-017-02662-2"}, {"db": "pmc", "key": "PMC5772647"}], "notes": [], "created": "2018-05-25T13:31:03.142Z", "modified": "2024-01-16T13:48:47.068Z"}, {"entity": "publication", "iuid": "f708a6aad749449f984959358cbbc4c9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f708a6aad749449f984959358cbbc4c9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f708a6aad749449f984959358cbbc4c9"}}, "title": "Rapid hybrid speciation in Darwin\u2019s finches", "authors": [{"family": "Lamichhaney", "given": "Sangeet", "initials": "S"}, {"family": "Han", "given": "Fan", "initials": "F"}, {"family": "Webster", "given": "Matthew T", "initials": "MT"}, {"family": "Andersson", "given": "Leif", "initials": "L"}, {"family": "Grant", "given": "B Rosemary", "initials": "BR"}, {"family": "Grant", "given": "Peter R", "initials": "PR"}], "type": "journal-article", "published": "2018-01-12", "journal": {"volume": "359", "issn": "1095-9203", "issue": "6372", "pages": "224-228", "title": "Science", "issn-l": "0036-8075"}, "abstract": null, "doi": "10.1126/science.aao4593", "pmid": "29170277", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "SRA", "description": null, "key": "PRJNA392917"}, {"db": "TreeBASE", "description": "https://treebase.org/treebase-web/search/study/summary.html?id=21803", "key": "S21803"}], "notes": [], "created": "2017-11-29T10:56:11.696Z", "modified": "2024-01-16T13:48:47.084Z"}, {"entity": "publication", "iuid": "5662650d5f3b43ccada077c1fd1d6431", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5662650d5f3b43ccada077c1fd1d6431.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5662650d5f3b43ccada077c1fd1d6431"}}, "title": "Meta-analysis of exome array data identifies six novel genetic loci for lung function.", "authors": [{"family": "Jackson", "given": "Victoria E", "initials": "VE"}, {"family": "Latourelle", "given": "Jeanne C", "initials": "JC"}, {"family": "Wain", "given": "Louise V", "initials": "LV"}, {"family": "Smith", "given": "Albert V", "initials": "AV"}, {"family": "Grove", "given": "Megan L", "initials": "ML"}, {"family": "Bartz", "given": "Traci M", "initials": "TM"}, {"family": "Obeidat", "given": "Ma'en", "initials": "M"}, {"family": "Province", "given": "Michael A", "initials": "MA"}, {"family": "Gao", "given": "Wei", "initials": "W"}, {"family": "Qaiser", "given": "Beenish", "initials": "B"}, {"family": "Porteous", "given": "David J", "initials": "DJ"}, {"family": "Cassano", "given": "Patricia A", "initials": "PA"}, {"family": "Ahluwalia", "given": "Tarunveer S", "initials": "TS"}, {"family": "Grarup", "given": "Niels", "initials": "N"}, {"family": "Li", "given": "Jin", "initials": "J"}, {"family": "Altmaier", "given": "Elisabeth", "initials": "E"}, {"family": "Marten", "given": "Jonathan", "initials": "J"}, {"family": "Harris", "given": "Sarah E", "initials": "SE"}, {"family": "Manichaikul", "given": "Ani", "initials": "A"}, {"family": "Pottinger", "given": "Tess D", "initials": "TD"}, {"family": "Li-Gao", "given": "Ruifang", "initials": "R"}, {"family": "Lind-Thomsen", "given": "Allan", "initials": "A"}, {"family": "Mahajan", "given": "Anubha", "initials": "A"}, {"family": "Lahousse", "given": "Lies", "initials": "L"}, {"family": "Imboden", "given": "Medea", "initials": "M"}, {"family": "Teumer", "given": "Alexander", "initials": "A"}, {"family": "Prins", "given": "Bram", "initials": "B"}, {"family": "Lyytik\u00e4inen", "given": "Leo-Pekka", "initials": "LP"}, {"family": "Eiriksdottir", "given": "Gudny", "initials": "G"}, {"family": "Franceschini", "given": "Nora", "initials": "N"}, {"family": "Sitlani", "given": "Colleen M", "initials": "CM"}, {"family": "Brody", "given": "Jennifer A", "initials": "JA"}, {"family": "Boss\u00e9", "given": "Yohan", "initials": "Y"}, {"family": "Timens", "given": "Wim", "initials": "W"}, {"family": "Kraja", "given": "Aldi", "initials": "A"}, {"family": "Loukola", "given": "Anu", "initials": "A"}, {"family": "Tang", "given": "Wenbo", "initials": "W"}, {"family": "Liu", "given": "Yongmei", "initials": "Y"}, {"family": "Bork-Jensen", "given": "Jette", "initials": "J"}, {"family": "Justesen", "given": "Johanne M", "initials": "JM"}, {"family": "Linneberg", "given": "Allan", "initials": "A"}, {"family": "Lange", "given": "Leslie A", "initials": "LA"}, {"family": "Rawal", "given": "Rajesh", "initials": "R"}, {"family": "Karrasch", "given": "Stefan", "initials": "S"}, {"family": "Huffman", "given": "Jennifer E", "initials": "JE"}, {"family": "Smith", "given": "Blair H", "initials": "BH"}, {"family": "Davies", "given": "Gail", "initials": "G"}, {"family": "Burkart", "given": "Kristin M", "initials": "KM"}, {"family": "Mychaleckyj", "given": "Josyf C", "initials": "JC"}, {"family": "Bonten", "given": "Tobias N", "initials": "TN"}, {"family": "Enroth", "given": "Stefan", "initials": "S"}, {"family": "Lind", "given": "Lars", "initials": "L"}, {"family": "Brusselle", "given": "Guy G", "initials": "GG"}, {"family": "Kumar", "given": "Ashish", "initials": "A"}, {"family": "Stubbe", "given": "Beate", "initials": "B"}, {"family": "Understanding Society Scientific Group", "given": "", "initials": ""}, {"family": "K\u00e4h\u00f6nen", "given": "Mika", "initials": "M"}, {"family": "Wyss", "given": "Annah B", "initials": "AB"}, {"family": "Psaty", "given": "Bruce M", "initials": "BM"}, {"family": "Heckbert", "given": "Susan R", "initials": "SR"}, {"family": "Hao", "given": "Ke", "initials": "K"}, {"family": "Rantanen", "given": "Taina", "initials": "T"}, {"family": "Kritchevsky", "given": "Stephen B", "initials": "SB"}, {"family": "Lohman", "given": "Kurt", "initials": "K"}, {"family": "Skaaby", "given": "Tea", "initials": "T"}, {"family": "Pisinger", "given": "Charlotta", "initials": "C"}, {"family": "Hansen", "given": "Torben", "initials": "T"}, {"family": "Schulz", "given": "Holger", "initials": "H"}, {"family": "Polasek", "given": "Ozren", "initials": "O"}, {"family": "Campbell", "given": "Archie", "initials": "A"}, {"family": "Starr", "given": "John M", "initials": "JM"}, {"family": "Rich", "given": "Stephen S", "initials": "SS"}, {"family": "Mook-Kanamori", "given": "Dennis O", "initials": "DO"}, {"family": "Johansson", "given": "\u00c5sa", "initials": "\u00c5"}, {"family": "Ingelsson", "given": "Erik", "initials": "E"}, {"family": "Uitterlinden", "given": "Andr\u00e9 G", "initials": "AG"}, {"family": "Weiss", "given": "Stefan", "initials": "S"}, {"family": "Raitakari", "given": "Olli T", "initials": "OT"}, {"family": "Gudnason", "given": "Vilmundur", "initials": "V"}, {"family": "North", "given": "Kari E", "initials": "KE"}, {"family": "Gharib", "given": "Sina A", "initials": "SA"}, {"family": "Sin", "given": "Don D", "initials": "DD"}, {"family": "Taylor", "given": "Kent D", "initials": "KD"}, {"family": "O'Connor", "given": "George T", "initials": "GT"}, {"family": "Kaprio", "given": "Jaakko", "initials": "J"}, {"family": "Harris", "given": "Tamara B", "initials": "TB"}, {"family": "Pederson", "given": "Oluf", "initials": "O"}, {"family": "Vestergaard", "given": "Henrik", "initials": "H"}, {"family": "Wilson", "given": "James G", "initials": "JG"}, {"family": "Strauch", "given": "Konstantin", "initials": "K"}, {"family": "Hayward", "given": "Caroline", "initials": "C"}, {"family": "Kerr", "given": "Shona", "initials": "S"}, {"family": "Deary", "given": "Ian J", "initials": "IJ"}, {"family": "Barr", "given": "R Graham", "initials": "RG"}, {"family": "de Mutsert", "given": "Ren\u00e9e", "initials": "R"}, {"family": "Gyllensten", "given": "Ulf", "initials": "U"}, {"family": "Morris", "given": "Andrew P", "initials": "AP"}, {"family": "Ikram", "given": "M Arfan", "initials": "MA"}, {"family": "Probst-Hensch", "given": "Nicole", "initials": "N"}, {"family": "Gl\u00e4ser", "given": "Sven", "initials": "S"}, {"family": "Zeggini", "given": "Eleftheria", "initials": "E"}, {"family": "Lehtim\u00e4ki", "given": "Terho", "initials": "T"}, {"family": "Strachan", "given": "David P", "initials": "DP"}, {"family": "Dupuis", "given": "Jos\u00e9e", "initials": "J"}, {"family": "Morrison", "given": "Alanna C", "initials": "AC"}, {"family": "Hall", "given": "Ian P", "initials": "IP"}, {"family": "Tobin", "given": "Martin D", "initials": "MD"}, {"family": "London", "given": "Stephanie J", "initials": "SJ"}], "type": "journal article", "published": "2018-01-12", "journal": {"volume": "3", "issn": "2398-502X", "issue": null, "pages": "4", "title": "Wellcome Open Res", "issn-l": "2398-502X"}, "abstract": "Background: Over 90 regions of the genome have been associated with lung function to date, many of which have also been implicated in chronic obstructive pulmonary disease. Methods: We carried out meta-analyses of exome array data and three lung function measures: forced expiratory volume in one second (FEV 1), forced vital capacity (FVC) and the ratio of FEV 1 to FVC (FEV 1/FVC). These analyses by the SpiroMeta and CHARGE consortia included 60,749 individuals of European ancestry from 23 studies, and 7,721 individuals of African Ancestry from 5 studies in the discovery stage, with follow-up in up to 111,556 independent individuals. Results: We identified significant (P<2\u00b78x10 -7) associations with six SNPs: a nonsynonymous variant in RPAP1, which is predicted to be damaging, three intronic SNPs ( SEC24C, CASC17 and UQCC1) and two intergenic SNPs near to LY86 and FGF10. Expression quantitative trait loci analyses found evidence for regulation of gene expression at three signals and implicated several genes, including TYRO3 and PLAU. Conclusions: Further interrogation of these loci could provide greater understanding of the determinants of lung function and pulmonary disease.", "doi": "10.12688/wellcomeopenres.12583.3", "pmid": "30175238", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC6081985"}], "notes": [], "created": "2019-01-09T07:22:16.762Z", "modified": "2020-01-21T13:56:13.690Z"}, {"entity": "publication", "iuid": "fcd37a8280914a0bb0b0796744b1796a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/fcd37a8280914a0bb0b0796744b1796a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/fcd37a8280914a0bb0b0796744b1796a"}}, "title": "Identification of shared genetic variants between schizophrenia and lung cancer.", "authors": [{"family": "Zuber", "given": "Verena", "initials": "V"}, {"family": "J\u00f6nsson", "given": "Erik G", "initials": "EG"}, {"family": "Frei", "given": "Oleksandr", "initials": "O"}, {"family": "Witoelar", "given": "Aree", "initials": "A"}, {"family": "Thompson", "given": "Wesley K", "initials": "WK"}, {"family": "Schork", "given": "Andrew J", "initials": "AJ"}, {"family": "Bettella", "given": "Francesco", "initials": "F"}, {"family": "Wang", "given": "Yunpeng", "initials": "Y"}, {"family": "Djurovic", "given": "Srdjan", "initials": "S"}, {"family": "Smeland", "given": "Olav B", "initials": "OB"}, {"family": "Dieset", "given": "Ingrid", "initials": "I"}, {"family": "Fanous", "given": "Ayman H", "initials": "AH"}, {"family": "Desikan", "given": "Rahul S", "initials": "RS"}, {"family": "K\u00fcry", "given": "S\u00e9bastien", "initials": "S"}, {"family": "B\u00e9zieau", "given": "St\u00e9phane", "initials": "S"}, {"family": "Dale", "given": "Anders M", "initials": "AM"}, {"family": "Mills", "given": "Ian G", "initials": "IG"}, {"family": "Andreassen", "given": "Ole A", "initials": "OA"}], "type": "journal article", "published": "2018-01-12", "journal": {"volume": "8", "issn": "2045-2322", "issue": "1", "pages": "674", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "Epidemiology studies suggest associations between schizophrenia and cancer. However, the underlying genetic mechanisms are not well understood, and difficult to identify from epidemiological data. We investigated if there is a shared genetic architecture between schizophrenia and cancer, with the aim to identify specific overlapping genetic loci. First, we performed genome-wide enrichment analysis and second, we analyzed specific loci jointly associated with schizophrenia and cancer by the conjunction false discovery rate. We analyzed the largest genome-wide association studies of schizophrenia and lung, breast, prostate, ovary, and colon-rectum cancer including more than 220,000 subjects, and included genetic association with smoking behavior. Polygenic enrichment of associations with lung cancer was observed in schizophrenia, and weak enrichment for the remaining cancer sites. After excluding the major histocompatibility complex region, we identified three independent loci jointly associated with schizophrenia and lung cancer. The strongest association included nicotinic acetylcholine receptors and is an established pleiotropic locus shared between lung cancer and smoking. The two other loci were independent of genetic association with smoking. Functional analysis identified downstream pleiotropic effects on epigenetics and gene-expression in lung and brain tissue. These findings suggest that genetic factors may explain partly the observed epidemiological association of lung cancer and schizophrenia.", "doi": "10.1038/s41598-017-16481-4", "pmid": "29330379", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-017-16481-4"}, {"db": "pmc", "key": "PMC5766533"}], "notes": [], "created": "2018-05-25T13:31:03.834Z", "modified": "2020-01-21T13:56:10.912Z"}, {"entity": "publication", "iuid": "8b76cc6199e946b29b91c243ab626ddb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8b76cc6199e946b29b91c243ab626ddb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8b76cc6199e946b29b91c243ab626ddb"}}, "title": "Angiopoietin-1 deficiency increases renal capillary rarefaction and tubulointerstitial fibrosis in mice", "authors": [{"family": "Loganathan", "given": "Krishnapriya", "initials": "K"}, {"family": "Salem Said", "given": "Ebtisam", "initials": "E"}, {"family": "Winterrowd", "given": "Emily", "initials": "E"}, {"family": "Orebrand", "given": "Martina", "initials": "M"}, {"family": "He", "given": "Liqun", "initials": "L"}, {"family": "Vanlandewijck", "given": "Michael", "initials": "M"}, {"family": "Betsholtz", "given": "Christer", "initials": "C"}, {"family": "Quaggin", "given": "Susan E", "initials": "SE"}, {"family": "Jeansson", "given": "Marie", "initials": "M"}], "type": "journal-article", "published": "2018-01-02", "journal": {"volume": "13", "issn": "1932-6203", "issue": "1", "pages": "e0189433", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": null, "doi": "10.1371/journal.pone.0189433", "pmid": "29293543", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2018-09-14T12:06:32.744Z", "modified": "2024-01-16T13:48:47.124Z"}, {"entity": "publication", "iuid": "a56ea7ef06e84a569067539347cf845b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a56ea7ef06e84a569067539347cf845b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a56ea7ef06e84a569067539347cf845b"}}, "title": "Cytokine Autoantibody Screening in the Swedish Addison Registry Identifies Patients With Undiagnosed APS1", "authors": [{"family": "Eriksson", "given": "Daniel", "initials": "D"}, {"family": "Dalin", "given": "Frida", "initials": "F"}, {"family": "Eriksson", "given": "Gabriel Nordling", "initials": "GN"}, {"family": "Landegren", "given": "Nils", "initials": "N"}, {"family": "Bianchi", "given": "Matteo", "initials": "M"}, {"family": "Hallgren", "given": "\u00c5sa", "initials": "\u00c5"}, {"family": "Dahlqvist", "given": "Per", "initials": "P"}, {"family": "Wahlberg", "given": "Jeanette", "initials": "J"}, {"family": "Ekwall", "given": "Olov", "initials": "O"}, {"family": "Winqvist", "given": "Ola", "initials": "O"}, {"family": "Catrina", "given": "Sergiu Bogdan", "initials": "SB"}, {"family": "R\u00f6nnelid", "given": "Johan", "initials": "J"}, {"family": "Hulting", "given": "Anna Lena", "initials": "AL"}, {"family": "Lindblad-Toh", "given": "Kerstin", "initials": "K", "orcid": "0000-0001-8338-0253", "researcher": {"href": "https://publications.scilifelab.se/researcher/e0063145f7d6476f80ab42f94833f4cf.json"}}, {"family": "Alimohammadi", "given": "Mohammad", "initials": "M"}, {"family": "Husebye", "given": "Eystein S", "initials": "ES"}, {"family": "Knappskog", "given": "Per Morten", "initials": "PM"}, {"family": "Rosengren Pielberg", "given": "Gerli", "initials": "G"}, {"family": "Bensing", "given": "Sophie", "initials": "S"}, {"family": "K\u00e4mpe", "given": "Olle", "initials": "O"}, {"family": "Bensing", "given": "Sophie", "initials": "S"}, {"family": "Hulting", "given": "Anna Lena", "initials": "AL"}, {"family": "Ekwall", "given": "Olov", "initials": "O"}, {"family": "Dahlqvist", "given": "Per", "initials": "P"}, {"family": "Wahlberg", "given": "Jeanette", "initials": "J"}, {"family": "Olsson", "given": "Tommy", "initials": "T"}, {"family": "Kristr\u00f6m", "given": "Berit", "initials": "B"}, {"family": "Laudius", "given": "Maria", "initials": "M"}, {"family": "K\u00e4mpe", "given": "Olle", "initials": "O"}, {"family": "Isaksson", "given": "Magnus", "initials": "M"}, {"family": "Stenlid", "given": "Maria Halldin", "initials": "MH"}, {"family": "Gustafsson", "given": "Jan", "initials": "J"}, {"family": "Gebre-Medhin", "given": "Gennet", "initials": "G"}, {"family": "Bj\u00f6rnsdottir", "given": "Sigridur", "initials": "S"}, {"family": "Eriksson", "given": "Gabriel Nordling", "initials": "GN"}, {"family": "Janson", "given": "Annika", "initials": "A"}, {"family": "\u00c5kerman", "given": "Anna Karin", "initials": "AK"}, {"family": "Bergthorsdottir", "given": "Ragnhildur", "initials": "R"}, {"family": "Johannsson", "given": "Gudmundur", "initials": "G"}, {"family": "Lindskog", "given": "Emma", "initials": "E"}, {"family": "Elfving", "given": "Maria", "initials": "M"}, {"family": "Waldenstr\u00f6m", "given": "Erik", "initials": "E"}, {"family": "Svensson", "given": "Johan", "initials": "J"}, {"family": "Kalcheva", "given": "Zlatka", "initials": "Z"}, {"family": "Eliasson", "given": "Mats", "initials": "M"}, {"family": "Hedman", "given": "Erik", "initials": "E"}, {"family": "Wahlin", "given": "Karin", "initials": "K"}, {"family": "Magnusson", "given": "Anders", "initials": "A"}, {"family": "Ekman", "given": "Bertil", "initials": "B"}, {"family": "Munoz", "given": "Karel Duchen", "initials": "KD"}, {"family": "None", "given": "", "initials": ""}], "type": "journal-article", "published": "2018-01-01", "journal": {"volume": "103", "issn": "0021-972X", "issue": "1", "pages": "179-186", "title": "J. Clin. Endocrinol. Metab.", "issn-l": null}, "abstract": "Autoimmune polyendocrine syndrome type 1 (APS1) is a monogenic disorder that features autoimmune Addison disease as a major component. Although APS1 accounts for only a small fraction of all patients with Addison disease, early identification of these individuals is vital to prevent the potentially lethal complications of APS1.\n\nTo determine whether available serological and genetic markers are valuable screening tools for the identification of APS1 among patients diagnosed with Addison disease.\n\nWe systematically screened 677 patients with Addison disease enrolled in the Swedish Addison Registry for autoantibodies against interleukin-22 and interferon-\u03b14. Autoantibody-positive patients were investigated for clinical manifestations of APS1, additional APS1-specific autoantibodies, and DNA sequence and copy number variations of AIRE.\n\nIn total, 17 patients (2.5%) displayed autoantibodies against interleukin-22 and/or interferon-\u03b14, of which nine were known APS1 cases. Four patients previously undiagnosed with APS1 fulfilled clinical, genetic, and serological criteria. Hence, we identified four patients with undiagnosed APS1 with this screening procedure.\n\nWe propose that patients with Addison disease should be routinely screened for cytokine autoantibodies. Clinical or serological support for APS1 should warrant DNA sequencing and copy number analysis of AIRE to enable early diagnosis and prevention of lethal complications.", "doi": "10.1210/jc.2017-01957", "pmid": "29069385", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2018-04-24T12:29:05.572Z", "modified": "2024-01-16T13:48:47.139Z"}, {"entity": "publication", "iuid": "384d92a33adf43dab39328798c66dd44", "links": {"self": {"href": "https://publications.scilifelab.se/publication/384d92a33adf43dab39328798c66dd44.json"}, "display": {"href": "https://publications.scilifelab.se/publication/384d92a33adf43dab39328798c66dd44"}}, "title": "Protein-altering variants associated with body mass index implicate pathways that control energy intake and expenditure in obesity.", "authors": [{"family": "Turcot", "given": "Val\u00e9rie", "initials": "V"}, {"family": "Lu", "given": "Yingchang", "initials": "Y"}, {"family": "Highland", "given": "Heather M", "initials": "HM"}, {"family": "Schurmann", "given": "Claudia", "initials": "C"}, {"family": "Justice", "given": "Anne E", "initials": "AE"}, {"family": "Fine", "given": "Rebecca S", "initials": "RS"}, {"family": "Bradfield", "given": "Jonathan P", "initials": "JP"}, {"family": "Esko", "given": "T\u00f5nu", "initials": "T"}, {"family": "Giri", "given": "Ayush", "initials": "A"}, {"family": "Graff", "given": "Mariaelisa", "initials": "M"}, {"family": "Guo", "given": "Xiuqing", "initials": "X"}, {"family": "Hendricks", "given": "Audrey E", "initials": "AE"}, {"family": "Karaderi", "given": "Tugce", "initials": "T"}, {"family": "Lempradl", "given": "Adelheid", "initials": "A"}, {"family": "Locke", "given": "Adam E", "initials": "AE"}, {"family": "Mahajan", "given": "Anubha", "initials": "A"}, {"family": "Marouli", "given": "Eirini", "initials": "E"}, {"family": "Sivapalaratnam", "given": "Suthesh", "initials": "S"}, {"family": "Young", "given": "Kristin L", "initials": "KL"}, {"family": "Alfred", "given": "Tamuno", "initials": "T"}, {"family": "Feitosa", "given": "Mary F", "initials": "MF"}, {"family": "Masca", "given": "Nicholas G D", "initials": "NGD"}, {"family": "Manning", "given": "Alisa K", "initials": "AK"}, {"family": "Medina-Gomez", "given": "Carolina", "initials": "C"}, {"family": "Mudgal", "given": "Poorva", "initials": "P"}, {"family": "Ng", "given": "Maggie C Y", "initials": "MCY"}, {"family": "Reiner", "given": "Alex P", "initials": "AP"}, {"family": "Vedantam", "given": "Sailaja", "initials": "S"}, {"family": "Willems", "given": "Sara M", "initials": "SM"}, {"family": "Winkler", "given": "Thomas W", "initials": "TW"}, {"family": "Abecasis", "given": "Gon\u00e7alo", "initials": "G"}, {"family": "Aben", "given": "Katja K", "initials": "KK"}, {"family": "Alam", "given": "Dewan S", "initials": "DS"}, {"family": "Alharthi", "given": "Sameer E", "initials": "SE"}, {"family": "Allison", "given": "Matthew", "initials": "M"}, {"family": "Amouyel", "given": "Philippe", "initials": "P"}, {"family": "Asselbergs", "given": "Folkert W", "initials": "FW"}, {"family": "Auer", "given": "Paul L", "initials": "PL"}, {"family": "Balkau", "given": "Beverley", "initials": "B"}, {"family": "Bang", "given": "Lia E", "initials": "LE"}, {"family": "Barroso", "given": "In\u00eas", "initials": "I"}, {"family": "Bastarache", "given": "Lisa", "initials": "L"}, {"family": "Benn", "given": "Marianne", "initials": "M"}, {"family": "Bergmann", "given": "Sven", "initials": "S"}, {"family": "Bielak", "given": "Lawrence F", "initials": "LF"}, {"family": "Bl\u00fcher", "given": "Matthias", "initials": "M"}, {"family": "Boehnke", "given": "Michael", "initials": "M"}, {"family": "Boeing", "given": "Heiner", "initials": "H"}, {"family": "Boerwinkle", "given": "Eric", "initials": "E"}, {"family": "B\u00f6ger", "given": "Carsten 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{"family": "Wallentin", "given": "Lars", "initials": "L"}, {"family": "Wang", "given": "Feijie", "initials": "F"}, {"family": "Wang", "given": "Carol A", "initials": "CA"}, {"family": "Wang", "given": "Shuai", "initials": "S"}, {"family": "Wang", "given": "Yiqin", "initials": "Y"}, {"family": "Ware", "given": "Erin B", "initials": "EB"}, {"family": "Wareham", "given": "Nicholas J", "initials": "NJ"}, {"family": "Warren", "given": "Helen R", "initials": "HR"}, {"family": "Waterworth", "given": "Dawn M", "initials": "DM"}, {"family": "Wessel", "given": "Jennifer", "initials": "J"}, {"family": "White", "given": "Harvey D", "initials": "HD"}, {"family": "Willer", "given": "Cristen J", "initials": "CJ"}, {"family": "Wilson", "given": "James G", "initials": "JG"}, {"family": "Witte", "given": "Daniel R", "initials": "DR"}, {"family": "Wood", "given": "Andrew R", "initials": "AR"}, {"family": "Wu", "given": "Ying", "initials": "Y"}, {"family": "Yaghootkar", "given": "Hanieh", "initials": "H"}, {"family": "Yao", "given": "Jie", "initials": "J"}, {"family": "Yao", "given": "Pang", "initials": "P"}, {"family": "Yerges-Armstrong", "given": "Laura M", "initials": "LM"}, {"family": "Young", "given": "Robin", "initials": "R"}, {"family": "Zeggini", "given": "Eleftheria", "initials": "E"}, {"family": "Zhan", "given": "Xiaowei", "initials": "X"}, {"family": "Zhang", "given": "Weihua", "initials": "W"}, {"family": "Zhao", "given": "Jing Hua", "initials": "JH"}, {"family": "Zhao", "given": "Wei", "initials": "W"}, {"family": "Zhou", "given": "Wei", "initials": "W"}, {"family": "Zondervan", "given": "Krina T", "initials": "KT"}, {"family": "Rotter", "given": "Jerome I", "initials": "JI"}, {"family": "Pospisilik", "given": "John A", "initials": "JA"}, {"family": "Rivadeneira", "given": "Fernando", "initials": "F"}, {"family": "Borecki", "given": "Ingrid B", "initials": "IB"}, {"family": "Deloukas", "given": "Panos", "initials": "P"}, {"family": "Frayling", "given": "Timothy M", "initials": "TM"}, {"family": "Lettre", "given": "Guillaume", "initials": "G"}, {"family": "North", "given": "Kari E", "initials": "KE"}, {"family": "Lindgren", "given": "Cecilia M", "initials": "CM"}, {"family": "Hirschhorn", "given": "Joel N", "initials": "JN"}, {"family": "Loos", "given": "Ruth J F", "initials": "RJF"}, {"family": "CHD Exome+ Consortium", "given": "", "initials": ""}, {"family": "EPIC-CVD Consortium", "given": "", "initials": ""}, {"family": "ExomeBP Consortium", "given": "", "initials": ""}, {"family": "Global Lipids Genetic Consortium", "given": "", "initials": ""}, {"family": "GoT2D Genes Consortium", "given": "", "initials": ""}, {"family": "EPIC\u00a0InterAct\u00a0Consortium", "given": "", "initials": ""}, {"family": "INTERVAL Study", "given": "", "initials": ""}, {"family": "ReproGen Consortium", "given": "", "initials": ""}, {"family": "T2D-Genes Consortium", "given": "", "initials": ""}, {"family": "MAGIC Investigators", "given": "", "initials": ""}, {"family": "Understanding Society Scientific Group", "given": "", "initials": ""}], "type": "journal article", "published": "2018-01-00", "journal": {"volume": "50", "issn": "1546-1718", "issue": "1", "pages": "26-41", "title": "Nat. Genet.", "issn-l": "1061-4036"}, "abstract": "Genome-wide association studies (GWAS) have identified >250 loci for body mass index (BMI), implicating pathways related to neuronal biology. Most GWAS loci represent clusters of common, noncoding variants from which pinpointing causal genes remains challenging. Here we combined data from 718,734 individuals to discover rare and low-frequency (minor allele frequency (MAF) < 5%) coding variants associated with BMI. We identified 14 coding variants in 13 genes, of which 8 variants were in genes (ZBTB7B, ACHE, RAPGEF3, RAB21, ZFHX3, ENTPD6, ZFR2 and ZNF169) newly implicated in human obesity, 2 variants were in genes (MC4R and KSR2) previously observed\u00a0to be mutated in extreme obesity and 2 variants were in GIPR. The effect sizes of rare variants are ~10 times larger than those of common variants, with the largest effect observed in carriers of an MC4R mutation introducing a stop codon (p.Tyr35Ter, MAF = 0.01%), who weighed ~7 kg more than non-carriers. Pathway analyses based on the variants associated with BMI\u00a0confirm enrichment of neuronal genes and provide new evidence for adipocyte and energy expenditure biology, widening the potential of genetically supported therapeutic targets in obesity.", "doi": "10.1038/s41588-017-0011-x", "pmid": "29273807", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41588-017-0011-x"}, {"db": "pmc", "key": "PMC5945951"}, {"db": "mid", "key": "NIHMS920811"}], "notes": [], "created": "2018-01-02T15:37:53.466Z", "modified": "2024-01-16T13:48:47.176Z"}, {"entity": "publication", "iuid": "79a097bcd5394e09a35047c3eb9dac7a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/79a097bcd5394e09a35047c3eb9dac7a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/79a097bcd5394e09a35047c3eb9dac7a"}}, "title": "Population genomics of Mesolithic Scandinavia: Investigating early postglacial migration routes and high-latitude adaptation.", "authors": [{"family": "G\u00fcnther", "given": "Torsten", "initials": "T", "orcid": "0000-0001-9460-390X", "researcher": {"href": "https://publications.scilifelab.se/researcher/84159bff82a64a938bcff107f550c901.json"}}, {"family": "Malmstr\u00f6m", "given": "Helena", "initials": "H"}, {"family": "Svensson", "given": "Emma M", "initials": "EM"}, {"family": "Omrak", "given": "Ay\u00e7a", "initials": "A"}, {"family": "S\u00e1nchez-Quinto", "given": "Federico", "initials": "F"}, {"family": "K\u0131l\u0131n\u00e7", "given": "G\u00fcl\u015fah M", "initials": "GM"}, {"family": "Krzewi\u0144ska", "given": "Maja", "initials": "M"}, {"family": "Eriksson", "given": "Gunilla", "initials": "G"}, {"family": "Fraser", "given": "Magdalena", "initials": "M"}, {"family": "Edlund", "given": "Hanna", "initials": "H"}, {"family": "Munters", "given": "Arielle R", "initials": "AR"}, {"family": "Coutinho", "given": "Alexandra", "initials": "A"}, {"family": "Sim\u00f5es", "given": "Luciana G", "initials": "LG"}, {"family": "Vicente", "given": "M\u00e1rio", "initials": "M"}, {"family": "Sj\u00f6lander", "given": "Anders", "initials": "A"}, {"family": "Jansen Sellevold", "given": "Berit", "initials": "B"}, {"family": "J\u00f8rgensen", "given": "Roger", "initials": "R"}, {"family": "Claes", "given": "Peter", "initials": "P"}, {"family": "Shriver", "given": "Mark D", "initials": "MD"}, {"family": "Valdiosera", "given": "Cristina", "initials": "C", "orcid": "0000-0003-4948-2226", "researcher": {"href": "https://publications.scilifelab.se/researcher/113ef0dde1dd48e388f75c43bd672005.json"}}, {"family": "Netea", "given": "Mihai G", "initials": "MG"}, {"family": "Apel", "given": "Jan", "initials": "J"}, {"family": "Lid\u00e9n", "given": "Kerstin", "initials": "K"}, {"family": "Skar", "given": "Birgitte", "initials": "B"}, {"family": "Stor\u00e5", "given": "Jan", "initials": "J"}, {"family": "G\u00f6therstr\u00f6m", "given": "Anders", "initials": "A", "orcid": "0000-0001-6307-8188", "researcher": {"href": "https://publications.scilifelab.se/researcher/2a1a0a680ab8456cbf5a941e9718fd5a.json"}}, {"family": "Jakobsson", "given": "Mattias", "initials": "M", "orcid": "0000-0001-7840-7853", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a4abe0fcb20492d9ec849c9fbf58a71.json"}}], "type": "historical article", "published": "2018-01-00", "journal": {"volume": "16", "issn": "1545-7885", "issue": "1", "pages": "e2003703", "title": "PLoS Biol.", "issn-l": "1544-9173"}, "abstract": "Scandinavia was one of the last geographic areas in Europe to become habitable for humans after the Last Glacial Maximum (LGM). However, the routes and genetic composition of these postglacial migrants remain unclear. We sequenced the genomes, up to 57\u00d7 coverage, of seven hunter-gatherers excavated across Scandinavia and dated from 9,500-6,000 years before present (BP). Surprisingly, among the Scandinavian Mesolithic individuals, the genetic data display an east-west genetic gradient that opposes the pattern seen in other parts of Mesolithic Europe. Our results suggest two different early postglacial migrations into Scandinavia: initially from the south, and later, from the northeast. The latter followed the ice-free Norwegian north Atlantic coast, along which novel and advanced pressure-blade stone-tool techniques may have spread. These two groups met and mixed in Scandinavia, creating a genetically diverse population, which shows patterns of genetic adaptation to high latitude environments. These potential adaptations include high frequencies of low pigmentation variants and a gene region associated with physical performance, which shows strong continuity into modern-day northern Europeans.", "doi": "10.1371/journal.pbio.2003703", "pmid": "29315301", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC5760011"}, {"db": "pii", "key": "pbio.2003703"}], "notes": [], "created": "2018-01-11T10:03:24.352Z", "modified": "2024-01-16T13:48:47.193Z"}, {"entity": "publication", "iuid": "82538c64afec43e48eff87f29b1c79c9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/82538c64afec43e48eff87f29b1c79c9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/82538c64afec43e48eff87f29b1c79c9"}}, "title": "Genomic consequences of intensive inbreeding in an isolated wolf population", "authors": [{"family": "Kardos", "given": "Marty", "initials": "M"}, {"family": "\u00c5kesson", "given": "Mikael", "initials": "M"}, {"family": "Fountain", "given": "Toby", "initials": "T"}, {"family": "Flagstad", "given": "\u00d8ystein", "initials": "\u00d8"}, {"family": "Liberg", "given": "Olof", "initials": "O"}, {"family": "Olason", "given": "Pall", "initials": "P"}, {"family": "Sand", "given": "H\u00e5kan", "initials": "H"}, {"family": "Wabakken", "given": "Petter", "initials": "P"}, {"family": "Wikenros", "given": "Camilla", "initials": "C"}, {"family": "Ellegren", "given": "Hans", "initials": "H"}], "type": "journal-article", "published": "2018-01-00", "journal": {"volume": "2", "issn": "2397-334X", "issue": "1", "pages": "124-131", "title": "Nat Ecol Evol", "issn-l": "2397-334X"}, "abstract": "Inbreeding (mating between relatives) is a major concern for conservation as it decreases individual fitness and can increase the risk of population extinction. We used whole-genome resequencing of 97 grey wolves (Canis lupus) from the highly inbred Scandinavian wolf population to identify 'identical-by-descent' (IBD) chromosome segments as runs of homozygosity (ROH). This gave the high resolution required to precisely measure realized inbreeding as the IBD fraction of the genome in ROH (F \n            ROH). We found a striking pattern of complete or near-complete homozygosity of entire chromosomes in many individuals.\u00a0The majority of individual inbreeding was due to long IBD segments (>5 cM) originating from ancestors\u00a0\u226410 generations ago,\u00a0with 10 genomic regions showing very few ROH and forming candidate regions for containing loci contributing strongly to inbreeding depression. Inbreeding estimated with an extensive pedigree (F P) was strongly correlated with realized inbreeding measured with the entire genome (r 2\u2009=\u20090.86). However, inbreeding measured with the whole genome was more strongly correlated with multi-locus heterozygosity estimated with as few as 500 single nucleotide polymorphisms, and with F ROH estimated with as few as 10,000 single nucleotide polymorphisms, than with F P. These results document in fine detail the genomic consequences of intensive inbreeding in a population of conservation concern.", "doi": "10.1038/s41559-017-0375-4", "pmid": "29158554", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "BioProject", "description": "Whole-genome re-sequencing of Scandinavian wolves", "key": "PRJEB20635"}], "notes": [], "created": "2018-01-09T20:57:48.541Z", "modified": "2024-01-16T13:48:47.222Z"}, {"entity": "publication", "iuid": "431bba8f47de417d9d05371783803c07", "links": {"self": {"href": "https://publications.scilifelab.se/publication/431bba8f47de417d9d05371783803c07.json"}, "display": {"href": "https://publications.scilifelab.se/publication/431bba8f47de417d9d05371783803c07"}}, "title": "Epigenetic Changes in the CRH Gene are Related to Severity of Suicide Attempt and a General Psychiatric Risk Score in Adolescents.", "authors": [{"family": "Jokinen", "given": "Jussi", "initials": "J"}, {"family": "Bostr\u00f6m", "given": "Adrian E", "initials": "AE"}, {"family": "Dadfar", "given": "Ali", "initials": "A"}, {"family": "Ciuculete", "given": "Diana M", "initials": "DM"}, {"family": "Chatzittofis", "given": "Andreas", "initials": "A"}, {"family": "\u00c5sberg", "given": "Marie", "initials": "M"}, {"family": "Schi\u00f6th", "given": "Helgi B", "initials": "HB"}], "type": "journal article", "published": "2018-01-00", "journal": {"volume": "27", "issn": "2352-3964", "issue": null, "pages": "123-133", "title": "EBioMedicine", "issn-l": "2352-3964"}, "abstract": "The aim of this study, comprising 88 suicide attempters, was to identify hypothalamic-pituitary-adrenal (HPA) -axis coupled CpG-sites showing methylation shifts linked to severity of the suicide attempt. Candidate methylation loci were further investigated as risk loci for a general psychiatric risk score in two cohorts of adolescents (cohort 1 and 2). The genome-wide methylation pattern was measured in whole blood using the Illumina Infinium Methylation EPIC BeadChip. Subjects were stratified into high-risk and low-risk groups based on the severity of the suicidal behavior. We included CpG sites located within 2000 basepairs away from transcriptional start site of the following HPA-axis coupled genes: corticotropin releasing hormone (CRH), corticotropin releasing hormone binding protein (CRHBP), corticotropin releasing hormone receptor 1 (CRHR1), corticotropin releasing hormone receptor 2 (CRHR2), FK506-binding protein 51 (FKBP5) and the glucocorticoid receptor (NR3C1). The methylation state of two corticotropin releasing hormone (CRH)-associated CpG sites were significantly hypomethylated in the high-risk group of suicide attempters (n=31) (cg19035496 and cg23409074) (p<0.001). Adolescent cohort 1 and 2 consisted of 129 and 93 subjects, respectively, and were stratified by the in silico generated DAWBA measurements of a general psychiatric risk score into high-risk group (>~50% risk) or controls. In adolescent cohort 2, cg19035496 was hypermethylated in subjects with a high general psychiatric risk score. Our results show epigenetic changes in the CRH gene related to severity of suicide attempt in adults and a general psychiatric risk score in adolescents.", "doi": "10.1016/j.ebiom.2017.12.018", "pmid": "29277323", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "S2352-3964(17)30499-1"}, {"db": "pmc", "key": "PMC5828554"}], "notes": [], "created": "2018-01-02T15:37:52.855Z", "modified": "2020-01-21T13:56:10.927Z"}, {"entity": "publication", "iuid": "4b8cf50284584cbc8be8ef1a2e357666", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4b8cf50284584cbc8be8ef1a2e357666.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4b8cf50284584cbc8be8ef1a2e357666"}}, "title": "Abundant recent activity of retrovirus-like retrotransposons within and among flycatcher species implies a rich source of structural variation in songbird genomes", "authors": [{"family": "Suh", "given": "Alexander", "initials": "A"}, {"family": "Smeds", "given": "Linn\u00e9a", "initials": "L"}, {"family": "Ellegren", "given": "Hans", "initials": "H"}], "type": "journal-article", "published": "2018-01-00", "journal": {"volume": "27", "issn": "0962-1083", "issue": "1", "pages": "99-111", "title": "Mol Ecol", "issn-l": "0962-1083"}, "abstract": null, "doi": "10.1111/mec.14439", "pmid": "29171119", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2018-09-14T12:09:55.724Z", "modified": "2024-01-16T13:48:47.244Z"}, {"entity": "publication", "iuid": "999dde89b4de4148b7bf42e4407bdfc3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/999dde89b4de4148b7bf42e4407bdfc3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/999dde89b4de4148b7bf42e4407bdfc3"}}, "title": "Methylation-based estimated biological age and cardiovascular disease", "authors": [{"family": "Lind", "given": "Lars", "initials": "L"}, {"family": "Ingelsson", "given": "Erik", "initials": "E"}, {"family": "Sundstr\u00f6m", "given": "Johan", "initials": "J"}, {"family": "Siegbahn", "given": "Agneta", "initials": "A"}, {"family": "Lampa", "given": "Erik", "initials": "E"}], "type": "journal-article", "published": "2017-12-27", "journal": {"volume": null, "issn": "0014-2972", "issue": null, "pages": "e12872", "title": "Eur J Clin Invest", "issn-l": null}, "abstract": "DNA methylation changes over life at specific sites in the genome, which can be used to estimate \"biological age.\" The aim of this population-based longitudinal cohort study was to investigate the association between estimated biological age and incident cardiovascular disease (CVD).\n\nBased on formulas published by Hannum et\u00a0al and Horvath et\u00a0al, \"biological age\" was calculated using data from the Illumina 450k Bead Methylation chip in 832 participants free from cardiovascular disease in the Prospective Study of the Vasculature in Uppsala Seniors (PIVUS) study (50% women, all aged 70\u00a0years at the examination). The difference between estimated biological and chronological age was calculated (DiffAge).\n\nDuring 10\u00a0years of follow-up, 153 incident cases of cardiovascular disease occurred. In the sex-adjusted analyses, the Horvath estimation of DiffAge was significantly related to incident cardiovascular disease (HR 1.040, 95% CI 1.010-1.071, P\u00a0=\u00a0.0079). Thus, for each year of increased biological age, a 4% increased risk of future cardiovascular disease was observed. This relationship was still significant following adjustment for the traditional risk factors sex, BMI, diabetes, HDL and LDL-cholesterol, systolic blood pressure and smoking (HR 1.033, 95% CI 1.004-1.063, P\u00a0=\u00a0.024). No such significant association was found using the Hannum formula.\n\nDNA methylation-based estimation of \"biological age\" per Horvath was associated with incident cardiovascular disease.", "doi": "10.1111/eci.12872", "pmid": "29231988", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [], "notes": [], "created": "2018-01-02T15:37:53.992Z", "modified": "2020-01-21T13:56:13.762Z"}, {"entity": "publication", "iuid": "63ef8af7a9eb43c2837e989c5f0510a5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/63ef8af7a9eb43c2837e989c5f0510a5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/63ef8af7a9eb43c2837e989c5f0510a5"}}, "title": "A family-based genome-wide association study of chronic rhinosinusitis with nasal polyps implicates several genes in the disease pathogenesis", "authors": [{"family": "Bohman", "given": "Anton", "initials": "A"}, {"family": "Juodakis", "given": "Julius", "initials": "J"}, {"family": "Oscarsson", "given": "Martin", "initials": "M"}, {"family": "Bacelis", "given": "Jonas", "initials": "J"}, {"family": "Bende", "given": "Mats", "initials": "M"}, {"family": "Torinsson Naluai", "given": "\u00c5sa", "initials": "\u00c5"}], "type": "journal-article", "published": "2017-12-18", "journal": {"volume": "12", "issn": "1932-6203", "issue": "12", "pages": "e0185244", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": null, "doi": "10.1371/journal.pone.0185244", "pmid": "29253858", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "EGA", "description": "sequence reads", "key": "EGAD00010001447"}], "notes": [], "created": "2018-01-02T15:37:55.021Z", "modified": "2020-01-21T13:56:12.063Z"}, {"entity": "publication", "iuid": "fe02c4674f4d493aa4b9f694a14029a8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/fe02c4674f4d493aa4b9f694a14029a8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/fe02c4674f4d493aa4b9f694a14029a8"}}, "title": "Cancer risk susceptibility loci in a Swedish population.", "authors": [{"family": "Liu", "given": "Wen", "initials": "W"}, {"family": "Jiao", "given": "Xiang", "initials": "X"}, {"family": "Thutkawkorapin", "given": "Jessada", "initials": "J"}, {"family": "Mahdessian", "given": "Hovsep", "initials": "H"}, {"family": "Lindblom", "given": "Annika", "initials": "A"}], "type": "journal article", "published": "2017-12-15", "journal": {"volume": "8", "issn": "1949-2553", "issue": "66", "pages": "110300-110310", "title": "Oncotarget", "issn-l": "1949-2553"}, "abstract": "A germline mutation in cancer predisposing genes is known to increase the risk of more than one tumor type. In order to find loci associated with many types of cancer, a genome-wide association study (GWAS) was conducted, and 3,555 Swedish cancer cases and 15,581 controls were analyzed for 226,883 SNPs. The study used haplotype analysis instead of single SNP analysis in order to find putative founder effects. Haplotype association studies identified seven risk loci associated with cancer risk, on chromosomes 1, 7, 11, 14, 16, 17 and 21. Four of the haplotypes, on chromosomes 7, 14, 16 and 17, were confirmed in Swedish familial cancer cases. It was possible to perform exome sequencing in one patient for each of those four loci. No clear disease-causing exonic mutation was found in any of the four loci. Some of the candidate loci hold several cancer genes, suggesting that the risk associated with one locus could involve more than one gene associated with cancer risk. In summary, this study identified seven novel candidate loci associated with cancer risk. It was also suggested that cancer risk at one locus could depend on multiple contributing risk mutations/genes.", "doi": "10.18632/oncotarget.22687", "pmid": "29299148", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "22687"}, {"db": "pmc", "key": "PMC5746383"}], "notes": [], "created": "2018-01-09T13:55:52.931Z", "modified": "2021-06-21T15:01:18.619Z"}, {"entity": "publication", "iuid": "105ffce64b2d49f09088d4300f162663", "links": {"self": {"href": "https://publications.scilifelab.se/publication/105ffce64b2d49f09088d4300f162663.json"}, "display": {"href": "https://publications.scilifelab.se/publication/105ffce64b2d49f09088d4300f162663"}}, "title": "CELSR2 is a candidate susceptibility gene in idiopathic scoliosis", "authors": [{"family": "Einarsdottir", "given": "Elisabet", "initials": "E"}, {"family": "Grauers", "given": "Anna", "initials": "A"}, {"family": "Wang", "given": "Jingwen", "initials": "J"}, {"family": "Jiao", "given": "Hong", "initials": "H"}, {"family": "Escher", "given": "Stefan A", "initials": "SA"}, {"family": "Danielsson", "given": "Aina", "initials": "A"}, {"family": "Simony", "given": "Ane", "initials": "A"}, {"family": "Andersen", "given": "Mikkel", "initials": "M"}, {"family": "Christensen", "given": "Steen Bach", "initials": "SB"}, {"family": "\u00c5kesson", "given": "Kristina", "initials": "K"}, {"family": "Kou", "given": "Ikuyo", "initials": "I"}, {"family": "Khanshour", "given": "Anas M", "initials": "AM"}, {"family": "Ohlin", "given": "Acke", "initials": "A"}, {"family": "Wise", "given": "Carol", "initials": "C"}, {"family": "Ikegawa", "given": "Shiro", "initials": "S"}, {"family": "Kere", "given": "Juha", "initials": "J"}, {"family": "Gerdhem", "given": "Paul", "initials": "P"}], "type": "journal-article", "published": "2017-12-14", "journal": {"volume": "12", "issn": "1932-6203", "issue": "12", "pages": "e0189591", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": null, "doi": "10.1371/journal.pone.0189591", "pmid": "29240829", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "ENA", "description": "sequences", "key": "PRJEB22953"}], "notes": [], "created": "2018-01-02T15:37:54.529Z", "modified": "2020-01-21T13:56:12.055Z"}, {"entity": "publication", "iuid": "812369ae8ecd493db7a2b7cb3c8387f9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/812369ae8ecd493db7a2b7cb3c8387f9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/812369ae8ecd493db7a2b7cb3c8387f9"}}, "title": "Heterogeneous Patterns of Genetic Diversity and Differentiation in European and Siberian Chiffchaff ( Phylloscopus collybita abietinus/P. tristis).", "authors": [{"family": "Talla", "given": "Venkat", "initials": "V"}, {"family": "Kalsoom", "given": "Faheema", "initials": "F"}, {"family": "Shipilina", "given": "Daria", "initials": "D"}, {"family": "Marova", "given": "Irina", "initials": "I"}, {"family": "Backstr\u00f6m", "given": "Niclas", "initials": "N", "orcid": "0000-0002-0961-8427", "researcher": {"href": "https://publications.scilifelab.se/researcher/674a0756dcf44e79ac6a6a2499b01760.json"}}], "type": "journal article", "published": "2017-12-04", "journal": {"volume": "7", "issn": "2160-1836", "issue": "12", "pages": "3983-3998", "title": "G3 (Bethesda)", "issn-l": "2160-1836"}, "abstract": "Identification of candidate genes for trait variation in diverging lineages and characterization of mechanistic underpinnings of genome differentiation are key steps toward understanding the processes underlying the formation of new species. Hybrid zones provide a valuable resource for such investigations, since they allow us to study how genomes evolve as species exchange genetic material and to associate particular genetic regions with phenotypic traits of interest. Here, we use whole-genome resequencing of both allopatric and hybridizing populations of the European ( Phylloscopus collybita abietinus) and the Siberian chiffchaff (P. tristis)-two recently diverged species which differ in morphology, plumage, song, habitat, and migration-to quantify the regional variation in genome-wide genetic diversity and differentiation, and to identify candidate regions for trait variation. We find that the levels of diversity, differentiation, and divergence are highly heterogeneous, with significantly reduced global differentiation, and more pronounced differentiation peaks in sympatry than in allopatry. This pattern is consistent with regional differences in effective population size and recurrent background selection or selective sweeps reducing the genetic diversity in specific regions prior to lineage divergence, but the data also suggest that postdivergence selection has resulted in increased differentiation and fixed differences in specific regions. We find that hybridization and backcrossing is common in sympatry, and that phenotype is a poor predictor of the genomic composition of sympatric birds. The combination of a differentiation scan approach with identification of fixed differences pinpoint a handful of candidate regions that might be important for trait variation between the two species.", "doi": "10.1534/g3.117.300152", "pmid": "29054864", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pii", "key": "g3.117.300152"}, {"db": "pmc", "key": "PMC5714495"}], "notes": [], "created": "2017-11-03T16:22:15.701Z", "modified": "2021-06-21T14:59:08.098Z"}, {"entity": "publication", "iuid": "a3142a603e7a4accb9d367851765f150", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a3142a603e7a4accb9d367851765f150.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a3142a603e7a4accb9d367851765f150"}}, "title": "Shared genetic origin of asthma, hay fever and eczema elucidates allergic disease biology.", "authors": [{"family": "Ferreira", "given": "Manuel A", "initials": "MA", "orcid": "0000-0001-9059-1825", "researcher": {"href": "https://publications.scilifelab.se/researcher/d27aef5015494b018b22352125c0225d.json"}}, {"family": "Vonk", "given": "Judith M", "initials": "JM"}, {"family": "Baurecht", "given": "Hansj\u00f6rg", "initials": "H"}, {"family": "Marenholz", "given": "Ingo", "initials": "I"}, {"family": "Tian", "given": "Chao", "initials": "C"}, {"family": "Hoffman", "given": "Joshua D", "initials": "JD"}, {"family": "Helmer", "given": "Quinta", "initials": "Q"}, {"family": "Tillander", "given": "Annika", "initials": "A"}, {"family": "Ullemar", "given": "Vilhelmina", "initials": "V"}, {"family": "van Dongen", "given": "Jenny", "initials": "J"}, {"family": "Lu", "given": "Yi", "initials": "Y"}, {"family": "R\u00fcschendorf", "given": "Franz", "initials": "F", "orcid": "0000-0001-5640-810X", "researcher": {"href": "https://publications.scilifelab.se/researcher/e02ac817ef224343ba9d9a9ac7cdc43e.json"}}, {"family": "Esparza-Gordillo", "given": "Jorge", "initials": "J"}, {"family": "Medway", "given": "Chris W", "initials": "CW"}, {"family": "Mountjoy", "given": "Edward", "initials": "E", "orcid": "0000-0002-0626-1821", "researcher": {"href": "https://publications.scilifelab.se/researcher/16fc9f5da5c34418a207b9bd468a0403.json"}}, {"family": "Burrows", "given": "Kimberley", "initials": "K"}, {"family": "Hummel", "given": "Oliver", "initials": "O"}, {"family": "Grosche", "given": "Sarah", "initials": "S"}, {"family": "Brumpton", "given": "Ben M", "initials": "BM"}, {"family": "Witte", "given": "John S", "initials": "JS"}, {"family": "Hottenga", "given": "Jouke-Jan", "initials": "JJ"}, {"family": "Willemsen", "given": "Gonneke", "initials": "G"}, {"family": "Zheng", "given": "Jie", "initials": "J"}, {"family": "Rodr\u00edguez", "given": "Elke", "initials": "E"}, {"family": "Hotze", "given": "Melanie", "initials": "M"}, {"family": "Franke", "given": "Andre", "initials": "A", "orcid": "0000-0003-1530-5811", "researcher": {"href": "https://publications.scilifelab.se/researcher/8fffe3df068c4283a8b8b583717e6bb6.json"}}, {"family": "Revez", "given": "Joana A", "initials": "JA"}, {"family": "Beesley", "given": "Jonathan", "initials": "J"}, {"family": "Matheson", "given": "Melanie C", "initials": "MC"}, {"family": "Dharmage", "given": "Shyamali C", "initials": "SC"}, {"family": "Bain", "given": "Lisa M", "initials": "LM"}, {"family": "Fritsche", "given": "Lars G", "initials": "LG"}, {"family": "Gabrielsen", "given": "Maiken E", "initials": "ME"}, {"family": "Balliu", "given": "Brunilda", "initials": "B"}, {"family": "23andMe Research Team", "given": "", "initials": ""}, {"family": "AAGC collaborators", "given": "", "initials": ""}, {"family": "BIOS consortium", "given": "", "initials": ""}, {"family": "LifeLines Cohort Study", "given": "", "initials": ""}, {"family": "Nielsen", "given": "Jonas B", "initials": "JB", "orcid": "0000-0002-6654-2852", "researcher": {"href": "https://publications.scilifelab.se/researcher/4e2c20e3817a4c79b8ae7110d197e69d.json"}}, {"family": "Zhou", "given": "Wei", "initials": "W"}, {"family": "Hveem", "given": "Kristian", "initials": "K"}, {"family": "Langhammer", "given": "Arnulf", "initials": "A"}, {"family": "Holmen", "given": "Oddgeir L", "initials": "OL"}, {"family": "L\u00f8set", "given": "Mari", "initials": "M"}, {"family": "Abecasis", "given": "Gon\u00e7alo R", "initials": "GR"}, {"family": "Willer", "given": "Cristen J", "initials": "CJ", "orcid": "0000-0001-5645-4966", "researcher": {"href": "https://publications.scilifelab.se/researcher/b3a8e1d33146452b87e7e21eb5339f80.json"}}, {"family": "Arnold", "given": "Andreas", "initials": "A"}, {"family": "Homuth", "given": "Georg", "initials": "G"}, {"family": "Schmidt", "given": "Carsten O", "initials": "CO"}, {"family": "Thompson", "given": "Philip J", "initials": "PJ"}, {"family": "Martin", "given": "Nicholas G", "initials": "NG"}, {"family": "Duffy", "given": "David L", "initials": "DL", "orcid": "0000-0002-8875-2308", "researcher": {"href": "https://publications.scilifelab.se/researcher/dce1a0fd17154c73b30f23c2a58bd390.json"}}, {"family": "Novak", "given": "Natalija", "initials": "N"}, {"family": "Schulz", "given": "Holger", "initials": "H"}, {"family": "Karrasch", "given": "Stefan", "initials": "S"}, {"family": "Gieger", "given": "Christian", "initials": "C", "orcid": "0000-0001-6986-9554", "researcher": {"href": "https://publications.scilifelab.se/researcher/86f44e76061c403fadd97b768e2a7e62.json"}}, {"family": "Strauch", "given": "Konstantin", "initials": "K"}, {"family": "Melles", "given": "Ronald B", "initials": "RB"}, {"family": "Hinds", "given": "David A", "initials": "DA", "orcid": "0000-0002-4911-803X", "researcher": {"href": "https://publications.scilifelab.se/researcher/ba56969917d14df0bd923a54ce9f911d.json"}}, {"family": "H\u00fcbner", "given": "Norbert", "initials": "N", "orcid": "0000-0002-1218-6223", "researcher": {"href": "https://publications.scilifelab.se/researcher/1d84f34739c743838cea107286522e42.json"}}, {"family": "Weidinger", "given": "Stephan", "initials": "S"}, {"family": "Magnusson", "given": "Patrik K E", "initials": "PKE"}, {"family": "Jansen", "given": "Rick", "initials": "R", "orcid": "0000-0002-3333-6737", "researcher": {"href": "https://publications.scilifelab.se/researcher/bcd392c9b9784ebe8c8730e05463377a.json"}}, {"family": "Jorgenson", "given": "Eric", "initials": "E", "orcid": "0000-0002-5829-8191", "researcher": {"href": "https://publications.scilifelab.se/researcher/38ef095c3de94bbc884d80c8949d16f5.json"}}, {"family": "Lee", "given": "Young-Ae", "initials": "YA"}, {"family": "Boomsma", "given": "Dorret I", "initials": "DI", "orcid": "0000-0002-7099-7972", "researcher": {"href": "https://publications.scilifelab.se/researcher/4b66ab2525fd4a468e7a4ad14c955cb4.json"}}, {"family": "Almqvist", "given": "Catarina", "initials": "C", "orcid": "0000-0002-1045-1898", "researcher": {"href": "https://publications.scilifelab.se/researcher/c7b0899897f046499272a916fd0c6ba5.json"}}, {"family": "Karlsson", "given": "Robert", "initials": "R", "orcid": "0000-0002-8949-2587", "researcher": {"href": "https://publications.scilifelab.se/researcher/9df14bf33f3342408d624caa70d45b7c.json"}}, {"family": "Koppelman", "given": "Gerard H", "initials": "GH", "orcid": "0000-0001-8567-3252", "researcher": {"href": "https://publications.scilifelab.se/researcher/cd7e0158050a4ab3860e288c4eb9ae87.json"}}, {"family": "Paternoster", "given": "Lavinia", "initials": "L", "orcid": "0000-0003-2514-0889", "researcher": {"href": "https://publications.scilifelab.se/researcher/826f9852c56d4922ab255ab83d26faa8.json"}}], "type": "journal article", "published": "2017-12-00", "journal": {"volume": "49", "issn": "1546-1718", "issue": "12", "title": "Nat. Genet.", "pages": "1752-1757", "issn-l": "1061-4036"}, "abstract": "Asthma, hay fever (or allergic rhinitis) and eczema (or atopic dermatitis) often coexist in the same individuals, partly because of a shared genetic origin. To identify shared risk variants, we performed a genome-wide association study (GWAS; n = 360,838) of a broad allergic disease phenotype that considers the presence of any one of these three diseases. We identified 136 independent risk variants (P < 3 \u00d7 10-8), including 73 not previously reported, which implicate 132 nearby genes in allergic disease pathophysiology. Disease-specific effects were detected for only six variants, confirming that most represent shared risk factors. Tissue-specific heritability and biological process enrichment analyses suggest that shared risk variants influence lymphocyte-mediated immunity. Six target genes provide an opportunity for drug repositioning, while for 36 genes CpG methylation was found to influence transcription independently of genetic effects. Asthma, hay fever and eczema partly coexist because they share many genetic risk variants that dysregulate the expression of immune-related genes.", "doi": "10.1038/ng.3985", "pmid": "29083406", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "mid", "key": "EMS74439"}, {"db": "pmc", "key": "PMC5989923"}, {"db": "pii", "key": "ng.3985"}], "notes": [], "created": "2017-11-09T16:02:23.965Z", "modified": "2023-06-19T10:57:00.779Z"}, {"entity": "publication", "iuid": "772771bb3bbc4cbcb15ffb55d59a1acb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/772771bb3bbc4cbcb15ffb55d59a1acb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/772771bb3bbc4cbcb15ffb55d59a1acb"}}, "title": "RNA-sequence data normalization through in silico prediction of reference genes: the bacterial response to DNA damage as case study", "authors": [{"family": "Berghoff", "given": "Bork A", "initials": "BA"}, {"family": "Karlsson", "given": "Torgny", "initials": "T"}, {"family": "K\u00e4llman", "given": "Thomas", "initials": "T"}, {"family": "Wagner", "given": "E Gerhart H", "initials": "EGH"}, {"family": "Grabherr", "given": "Manfred G", "initials": "MG"}], "type": "journal-article", "published": "2017-12-00", "journal": {"volume": "10", "issn": "1756-0381", "issue": "1", "pages": null, "title": "BioData Mining", "issn-l": "1756-0381"}, "abstract": "Measuring how gene expression changes in the course of an experiment assesses how an organism responds on a molecular level. Sequencing of RNA molecules, and their subsequent quantification, aims to assess global gene expression changes on the RNA level (transcriptome). While advances in high-throughput RNA-sequencing (RNA-seq) technologies allow for inexpensive data generation, accurate post-processing and normalization across samples is required to eliminate any systematic noise introduced by the biochemical and/or technical processes. Existing methods thus either normalize on selected known reference genes that are invariant in expression across the experiment, assume that the majority of genes are invariant, or that the effects of up- and down-regulated genes cancel each other out during the normalization.\n\nHere, we present a novel method, \n                moose\n                         , which predicts invariant genes in silico through a dynamic programming (DP) scheme and applies a quadratic normalization based on this subset. The method allows for specifying a set of known or experimentally validated invariant genes, which guides the DP. We experimentally verified the predictions of this method in the bacterium 2\n                    Escherichia coli, and show how moose\n                         is able to (i) estimate the expression value distances between RNA-seq samples, (ii) reduce the variation of expression values across all samples, and (iii) to subsequently reveal new functional groups of genes during the late stages of DNA damage. We further applied the method to three eukaryotic data sets, on which its performance compares favourably to other methods. The software is implemented in C++ and is publicly available from http://grabherr.github.io/moose2/.2\n\nThe proposed RNA-seq normalization method, \n            moose\n                         , is a valuable alternative to existing methods, with two major advantages: (i) in silico prediction of invariant genes provides a list of potential reference genes for downstream analyses, and (ii) non-linear artefacts in RNA-seq data are handled adequately to minimize variations between replicates.2", "doi": "10.1186/s13040-017-0150-8", "pmid": "28878825", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [], "notes": [], "created": "2017-10-30T09:27:45.065Z", "modified": "2024-01-16T13:48:47.258Z"}, {"entity": "publication", "iuid": "21aaff4ed48e45438079d2d7652600df", "links": {"self": {"href": "https://publications.scilifelab.se/publication/21aaff4ed48e45438079d2d7652600df.json"}, "display": {"href": "https://publications.scilifelab.se/publication/21aaff4ed48e45438079d2d7652600df"}}, "title": "Overexpression of PaNAC03, a stress induced NAC gene family transcription factor in Norway spruce leads to reduced flavonol biosynthesis and aberrant embryo development", "authors": [{"family": "Dalman", "given": "Kerstin", "initials": "K"}, {"family": "Wind", "given": "Julia Johanna", "initials": "JJ"}, {"family": "Nemesio-Gorriz", "given": "Miguel", "initials": "M"}, {"family": "Hammerbacher", "given": "Almuth", "initials": "A"}, {"family": "Lund\u00e9n", "given": "Karl", "initials": "K"}, {"family": "Ezcurra", "given": "Ines", "initials": "I"}, {"family": "Elfstrand", "given": "Malin", "initials": "M"}], "type": "journal-article", "published": "2017-12-00", "journal": {"volume": "17", "issn": "1471-2229", "issue": "1", "pages": null, "title": "BMC Plant Biol.", "issn-l": "1471-2229"}, "abstract": null, "doi": "10.1186/s12870-016-0952-8", "pmid": "28061815", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "BioProject", "description": "Picea abies cell lines transcriptome project", "key": "PRJNA350779"}, {"db": "SRA", "description": null, "key": "SRP093366"}], "notes": [], "created": "2018-01-09T20:49:55.957Z", "modified": "2020-01-21T13:56:11.999Z"}, {"entity": "publication", "iuid": "8be977a6fe724420894f3df784d9aff1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8be977a6fe724420894f3df784d9aff1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8be977a6fe724420894f3df784d9aff1"}}, "title": "Novel risk genes for systemic lupus erythematosus predicted by random forest classification", "authors": 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{"family": "Esberg", "given": "Anders", "initials": "A"}, {"family": "Sheng", "given": "Nongfei", "initials": "N"}, {"family": "M\u00e5rell", "given": "Lena", "initials": "L"}, {"family": "L\u00f6fgren-Burstr\u00f6m", "given": "Anna", "initials": "A"}, {"family": "Danielsson", "given": "Karin", "initials": "K"}, {"family": "K\u00e4llest\u00e5l", "given": "Carina", "initials": "C"}], "type": "journal-article", "published": "2017-12-00", "journal": {"volume": "26", "issn": "2352-3964", "issue": null, "pages": "38-46", "title": "EBioMedicine", "issn-l": "2352-3964"}, "abstract": null, "doi": "10.1016/j.ebiom.2017.11.019", "pmid": "29191562", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [], "notes": [], "created": "2018-01-09T13:55:52.544Z", "modified": "2020-01-21T13:56:12.007Z"}, {"entity": "publication", "iuid": "79290fe0255d450fbbb5b0817adda42a", "links": {"self": {"href": 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"49", "issn": "0049-4747", "issue": "8", "pages": "1657-1662", "title": "Trop Anim Health Prod", "issn-l": null}, "abstract": null, "doi": "10.1007/s11250-017-1373-x", "pmid": "28801813", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [], "notes": [], "created": "2018-01-09T13:55:54.961Z", "modified": "2020-01-21T13:56:12.030Z"}, {"entity": "publication", "iuid": "b16e57c3e23a42a7a678a2b216cebed3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b16e57c3e23a42a7a678a2b216cebed3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b16e57c3e23a42a7a678a2b216cebed3"}}, "title": "Correspondence on Lovell et al.: identification of chicken genes previously assumed to be evolutionarily lost", "authors": [{"family": "Bornel\u00f6v", "given": "Susanne", "initials": "S"}, {"family": "Seroussi", "given": "Eyal", "initials": "E"}, {"family": "Yosefi", "given": "Sara", "initials": "S"}, {"family": "Pendavis", "given": "Ken", "initials": "K"}, {"family": "Burgess", "given": "Shane C", "initials": "SC"}, {"family": "Grabherr", "given": "Manfred", "initials": "M"}, {"family": "Friedman-Einat", "given": "Miriam", "initials": "M"}, {"family": "Andersson", "given": "Leif", "initials": "L"}], "type": "journal-article", "published": "2017-12-00", "journal": {"volume": "18", "issn": "1474-760X", "issue": "1", "pages": null, "title": "Genome Biol.", "issn-l": "1474-7596"}, "abstract": null, "doi": "10.1186/s13059-017-1231-1", "pmid": "28615067", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2017-11-02T18:40:30.126Z", "modified": "2024-01-16T13:48:47.303Z"}, {"entity": "publication", "iuid": "61c4edd44f7c449aac10aa3423c4a688", "links": {"self": {"href": "https://publications.scilifelab.se/publication/61c4edd44f7c449aac10aa3423c4a688.json"}, "display": {"href": "https://publications.scilifelab.se/publication/61c4edd44f7c449aac10aa3423c4a688"}}, "title": "Southern African ancient genomes estimate modern human divergence to 350,000 to 260,000 years ago.", "authors": [{"family": "Schlebusch", "given": "Carina M", "initials": "CM", "orcid": "0000-0002-8160-9621", "researcher": {"href": "https://publications.scilifelab.se/researcher/682f10853c1145649b8c76680605dd9b.json"}}, {"family": "Malmstr\u00f6m", "given": "Helena", "initials": "H", "orcid": "0000-0002-6456-8055", "researcher": {"href": "https://publications.scilifelab.se/researcher/3b3397b2842142bea34c222f6683c0eb.json"}}, {"family": "G\u00fcnther", "given": "Torsten", "initials": "T", "orcid": "0000-0001-9460-390X", "researcher": {"href": "https://publications.scilifelab.se/researcher/84159bff82a64a938bcff107f550c901.json"}}, {"family": "Sj\u00f6din", "given": "Per", "initials": "P"}, {"family": "Coutinho", "given": "Alexandra", "initials": "A", "orcid": "0000-0002-1756-9469", "researcher": {"href": "https://publications.scilifelab.se/researcher/1863fb821bdf444ba26e351f764e4a70.json"}}, {"family": "Edlund", "given": "Hanna", "initials": "H", "orcid": "0000-0003-3784-4285", "researcher": {"href": "https://publications.scilifelab.se/researcher/d56063f091264c0587c973a82335c578.json"}}, {"family": "Munters", "given": "Arielle R", "initials": "AR", "orcid": "0000-0003-1512-6565", "researcher": {"href": "https://publications.scilifelab.se/researcher/5e089ee0008a4ea3a9603fa011f973de.json"}}, {"family": "Vicente", "given": "M\u00e1rio", "initials": "M", "orcid": "0000-0002-9122-4530", "researcher": {"href": "https://publications.scilifelab.se/researcher/603244b141da49dfa9ff3a8d17f42b70.json"}}, {"family": "Steyn", "given": "Maryna", "initials": "M", "orcid": "0000-0002-0215-9723", "researcher": {"href": "https://publications.scilifelab.se/researcher/9d9921b3dba248eab7b85488dda530ad.json"}}, {"family": "Soodyall", "given": "Himla", "initials": "H"}, {"family": "Lombard", "given": "Marlize", "initials": "M", "orcid": "0000-0002-0675-0414", "researcher": {"href": "https://publications.scilifelab.se/researcher/e04e97bbc9914f358864988174b9b58d.json"}}, {"family": "Jakobsson", "given": "Mattias", "initials": "M", "orcid": "0000-0001-7840-7853", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a4abe0fcb20492d9ec849c9fbf58a71.json"}}], "type": "journal article", "published": "2017-11-03", "journal": {"volume": "358", "issn": "1095-9203", "issue": "6363", "pages": "652-655", "title": "Science", "issn-l": "0036-8075"}, "abstract": "Southern Africa is consistently placed as a potential region for the evolution of Homo sapiens We present genome sequences, up to 13x coverage, from seven ancient individuals from KwaZulu-Natal, South Africa. The remains of three Stone Age hunter-gatherers (about 2000 years old) were genetically similar to current-day southern San groups, and those of four Iron Age farmers (300 to 500 years old) were genetically similar to present-day Bantu-language speakers. We estimate that all modern-day Khoe-San groups have been influenced by 9 to 30% genetic admixture from East Africans/Eurasians. Using traditional and new approaches, we estimate the first modern human population divergence time to between 350,000 and 260,000 years ago. This estimate increases the deepest divergence among modern humans, coinciding with anatomical developments of archaic humans into modern humans, as represented in the local fossil record.", "doi": "10.1126/science.aao6266", "pmid": "28971970", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "science.aao6266"}], "notes": [], "created": "2017-10-30T09:27:46.012Z", "modified": "2024-01-16T13:48:47.317Z"}, {"entity": "publication", "iuid": "ecc7551bf07d4ecf930ff13d013aeee3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ecc7551bf07d4ecf930ff13d013aeee3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ecc7551bf07d4ecf930ff13d013aeee3"}}, "title": "RNA-Seq de novo assembly and differential transcriptome analysis of the nematode Ascaridia galli in relation to in vivo exposure to flubendazole", "authors": [{"family": "Martis", "given": "Mihaela M", "initials": "MM"}, {"family": "Tarbiat", "given": "Behdad", "initials": "B"}, {"family": "Tyd\u00e9n", "given": "Eva", "initials": "E"}, {"family": "Jansson", "given": "D\u00e9sir\u00e9e S", "initials": "DS"}, {"family": "H\u00f6glund", "given": "Johan", "initials": "J"}], "type": "journal-article", "published": "2017-11-03", "journal": {"volume": "12", "issn": "1932-6203", "issue": "11", "pages": "e0185182", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": null, "doi": "10.1371/journal.pone.0185182", "pmid": "29099835", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "BioProject", "description": "RNA-seq of the nematode Ascaridia galli exposed to flubendazole against untreated control", "key": "PRJEB20558"}], "notes": [], "created": "2017-11-06T13:08:22.384Z", "modified": "2020-01-21T13:56:17.125Z"}, {"entity": "publication", "iuid": "f892ff63669141bc8f46e7fd8d8fde48", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f892ff63669141bc8f46e7fd8d8fde48.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f892ff63669141bc8f46e7fd8d8fde48"}}, "title": "SweGen: a whole-genome data resource of genetic variability in a cross-section of the Swedish population.", "authors": [{"family": "Ameur", "given": "Adam", "initials": "A", "orcid": "0000-0001-6085-6749", "researcher": {"href": "https://publications.scilifelab.se/researcher/e960811513664a78b2804a00ee70f7c3.json"}}, {"family": "Dahlberg", "given": "Johan", "initials": "J"}, {"family": "Olason", "given": "Pall", "initials": "P"}, {"family": "Vezzi", "given": "Francesco", "initials": "F"}, {"family": "Karlsson", "given": "Robert", "initials": "R", "orcid": "0000-0002-8949-2587", "researcher": {"href": "https://publications.scilifelab.se/researcher/9df14bf33f3342408d624caa70d45b7c.json"}}, {"family": "Martin", "given": "Marcel", "initials": "M"}, {"family": "Viklund", "given": "Johan", "initials": "J"}, {"family": "K\u00e4h\u00e4ri", "given": "Andreas Kusalananda", "initials": "AK"}, {"family": "Lundin", "given": "P\u00e4r", "initials": "P"}, {"family": "Che", "given": "Huiwen", "initials": "H"}, {"family": "Thutkawkorapin", "given": "Jessada", "initials": "J"}, {"family": "Eisfeldt", "given": "Jesper", "initials": "J"}, {"family": "Lampa", "given": "Samuel", "initials": "S"}, {"family": "Dahlberg", "given": "Mats", "initials": "M"}, {"family": "Hagberg", "given": "Jonas", "initials": "J", "orcid": "0000-0003-2370-6025", "researcher": {"href": "https://publications.scilifelab.se/researcher/181649773b3e451981f5ffb2da4c60b9.json"}}, {"family": "Jareborg", "given": "Niclas", "initials": "N", "orcid": "0000-0002-4520-044X", "researcher": {"href": "https://publications.scilifelab.se/researcher/09533c4bd4174ecab9ba866d22a1e585.json"}}, {"family": "Liljedahl", "given": "Ulrika", "initials": "U", "orcid": "0000-0002-1250-392X", "researcher": {"href": "https://publications.scilifelab.se/researcher/241618974ae142b38e5fe84236819f2b.json"}}, {"family": "Jonasson", "given": "Inger", "initials": "I"}, {"family": "Johansson", "given": "\u00c5sa", "initials": "\u00c5"}, {"family": "Feuk", "given": "Lars", "initials": "L", "orcid": "0000-0003-2355-2919", "researcher": {"href": "https://publications.scilifelab.se/researcher/3eb2f826b3554d4b9971bf0766b275c4.json"}}, {"family": "Lundeberg", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a4e6ca0f29b4ead8569e2729481c3e0.json"}}, {"family": "Syv\u00e4nen", "given": "Ann-Christine", "initials": "AC", "orcid": "0000-0002-9681-9146", "researcher": {"href": "https://publications.scilifelab.se/researcher/f7012e35025543379380cb90efd71243.json"}}, {"family": "Lundin", "given": "Sverker", "initials": "S"}, {"family": "Nilsson", "given": "Daniel", "initials": "D"}, {"family": "Nystedt", "given": "Bj\u00f6rn", "initials": "B", "orcid": "0000-0001-7809-7664", "researcher": {"href": "https://publications.scilifelab.se/researcher/f0af5a168baa4b00a6fab8d3447ebfb4.json"}}, {"family": "Magnusson", "given": "Patrik Ke", "initials": "PK"}, {"family": "Gyllensten", "given": "Ulf", "initials": "U"}], "type": "journal article", "published": "2017-11-00", "journal": {"volume": "25", "issn": "1476-5438", "issue": "11", "pages": "1253-1260", "title": "Eur. J. Hum. Genet.", "issn-l": "1018-4813"}, "abstract": "Here we describe the SweGen data set, a comprehensive map of genetic variation in the Swedish population. These data represent a basic resource for clinical genetics laboratories as well as for sequencing-based association studies by providing information on genetic variant frequencies in a cohort that is well matched to national patient cohorts. To select samples for this study, we first examined the genetic structure of the Swedish population using high-density SNP-array data from a nation-wide cohort of over 10 000 Swedish-born individuals included in the Swedish Twin Registry. A total of 1000 individuals, reflecting a cross-section of the population and capturing the main genetic structure, were selected for whole-genome sequencing. Analysis pipelines were developed for automated alignment, variant calling and quality control of the sequencing data. This resulted in a genome-wide collection of aggregated variant frequencies in the Swedish population that we have made available to the scientific community through the website https://swefreq.nbis.se. A total of 29.2 million single-nucleotide variants and 3.8 million indels were detected in the 1000 samples, with 9.9 million of these variants not present in current databases. Each sample contributed with an average of 7199 individual-specific variants. In addition, an average of 8645 larger structural variants (SVs) were detected per individual, and we demonstrate that the population frequencies of these SVs can be used for efficient filtering analyses. Finally, our results show that the genetic diversity within Sweden is substantial compared with the diversity among continental European populations, underscoring the relevance of establishing a local reference data set.", "doi": "10.1038/ejhg.2017.130", "pmid": "28832569", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "NGI Stockholm (Genomics Production)": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Uppsala (Uppsala Genome Center)": "Collaborative", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "ejhg2017130"}, {"db": "pmc", "key": "PMC5765326"}], "notes": [], "created": "2017-08-24T14:18:14.989Z", "modified": "2024-01-16T13:48:47.338Z"}, {"entity": "publication", "iuid": "13b3499da98c4b919399fe6ad45b6104", "links": {"self": {"href": "https://publications.scilifelab.se/publication/13b3499da98c4b919399fe6ad45b6104.json"}, "display": {"href": "https://publications.scilifelab.se/publication/13b3499da98c4b919399fe6ad45b6104"}}, "title": "Rare X Chromosome Abnormalities in Systemic Lupus Erythematosus and Sj\u00f6gren's Syndrome.", "authors": [{"family": "Sharma", "given": "Rohan", "initials": "R"}, {"family": "Harris", "given": "Valerie M", "initials": "VM"}, {"family": "Cavett", "given": "Joshua", "initials": "J"}, {"family": "Kurien", "given": "Biji T", "initials": "BT"}, {"family": "Liu", "given": "Ke", "initials": "K"}, {"family": "Koelsch", "given": "Kristi A", "initials": "KA"}, {"family": "Fayaaz", "given": "Anum", "initials": "A"}, {"family": "Chaudhari", "given": "Kaustubh S", "initials": "KS"}, {"family": "Radfar", "given": "Lida", "initials": "L"}, {"family": "Lewis", "given": "David", "initials": "D"}, {"family": "Stone", "given": "Donald U", "initials": "DU"}, {"family": "Kaufman", "given": "C Erick", "initials": "CE"}, {"family": "Li", "given": "Shibo", "initials": "S"}, {"family": "Segal", "given": "Barbara", "initials": "B"}, {"family": "Wallace", "given": "Daniel J", "initials": "DJ"}, {"family": "Weisman", "given": "Michael H", "initials": "MH"}, {"family": "Venuturupalli", "given": "Swamy", "initials": "S"}, {"family": "Kelly", "given": "Jennifer A", "initials": "JA"}, {"family": "Pons-Estel", "given": "Bernardo", "initials": "B"}, {"family": "Jonsson", "given": "Roland", "initials": "R"}, {"family": "Lu", "given": "Xianglan", "initials": "X"}, {"family": "Gottenberg", "given": "Jacques-Eric", "initials": "JE"}, {"family": "Anaya", "given": "Juan-Manuel", "initials": "JM"}, {"family": "Cunninghame-Graham", "given": "Deborah S", "initials": "DS"}, {"family": "Huang", "given": "Andrew J W", "initials": "AJW"}, {"family": "Brennan", "given": "Michael T", "initials": "MT"}, {"family": "Hughes", "given": "Pamela", "initials": "P"}, {"family": "Alevizos", "given": "Ilias", "initials": "I"}, {"family": "Miceli-Richard", "given": "Corinne", "initials": "C"}, {"family": "Keystone", "given": "Edward C", "initials": "EC"}, {"family": "Bykerk", "given": "Vivian P", "initials": "VP"}, {"family": "Hirschfield", "given": "Gideon", "initials": "G"}, {"family": "Nordmark", "given": "Gunnel", "initials": "G"}, {"family": "Bucher", "given": "Sara Magnusson", "initials": "SM"}, {"family": "Eriksson", "given": "Per", "initials": "P"}, {"family": "Omdal", "given": "Roald", "initials": "R"}, {"family": "Rhodus", "given": "Nelson L", "initials": "NL"}, {"family": "Rischmueller", "given": "Maureen", "initials": "M"}, {"family": "Rohrer", "given": "Michael", "initials": "M"}, {"family": "Wahren-Herlenius", "given": "Marie", "initials": "M"}, {"family": "Witte", "given": "Torsten", "initials": "T"}, {"family": "Alarc\u00f3n-Riquelme", "given": "Marta", "initials": "M"}, {"family": "Mariette", "given": "Xavier", "initials": "X"}, {"family": "Lessard", "given": "Christopher J", "initials": "CJ"}, {"family": "Harley", "given": "John B", "initials": "JB"}, {"family": "Ng", "given": "Wan-Fai", "initials": "WF"}, {"family": "Rasmussen", "given": "Astrid", "initials": "A"}, {"family": "Sivils", "given": "Kathy L", "initials": "KL"}, {"family": "Scofield", "given": "R Hal", "initials": "RH"}], "type": "journal article", "published": "2017-11-00", "journal": {"volume": "69", "issn": "2326-5205", "issue": "11", "pages": "2187-2192", "title": "Arthritis & rheumatology (Hoboken, N.J.)", "issn-l": "2326-5191"}, "abstract": "Sj\u00f6gren's syndrome (SS) and systemic lupus erythematosus (SLE) are related by clinical and serologic manifestations as well as genetic risks. Both diseases are more commonly found in women than in men, at a ratio of ~10 to 1. Common X chromosome aneuploidies, 47,XXY and 47,XXX, are enriched among men and women, respectively, in either disease, suggesting a dose effect on the X chromosome.\n\nWe examined cohorts of SS and SLE patients by constructing intensity plots of X chromosome single-nucleotide polymorphism alleles, along with determining the karyotype of selected patients.\n\nAmong ~2,500 women with SLE, we found 3 patients with a triple mosaic, consisting of 45,X/46,XX/47,XXX. Among ~2,100 women with SS, 1 patient had 45,X/46,XX/47,XXX, with a triplication of the distal p arm of the X chromosome in the 47,XXX cells. Neither the triple mosaic nor the partial triplication was found among the controls. In another SS cohort, we found a mother/daughter pair with partial triplication of this same region of the X chromosome. The triple mosaic occurs in ~1 in 25,000-50,000 live female births, while partial triplications are even rarer.\n\nVery rare X chromosome abnormalities are present among patients with either SS or SLE and may inform the location of a gene(s) that mediates an X dose effect, as well as critical cell types in which such an effect is operative.", "doi": "10.1002/art.40207", "pmid": "28692793", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [], "notes": [], "created": "2018-01-09T13:58:08.516Z", "modified": "2021-06-21T15:04:16.533Z"}, {"entity": "publication", "iuid": "df165d9fceca44289765656792099a8b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/df165d9fceca44289765656792099a8b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/df165d9fceca44289765656792099a8b"}}, "title": "Integrative studies implicate matrix metalloproteinase-12 as a culprit gene for large-artery atherosclerotic stroke", "authors": [{"family": "Mahdessian", "given": "H", "initials": "H"}, {"family": "Perisic Matic", "given": "L", "initials": "L"}, {"family": "Lengquist", "given": "M", "initials": "M"}, {"family": "Gertow", "given": "K", "initials": "K"}, {"family": "Sennblad", "given": "B", "initials": "B"}, {"family": "Baldassarre", "given": "D", "initials": "D"}, {"family": "Veglia", "given": "F", "initials": "F"}, {"family": "Humphries", "given": "S E", "initials": "SE"}, {"family": "Rauramaa", "given": "R", "initials": "R"}, {"family": "de Faire", "given": "U", "initials": "U"}, {"family": "Smit", "given": "A J", "initials": "AJ"}, {"family": "Giral", "given": "P", "initials": "P"}, {"family": "Kurl", "given": "S", "initials": "S"}, {"family": "Mannarino", "given": "E", "initials": "E"}, {"family": "Tremoli", "given": "E", "initials": "E"}, {"family": "Hamsten", "given": "A", "initials": "A"}, {"family": "Eriksson", "given": "P", "initials": "P"}, {"family": "Hedin", "given": "U", "initials": "U"}, {"family": "M\u00e4larstig", "given": "A", "initials": "A"}, {"family": null, "given": "", "initials": ""}], "type": "journal-article", "published": "2017-11-00", "journal": {"volume": "282", "issn": "0954-6820", "issue": "5", "pages": "429-444", "title": "J Intern Med", "issn-l": "0954-6820"}, "abstract": null, "doi": "10.1111/joim.12655", "pmid": "28734077", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [], "notes": [], "created": "2018-01-09T13:55:56.405Z", "modified": "2020-01-21T13:56:11.992Z"}, {"entity": "publication", "iuid": "84199c0fdcf3432a8f4e33a4246c420d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/84199c0fdcf3432a8f4e33a4246c420d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/84199c0fdcf3432a8f4e33a4246c420d"}}, "title": "Genotype-based recall to study metabolic effects of genetic variation: a pilot study of PPARG Pro12Ala carriers.", "authors": [{"family": "Kamble", "given": "Prasad G", "initials": "PG"}, {"family": "Gustafsson", "given": "Stefan", "initials": "S"}, {"family": "Pereira", "given": "Maria J", "initials": "MJ"}, {"family": "Lundkvist", "given": "Per", "initials": "P"}, {"family": "Cook", "given": "Naomi", "initials": "N"}, {"family": "Lind", "given": "Lars", "initials": "L"}, {"family": "Franks", "given": "Paul W", "initials": "PW"}, {"family": "Fall", "given": "Tove", "initials": "T"}, {"family": "Eriksson", "given": "Jan W", "initials": "JW"}, {"family": "Ingelsson", "given": "Erik", "initials": "E"}], "type": "journal article", "published": "2017-11-00", "journal": {"volume": "122", "issn": "2000-1967", "issue": "4", "pages": "234-242", "title": "Ups. J. Med. Sci.", "issn-l": "0300-9734"}, "abstract": "To assess practical implications of genotype-based recall (GBR) studies, an increasingly popular approach for in-depth characterization of genotype-phenotype relationships.\n\nWe genotyped 2500 participants from the Swedish EpiHealth cohort and considered loss-of-function and missense variants in genes with relation to cardiometabolic traits as the basis for our GBR study. Therefore, we focused on carriers and non-carriers of the PPARG Pro12Ala (rs1801282) variant, as it is a relatively common variant with a minor allele frequency (MAF) of 0.14. It has also been shown to affect ligand binding and transcription, and carriage of the minor allele (Ala12) is associated with a reduced risk of type 2 diabetes. We re-invited 39 Pro12Pro, 34 Pro12Ala, and 30 Ala12Ala carriers and performed detailed anthropometric and serological assessments.\n\nThe participation rates in the GBR study were 31%, 44%, and 40%, and accordingly we included 12, 15, and 13 individuals with Pro12Pro, Pro12Ala, and Ala12Ala variants, respectively. There were no differences in anthropometric or metabolic variables among the different genotype groups.\n\nOur report highlights that from a practical perspective, GBR can be used to study genotype-phenotype relationships. This approach can prove to be a valuable tool for follow-up findings from large-scale genetic discovery studies by undertaking detailed phenotyping procedures that might not be feasible in large studies. However, our study also illustrates the need for a larger pool of genotyped or sequenced individuals to allow for selection of rare variants with larger effects that can be examined in a GBR study of the present size.", "doi": "10.1080/03009734.2017.1405127", "pmid": "29303622", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC5810227"}], "notes": [], "created": "2018-05-25T13:31:05.888Z", "modified": "2020-01-21T13:56:10.921Z"}, {"entity": "publication", "iuid": "6919ea89c19846078b8eb8cd9e538de7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6919ea89c19846078b8eb8cd9e538de7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6919ea89c19846078b8eb8cd9e538de7"}}, "title": "An Expanded Genome-Wide Association Study of Type 2 Diabetes in Europeans", "authors": [{"family": "Scott", "given": "Robert A", "initials": "RA"}, {"family": "Scott", "given": "Laura J", "initials": "LJ"}, {"family": "M\u00e4gi", "given": "Reedik", "initials": "R"}, {"family": "Marullo", "given": "Letizia", "initials": "L"}, {"family": "Gaulton", "given": "Kyle J", "initials": "KJ"}, {"family": "Kaakinen", "given": "Marika", "initials": "M"}, {"family": "Pervjakova", "given": "Natalia", "initials": "N"}, {"family": "Pers", "given": "Tune H", "initials": "TH"}, {"family": "Johnson", "given": "Andrew D", "initials": "AD"}, {"family": "Eicher", "given": "John D", "initials": "JD"}, {"family": "Jackson", "given": "Anne U", "initials": "AU"}, {"family": "Ferreira", "given": "Teresa", "initials": "T"}, {"family": "Lee", "given": "Yeji", "initials": "Y"}, {"family": "Ma", "given": "Clement", "initials": "C"}, {"family": "Steinthorsdottir", "given": "Valgerdur", "initials": "V"}, {"family": "Thorleifsson", "given": "Gudmar", "initials": "G"}, {"family": "Qi", "given": "Lu", "initials": "L"}, {"family": "Van Zuydam", "given": "Natalie R", "initials": "NR"}, {"family": "Mahajan", "given": "Anubha", "initials": "A"}, {"family": "Chen", "given": "Han", "initials": "H"}, {"family": "Almgren", "given": "Peter", "initials": "P"}, {"family": "Voight", "given": "Ben F", "initials": "BF"}, {"family": "Grallert", "given": "Harald", "initials": "H"}, {"family": "M\u00fcller-Nurasyid", "given": "Martina", "initials": "M"}, {"family": "Ried", "given": "Janina S", "initials": "JS"}, {"family": "Rayner", "given": "Nigel W", "initials": "NW"}, {"family": "Robertson", "given": "Neil", "initials": "N"}, {"family": "Karssen", "given": "Lennart C", "initials": "LC"}, {"family": "van Leeuwen", "given": "Elisabeth M", "initials": "EM"}, {"family": "Willems", "given": "Sara M", "initials": "SM"}, {"family": "Fuchsberger", "given": "Christian", "initials": "C"}, {"family": "Kwan", "given": "Phoenix", "initials": "P"}, {"family": "Teslovich", "given": "Tanya M", "initials": "TM"}, {"family": "Chanda", "given": "Pritam", "initials": "P"}, {"family": "Li", "given": "Man", "initials": "M"}, {"family": "Lu", "given": "Yingchang", "initials": "Y"}, {"family": "Dina", "given": "Christian", "initials": "C"}, {"family": "Thuillier", "given": "Dorothee", "initials": "D"}, {"family": "Yengo", "given": "Loic", "initials": "L"}, {"family": "Jiang", "given": "Longda", "initials": "L"}, {"family": "Sparso", "given": "Thomas", "initials": "T"}, {"family": "Kestler", "given": "Hans A", "initials": "HA"}, {"family": "Chheda", "given": "Himanshu", "initials": "H"}, {"family": "Eisele", "given": "Lewin", "initials": "L"}, {"family": "Gustafsson", "given": "Stefan", "initials": "S"}, {"family": "Fr\u00e5nberg", "given": "Mattias", "initials": "M"}, {"family": "Strawbridge", "given": "Rona J", "initials": "RJ"}, {"family": "Benediktsson", "given": "Rafn", "initials": "R"}, {"family": "Hreidarsson", "given": "Astradur B", "initials": "AB"}, {"family": "Kong", "given": "Augustine", "initials": "A"}, {"family": "Sigur\u00f0sson", "given": "Gunnar", "initials": "G"}, {"family": "Kerrison", "given": "Nicola D", "initials": "ND"}, {"family": "Luan", "given": "Jian'an", "initials": "J"}, {"family": "Liang", "given": "Liming", "initials": "L"}, {"family": "Meitinger", "given": "Thomas", "initials": "T"}, {"family": "Roden", "given": "Michael", "initials": "M"}, {"family": "Thorand", "given": "Barbara", "initials": "B"}, {"family": "Esko", "given": "T\u00f5nu", "initials": "T"}, {"family": "Mihailov", "given": "Evelin", "initials": "E"}, {"family": "Fox", "given": "Caroline", "initials": "C"}, {"family": "Liu", "given": "Ching Ti", "initials": "CT"}, {"family": "Rybin", "given": "Denis", "initials": "D"}, {"family": "Isomaa", "given": "Bo", "initials": "B"}, {"family": "Lyssenko", "given": "Valeriya", "initials": "V"}, {"family": "Tuomi", "given": "Tiinamaija", "initials": "T"}, {"family": "Couper", "given": "David J", "initials": "DJ"}, {"family": "Pankow", "given": "James S", "initials": "JS"}, {"family": "Grarup", "given": 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"initials": "AD"}, {"family": "Palmer", "given": "Colin N A", "initials": "CNA"}, {"family": "Hu", "given": "Frank B", "initials": "FB"}, {"family": "Thorsteinsdottir", "given": "Unnur", "initials": "U"}, {"family": "Stefansson", "given": "Kari", "initials": "K"}, {"family": "Dupuis", "given": "Jos\u00e9e", "initials": "J"}, {"family": "Morris", "given": "Andrew P", "initials": "AP"}, {"family": "Boehnke", "given": "Michael", "initials": "M"}, {"family": "McCarthy", "given": "Mark I", "initials": "MI"}, {"family": "Prokopenko", "given": "Inga", "initials": "I"}], "type": "journal-article", "published": "2017-11-00", "journal": {"volume": "66", "issn": "1939-327X", "issue": "11", "pages": "2888-2902", "title": "Diabetes", "issn-l": "0012-1797"}, "abstract": null, "doi": "10.2337/db16-1253", "pmid": "28566273", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [], "notes": [], "created": "2018-01-09T13:58:10.604Z", "modified": "2020-01-21T13:56:11.979Z"}, {"entity": "publication", "iuid": "0ea140596e2947cbba1cff3d94b7655c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0ea140596e2947cbba1cff3d94b7655c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0ea140596e2947cbba1cff3d94b7655c"}}, "title": "Vitamin and Amino Acid Auxotrophy in Anaerobic Consortia Operating under Methanogenic Conditions", "authors": [{"family": "Hubalek", "given": "Valerie", "initials": "V"}, {"family": "Buck", "given": "Moritz", "initials": "M"}, {"family": "Tan", "given": "BoonFei", "initials": "B"}, {"family": "Foght", "given": "Julia", "initials": "J"}, {"family": "Wendeberg", "given": "Annelie", "initials": "A"}, {"family": "Berry", "given": "David", "initials": "D"}, {"family": "Bertilsson", "given": "Stefan", "initials": "S"}, {"family": "Eiler", "given": "Alexander", "initials": "A"}], "type": "journal-article", "published": "2017-10-31", "journal": {"volume": "2", "issn": "2379-5077", "issue": "5", "pages": "e00038-17", "title": "mSystems", "issn-l": "2379-5077"}, "abstract": "Syntrophy among \n            Archaea and Bacteria facilitates the anaerobic degradation of organic compounds to CH4 and CO2. Particularly during aliphatic and aromatic hydrocarbon mineralization, as in the case of crude oil reservoirs and petroleum-contaminated sediments, metabolic interactions between obligate mutualistic microbial partners are of central importance. Using micromanipulation combined with shotgun metagenomic approaches, we describe the genomes of complex consortia within short-chain alkane-degrading cultures operating under methanogenic conditions. Metabolic reconstruction revealed that only a small fraction of genes in the metagenome-assembled genomes encode the capacity for fermentation of alkanes facilitated by energy conservation linked to H2 metabolism. Instead, the presence of inferred lifestyles based on scavenging anabolic products and intermediate fermentation products derived from detrital biomass was a common feature. Additionally, inferred auxotrophy for vitamins and amino acids suggests that the hydrocarbon-degrading microbial assemblages are structured and maintained by multiple interactions beyond the canonical H2-producing and syntrophic alkane degrader-methanogen partnership. Compared to previous work, our report points to a higher order of complexity in microbial consortia engaged in anaerobic hydrocarbon transformation. IMPORTANCE Microbial interactions between Archaea and Bacteria mediate many important chemical transformations in the biosphere from degrading abundant polymers to synthesis of toxic compounds. Two of the most pressing issues in microbial interactions are how consortia are established and how we can modulate these microbial communities to express desirable functions. Here, we propose that public goods (i.e., metabolites of high energy demand in biosynthesis) facilitate energy conservation for life under energy-limited conditions and determine the assembly and function of the consortia. Our report suggests that an understanding of public good dynamics could result in new ways to improve microbial pollutant degradation in anaerobic systems.", "doi": "10.1128/msystems.00038-17", "pmid": "29104938", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [], "notes": [], "created": "2018-01-09T20:51:43.787Z", "modified": "2020-01-21T13:56:17.316Z"}, {"entity": "publication", "iuid": "143b472121a44e75898dd001f521485f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/143b472121a44e75898dd001f521485f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/143b472121a44e75898dd001f521485f"}}, "title": "Exome-wide association study of plasma lipids in >300,000 individuals.", "authors": 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"Eirini", "initials": "E"}, {"family": "Masca", "given": "Nicholas G D", "initials": "NGD"}, {"family": "Maschio", "given": "Andrea", "initials": "A"}, {"family": "Meigs", "given": "James B", "initials": "JB"}, {"family": "Melander", "given": "Olle", "initials": "O"}, {"family": "Metspalu", "given": "Andres", "initials": "A"}, {"family": "Morris", "given": "Andrew P", "initials": "AP"}, {"family": "Morrison", "given": "Alanna C", "initials": "AC"}, {"family": "Mulas", "given": "Antonella", "initials": "A"}, {"family": "M\u00fcller-Nurasyid", "given": "Martina", "initials": "M"}, {"family": "Munroe", "given": "Patricia B", "initials": "PB"}, {"family": "Neville", "given": "Matt J", "initials": "MJ"}, {"family": "Nielsen", "given": "Jonas B", "initials": "JB"}, {"family": "Nielsen", "given": "Sune F", "initials": "SF"}, {"family": "Nordestgaard", "given": "B\u00f8rge G", "initials": "BG"}, {"family": "Ordovas", "given": "Jose M", "initials": "JM"}, {"family": "Mehran", "given": "Roxana", "initials": "R"}, {"family": "O'Donnell", "given": "Christoper J", "initials": "CJ"}, {"family": "Orho-Melander", "given": "Marju", "initials": "M"}, {"family": "Molony", "given": "Cliona M", "initials": "CM"}, {"family": "Muntendam", "given": "Pieter", "initials": "P"}, {"family": "Padmanabhan", "given": "Sandosh", "initials": "S"}, {"family": "Palmer", "given": "Colin N A", "initials": "CNA"}, {"family": "Pasko", "given": "Dorota", "initials": "D"}, {"family": "Patel", "given": "Aniruddh P", "initials": "AP"}, {"family": "Pedersen", "given": "Oluf", "initials": "O"}, {"family": "Perola", "given": "Markus", "initials": "M"}, {"family": "Peters", "given": "Annette", "initials": "A"}, {"family": "Pisinger", "given": "Charlotta", "initials": "C"}, {"family": "Pistis", "given": "Giorgio", "initials": "G"}, {"family": "Polasek", "given": "Ozren", "initials": "O"}, {"family": "Poulter", "given": "Neil", "initials": "N"}, {"family": "Psaty", "given": "Bruce M", "initials": "BM"}, {"family": "Rader", "given": "Daniel J", "initials": "DJ"}, {"family": "Rasheed", "given": "Asif", "initials": "A"}, {"family": "Rauramaa", "given": "Rainer", "initials": "R"}, {"family": "Reilly", "given": "Dermot F", "initials": "DF"}, {"family": "Reiner", "given": "Alex P", "initials": "AP"}, {"family": "Renstr\u00f6m", "given": "Frida", "initials": "F"}, {"family": "Rich", "given": "Stephen S", "initials": "SS"}, {"family": "Ridker", "given": "Paul M", "initials": "PM"}, {"family": "Rioux", "given": "John D", "initials": "JD"}, {"family": "Robertson", "given": "Neil R", "initials": "NR"}, {"family": "Roden", "given": "Dan M", "initials": "DM"}, {"family": "Rotter", "given": "Jerome I", "initials": "JI"}, {"family": "Rudan", "given": "Igor", "initials": "I"}, {"family": "Salomaa", "given": "Veikko", "initials": "V"}, {"family": "Samani", "given": "Nilesh J", "initials": "NJ"}, {"family": "Sanna", "given": "Serena", "initials": "S"}, {"family": "Sattar", "given": "Naveed", "initials": "N"}, {"family": "Schmidt", "given": "Ellen M", "initials": "EM"}, {"family": "Scott", "given": "Robert A", "initials": "RA"}, {"family": "Sever", "given": "Peter", "initials": "P"}, {"family": "Sevilla", "given": "Raquel S", "initials": "RS"}, {"family": "Shaffer", "given": "Christian M", "initials": "CM"}, {"family": "Sim", "given": "Xueling", "initials": "X"}, {"family": "Sivapalaratnam", "given": "Suthesh", "initials": "S"}, {"family": "Small", "given": "Kerrin S", "initials": "KS"}, {"family": "Smith", "given": "Albert V", "initials": "AV"}, {"family": "Smith", "given": "Blair H", "initials": "BH"}, {"family": "Somayajula", "given": "Sangeetha", "initials": "S"}, {"family": "Southam", "given": "Lorraine", "initials": "L"}, {"family": "Spector", "given": "Timothy D", "initials": "TD"}, {"family": "Speliotes", "given": "Elizabeth K", "initials": "EK"}, {"family": "Starr", "given": "John M", "initials": "JM"}, {"family": "Stirrups", "given": "Kathleen E", "initials": "KE"}, {"family": "Stitziel", "given": "Nathan", "initials": "N"}, {"family": "Strauch", "given": "Konstantin", "initials": "K"}, {"family": "Stringham", "given": "Heather M", "initials": "HM"}, {"family": "Surendran", "given": "Praveen", "initials": "P"}, {"family": "Tada", "given": "Hayato", "initials": "H"}, {"family": "Tall", "given": "Alan R", "initials": "AR"}, {"family": "Tang", "given": "Hua", "initials": "H"}, {"family": "Tardif", "given": "Jean-Claude", "initials": "JC"}, {"family": "Taylor", "given": "Kent D", "initials": "KD"}, {"family": "Trompet", "given": "Stella", "initials": "S"}, {"family": "Tsao", "given": "Philip S", "initials": "PS"}, {"family": "Tuomilehto", "given": "Jaakko", "initials": "J"}, {"family": "Tybjaerg-Hansen", "given": "Anne", "initials": "A"}, {"family": "van Zuydam", "given": "Natalie R", "initials": "NR"}, {"family": "Varbo", "given": "Anette", "initials": "A"}, {"family": "Varga", "given": "Tibor V", "initials": "TV"}, {"family": "Virtamo", "given": "Jarmo", "initials": "J"}, {"family": "Waldenberger", "given": "Melanie", "initials": "M"}, {"family": "Wang", "given": "Nan", "initials": "N"}, {"family": "Wareham", "given": "Nick J", "initials": "NJ"}, {"family": "Warren", "given": "Helen R", "initials": "HR"}, {"family": "Weeke", "given": "Peter E", "initials": "PE"}, {"family": "Weinstock", "given": "Joshua", "initials": "J"}, {"family": "Wessel", "given": "Jennifer", "initials": "J"}, {"family": "Wilson", "given": "James G", "initials": "JG"}, {"family": "Wilson", "given": "Peter W F", "initials": "PWF"}, {"family": "Xu", "given": "Ming", "initials": "M"}, {"family": "Yaghootkar", "given": "Hanieh", "initials": "H"}, {"family": "Young", "given": "Robin", "initials": "R"}, {"family": "Zeggini", "given": "Eleftheria", "initials": "E"}, {"family": "Zhang", "given": "He", "initials": "H"}, {"family": "Zheng", "given": "Neil S", "initials": "NS"}, {"family": "Zhang", "given": "Weihua", "initials": "W"}, {"family": "Zhang", "given": "Yan", "initials": "Y"}, {"family": "Zhou", "given": "Wei", "initials": "W"}, {"family": "Zhou", "given": "Yanhua", "initials": "Y"}, {"family": "Zoledziewska", "given": "Magdalena", "initials": "M"}, {"family": "Charge Diabetes Working Group", "given": "", "initials": ""}, {"family": "EPIC-InterAct Consortium", "given": "", "initials": ""}, {"family": "EPIC-CVD Consortium", "given": "", "initials": ""}, {"family": "GOLD Consortium", "given": "", "initials": ""}, {"family": "VA Million Veteran Program", "given": "", "initials": ""}, {"family": "Howson", "given": "Joanna M M", "initials": "JMM"}, {"family": "Danesh", "given": "John", "initials": "J"}, {"family": "McCarthy", "given": "Mark I", "initials": "MI"}, {"family": "Cowan", "given": "Chad A", "initials": "CA"}, {"family": "Abecasis", "given": "Goncalo", "initials": "G"}, {"family": "Deloukas", "given": "Panos", "initials": "P"}, {"family": "Musunuru", "given": "Kiran", "initials": "K"}, {"family": "Willer", "given": "Cristen J", "initials": "CJ"}, {"family": "Kathiresan", "given": "Sekar", "initials": "S"}], "type": "journal article", "published": "2017-10-30", "journal": {"volume": null, "issn": "1546-1718", "issue": null, "title": "Nat. Genet.", "issn-l": "1061-4036"}, "abstract": "We screened variants on an exome-focused genotyping array in >300,000 participants (replication in >280,000 participants) and identified 444 independent variants in 250 loci significantly associated with total cholesterol (TC), high-density-lipoprotein cholesterol (HDL-C), low-density-lipoprotein cholesterol (LDL-C), and/or triglycerides (TG). At two loci (JAK2 and A1CF), experimental analysis in mice showed lipid changes consistent with the human data. We also found that: (i) beta-thalassemia trait carriers displayed lower TC and were protected from coronary artery disease (CAD); (ii) excluding the CETP locus, there was not a predictable relationship between plasma HDL-C and risk for age-related macular degeneration; (iii) only some mechanisms of lowering LDL-C appeared to increase risk for type 2 diabetes (T2D); and (iv) TG-lowering alleles involved in hepatic production of TG-rich lipoproteins (TM6SF2 and PNPLA3) tracked with higher liver fat, higher risk for T2D, and lower risk for CAD, whereas TG-lowering alleles involved in peripheral lipolysis (LPL and ANGPTL4) had no effect on liver fat but decreased risks for both T2D and CAD.", "doi": "10.1038/ng.3977", "pmid": "29083408", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "ng.3977"}], "notes": [], "created": "2017-11-09T16:02:23.213Z", "modified": "2020-01-21T13:56:10.219Z"}, {"entity": "publication", "iuid": "dbef244a97744185a5325c6bdeaf9b13", "links": {"self": {"href": "https://publications.scilifelab.se/publication/dbef244a97744185a5325c6bdeaf9b13.json"}, "display": {"href": "https://publications.scilifelab.se/publication/dbef244a97744185a5325c6bdeaf9b13"}}, "title": "The Evolution of Dark Matter in the Mitogenome of Seed Beetles", "authors": [{"family": "Sayadi", "given": "Ahmed", "initials": "A"}, {"family": "Immonen", "given": "Elina", "initials": "E"}, {"family": "Tellgren-Roth", "given": "Christian", "initials": "C"}, {"family": "Arnqvist", "given": "G\u00f6ran", "initials": "G"}], "type": "journal-article", "published": "2017-10-01", "journal": {"volume": "9", "issn": "1759-6653", "issue": "10", "pages": "2697-2706", "title": "Genome Biol Evol", "issn-l": "1759-6653"}, "abstract": null, "doi": "10.1093/gbe/evx205", "pmid": "29048527", "labels": {"Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Long-term Support WABI": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Uppsala (Uppsala Genome Center)": "Collaborative", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "GENBANK", "description": "Callosobruchus maculatus from India mitochondrion, complete genome", "key": "KY856743"}, {"db": "GENBANK", "description": "Callosobruchus chinensis mitochondrion, complete genome", "key": "KY856744"}, {"db": "GENBANK", "description": "Callosobruchus analis mitochondrion, complete genome", "key": "KY856745"}, {"db": "GENBANK", "description": "Callosobruchus maculatus from Brazil mitochondrion, complete genome", "key": "KY942060"}, {"db": "GENBANK", "description": "Callosobruchus maculatus from USA mitochondrion, complete genome", "key": "KY942061"}, {"db": "GENBANK", "description": "Callosobruchus maculatus from Yemen mitochondrion, complete genome", "key": "KY942062"}, {"db": "GENBANK", "description": "Acanthoscelides obtectus mitochondrion, complete genome", "key": "MF925724"}], "notes": [], "created": "2017-10-13T08:02:37.993Z", "modified": "2024-01-16T13:48:47.441Z"}, {"entity": "publication", "iuid": "7288c350f11e45b4986bd6fa6331f24d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7288c350f11e45b4986bd6fa6331f24d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7288c350f11e45b4986bd6fa6331f24d"}}, "title": "Rapid Increase in Genome Size as a Consequence of Transposable Element Hyperactivity in Wood-White (Leptidea) Butterflies.", "authors": [{"family": "Talla", "given": "Venkat", "initials": "V"}, {"family": "Suh", "given": "Alexander", "initials": "A"}, {"family": "Kalsoom", "given": "Faheema", "initials": "F"}, {"family": "Dinca", "given": "Vlad", "initials": "V"}, {"family": "Vila", "given": "Roger", "initials": "R"}, {"family": "Friberg", "given": "Magne", "initials": "M"}, {"family": "Wiklund", "given": "Christer", "initials": "C"}, {"family": "Backstr\u00f6m", "given": "Niclas", "initials": "N"}], "type": "journal article", "published": "2017-10-01", "journal": {"volume": "9", "issn": "1759-6653", "issue": "10", "pages": "2491-2505", "title": "Genome Biol Evol", "issn-l": "1759-6653"}, "abstract": "Characterizing and quantifying genome size variation among organisms and understanding if genome size evolves as a consequence of adaptive or stochastic processes have been long-standing goals in evolutionary biology. Here, we investigate genome size variation and association with transposable elements (TEs) across lepidopteran lineages using a novel genome assembly of the common wood-white (Leptidea sinapis) and population re-sequencing data from both L. sinapis and the closely related L. reali and L. juvernica together with 12 previously available lepidopteran genome assemblies. A phylogenetic analysis confirms established relationships among species, but identifies previously unknown intraspecific structure within Leptidea lineages. The genome assembly of L. sinapis is one of the largest of any lepidopteran taxon so far (643\u2009Mb) and genome size is correlated with abundance of TEs, both in Lepidoptera in general and within Leptidea where L. juvernica from Kazakhstan has considerably larger genome size than any other Leptidea population. Specific TE subclasses have been active in different Lepidoptera lineages with a pronounced expansion of predominantly LINEs, DNA elements, and unclassified TEs in the Leptidea lineage after the split from other Pieridae. The rate of genome expansion in Leptidea in general has been in the range of four Mb/Million year (My), with an increase in a particular L. juvernica population to 72\u2009Mb/My. The considerable differences in accumulation rates of specific TE classes in different lineages indicate that TE activity plays a major role in genome size evolution in butterflies and moths.", "doi": "10.1093/gbe/evx163", "pmid": "28981642", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "4091610"}, {"db": "BioProject", "description": "Rapid increase in genome size as a consequence of transposable element hyperactivity in wood-white (Leptidea) butterflies.", "key": "PRJEB21838"}, {"db": "GENBANK", "description": "Leptidea sinapis, whole genome shotgun sequencing project", "key": "FZQP00000000"}], "notes": [], "created": "2017-10-30T09:27:46.367Z", "modified": "2024-01-16T13:48:47.456Z"}, {"entity": "publication", "iuid": "fcf6935e1c56441cb92e0dbb3fde5b21", "links": {"self": {"href": "https://publications.scilifelab.se/publication/fcf6935e1c56441cb92e0dbb3fde5b21.json"}, "display": {"href": "https://publications.scilifelab.se/publication/fcf6935e1c56441cb92e0dbb3fde5b21"}}, "title": "A MIR4646 associated methylation locus is hypomethylated in adolescent depression.", "authors": [{"family": "Bostr\u00f6m", "given": "Adrian E", "initials": "AE"}, {"family": "Ciuculete", "given": "Diana-Maria", "initials": "DM"}, {"family": "Attwood", "given": "Misty", "initials": "M"}, {"family": "Krattinger", "given": "Regina", "initials": "R"}, {"family": "Nikontovic", "given": "Lamia", "initials": "L"}, {"family": "Titova", "given": "Olga E", "initials": "OE"}, {"family": "Kullak-Ublick", "given": "Gerd A", "initials": "GA"}, {"family": "Mwinyi", "given": "Jessica", "initials": "J"}, {"family": "Schi\u00f6th", "given": "Helgi B", "initials": "HB"}], "type": "journal article", "published": "2017-10-01", "journal": {"volume": "220", "issn": "1573-2517", "issue": null, "pages": "117-128", "title": "J Affect Disord", "issn-l": "0165-0327"}, "abstract": "Studies of epigenetics and transcriptional activity in adolescents may provide knowledge about possible preventive strategies of depression.\n\nWe present a methylome-wide association study (MWAS) and cohort validation analysis of depression in adolescents, in two separate cohorts: discovery (n=93) and validation data set 1 (n=78). The genome-wide methylation pattern was measured from whole blood using the Illumina 450K array. A second validation cohort, validation data set 2, consists of post-mortem brain biopsies from depressed adults (n=58). We performed a MWAS by robust multiple linear regressions of methylation to a modified risk-score assessment of depression. Methylation levels of candidate CpG sites were correlated with expression levels of the associated gene in an independent cohort of 11 healthy volunteers.\n\nThe methylation state of two CpG sites reliably predicted ratings of depression in adolescents (cg13227623 and cg04102384) (p<10E-06). Cohort validation analysis confirmed cg04102384 - located in the promoter region of microRNA 4646 (MIR4646) - to be hypomethylated in both validation data set 1 and validation data set 2 (p<0.05). Cg04102384 was inversely correlated to expression levels of MIR4646-3p in healthy controls (p<0.05).\n\nMIR4646 was not differentially expressed in a subset of samples with adolescent depression measured by qRT-PCR measurements.\n\nWe identify a specific MIR4646 associated epigenetic risk site to be associated with depression in adolescents. Cg04102384 putatively regulates gene expression of MIR4646-3p. Target gene prediction and gene set overrepresentation analysis revealed involvement of this miRNA in fatty acid elongation, a process related to omega-3 fatty acids, previously associated with depression.", "doi": "10.1016/j.jad.2017.05.017", "pmid": "28618313", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "S0165-0327(16)32420-X"}], "notes": [], "created": "2017-10-25T15:27:44.326Z", "modified": "2020-01-21T13:56:08.027Z"}, {"entity": "publication", "iuid": "08d96437e2804f3f8139651b56ca60ce", "links": {"self": {"href": "https://publications.scilifelab.se/publication/08d96437e2804f3f8139651b56ca60ce.json"}, "display": {"href": "https://publications.scilifelab.se/publication/08d96437e2804f3f8139651b56ca60ce"}}, "title": "The evolutionary history of the DMRT3 \u2018Gait keeper\u2019 haplotype", "authors": [{"family": "Staiger", "given": "E A", "initials": "EA"}, {"family": "Alm\u00e9n", "given": "M S", "initials": "MS"}, {"family": "Promerov\u00e1", "given": "M", "initials": "M"}, {"family": "Brooks", "given": "S", "initials": "S"}, {"family": "Cothran", "given": "E G", "initials": "EG"}, {"family": "Imsland", "given": "F", "initials": "F"}, {"family": "J\u00e4derkvist Fegraeus", "given": "K", "initials": "K"}, {"family": "Lindgren", "given": "G", "initials": "G"}, {"family": "Mehrabani Yeganeh", "given": "H", "initials": "H"}, {"family": "Mikko", "given": "S", "initials": "S"}, {"family": "Vega-Pla", "given": "J L", "initials": "JL"}, {"family": "Tozaki", "given": "T", "initials": "T"}, {"family": "Rubin", "given": "C J", "initials": "CJ"}, {"family": "Andersson", "given": "L", "initials": "L"}], "type": "journal-article", "published": "2017-10-00", "journal": {"volume": "48", "issn": "0268-9146", "issue": "5", "pages": "551-559", "title": "Anim Genet", "issn-l": null}, "abstract": null, "doi": "10.1111/age.12580", "pmid": "28741731", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [], "notes": [], "created": "2018-01-09T20:54:59.924Z", "modified": "2020-01-21T13:56:14.875Z"}, {"entity": "publication", "iuid": "14eb5706d8aa4e83800ec409e0517584", "links": {"self": {"href": "https://publications.scilifelab.se/publication/14eb5706d8aa4e83800ec409e0517584.json"}, "display": {"href": "https://publications.scilifelab.se/publication/14eb5706d8aa4e83800ec409e0517584"}}, "title": "Reduced cell surface levels of GPI-linked markers in a new case with PIGG loss of function.", "authors": [{"family": "Zhao", "given": "Jin James", "initials": "JJ", "orcid": "0000-0001-8367-8391", "researcher": {"href": "https://publications.scilifelab.se/researcher/fad3b22c21064a85a351f549bedfc36e.json"}}, {"family": "Halvardson", "given": "Jonatan", "initials": "J"}, {"family": "Knaus", "given": "Alexej", "initials": "A"}, {"family": "Georgii-Hemming", "given": "Patrik", "initials": "P"}, {"family": "Baeck", "given": "Peter", "initials": "P"}, {"family": "Krawitz", "given": "Peter M", "initials": "PM"}, {"family": "Thuresson", "given": "Ann-Charlotte", "initials": "AC"}, {"family": "Feuk", "given": "Lars", "initials": "L", "orcid": "0000-0003-2355-2919", "researcher": {"href": "https://publications.scilifelab.se/researcher/3eb2f826b3554d4b9971bf0766b275c4.json"}}], "type": "journal article", "published": "2017-10-00", "journal": {"volume": "38", "issn": "1098-1004", "issue": "10", "pages": "1394-1401", "title": "Hum. Mutat.", "issn-l": "1059-7794"}, "abstract": "Glycosylphosphatidylinositol (GPI) is a glycolipid that tethers more than 150 different proteins to the cell surface. Aberrations in biosynthesis of GPI anchors cause congenital disorders of glycosylation with clinical features including intellectual disability (ID), seizures, and facial dysmorphism. Here, we present two siblings with ID, cerebellar hypoplasia, cerebellar ataxia, early-onset seizures, and minor facial dysmorphology. Using exome sequencing, we identified a homozygous nonsense variant (NM_001127178.1:c.1640G>A, p.Trp547*) in the gene Phosphatidylinositol Glycan Anchor Biosynthesis, Class G (PIGG) in both the patients. Variants in several other GPI anchor synthesis genes lead to a reduced expression of GPI-anchored proteins (GPI-APs) that can be measured by flow cytometry. No significant differences in GPI-APs could be detected in patient granulocytes, consistent with recent findings. However, fibroblasts showed a reduced global level of GPI anchors and of specific GPI-linked markers. These findings suggest that fibroblasts might be more sensitive to pathogenic variants in GPI synthesis pathway and are well suited to screen for GPI-anchor deficiencies. Based on genetic and functional evidence, we confirm that pathogenic variants in PIGG cause an ID syndrome, and we find that loss of function of PIGG is associated with GPI deficiency.", "doi": "10.1002/humu.23268", "pmid": "28581210", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC6180480"}], "notes": [], "created": "2017-10-17T09:44:01.955Z", "modified": "2024-01-16T13:48:47.470Z"}, {"entity": "publication", "iuid": "16781fb9aaae414bb5b27ea73128ba92", "links": {"self": {"href": "https://publications.scilifelab.se/publication/16781fb9aaae414bb5b27ea73128ba92.json"}, "display": {"href": "https://publications.scilifelab.se/publication/16781fb9aaae414bb5b27ea73128ba92"}}, "title": "Novel genetic loci associated HLA-B*08:01 positive myasthenia gravis", "authors": [{"family": "Varade", "given": "Jezabel", "initials": "J"}, {"family": "Wang", "given": "Ning", "initials": "N"}, {"family": "Lim", "given": "Che Kang", "initials": "CK"}, {"family": "Zhang", "given": "Tao", "initials": "T"}, {"family": "Zhang", "given": "Yuanwei", "initials": "Y"}, {"family": "Liu", "given": "Xiaomin", "initials": "X"}, {"family": "Piehl", "given": "Fredrik", "initials": "F"}, {"family": "Matell", "given": "Ritva", "initials": "R"}, {"family": "Cao", "given": "Hongzhi", "initials": "H"}, {"family": "Xu", "given": "Xun", "initials": "X"}, {"family": "Hammarstr\u00f6m", "given": "Lennart", "initials": "L"}], "type": "journal-article", "published": "2017-10-00", "journal": {"volume": null, "issn": "0896-8411", "issue": null, "pages": null, "title": "Journal of Autoimmunity", "issn-l": "0896-8411"}, "abstract": null, "doi": "10.1016/j.jaut.2017.10.002", "pmid": "29037440", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [], "notes": [], "created": "2018-01-09T13:55:53.289Z", "modified": "2020-01-21T13:56:11.955Z"}, {"entity": "publication", "iuid": "bb30b72c6f4547829967dbcf17c35eb7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/bb30b72c6f4547829967dbcf17c35eb7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/bb30b72c6f4547829967dbcf17c35eb7"}}, "title": "Artificial Selection Response due to Polygenic Adaptation from a Multilocus, Multiallelic Genetic Architecture", "authors": [{"family": "Zan", "given": "Yanjun", "initials": "Y"}, {"family": "Sheng", "given": "Zheya", "initials": "Z"}, {"family": "Lillie", "given": "Mette", "initials": "M"}, {"family": "R\u00f6nneg\u00e5rd", "given": "Lars", "initials": "L"}, {"family": "Honaker", "given": "Christa F", "initials": "CF"}, {"family": "Siegel", "given": "Paul B", "initials": "PB"}, {"family": "Carlborg", "given": "\u00d6rjan", "initials": "\u00d6"}], "type": "journal-article", "published": "2017-10-00", "journal": {"volume": "34", "issn": "0737-4038", "issue": "10", "pages": "2678-2689", "title": "", "issn-l": null}, "abstract": null, "doi": "10.1093/molbev/msx194", "pmid": "28957504", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [], "notes": [], "created": "2017-12-05T12:58:21.130Z", "modified": "2020-01-21T13:56:11.962Z"}, {"entity": "publication", "iuid": "38ade6881a5c4c4aa4aeabe2fe7eb85d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/38ade6881a5c4c4aa4aeabe2fe7eb85d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/38ade6881a5c4c4aa4aeabe2fe7eb85d"}}, "title": "Identification of a novel proinsulin-associated SNP and demonstration that proinsulin is unlikely to be a causal factor in subclinical vascular remodelling using Mendelian randomisation.", "authors": [{"family": "Strawbridge", "given": "Rona J", "initials": "RJ"}, {"family": "Silveira", "given": "Angela", "initials": "A"}, {"family": "Hoed", "given": "Marcel den", "initials": "MD"}, {"family": "Gustafsson", "given": "Stefan", "initials": "S"}, {"family": "Luan", "given": "Jian'an", "initials": "J"}, {"family": "Rybin", "given": "Denis", "initials": "D"}, {"family": "Dupuis", "given": "Jos\u00e9e", "initials": "J"}, {"family": "Li-Gao", "given": "Ruifang", "initials": "R"}, {"family": "Kavousi", "given": "Maryam", "initials": "M"}, {"family": "Dehghan", "given": "Abbas", "initials": "A"}, {"family": "Haljas", "given": "Kadri", "initials": "K"}, {"family": "Lahti", "given": "Jari", "initials": "J"}, {"family": "G\u00e5din", "given": "Jesper R", "initials": "JR"}, {"family": "B\u00e4cklund", "given": "Alexandra", "initials": "A"}, {"family": "de Faire", "given": "Ulf", "initials": "U"}, {"family": "Gertow", "given": "Karl", "initials": "K"}, {"family": "Giral", "given": "Phillipe", "initials": "P"}, {"family": "Goel", "given": "Anuj", "initials": "A"}, {"family": "Humphries", "given": "Steve E", "initials": "SE"}, {"family": "Kurl", "given": "Sudhir", "initials": "S"}, {"family": "Langenberg", "given": "Claudia", "initials": "C"}, {"family": "Lannfelt", "given": "Lars L", "initials": "LL"}, {"family": "Lind", "given": "Lars", "initials": "L"}, {"family": "Lindgren", "given": "Cecilia C M", "initials": "CCM"}, {"family": "Mannarino", "given": "Elmo", "initials": "E"}, {"family": "Mook-Kanamori", "given": "Dennis O", "initials": "DO"}, {"family": "Morris", "given": "Andrew P", "initials": "AP"}, {"family": "de Mutsert", "given": "Ren\u00e9e", "initials": "R"}, {"family": "Rauramaa", "given": "Rainer", "initials": "R"}, {"family": "Saliba-Gustafsson", "given": "Peter", "initials": "P"}, {"family": "Sennblad", "given": "Bengt", "initials": "B"}, {"family": "Smit", "given": "Andries J", "initials": "AJ"}, {"family": "Syv\u00e4nen", "given": "Ann-Christine", "initials": "AC", "orcid": "0000-0002-9681-9146", "researcher": {"href": "https://publications.scilifelab.se/researcher/f7012e35025543379380cb90efd71243.json"}}, {"family": "Tremoli", "given": "Elena", "initials": "E"}, {"family": "Veglia", "given": "Fabrizio", "initials": "F"}, {"family": "Zethelius", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Bj\u00f6rck", "given": "Hanna M", "initials": "HM"}, {"family": "Eriksson", "given": "Johan G", "initials": "JG"}, {"family": "Hofman", "given": "Albert", "initials": "A"}, {"family": "Franco", "given": "Oscar H", "initials": "OH"}, {"family": "Watkins", "given": "Hugh", "initials": "H"}, {"family": "Jukema", "given": "J Wouter", "initials": "JW"}, {"family": "Florez", "given": "Jose C", "initials": "JC"}, {"family": "Wareham", "given": "Nicholas J", "initials": "NJ"}, {"family": "Meigs", "given": "James B", "initials": "JB"}, {"family": "Ingelsson", "given": "Erik", "initials": "E"}, {"family": "Baldassarre", "given": "Damiano", "initials": "D"}, {"family": "Hamsten", "given": "Anders", "initials": "A"}, {"family": "IMPROVE study group", "given": "", "initials": ""}], "type": "journal article", "published": "2017-09-28", "journal": {"volume": "266", "issn": "1879-1484", "issue": null, "pages": "196-204", "title": "Atherosclerosis", "issn-l": "0021-9150"}, "abstract": "Increased proinsulin relative to insulin levels have been associated with subclinical atherosclerosis (measured by carotid intima-media thickness (cIMT)) and are predictive of future cardiovascular disease (CVD), independently of established risk factors. The mechanisms linking proinsulin to atherosclerosis and CVD are unclear. A genome-wide meta-analysis has identified nine loci associated with circulating proinsulin levels. Using proinsulin-associated SNPs, we set out to use a Mendelian randomisation approach to test the hypothesis that proinsulin plays a causal role in subclinical vascular remodelling.\n\nWe studied the high CVD-risk IMPROVE cohort (n\u00a0=\u00a03345), which has detailed biochemical phenotyping and repeated, state-of-the-art, high-resolution carotid ultrasound examinations. Genotyping was performed using Illumina Cardio-Metabo and Immuno arrays, which include reported proinsulin-associated loci. Participants with type 2 diabetes (n\u00a0=\u00a0904) were omitted from the analysis. Linear regression was used to identify proinsulin-associated genetic variants.\n\nWe identified a proinsulin locus on chromosome 15 (rs8029765) and replicated it in data from 20,003 additional individuals. An 11-SNP score, including the previously identified and the chromosome 15 proinsulin-associated loci, was significantly and negatively associated with baseline IMTmean and IMTmax (the primary cIMT phenotypes) but not with progression measures. However, MR-Eggers refuted any significant effect of the proinsulin-associated 11-SNP score, and a non-pleiotropic SNP score of three variants (including rs8029765) demonstrated no effect on baseline or progression cIMT measures.\n\nWe identified a novel proinsulin-associated locus and demonstrated that whilst proinsulin levels are associated with cIMT measures, proinsulin per se is unlikely to have a causative effect on cIMT.", "doi": "10.1016/j.atherosclerosis.2017.09.031", "pmid": "29040868", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "S0021-9150(17)31317-5"}], "notes": [], "created": "2017-10-25T15:41:50.212Z", "modified": "2024-01-16T13:48:47.500Z"}, {"entity": "publication", "iuid": "da31c112341047c5a5ca23114213fd81", "links": {"self": {"href": "https://publications.scilifelab.se/publication/da31c112341047c5a5ca23114213fd81.json"}, "display": {"href": "https://publications.scilifelab.se/publication/da31c112341047c5a5ca23114213fd81"}}, "title": "Epidemiological characterization of a nosocomial outbreak of extended spectrum \u03b2-lactamase Escherichia coli ST-131 confirms the clinical value of core genome multilocus sequence typing", "authors": [{"family": "Woksepp", "given": "Hanna", "initials": "H"}, {"family": "Ryberg", "given": "Anna", "initials": "A"}, {"family": "Berglind", "given": "Linda", "initials": "L"}, {"family": "Sch\u00f6n", "given": "Thomas", "initials": "T"}, {"family": "S\u00f6derman", "given": "Jan", "initials": "J"}], "type": "journal-article", "published": "2017-09-28", "journal": {"volume": null, "issn": "0903-4641", "issue": null, "pages": null, "title": "APMIS", "issn-l": null}, "abstract": null, "doi": "10.1111/apm.12753", "pmid": "28960453", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "BioProject", "description": "Genome sequencing and assembly", "key": "PRJEB15588"}], "notes": [], "created": "2017-10-30T09:30:03.674Z", "modified": "2020-01-21T13:56:14.881Z"}, {"entity": "publication", "iuid": "1e2ade93efce4c0f8d791467a61493cb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1e2ade93efce4c0f8d791467a61493cb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1e2ade93efce4c0f8d791467a61493cb"}}, "title": "Anti-mycobacterial activity correlates with altered DNA methylation pattern in immune cells from BCG-vaccinated subjects.", "authors": [{"family": "Verma", "given": "Deepti", "initials": "D"}, {"family": "Parasa", "given": "Venkata Ramanarao", "initials": "VR"}, {"family": "Raffetseder", "given": "Johanna", "initials": "J"}, {"family": "Martis", "given": "Mihaela", "initials": "M"}, {"family": "Mehta", "given": "Ratnesh B", "initials": "RB"}, {"family": "Netea", "given": "Mihai", "initials": "M"}, {"family": "Lerm", "given": "Maria", "initials": "M"}], "type": "journal article", "published": "2017-09-26", "journal": {"volume": "7", "issn": "2045-2322", "issue": "1", "pages": "12305", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "The reason for the largely variable protective effect against TB of the vaccine Bacille Calmette-Guerin (BCG) is not understood. In this study, we investigated whether epigenetic mechanisms are involved in the response of immune cells to the BCG vaccine. We isolated peripheral blood mononuclear cells (PBMCs) from BCG-vaccinated subjects and performed global DNA methylation analysis in combination with functional assays representative of innate immunity against Mycobacterium tuberculosis infection. Enhanced containment of replication was observed in monocyte-derived macrophages from a sub-group of BCG-vaccinated individuals (identified as 'responders'). A stable and robust differential DNA methylation pattern in response to BCG could be observed in PBMCs isolated from the responders but not from the non-responders. Gene ontology analysis revealed that promoters with altered DNA methylation pattern were strongly enriched among genes belonging to immune pathways in responders, however no enrichments could be observed in the non-responders. Our findings suggest that BCG-induced epigenetic reprogramming of immune cell function can enhance anti-mycobacterial immunity in macrophages. Understanding why BCG induces this response in responders but not in non-responders could provide clues to improvement of TB vaccine efficacy.", "doi": "10.1038/s41598-017-12110-2", "pmid": "28951586", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-017-12110-2"}, {"db": "pmc", "key": "PMC5615063"}], "notes": [], "created": "2017-10-25T15:27:48.394Z", "modified": "2024-01-16T13:48:47.507Z"}, {"entity": "publication", "iuid": "923f95c531b44fe183b15bd21bee0a6f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/923f95c531b44fe183b15bd21bee0a6f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/923f95c531b44fe183b15bd21bee0a6f"}}, "title": "Genetic risk scores and family history as predictors of schizophrenia in Nordic registers.", "authors": [{"family": "Lu", "given": "Y", "initials": "Y"}, {"family": "Pouget", "given": "J G", "initials": "JG"}, {"family": "Andreassen", "given": "O A", "initials": "OA"}, {"family": "Djurovic", "given": "S", "initials": "S"}, {"family": "Esko", "given": "T", "initials": "T"}, {"family": "Hultman", "given": "C M", "initials": "CM"}, {"family": "Metspalu", "given": "A", "initials": "A"}, {"family": "Milani", "given": "L", "initials": "L"}, {"family": "Werge", "given": "T", "initials": "T"}, {"family": "Sullivan", "given": "P F", "initials": "PF"}], "type": "journal article", "published": "2017-09-25", "journal": {"volume": null, "issn": "1469-8978", "issue": null, "pages": "1-9", "title": "Psychol Med", "issn-l": "0033-2917"}, "abstract": "Family history is a long-standing and readily obtainable risk factor for schizophrenia (SCZ). Low-cost genotyping technologies have enabled large genetic studies of SCZ, and the results suggest the utility of genetic risk scores (GRS, direct assessments of inherited common variant risk). Few studies have evaluated family history and GRS simultaneously to ask whether one can explain away the other.\n\nWe studied 5959 SCZ cases and 8717 controls from four Nordic countries. All subjects had family history data from national registers and genome-wide genotypes that were processed through the quality control procedures used by the Psychiatric Genomics Consortium. Using external training data, GRS were estimated for SCZ, bipolar disorder (BIP), major depression, autism, educational attainment, and body mass index. Multivariable modeling was used to estimate effect sizes.\n\nUsing harmonized genomic and national register data from Denmark, Estonia, Norway, and Sweden, we confirmed that family history of SCZ and GRS for SCZ and BIP were risk factors for SCZ. In a joint model, the effects of GRS for SCZ and BIP were essentially unchanged, and the effect of family history was attenuated but remained significant. The predictive capacity of a model including GRS and family history neared the minimum for clinical utility.\n\nCombining national register data with measured genetic risk factors represents an important investigative approach for psychotic disorders. Our findings suggest the potential clinical utility of combining GRS and family history for early prediction and diagnostic improvements.", "doi": "10.1017/S0033291717002665", "pmid": "28942743", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support and Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pii", "key": "S0033291717002665"}], "notes": [], "created": "2017-10-25T15:27:49.142Z", "modified": "2024-01-16T13:48:47.514Z"}, {"entity": "publication", "iuid": "ba5631775a314411b73ca7a1569aae73", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ba5631775a314411b73ca7a1569aae73.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ba5631775a314411b73ca7a1569aae73"}}, "title": "Impact of common genetic determinants of Hemoglobin A1c on type 2 diabetes risk and diagnosis in ancestrally diverse populations: A transethnic genome-wide meta-analysis", "authors": [{"family": "Wheeler", "given": "Eleanor", "initials": "E"}, {"family": "Leong", "given": "Aaron", "initials": "A"}, {"family": "Liu", "given": "Ching Ti", "initials": "CT"}, {"family": "Hivert", "given": "Marie France", "initials": "MF"}, {"family": "Strawbridge", "given": "Rona J", "initials": "RJ"}, {"family": "Podmore", "given": "Clara", "initials": "C"}, {"family": "Li", "given": "Man", "initials": "M"}, {"family": "Yao", "given": "Jie", "initials": "J"}, {"family": "Sim", "given": "Xueling", "initials": "X"}, {"family": "Hong", "given": "Jaeyoung", "initials": "J"}, {"family": "Chu", "given": "Audrey Y", "initials": "AY"}, {"family": "Zhang", "given": "Weihua", "initials": "W"}, {"family": "Wang", "given": "Xu", "initials": "X"}, {"family": "Chen", "given": "Peng", "initials": "P"}, {"family": "Maruthur", "given": "Nisa M", "initials": "NM"}, {"family": "Porneala", "given": "Bianca C", "initials": "BC"}, {"family": "Sharp", "given": "Stephen J", "initials": "SJ"}, {"family": "Jia", "given": "Yucheng", "initials": "Y"}, {"family": "Kabagambe", "given": "Edmond K", "initials": "EK"}, {"family": "Chang", "given": "Li Ching", "initials": "LC"}, {"family": "Chen", "given": "Wei Min", "initials": "WM"}, {"family": "Elks", "given": "Cathy E", "initials": "CE"}, {"family": "Evans", "given": "Daniel S", "initials": "DS"}, {"family": "Fan", "given": "Qiao", "initials": "Q"}, {"family": "Giulianini", "given": "Franco", "initials": "F"}, {"family": "Go", "given": "Min Jin", "initials": "MJ"}, {"family": "Hottenga", "given": "Jouke Jan", "initials": "JJ"}, {"family": "Hu", "given": "Yao", "initials": "Y"}, {"family": "Jackson", "given": "Anne U", "initials": "AU"}, {"family": "Kanoni", "given": "Stavroula", "initials": "S"}, {"family": "Kim", "given": "Young Jin", "initials": "YJ"}, {"family": "Kleber", "given": "Marcus E", "initials": "ME"}, {"family": "Ladenvall", "given": "Claes", "initials": "C"}, {"family": "Lecoeur", "given": "Cecile", "initials": "C"}, {"family": "Lim", "given": "Sing Hui", "initials": "SH"}, {"family": "Lu", "given": "Yingchang", "initials": "Y"}, {"family": "Mahajan", "given": "Anubha", "initials": "A"}, {"family": "Marzi", "given": "Carola", "initials": "C"}, {"family": "Nalls", "given": "Mike A", "initials": "MA"}, {"family": "Navarro", "given": "Pau", "initials": "P"}, {"family": "Nolte", "given": "Ilja M", "initials": "IM"}, {"family": "Rose", "given": "Lynda M", "initials": "LM"}, {"family": "Rybin", "given": "Denis V", "initials": "DV"}, {"family": "Sanna", "given": "Serena", "initials": "S"}, {"family": "Shi", "given": "Yuan", "initials": "Y"}, {"family": "Stram", "given": "Daniel O", "initials": "DO"}, {"family": "Takeuchi", "given": "Fumihiko", "initials": "F"}, {"family": "Tan", "given": "Shu Pei", "initials": "SP"}, {"family": "van der Most", "given": "Peter J", "initials": "PJ"}, {"family": "Van Vliet-Ostaptchouk", "given": "Jana V", "initials": "JV"}, {"family": "Wong", "given": "Andrew", "initials": "A"}, {"family": "Yengo", "given": "Loic", "initials": "L"}, {"family": "Zhao", "given": "Wanting", "initials": "W"}, {"family": "Goel", "given": "Anuj", "initials": "A"}, {"family": "Martinez Larrad", "given": "Maria Teresa", "initials": "MT"}, {"family": "Radke", "given": "D\u00f6rte", "initials": "D"}, {"family": "Salo", "given": "Perttu", "initials": "P"}, {"family": "Tanaka", "given": "Toshiko", "initials": "T"}, {"family": "van Iperen", "given": "Erik P A", "initials": "EPA"}, {"family": "Abecasis", "given": "Goncalo", "initials": "G"}, {"family": "Afaq", "given": "Saima", "initials": "S"}, {"family": "Alizadeh", "given": "Behrooz Z", "initials": "BZ"}, {"family": "Bertoni", "given": "Alain G", "initials": "AG"}, {"family": "Bonnefond", "given": "Amelie", "initials": "A"}, {"family": "B\u00f6ttcher", "given": "Yvonne", "initials": "Y"}, {"family": "Bottinger", "given": "Erwin P", "initials": "EP"}, {"family": "Campbell", "given": "Harry", "initials": "H"}, {"family": "Carlson", "given": "Olga D", "initials": "OD"}, {"family": "Chen", "given": "Chien Hsiun", "initials": "CH"}, {"family": "Cho", "given": "Yoon Shin", "initials": "YS"}, {"family": "Garvey", "given": "W Timothy", "initials": "WT"}, {"family": "Gieger", "given": "Christian", "initials": "C"}, {"family": "Goodarzi", "given": "Mark O", "initials": "MO"}, {"family": "Grallert", "given": "Harald", "initials": "H"}, {"family": "Hamsten", "given": "Anders", "initials": "A"}, {"family": "Hartman", "given": "Catharina A", "initials": "CA"}, {"family": "Herder", "given": "Christian", "initials": "C"}, {"family": "Hsiung", "given": "Chao Agnes", "initials": "CA"}, {"family": "Huang", "given": "Jie", "initials": "J"}, {"family": "Igase", "given": "Michiya", "initials": "M"}, {"family": "Isono", "given": "Masato", "initials": "M"}, {"family": "Katsuya", "given": "Tomohiro", "initials": "T"}, {"family": "Khor", "given": "Chiea Chuen", "initials": "CC"}, {"family": "Kiess", "given": "Wieland", "initials": "W"}, {"family": "Kohara", "given": "Katsuhiko", "initials": "K"}, {"family": "Kovacs", "given": "Peter", "initials": "P"}, {"family": "Lee", "given": "Juyoung", "initials": "J"}, {"family": "Lee", "given": "Wen Jane", "initials": "WJ"}, {"family": "Lehne", "given": "Benjamin", "initials": "B"}, {"family": "Li", "given": "Huaixing", "initials": "H"}, {"family": "Liu", "given": "Jianjun", "initials": "J"}, {"family": "Lobbens", "given": "Stephane", "initials": "S"}, {"family": "Luan", "given": "Jian'an", "initials": "J"}, {"family": "Lyssenko", "given": "Valeriya", "initials": "V"}, {"family": "Meitinger", "given": "Thomas", "initials": "T"}, {"family": "Miki", "given": "Tetsuro", "initials": "T"}, {"family": "Miljkovic", "given": "Iva", "initials": "I"}, {"family": "Moon", "given": "Sanghoon", "initials": "S"}, {"family": "Mulas", "given": "Antonella", "initials": "A"}, {"family": "M\u00fcller", "given": "Gabriele", "initials": "G"}, {"family": "M\u00fcller-Nurasyid", "given": "Martina", "initials": "M"}, {"family": "Nagaraja", "given": "Ramaiah", "initials": "R"}, {"family": "Nauck", "given": "Matthias", "initials": "M"}, {"family": "Pankow", "given": "James S", "initials": "JS"}, {"family": "Polasek", "given": "Ozren", "initials": "O"}, {"family": "Prokopenko", "given": "Inga", "initials": "I"}, {"family": "Ramos", "given": "Paula S", "initials": "PS"}, {"family": "Rasmussen-Torvik", "given": "Laura", "initials": "L"}, {"family": "Rathmann", "given": "Wolfgang", "initials": "W"}, {"family": "Rich", "given": "Stephen S", "initials": "SS"}, {"family": "Robertson", "given": "Neil R", "initials": "NR"}, {"family": "Roden", "given": "Michael", "initials": "M"}, {"family": "Roussel", "given": "Ronan", "initials": "R"}, {"family": "Rudan", "given": "Igor", "initials": "I"}, {"family": "Scott", "given": "Robert A", "initials": "RA"}, {"family": "Scott", "given": "William R", "initials": "WR"}, {"family": "Sennblad", "given": "Bengt", "initials": "B"}, {"family": "Siscovick", "given": "David S", "initials": "DS"}, {"family": "Strauch", "given": "Konstantin", "initials": "K"}, {"family": "Sun", "given": "Liang", "initials": "L"}, {"family": "Swertz", "given": "Morris", "initials": "M"}, {"family": "Tajuddin", "given": "Salman M", "initials": "SM"}, {"family": "Taylor", "given": "Kent D", "initials": "KD"}, {"family": "Teo", "given": "Yik Ying", "initials": "YY"}, {"family": "Tham", "given": "Yih Chung", "initials": "YC"}, {"family": "T\u00f6njes", "given": "Anke", "initials": "A"}, {"family": "Wareham", "given": "Nicholas J", "initials": "NJ"}, {"family": "Willemsen", "given": "Gonneke", "initials": "G"}, {"family": "Wilsgaard", "given": "Tom", "initials": "T"}, {"family": "Hingorani", "given": "Aroon D", "initials": "AD"}, {"family": "Egan", "given": "Josephine", "initials": "J"}, {"family": "Ferrucci", "given": "Luigi", "initials": "L"}, {"family": "Hovingh", "given": "G Kees", "initials": "GK"}, {"family": "Jula", "given": "Antti", "initials": "A"}, {"family": "Kivimaki", "given": "Mika", "initials": "M"}, {"family": "Kumari", "given": "Meena", "initials": "M"}, {"family": "Nj\u00f8lstad", "given": "Inger", "initials": "I"}, {"family": "Palmer", "given": "Colin N A", "initials": "CNA"}, {"family": "Serrano R\u00edos", "given": "Manuel", "initials": "M"}, {"family": "Stumvoll", "given": "Michael", "initials": "M"}, {"family": "Watkins", "given": "Hugh", "initials": "H"}, {"family": "Aung", "given": "Tin", "initials": "T"}, {"family": "Bl\u00fcher", "given": "Matthias", "initials": "M"}, {"family": "Boehnke", "given": "Michael", "initials": "M"}, {"family": "Boomsma", "given": "Dorret I", "initials": "DI"}, {"family": "Bornstein", "given": "Stefan R", "initials": "SR"}, {"family": "Chambers", "given": "John C", "initials": "JC"}, {"family": "Chasman", "given": "Daniel I", "initials": "DI"}, {"family": "Chen", "given": "Yii Der Ida", "initials": "YDI"}, {"family": "Chen", "given": "Yduan Tsong", "initials": "YT"}, {"family": "Cheng", "given": "Ching Yu", "initials": "CY"}, {"family": "Cucca", "given": "Francesco", "initials": "F"}, {"family": "de Geus", "given": "Eco J C", "initials": "EJC"}, {"family": "Deloukas", "given": "Panos", "initials": "P"}, {"family": "Evans", "given": "Michele K", "initials": "MK"}, {"family": "Fornage", "given": "Myriam", "initials": "M"}, {"family": "Friedlander", "given": "Yechiel", "initials": "Y"}, {"family": "Froguel", "given": "Philippe", "initials": "P"}, {"family": "Groop", "given": "Leif", "initials": "L"}, {"family": "Gross", "given": "Myron D", "initials": "MD"}, {"family": "Harris", "given": "Tamara B", "initials": "TB"}, {"family": "Hayward", "given": "Caroline", "initials": "C"}, {"family": "Heng", "given": "Chew Kiat", "initials": "CK"}, {"family": "Ingelsson", "given": "Erik", "initials": "E"}, {"family": "Kato", "given": "Norihiro", "initials": "N"}, {"family": "Kim", "given": "Bong Jo", "initials": "BJ"}, {"family": "Koh", "given": "Woon Puay", "initials": "WP"}, {"family": "Kooner", "given": "Jaspal S", "initials": "JS"}, {"family": "K\u00f6rner", "given": "Antje", "initials": "A"}, {"family": "Kuh", "given": "Diana", "initials": "D"}, {"family": "Kuusisto", "given": "Johanna", "initials": "J"}, {"family": "Laakso", "given": "Markku", "initials": "M"}, {"family": "Lin", "given": "Xu", "initials": "X"}, {"family": "Liu", "given": "Yongmei", "initials": "Y"}, {"family": "Loos", "given": "Ruth J F", "initials": "RJF"}, {"family": "Magnusson", "given": "Patrik K E", "initials": "PKE"}, {"family": "M\u00e4rz", "given": "Winfried", "initials": "W"}, {"family": "McCarthy", "given": "Mark I", "initials": "MI"}, {"family": "Oldehinkel", "given": "Albertine J", "initials": "AJ"}, {"family": "Ong", "given": "Ken K", "initials": "KK"}, {"family": "Pedersen", "given": "Nancy L", "initials": "NL"}, {"family": "Pereira", "given": "Mark A", "initials": "MA"}, {"family": "Peters", "given": "Annette", "initials": "A"}, {"family": "Ridker", "given": "Paul M", "initials": "PM"}, {"family": "Sabanayagam", "given": "Charumathi", "initials": "C"}, {"family": "Sale", "given": "Michele", "initials": "M"}, {"family": "Saleheen", "given": "Danish", "initials": "D"}, {"family": "Saltevo", "given": "Juha", "initials": "J"}, {"family": "Schwarz", "given": "Peter EH", "initials": "PE"}, {"family": "Sheu", "given": "Wayne H H", "initials": "WHH"}, {"family": "Snieder", "given": "Harold", "initials": "H"}, {"family": "Spector", "given": "Timothy D", "initials": "TD"}, {"family": "Tabara", "given": "Yasuharu", "initials": "Y"}, {"family": "Tuomilehto", "given": "Jaakko", "initials": "J"}, {"family": "van Dam", "given": "Rob M", "initials": "RM"}, {"family": "Wilson", "given": "James G", "initials": "JG"}, {"family": "Wilson", "given": "James F", "initials": "JF"}, {"family": "Wolffenbuttel", "given": "Bruce H R", "initials": "BHR"}, {"family": "Wong", "given": "Tien Yin", "initials": "TY"}, {"family": "Wu", "given": "Jer Yuarn", "initials": "JY"}, {"family": "Yuan", "given": "Jian Min", "initials": "JM"}, {"family": "Zonderman", "given": "Alan B", "initials": "AB"}, {"family": "Soranzo", "given": "Nicole", "initials": "N"}, {"family": "Guo", "given": "Xiuqing", "initials": "X"}, {"family": "Roberts", "given": "David J", "initials": "DJ"}, {"family": "Florez", "given": "Jose C", "initials": "JC"}, {"family": "Sladek", "given": "Robert", "initials": "R"}, {"family": "Dupuis", "given": "Jos\u00e9e", "initials": "J"}, {"family": "Morris", "given": "Andrew P", "initials": "AP"}, {"family": "Tai", "given": "E Shyong", "initials": "ES"}, {"family": "Selvin", "given": "Elizabeth", "initials": "E"}, {"family": "Rotter", "given": "Jerome I", "initials": "JI"}, {"family": "Langenberg", "given": "Claudia", "initials": "C"}, {"family": "Barroso", "given": "In\u00eas", "initials": "I"}, {"family": "Meigs", "given": "James B", "initials": "JB"}, {"family": null, "given": "", "initials": ""}, {"family": null, "given": "", "initials": ""}, {"family": null, "given": "", "initials": ""}], "type": "journal-article", "published": "2017-09-12", "journal": {"volume": "14", "issn": "1549-1676", "issue": "9", "pages": "e1002383", "title": "PLoS Med.", "issn-l": "1549-1277"}, "abstract": null, "doi": "10.1371/journal.pmed.1002383", "pmid": "28898252", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "MAGIC", "description": "spreadsheets (tsv)", "key": "https://www.magicinvestigators.org/downloads/"}], "notes": [], "created": "2018-01-09T13:55:53.834Z", "modified": "2020-01-21T13:56:11.937Z"}, {"entity": "publication", "iuid": "186d9c669252431592bb26afb3bcb39d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/186d9c669252431592bb26afb3bcb39d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/186d9c669252431592bb26afb3bcb39d"}}, "title": "A practical guide to build de-novo assemblies for single tissues of non-model organisms: the example of a Neotropical frog", "authors": [{"family": "Montero-Mendieta", "given": "Santiago", "initials": "S"}, {"family": "Grabherr", "given": "Manfred", "initials": "M"}, {"family": "Lantz", "given": "Henrik", "initials": "H"}, {"family": "De la Riva", "given": "Ignacio", "initials": "I"}, {"family": "Leonard", "given": "Jennifer A", "initials": "JA"}, {"family": "Webster", "given": "Matthew T", "initials": "MT"}, {"family": "Vil\u00e0", "given": "Carles", "initials": "C"}], "type": "journal-article", "published": "2017-09-01", "journal": {"volume": "5", "issn": "2167-8359", "issue": null, "pages": "e3702", "title": "PeerJ", "issn-l": "2167-8359"}, "abstract": "Whole genome sequencing (WGS) is a very valuable resource to understand the evolutionary history of poorly known species. However, in organisms with large genomes, as most amphibians, WGS is still excessively challenging and transcriptome sequencing (RNA-seq) represents a cost-effective tool to explore genome-wide variability. Non-model organisms do not usually have a reference genome and the transcriptome must be assembled \n            de-novo. We used RNA-seq to obtain the transcriptomic profile for Oreobates cruralis, a poorly known South American direct-developing frog. In total, 550,871 transcripts were assembled, corresponding to 422,999 putative genes. Of those, we identified 23,500, 37,349, 38,120 and 45,885 genes present in the Pfam, EggNOG, KEGG and GO databases, respectively. Interestingly, our results suggested that genes related to immune system and defense mechanisms are abundant in the transcriptome of O. cruralis. We also present a pipeline to assist with pre-processing, assembling, evaluating and functionally annotating a de-novo transcriptome from RNA-seq data of non-model organisms. Our pipeline guides the inexperienced user in an intuitive way through all the necessary steps to build de-novo transcriptome assemblies using readily available software and is freely available at: https://github.com/biomendi/TRANSCRIPTOME-ASSEMBLY-PIPELINE/wiki.", "doi": "10.7717/peerj.3702", "pmid": "28879061", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "SRA", "description": null, "key": "SRP106442"}, {"db": "GENBANK", "description": "TSA: Oreobates cruralis, transcriptome shotgun assembly", "key": "GFNJ00000000"}, {"db": "BioProject", "description": "Oreobates cruralis isolate:MNCN/ADN:65263 Transcriptome or Gene expression", "key": "PRJNA384528"}], "notes": [], "created": "2017-10-30T09:27:45.542Z", "modified": "2024-01-16T13:48:47.564Z"}, {"entity": "publication", "iuid": "e3ed08c8a4f04017b148c7c3bd163285", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e3ed08c8a4f04017b148c7c3bd163285.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e3ed08c8a4f04017b148c7c3bd163285"}}, "title": "The relative contribution of DNA methylation and genetic variants on protein biomarkers for human diseases.", "authors": [{"family": "Ahsan", "given": "Muhammad", "initials": "M"}, {"family": "Ek", "given": "Weronica E", "initials": "WE"}, {"family": "Rask-Andersen", "given": "Mathias", "initials": "M"}, {"family": "Karlsson", "given": "Torgny", "initials": "T"}, {"family": "Lind-Thomsen", "given": "Allan", "initials": "A"}, {"family": "Enroth", "given": "Stefan", "initials": "S"}, {"family": "Gyllensten", "given": "Ulf", "initials": "U"}, {"family": "Johansson", "given": "\u00c5sa", "initials": "\u00c5"}], "type": "journal article", "published": "2017-09-00", "journal": {"volume": "13", "issn": "1553-7404", "issue": "9", "pages": "e1007005", "title": "PLoS Genet.", "issn-l": "1553-7390"}, "abstract": "Associations between epigenetic alterations and disease status have been identified for many diseases. However, there is no strong evidence that epigenetic alterations are directly causal for disease pathogenesis. In this study, we combined SNP and DNA methylation data with measurements of protein biomarkers for cancer, inflammation or cardiovascular disease, to investigate the relative contribution of genetic and epigenetic variation on biomarker levels. A total of 121 protein biomarkers were measured and analyzed in relation to DNA methylation at 470,000 genomic positions and to over 10 million SNPs. We performed epigenome-wide association study (EWAS) and genome-wide association study (GWAS) analyses, and integrated biomarker, DNA methylation and SNP data using between 698 and 1033 samples depending on data availability for the different analyses. We identified 124 and 45 loci (Bonferroni adjusted P < 0.05) with effect sizes up to 0.22 standard units' change per 1% change in DNA methylation levels and up to four standard units' change per copy of the effective allele in the EWAS and GWAS respectively. Most GWAS loci were cis-regulatory whereas most EWAS loci were located in trans. Eleven EWAS loci were associated with multiple biomarkers, including one in NLRC5 associated with CXCL11, CXCL9, IL-12, and IL-18 levels. All EWAS signals that overlapped with a GWAS locus were driven by underlying genetic variants and three EWAS signals were confounded by smoking. While some cis-regulatory SNPs for biomarkers appeared to have an effect also on DNA methylation levels, cis-regulatory SNPs for DNA methylation were not observed to affect biomarker levels. We present associations between protein biomarker and DNA methylation levels at numerous loci in the genome. The associations are likely to reflect the underlying pattern of genetic variants, specific environmental exposures, or represent secondary effects to the pathogenesis of disease.", "doi": "10.1371/journal.pgen.1007005", "pmid": "28915241", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "PGENETICS-D-17-00622"}, {"db": "pmc", "key": "PMC5617224"}, {"db": "GEO", "description": "sequences", "key": "GSE87571"}], "notes": [], "created": "2017-10-25T15:27:49.784Z", "modified": "2024-01-16T13:48:47.571Z"}, {"entity": "publication", "iuid": "d07e00d31a13460682d9cb1e01855da0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d07e00d31a13460682d9cb1e01855da0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d07e00d31a13460682d9cb1e01855da0"}}, "title": "Regulation of gene expression is associated with tolerance of the Arctic copepod Calanus glacialis to CO2-acidified sea water", "authors": [{"family": "Bailey", "given": "Allison", "initials": "A"}, {"family": "De Wit", "given": "Pierre", "initials": "P"}, {"family": "Thor", "given": "Peter", "initials": "P"}, {"family": "Browman", "given": "Howard I", "initials": "HI"}, {"family": "Bjelland", "given": "Reidun", "initials": "R"}, {"family": "Shema", "given": "Steven", "initials": "S"}, {"family": "Fields", "given": "David M", "initials": "DM"}, {"family": "Runge", "given": "Jeffrey A", "initials": "JA"}, {"family": "Thompson", "given": "Cameron", "initials": "C"}, {"family": "Hop", "given": "Haakon", "initials": "H"}], "type": "journal-article", "published": "2017-09-00", "journal": {"volume": "7", "issn": "2045-7758", "issue": "18", "pages": "7145-7160", "title": "Ecol Evol", "issn-l": "2045-7758"}, "abstract": null, "doi": "10.1002/ece3.3063", "pmid": "28944006", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "BioProject", "description": "Calanus glacialis Transcriptome or Gene expression", "key": "PRJNA352656"}, {"db": "SRA", "description": null, "key": "SRP092884"}], "notes": [], "created": "2018-01-09T20:49:54.365Z", "modified": "2020-01-21T13:56:14.887Z"}, {"entity": "publication", "iuid": "fd24c7f3c9d14b86bcabb5a7734c46a5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/fd24c7f3c9d14b86bcabb5a7734c46a5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/fd24c7f3c9d14b86bcabb5a7734c46a5"}}, "title": "A genomic exploration identifies mechanisms that may explain adverse cardiovascular effects of COX-2 inhibitors.", "authors": [{"family": "Br\u00e6nne", "given": "Ingrid", "initials": "I"}, {"family": "Willenborg", "given": "Christina", "initials": "C"}, {"family": "Tragante", "given": "Vinicius", "initials": "V"}, {"family": "Kessler", "given": "Thorsten", "initials": "T"}, {"family": "Zeng", "given": "Lingyao", "initials": "L"}, {"family": "Reiz", "given": "Benedikt", "initials": "B"}, {"family": "Kleinecke", "given": "Mariana", "initials": "M"}, {"family": "von Ameln", "given": "Simon", "initials": "S"}, {"family": "Willer", "given": "Cristen J", "initials": "CJ"}, {"family": "Laakso", "given": "Markku", "initials": "M"}, {"family": "Wild", "given": "Philipp S", "initials": "PS"}, {"family": "Zeller", "given": "Tanja", "initials": "T"}, {"family": "Wallentin", "given": "Lars", "initials": "L"}, {"family": "Franks", "given": "Paul W", "initials": "PW"}, {"family": "Salomaa", "given": "Veikko", "initials": "V"}, {"family": "Dehghan", "given": "Abbas", "initials": "A"}, {"family": "Meitinger", "given": "Thomas", "initials": "T"}, {"family": "Samani", "given": "Nilesh J", "initials": "NJ"}, {"family": "Asselbergs", "given": "Folkert W", "initials": "FW"}, {"family": "Erdmann", "given": "Jeanette", "initials": "J"}, {"family": "Schunkert", "given": "Heribert", "initials": "H"}], "type": "journal article", "published": "2017-08-31", "journal": {"volume": "7", "issn": "2045-2322", "issue": "1", "pages": "10252", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "Cyclooxygenase-2 inhibitors (coxibs) are characterized by multiple molecular off-target effects and increased coronary artery disease (CAD) risk. Here, we systematically explored common variants of genes representing molecular targets of coxibs for association with CAD. Given a broad spectrum of pleiotropic effects of coxibs, our intention was to narrow potential mechanisms affecting CAD risk as we hypothesized that the affected genes may also display genomic signals of coronary disease risk. A Drug Gene Interaction Database search identified 47 gene products to be affected by coxibs. We traced association signals in 200-kb regions surrounding these genes in 84,813 CAD cases and 202,543 controls. Based on a threshold of 1\u2009\u00d7\u200910(-5) (Bonferroni correction for 3131 haplotype blocks), four gene loci yielded significant associations. The lead SNPs were rs7270354 (MMP9), rs4888383 (BCAR1), rs6905288 (VEGFA1), and rs556321 (CACNA1E). By additional genotyping, rs7270354 at MMP9 and rs4888383 at BCAR1 also reached the established GWAS threshold for genome-wide significance. The findings demonstrate overlap of genes affected by coxibs and those mediating CAD risk and points to further mechanisms, which are potentially responsible for coxib-associated CAD risk. The novel approach furthermore suggests that genetic studies may be useful to explore the clinical relevance of off-target drug effects.", "doi": "10.1038/s41598-017-10928-4", "pmid": "28860667", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-017-10928-4"}, {"db": "pmc", "key": "PMC5579257"}], "notes": [], "created": "2017-10-25T15:27:50.730Z", "modified": "2024-01-16T13:48:47.586Z"}, {"entity": "publication", "iuid": "f29099c2af6a4d45a91f29c169b87c86", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f29099c2af6a4d45a91f29c169b87c86.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f29099c2af6a4d45a91f29c169b87c86"}}, "title": "Genomic correlates of glatiramer acetate adverse cardiovascular effects lead to a novel locus mediating coronary risk", "authors": [{"family": "Br\u00e6nne", "given": "Ingrid", "initials": "I"}, {"family": "Zeng", "given": "Lingyao", "initials": "L"}, {"family": "Willenborg", "given": "Christina", "initials": "C"}, {"family": "Tragante", "given": "Vinicius", "initials": "V"}, {"family": "Kessler", "given": "Thorsten", "initials": "T"}, {"family": "Willer", "given": "Cristen J", "initials": "CJ"}, {"family": "Laakso", "given": "Markku", "initials": "M"}, {"family": "Wallentin", "given": "Lars", "initials": "L"}, {"family": "Franks", "given": "Paul W", "initials": "PW"}, {"family": "Salomaa", "given": "Veikko", "initials": "V"}, {"family": "Dehghan", "given": "Abbas", "initials": "A"}, {"family": "Meitinger", "given": "Thomas", "initials": "T"}, {"family": "Samani", "given": "Nilesh J", "initials": "NJ"}, {"family": "Asselbergs", "given": "Folkert W", "initials": "FW"}, {"family": "Erdmann", "given": "Jeanette", "initials": "J"}, {"family": "Schunkert", "given": "Heribert", "initials": "H"}, {"family": null, "given": "", "initials": ""}, {"family": null, "given": "", "initials": ""}], "type": "journal-article", "published": "2017-08-22", "journal": {"volume": "12", "issn": "1932-6203", "issue": "8", "pages": "e0182999", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": null, "doi": "10.1371/journal.pone.0182999", "pmid": "28829817", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [], "notes": [], "created": "2018-01-09T13:55:54.435Z", "modified": "2020-01-21T13:56:11.919Z"}, {"entity": "publication", "iuid": "142739defdfa4835934e427e05a7af39", "links": {"self": {"href": "https://publications.scilifelab.se/publication/142739defdfa4835934e427e05a7af39.json"}, "display": {"href": "https://publications.scilifelab.se/publication/142739defdfa4835934e427e05a7af39"}}, "title": "Tea and coffee consumption in relation to DNA methylation in four European cohorts.", "authors": [{"family": "Ek", "given": "Weronica E", "initials": "WE"}, {"family": "Tobi", "given": "Elmar W", "initials": "EW"}, {"family": "Ahsan", "given": "Muhammad", "initials": "M"}, {"family": "Lampa", "given": "Erik", "initials": "E"}, {"family": "Ponzi", "given": "Erica", "initials": "E"}, {"family": "Kyrtopoulos", "given": "Soterios A", "initials": "SA"}, {"family": "Georgiadis", "given": "Panagiotis", "initials": "P"}, {"family": "Lumey", "given": "L H", "initials": "LH"}, {"family": "Heijmans", "given": "Bastiaan T", "initials": "BT"}, {"family": "Botsivali", "given": "Maria", "initials": "M"}, {"family": "Bergdahl", "given": "Ingvar A", "initials": "IA"}, {"family": "Karlsson", "given": "Torgny", "initials": "T"}, {"family": "Rask-Andersen", "given": "Mathias", "initials": "M"}, {"family": "Palli", "given": "Domenico", "initials": "D"}, {"family": "Ingelsson", "given": "Erik", "initials": "E"}, {"family": "Hedman", "given": "\u00c5sa K", "initials": "\u00c5K"}, {"family": "Nilsson", "given": "Lena M", "initials": "LM"}, {"family": "Vineis", "given": "Paolo", "initials": "P"}, {"family": "Lind", "given": "Lars", "initials": "L"}, {"family": "Flanagan", "given": "James M", "initials": "JM"}, {"family": "Johansson", "given": "\u00c5sa", "initials": "\u00c5"}, {"family": "Epigenome-Wide Association Study Consortium", "given": "", "initials": ""}], "type": "journal article", "published": "2017-08-15", "journal": {"volume": "26", "issn": "1460-2083", "issue": "16", "pages": "3221-3231", "title": "Hum. Mol. Genet.", "issn-l": "0964-6906"}, "abstract": "Lifestyle factors, such as food choices and exposure to chemicals, can alter DNA methylation and lead to changes in gene activity. Two such exposures with pharmacologically active components are coffee and tea consumption. Both coffee and tea have been suggested to play an important role in modulating disease-risk in humans by suppressing tumour progression, decreasing inflammation and influencing estrogen metabolism. These mechanisms may be mediated by changes in DNA methylation. To investigate if DNA methylation in blood is associated with coffee and tea consumption, we performed a genome-wide DNA methylation study for coffee and tea consumption in four European cohorts (N\u2009=\u20093,096). DNA methylation was measured from whole blood at 421,695 CpG sites distributed throughout the genome and analysed in men and women both separately and together in each cohort. Meta-analyses of the results and additional regional-level analyses were performed. After adjusting for multiple testing, the meta-analysis revealed that two individual CpG-sites, mapping to DNAJC16 and TTC17, were differentially methylated in relation to tea consumption in women. No individual sites were associated with men or with the sex-combined analysis for tea or coffee. The regional analysis revealed that 28 regions were differentially methylated in relation to tea consumption in women. These regions contained genes known to interact with estradiol metabolism and cancer. No significant regions were found in the sex-combined and male-only analysis for either tea or coffee consumption.", "doi": "10.1093/hmg/ddx194", "pmid": "28535255", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "3848993"}], "notes": [], "created": "2017-10-25T15:18:22.652Z", "modified": "2024-01-16T13:48:47.609Z"}, {"entity": "publication", "iuid": "29256f43a3fd4115a18d255f5802b221", "links": {"self": {"href": "https://publications.scilifelab.se/publication/29256f43a3fd4115a18d255f5802b221.json"}, "display": {"href": "https://publications.scilifelab.se/publication/29256f43a3fd4115a18d255f5802b221"}}, "title": "Transcriptome sequencing in pediatric acute lymphoblastic leukemia identifies fusion genes associated with distinct DNA methylation profiles.", "authors": [{"family": "Marincevic-Zuniga", "given": "Yanara", "initials": "Y"}, {"family": "Dahlberg", "given": "Johan", "initials": "J"}, {"family": "Nilsson", "given": "Sara", "initials": "S"}, {"family": "Raine", "given": "Amanda", "initials": "A"}, {"family": "Nystedt", "given": "Sara", "initials": "S"}, {"family": "Lindqvist", "given": "Carl M\u00e5rten", "initials": "CM"}, {"family": "Berglund", "given": "Eva C", "initials": "EC"}, {"family": "Abrahamsson", "given": "Jonas", "initials": "J"}, {"family": "Cavelier", "given": "Lucia", "initials": "L", "orcid": "0009-0003-8195-370X", "researcher": {"href": "https://publications.scilifelab.se/researcher/f01226edb140436da0c9d166c1f5fe51.json"}}, {"family": "Forestier", "given": "Erik", "initials": "E"}, {"family": "Heyman", "given": "Mats", "initials": "M"}, {"family": "L\u00f6nnerholm", "given": "Gudmar", "initials": "G"}, {"family": "Nordlund", "given": "Jessica", "initials": "J", "orcid": "0000-0001-8699-9959", "researcher": {"href": "https://publications.scilifelab.se/researcher/ddf48c9262134821bcc6ce1180049753.json"}}, {"family": "Syv\u00e4nen", "given": "Ann-Christine", "initials": "AC", "orcid": "0000-0002-9681-9146", "researcher": {"href": "https://publications.scilifelab.se/researcher/f7012e35025543379380cb90efd71243.json"}}], "type": "journal article", "published": "2017-08-14", "journal": {"volume": "10", "issn": "1756-8722", "issue": "1", "pages": "148", "title": "J Hematol Oncol", "issn-l": "1756-8722"}, "abstract": "Structural chromosomal rearrangements that lead to expressed fusion genes are a hallmark of acute lymphoblastic leukemia (ALL). In this study, we performed transcriptome sequencing of 134 primary ALL patient samples to comprehensively detect fusion transcripts.\n\nWe combined fusion gene detection with genome-wide DNA methylation analysis, gene expression profiling, and targeted sequencing to determine molecular signatures of emerging ALL subtypes.\n\nWe identified 64 unique fusion events distributed among 80 individual patients, of which over 50% have not previously been reported in ALL. Although the majority of the fusion genes were found only in a single patient, we identified several recurrent fusion gene families defined by promiscuous fusion gene partners, such as ETV6, RUNX1, PAX5, and ZNF384, or recurrent fusion genes, such as DUX4-IGH. Our data show that patients harboring these fusion genes displayed characteristic genome-wide DNA methylation and gene expression signatures in addition to distinct patterns in single nucleotide variants and recurrent copy number alterations.\n\nOur study delineates the fusion gene landscape in pediatric ALL, including both known and novel fusion genes, and highlights fusion gene families with shared molecular etiologies, which may provide additional information for prognosis and therapeutic options in the future.", "doi": "10.1186/s13045-017-0515-y", "pmid": "28806978", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Clinical Genomics Uppsala": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Clinical Genomics": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1186/s13045-017-0515-y"}, {"db": "pmc", "key": "PMC5557398"}], "notes": [], "created": "2017-10-30T09:26:29.124Z", "modified": "2024-01-16T13:48:47.617Z"}, {"entity": "publication", "iuid": "8b7c4d75fc1a4d75ab4c9519a85a6c35", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8b7c4d75fc1a4d75ab4c9519a85a6c35.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8b7c4d75fc1a4d75ab4c9519a85a6c35"}}, "title": "Drift, selection, or migration? Processes affecting genetic differentiation and variation along a latitudinal gradient in an amphibian.", "authors": [{"family": "Cort\u00e1zar-Chinarro", "given": "Maria", "initials": "M"}, {"family": "Lattenkamp", "given": "Ella Z", "initials": "EZ"}, {"family": "Meyer-Lucht", "given": "Yvonne", "initials": "Y"}, {"family": "Luquet", "given": "Emilien", "initials": "E"}, {"family": "Laurila", "given": "Anssi", "initials": "A"}, {"family": "H\u00f6glund", "given": "Jacob", "initials": "J"}], "type": "journal article", "published": "2017-08-14", "journal": {"volume": "17", "issn": "1471-2148", "issue": "1", "pages": "189", "title": "BMC Evol. Biol.", "issn-l": "1471-2148"}, "abstract": "Past events like fluctuations in population size and post-glacial colonization processes may influence the relative importance of genetic drift, migration and selection when determining the present day patterns of genetic variation. We disentangle how drift, selection and migration shape neutral and adaptive genetic variation in 12 moor frog populations along a 1700 km latitudinal gradient. We studied genetic differentiation and variation at a MHC exon II locus and a set of 18 microsatellites.\n\nUsing outlier analyses, we identified the MHC II exon 2 (corresponding to the \u03b2-2 domain) locus and one microsatellite locus (RCO8640) to be subject to diversifying selection, while five microsatellite loci showed signals of stabilizing selection among populations. STRUCTURE and DAPC analyses on the neutral microsatellites assigned populations to a northern and a southern cluster, reflecting two different post-glacial colonization routes found in previous studies. Genetic variation overall was lower in the northern cluster. The signature of selection on MHC exon II was weaker in the northern cluster, possibly as a consequence of smaller and more fragmented populations.\n\nOur results show that historical demographic processes combined with selection and drift have led to a complex pattern of differentiation along the gradient where some loci are more divergent among populations than predicted from drift expectations due to diversifying selection, while other loci are more uniform among populations due to stabilizing selection. Importantly, both overall and MHC genetic variation are lower at northern latitudes. Due to lower evolutionary potential, the low genetic variation in northern populations may increase the risk of extinction when confronted with emerging pathogens and climate change.", "doi": "10.1186/s12862-017-1022-z", "pmid": "28806900", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1186/s12862-017-1022-z"}, {"db": "pmc", "key": "PMC5557520"}], "notes": [], "created": "2018-01-09T20:49:55.495Z", "modified": "2021-06-21T14:58:37.712Z"}, {"entity": "publication", "iuid": "61acb9a9d7df4876a2dfbd51ace9511a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/61acb9a9d7df4876a2dfbd51ace9511a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/61acb9a9d7df4876a2dfbd51ace9511a"}}, "title": "Genomic exploration of the diversity, ecology, and evolution of the archaeal domain of life", "authors": [{"family": "Spang", "given": "Anja", "initials": "A"}, {"family": "Caceres", "given": "Eva F", "initials": "EF"}, {"family": "Ettema", "given": "Thijs J G", "initials": "TJG"}], "type": "journal-article", "published": "2017-08-11", "journal": {"volume": "357", "issn": "1095-9203", "issue": "6351", "pages": "eaaf3883", "title": "Science", "issn-l": "0036-8075"}, "abstract": null, "doi": "10.1126/science.aaf3883", "pmid": "28798101", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2017-10-30T09:27:44.609Z", "modified": "2024-01-16T13:48:47.624Z"}, {"entity": "publication", "iuid": "9b3c47e1ea0843e3a015238ec949a229", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9b3c47e1ea0843e3a015238ec949a229.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9b3c47e1ea0843e3a015238ec949a229"}}, "title": "Comparison of four DNA extraction methods for comprehensive assessment of 16S rRNA bacterial diversity in marine biofilms using high-throughput sequencing", "authors": [{"family": "Corcoll", "given": "Nat\u00e0lia", "initials": "N"}, {"family": "\u00d6sterlund", "given": "Tobias", "initials": "T"}, {"family": "Sinclair", "given": "Lucas", "initials": "L"}, {"family": "Eiler", "given": "Alexander", "initials": "A"}, {"family": "Kristiansson", "given": "Erik", "initials": "E"}, {"family": "Backhaus", "given": "Thomas", "initials": "T"}, {"family": "Eriksson", "given": "K Martin", "initials": "KM"}], "type": "journal-article", "published": "2017-08-01", "journal": {"volume": "364", "issn": "1574-6968", "issue": "14", "pages": null, "title": "FEMS Microbiol. Lett.", "issn-l": "0378-1097"}, "abstract": null, "doi": "10.1093/femsle/fnx139", "pmid": "28673033", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "BioProject", "description": null, "key": "PRJNA378915"}], "notes": [], "created": "2017-10-30T09:27:43.376Z", "modified": "2024-01-16T13:48:47.653Z"}, {"entity": "publication", "iuid": "d7cca67c91f44fdeb9f673db8956d17b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d7cca67c91f44fdeb9f673db8956d17b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d7cca67c91f44fdeb9f673db8956d17b"}}, "title": "Whole-genome patterns of linkage disequilibrium across flycatcher populations clarify the causes and consequences of fine-scale recombination rate variation in birds", "authors": [{"family": "Kawakami", "given": "Takeshi", "initials": "T"}, {"family": "Mugal", "given": "Carina F", "initials": "CF"}, {"family": "Suh", "given": "Alexander", "initials": "A"}, {"family": "Nater", "given": "Alexander", "initials": "A"}, {"family": "Burri", "given": "Reto", "initials": "R"}, {"family": "Smeds", "given": "Linn\u00e9a", "initials": "L"}, {"family": "Ellegren", "given": "Hans", "initials": "H"}], "type": "journal-article", "published": "2017-08-00", "journal": {"volume": "26", "issn": "0962-1083", "issue": "16", "pages": "4158-4172", "title": "Mol Ecol", "issn-l": "0962-1083"}, "abstract": null, "doi": "10.1111/mec.14197", "pmid": "28597534", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "BioProject", "description": "Genetic variation in Ficedula flycatchers", "key": "PRJEB7359"}, {"db": "Dryad", "description": null, "key": "https://doi.org/10.5061/dryad.hp5h2"}], "notes": [], "created": "2018-01-09T20:51:44.961Z", "modified": "2020-01-21T13:56:11.900Z"}, {"entity": "publication", "iuid": "afb5a02c1c6643a6b4c048017818af1b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/afb5a02c1c6643a6b4c048017818af1b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/afb5a02c1c6643a6b4c048017818af1b"}}, "title": "Poorly known microbial taxa dominate the microbiome of permafrost thaw ponds", "authors": [{"family": "Wurzbacher", "given": "Christian", "initials": "C"}, {"family": "Nilsson", "given": "R Henrik", "initials": "RH"}, {"family": "Rautio", "given": "Milla", "initials": "M"}, {"family": "Peura", "given": "Sari", "initials": "S"}], "type": "journal-article", "published": "2017-08-00", "journal": {"volume": "11", "issn": "1751-7370", "issue": "8", "pages": "1938-1941", "title": "ISME J", "issn-l": "1751-7362"}, "abstract": null, "doi": "10.1038/ismej.2017.54", "pmid": "28430187", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "BioProject", "description": "Poorly known microbial taxa dominate the microbiome of permafrost thaw ponds", "key": "PRJEB18117"}], "notes": [], "created": "2018-01-09T20:57:48.038Z", "modified": "2020-01-21T13:56:11.889Z"}, {"entity": "publication", "iuid": "7119a4bbab9f46d2a03b17b778804251", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7119a4bbab9f46d2a03b17b778804251.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7119a4bbab9f46d2a03b17b778804251"}}, "title": "Northeast African genomic variation shaped by the continuity of indigenous groups and Eurasian migrations.", "authors": [{"family": "Hollfelder", "given": "Nina", "initials": "N"}, {"family": "Schlebusch", "given": "Carina M", "initials": "CM", "orcid": "0000-0002-8160-9621", "researcher": {"href": "https://publications.scilifelab.se/researcher/682f10853c1145649b8c76680605dd9b.json"}}, {"family": "G\u00fcnther", "given": "Torsten", "initials": "T", "orcid": "0000-0001-9460-390X", "researcher": {"href": "https://publications.scilifelab.se/researcher/84159bff82a64a938bcff107f550c901.json"}}, {"family": "Babiker", "given": "Hiba", "initials": "H"}, {"family": "Hassan", "given": "Hisham Y", "initials": "HY", "orcid": "0000-0003-0026-5781", "researcher": {"href": "https://publications.scilifelab.se/researcher/df40ecb572c5470e9bd4368095fdb308.json"}}, {"family": "Jakobsson", "given": "Mattias", "initials": "M", "orcid": "0000-0001-7840-7853", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a4abe0fcb20492d9ec849c9fbf58a71.json"}}], "type": "journal article", "published": "2017-08-00", "journal": {"volume": "13", "issn": "1553-7404", "issue": "8", "pages": "e1006976", "title": "PLoS Genet.", "issn-l": "1553-7390"}, "abstract": "Northeast Africa has a long history of human habitation, with fossil-finds from the earliest anatomically modern humans, and housing ancient civilizations. The region is also the gate-way out of Africa, as well as a portal for migration into Africa from Eurasia via the Middle East and the Arabian Peninsula. We investigate the population history of northeast Africa by genotyping ~3.9 million SNPs in 221 individuals from 18 populations sampled in Sudan and South Sudan and combine this data with published genome-wide data from surrounding areas. We find a strong genetic divide between the populations from the northeastern parts of the region (Nubians, central Arab populations, and the Beja) and populations towards the west and south (Nilotes, Darfur and Kordofan populations). This differentiation is mainly caused by a large Eurasian ancestry component of the northeast populations likely driven by migration of Middle Eastern groups followed by admixture that affected the local populations in a north-to-south succession of events. Genetic evidence points to an early admixture event in the Nubians, concurrent with historical contact between North Sudanese and Arab groups. We estimate the admixture in current-day Sudanese Arab populations to about 700 years ago, coinciding with the fall of Dongola in 1315/1316 AD, a wave of admixture that reached the Darfurian/Kordofanian populations some 400-200 years ago. In contrast to the northeastern populations, the current-day Nilotic populations from the south of the region display little or no admixture from Eurasian groups indicating long-term isolation and population continuity in these areas of northeast Africa.", "doi": "10.1371/journal.pgen.1006976", "pmid": "28837655", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "PGENETICS-D-17-00483"}, {"db": "pmc", "key": "PMC5587336"}], "notes": [], "created": "2017-10-25T15:27:45.744Z", "modified": "2024-01-16T13:48:47.667Z"}, {"entity": "publication", "iuid": "11a0e20f7a4b4d8fb8049f4e5f2d5e70", "links": {"self": {"href": "https://publications.scilifelab.se/publication/11a0e20f7a4b4d8fb8049f4e5f2d5e70.json"}, "display": {"href": "https://publications.scilifelab.se/publication/11a0e20f7a4b4d8fb8049f4e5f2d5e70"}}, "title": "Low-Frequency Synonymous Coding Variation in  CYP2R1  Has Large Effects on Vitamin D Levels and Risk of Multiple Sclerosis", "authors": [{"family": "Manousaki", "given": "Despoina", "initials": "D"}, {"family": "Dudding", "given": "Tom", "initials": "T"}, {"family": "Haworth", "given": "Simon", "initials": "S"}, {"family": "Hsu", "given": "Yi Hsiang", "initials": "YH"}, {"family": "Liu", "given": "Ching Ti", "initials": "CT"}, {"family": "Medina-G\u00f3mez", "given": "Carolina", "initials": "C"}, {"family": "Voortman", "given": "Trudy", "initials": "T"}, {"family": "van der Velde", "given": "Nathalie", "initials": "N"}, {"family": "Melhus", "given": "H\u00e5kan", "initials": "H"}, {"family": "Robinson-Cohen", "given": "Cassianne", "initials": "C"}, {"family": "Cousminer", "given": "Diana L", "initials": "DL"}, {"family": "Nethander", "given": "Maria", "initials": "M"}, {"family": "Vandenput", "given": "Liesbeth", "initials": "L"}, {"family": "Noordam", "given": "Raymond", "initials": "R"}, 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"Rie", "initials": "R"}, {"family": "Pietil\u00e4inen", "given": "Kirsi H", "initials": "KH"}, {"family": "Rissanen", "given": "Aila", "initials": "A"}, {"family": "Siribaddana", "given": "Sisira H", "initials": "SH"}, {"family": "Hotopf", "given": "Matthew", "initials": "M"}, {"family": "Sumathipala", "given": "Athula", "initials": "A"}, {"family": "Rijsdijk", "given": "Fruhling", "initials": "F"}, {"family": "Tan", "given": "Qihua", "initials": "Q"}, {"family": "Zhang", "given": "Dongfeng", "initials": "D"}, {"family": "Pang", "given": "Zengchang", "initials": "Z"}, {"family": "Piirtola", "given": "Maarit", "initials": "M"}, {"family": "Aaltonen", "given": "Sari", "initials": "S"}, {"family": "\u00d6ncel", "given": "Sevgi Y", "initials": "SY"}, {"family": "Aliev", "given": "Fazil", "initials": "F"}, {"family": "Rebato", "given": "Esther", "initials": "E"}, {"family": "Hjelmborg", "given": "Jacob B", "initials": "JB"}, {"family": "Christensen", "given": "Kaare", "initials": "K"}, {"family": "Skytthe", "given": "Axel", "initials": "A"}, {"family": "Kyvik", "given": "Kirsten O", "initials": "KO"}, {"family": "Silberg", "given": "Judy L", "initials": "JL"}, {"family": "Eaves", "given": "Lindon J", "initials": "LJ"}, {"family": "Cutler", "given": "Tessa L", "initials": "TL"}, {"family": "Ordo\u00f1ana", "given": "Juan R", "initials": "JR"}, {"family": "S\u00e1nchez-Romera", "given": "Juan F", "initials": "JF"}, {"family": "Colodro-Conde", "given": "Lucia", "initials": "L"}, {"family": "Song", "given": "Yun Mi", "initials": "YM"}, {"family": "Yang", "given": "Sarah", "initials": "S"}, {"family": "Lee", "given": "Kayoung", "initials": "K"}, {"family": "Franz", "given": "Carol E", "initials": "CE"}, {"family": "Kremen", "given": "William S", "initials": "WS"}, {"family": "Lyons", "given": "Michael J", "initials": "MJ"}, {"family": "Busjahn", "given": "Andreas", "initials": "A"}, {"family": "Nelson", "given": "Tracy L", "initials": "TL"}, {"family": "Whitfield", 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"PK"}, {"family": "Pedersen", "given": "Nancy L", "initials": "NL"}, {"family": "Dahl Aslan", "given": "Anna K", "initials": "AK"}, {"family": "McAdams", "given": "Tom A", "initials": "TA"}, {"family": "Eley", "given": "Thalia C", "initials": "TC"}, {"family": "Gregory", "given": "Alice M", "initials": "AM"}, {"family": "Tynelius", "given": "Per", "initials": "P"}, {"family": "Baker", "given": "Laura A", "initials": "LA"}, {"family": "Tuvblad", "given": "Catherine", "initials": "C"}, {"family": "Bayasgalan", "given": "Gombojav", "initials": "G"}, {"family": "Narandalai", "given": "Danshiitsoodol", "initials": "D"}, {"family": "Spector", "given": "Timothy D", "initials": "TD"}, {"family": "Mangino", "given": "Massimo", "initials": "M"}, {"family": "Lachance", "given": "Genevieve", "initials": "G"}, {"family": "Burt", "given": "S Alexandra", "initials": "SA"}, {"family": "Klump", "given": "Kelly L", "initials": "KL"}, {"family": "Harris", "given": "Jennifer R", "initials": "JR"}, {"family": "Brandt", "given": "Ingunn", "initials": "I"}, {"family": "Nilsen", "given": "Thomas S", "initials": "TS"}, {"family": "Krueger", "given": "Robert F", "initials": "RF"}, {"family": "McGue", "given": "Matt", "initials": "M"}, {"family": "Pahlen", "given": "Shandell", "initials": "S"}, {"family": "Corley", "given": "Robin P", "initials": "RP"}, {"family": "Huibregtse", "given": "Brooke M", "initials": "BM"}, {"family": "Bartels", "given": "Meike", "initials": "M"}, {"family": "van Beijsterveldt", "given": "Catharina EM", "initials": "CE"}, {"family": "Willemsen", "given": "Gonneke", "initials": "G"}, {"family": "Goldberg", "given": "Jack H", "initials": "JH"}, {"family": "Rasmussen", "given": "Finn", "initials": "F"}, {"family": "Tarnoki", "given": "Adam D", "initials": "AD"}, {"family": "Tarnoki", "given": "David L", "initials": "DL"}, {"family": "Derom", "given": "Catherine A", "initials": "CA"}, {"family": "Vlietinck", "given": "Robert F", "initials": "RF"}, {"family": "Loos", "given": "Ruth JF", "initials": "RJ"}, {"family": "Hopper", "given": "John L", "initials": "JL"}, {"family": "Sung", "given": "Joohon", "initials": "J"}, {"family": "Maes", "given": "Hermine H", "initials": "HH"}, {"family": "Turkheimer", "given": "Eric", "initials": "E"}, {"family": "Boomsma", "given": "Dorret I", "initials": "DI"}, {"family": "S\u00f8rensen", "given": "Thorkild IA", "initials": "TI"}, {"family": "Kaprio", "given": "Jaakko", "initials": "J"}], "type": "journal-article", "published": "2017-08-00", "journal": {"volume": "106", "issn": "0002-9165", "issue": "2", "pages": "457-466", "title": "Am J Clin Nutr", "issn-l": "0002-9165"}, "abstract": null, "doi": "10.3945/ajcn.117.153643", "pmid": "28679550", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [], "notes": [], "created": "2018-01-09T13:58:09.302Z", "modified": "2020-01-21T13:56:11.877Z"}, {"entity": "publication", "iuid": "132b02e3f2a04a58a7a4909db3048757", "links": {"self": {"href": "https://publications.scilifelab.se/publication/132b02e3f2a04a58a7a4909db3048757.json"}, "display": {"href": "https://publications.scilifelab.se/publication/132b02e3f2a04a58a7a4909db3048757"}}, "title": "CKM Glu83Gly Is Associated With Blunted Creatine Kinase Variation, but Not With Myalgia.", "authors": [{"family": "Siddiqui", "given": "Moneeza Kalhan", "initials": "MK"}, {"family": "Veluchamy", "given": "Abirami", "initials": "A"}, {"family": "Maroteau", "given": "Cyrielle", "initials": "C"}, {"family": "Tavendale", "given": "Roger", "initials": "R"}, {"family": "Carr", "given": "Fiona", "initials": "F"}, {"family": "Pearson", "given": "Ewan", "initials": "E"}, {"family": "Colhoun", "given": "Helen", "initials": "H"}, {"family": "Morris", "given": "Andrew D", "initials": "AD"}, {"family": "George", "given": "Jacob", "initials": "J"}, {"family": "Doney", "given": "Alexander", "initials": "A"}, {"family": "Pirmohamed", "given": "Munir", "initials": "M"}, {"family": "Alfirevic", "given": "Ana", "initials": "A"}, {"family": "Wadelius", "given": "Mia", "initials": "M"}, {"family": "Maitland van der Zee", "given": "Anke H", "initials": "AH"}, {"family": "Ridker", "given": "Paul M", "initials": "PM"}, {"family": "Chasman", "given": "Daniel I", "initials": "DI"}, {"family": "Palmer", "given": "Colin N A", "initials": "CNA"}, {"family": "PREDICTION-ADR Consortium", "given": "", "initials": ""}], "type": "journal article", "published": "2017-08-00", "journal": {"volume": "10", "issn": "1942-3268", "issue": "4", "pages": "e001737", "title": "Circ Cardiovasc Genet", "issn-l": null}, "abstract": "To test the association of a recently reported variant in the creatine kinase (CK) muscle gene, CKM Glu83Gly (rs11559024) with constitutive creatine phosphokinase (CK) levels, CK variation, and inducibility. Given the diagnostic importance of CK in determining muscle damage, we tested the association of the variant with myalgia.\n\nMeta-analysis between longitudinal cohort GoDARTS (Genetics of Diabetes Audit and Research, Tayside Scotland), minor allele frequency (=0.02), and randomized clinical trial (JUPITER [Justification for the Use of Statins in Primary Prevention: An Intervention Trial Evaluating Rosuvastatin], minor allele frequency=0.018) was used to replicate the association with baseline CK measures. GoDARTS was used to study the relationship with CK variability. Myalgia was studied in JUPITER trial participants. Baseline and SDs of CK were on average 18% ( P value=6\u00d710-63) and 24% (P value=2\u00d710-5) lower for carriers of the variant, respectively. The variant was not associated with myalgia (odds ratio, 0.84; 95% confidence interval, 0.52-1.38).\n\nThis study highlights that a genetic factor known to be associated with constitutive CK levels is also associated with CK variability and inducibility. This is discussed in the context of evidence to suggest that the variant has an impact on inducibility of CK by trauma through a previously reported case of a homozygous carrier. However, the lack of association between the variant and myalgia suggests that it cannot reliably be used as a biomarker for muscle symptoms.", "doi": "10.1161/CIRCGENETICS.117.001737", "pmid": "28790154", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "CIRCGENETICS.117.001737"}], "notes": [], "created": "2018-01-09T20:54:59.536Z", "modified": "2021-06-21T15:34:34.341Z"}, {"entity": "publication", "iuid": "9b17776095cb4586a4ed84d38eaa61f7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9b17776095cb4586a4ed84d38eaa61f7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9b17776095cb4586a4ed84d38eaa61f7"}}, "title": "Bioinformatic processing of RAD\u2010seq data dramatically impacts downstream population genetic inference", "authors": [{"family": "Shafer", "given": "Aaron B A", "initials": "ABA"}, {"family": "Peart", "given": "Claire R", "initials": "CR"}, {"family": "Tusso", "given": "Sergio", "initials": "S"}, {"family": "Maayan", "given": "Inbar", "initials": "I"}, {"family": "Brelsford", "given": "Alan", "initials": "A"}, {"family": "Wheat", "given": "Christopher W", "initials": "CW"}, {"family": "Wolf", "given": "Jochen B W", "initials": "JBW"}], "type": "journal-article", "published": "2017-08-00", "journal": {"volume": "8", "issn": "2041-210X", "issue": "8", "pages": "907-917", "title": "Methods Ecol Evol", "issn-l": "2041-210X"}, "abstract": null, "doi": "10.1111/2041-210x.12700", "pmid": null, "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "BioProject", "description": "Galapagos sea lion resequencing", "key": "PRJNA349123"}, {"db": "Dryad", "description": "Data from: Bioinformatic processing of RAD-seq data dramatically impacts downstream population genetic inference", "key": "https://doi.org/10.5061/dryad.q14c1"}, {"db": "Dryad", "description": "Data from: A draft fur seal genome provides insights into factors affecting SNP validation and how to mitigate them", "key": "https://doi.org/10.5061/dryad.8kn8c.2"}, {"db": "Assembly", "description": "https://www.ncbi.nlm.nih.gov/assembly/GCF_000349705.1/", "key": "GCF_000349705.1"}, {"db": "Assembly", "description": "https://www.ncbi.nlm.nih.gov/assembly/GCF_000321225.1/", "key": "GCF_000321225.1"}], "notes": [], "created": "2017-10-19T20:42:24.110Z", "modified": "2024-01-16T13:48:47.696Z"}, {"entity": "publication", "iuid": "f46452abecc647e3bb3780c1224e3e42", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f46452abecc647e3bb3780c1224e3e42.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f46452abecc647e3bb3780c1224e3e42"}}, "title": "Haploid selection within a single ejaculate increases offspring fitness", "authors": [{"family": "Alavioon", "given": "Ghazal", "initials": "G"}, {"family": "Hotzy", "given": "Cosima", "initials": "C"}, {"family": "Nakhro", "given": "Khriezhanuo", "initials": "K"}, {"family": "Rudolf", "given": "Sandra", "initials": "S"}, {"family": "Scofield", "given": "Douglas G", "initials": "DG"}, {"family": "Zajitschek", "given": "Susanne", "initials": "S"}, {"family": "Maklakov", "given": "Alexei A", "initials": "AA"}, {"family": "Immler", "given": "Simone", "initials": "S"}], "type": "journal-article", "published": "2017-07-25", "journal": {"volume": "114", "issn": "0027-8424", "issue": "30", "pages": "8053-8058", "title": "Proc Natl Acad Sci USA", "issn-l": "0027-8424"}, "abstract": null, "doi": "10.1073/pnas.1705601114", "pmid": "28698378", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Genome Engineering Zebrafish": "Service"}, "xrefs": [], "notes": [], "created": "2017-10-26T09:20:47.508Z", "modified": "2020-01-21T13:56:11.851Z"}, 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{"family": "Strachan", "given": "David P", "initials": "DP"}, {"family": "Palmas", "given": "Walter", "initials": "W"}, {"family": "Metspalu", "given": "Andres", "initials": "A"}, {"family": "Ingelsson", "given": "Erik", "initials": "E"}, {"family": "Boomsma", "given": "Dorret I", "initials": "DI"}, {"family": "Franco", "given": "Oscar H", "initials": "OH"}, {"family": "Bochud", "given": "Murielle", "initials": "M"}, {"family": "Newton-Cheh", "given": "Christopher", "initials": "C"}, {"family": "Munroe", "given": "Patricia B", "initials": "PB"}, {"family": "Elliott", "given": "Paul", "initials": "P"}, {"family": "Chasman", "given": "Daniel I", "initials": "DI"}, {"family": "Chakravarti", "given": "Aravinda", "initials": "A"}, {"family": "Knight", "given": "Joanne", "initials": "J"}, {"family": "Morris", "given": "Andrew P", "initials": "AP"}, {"family": "Levy", "given": "Daniel", "initials": "D"}, {"family": "Tobin", "given": "Martin D", "initials": "MD"}, {"family": "Snieder", "given": "Harold", "initials": "H"}, {"family": "Caulfield", "given": "Mark J", "initials": "MJ"}, {"family": "Ehret", "given": "Georg B", "initials": "GB"}], "type": "journal article", "published": "2017-07-24", "journal": {"volume": "70", "issn": "1524-4563", "issue": "3", "pages": "e4-e19", "title": "Hypertension", "issn-l": "0194-911X"}, "abstract": "Elevated blood pressure is a major risk factor for cardiovascular disease and has a substantial genetic contribution. Genetic variation influencing blood pressure has the potential to identify new pharmacological targets for the treatment of hypertension. To discover additional novel blood pressure loci, we used 1000 Genomes Project-based imputation in 150 134 European ancestry individuals and sought significant evidence for independent replication in a further 228 245 individuals. We report 6 new signals of association in or near HSPB7, TNXB, LRP12, LOC283335, SEPT9, and AKT2, and provide new replication evidence for a further 2 signals in EBF2 and NFKBIA Combining large whole-blood gene expression resources totaling 12 607 individuals, we investigated all novel and previously reported signals and identified 48 genes with evidence for involvement in blood pressure regulation that are significant in multiple resources. Three novel kidney-specific signals were also detected. These robustly implicated genes may provide new leads for therapeutic innovation.", "doi": "10.1161/HYPERTENSIONAHA.117.09438", "pmid": "28739976", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "HYPERTENSIONAHA.117.09438"}, {"db": "pmc", "key": "PMC5783787"}, {"db": "mid", "key": "NIHMS902240"}], "notes": [], "created": "2018-01-09T13:55:55.847Z", "modified": "2021-06-21T15:30:31.426Z"}, {"entity": "publication", "iuid": "2fc4e31b250e495ca1b009d046c37ce5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2fc4e31b250e495ca1b009d046c37ce5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2fc4e31b250e495ca1b009d046c37ce5"}}, "title": "Large meta-analysis of genome-wide association studies identifies five loci for lean body mass.", "authors": [{"family": "Zillikens", "given": "M Carola", "initials": "MC"}, {"family": "Demissie", "given": 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"HE"}, {"family": "Widen", "given": "Elisabeth", "initials": "E"}, {"family": "Williams", "given": "Frances M K", "initials": "FMK"}, {"family": "Wilson", "given": "James F", "initials": "JF"}, {"family": "Wright", "given": "Nicole C", "initials": "NC"}, {"family": "Xie", "given": "Weijia", "initials": "W"}, {"family": "Yu", "given": "Lei", "initials": "L"}, {"family": "Zhou", "given": "Yanhua", "initials": "Y"}, {"family": "Chambers", "given": "John C", "initials": "JC"}, {"family": "D\u00f6ring", "given": "Angela", "initials": "A"}, {"family": "van Duijn", "given": "Cornelia M", "initials": "CM"}, {"family": "Econs", "given": "Michael J", "initials": "MJ"}, {"family": "Gudnason", "given": "Vilmundur", "initials": "V"}, {"family": "Kooner", "given": "Jaspal S", "initials": "JS"}, {"family": "Psaty", "given": "Bruce M", "initials": "BM"}, {"family": "Spector", "given": "Timothy D", "initials": "TD"}, {"family": "Stefansson", "given": "Kari", "initials": "K"}, {"family": "Rivadeneira", "given": "Fernando", "initials": "F"}, {"family": "Uitterlinden", "given": "Andr\u00e9 G", "initials": "AG"}, {"family": "Wareham", "given": "Nicholas J", "initials": "NJ"}, {"family": "Ossowski", "given": "Vicky", "initials": "V"}, {"family": "Waterworth", "given": "Dawn", "initials": "D"}, {"family": "Loos", "given": "Ruth J F", "initials": "RJF"}, {"family": "Karasik", "given": "David", "initials": "D"}, {"family": "Harris", "given": "Tamara B", "initials": "TB"}, {"family": "Ohlsson", "given": "Claes", "initials": "C"}, {"family": "Kiel", "given": "Douglas P", "initials": "DP"}], "type": "journal article", "published": "2017-07-19", "journal": {"volume": "8", "issn": "2041-1723", "issue": "1", "pages": "80", "title": "Nat Commun", "issn-l": "2041-1723"}, "abstract": "Lean body mass, consisting mostly of skeletal muscle, is important for healthy aging. We performed a genome-wide association study for whole body (20 cohorts of European ancestry with n = 38,292) and appendicular (arms and legs) lean body mass (n = 28,330) measured using dual energy X-ray absorptiometry or bioelectrical impedance analysis, adjusted for sex, age, height, and fat mass. Twenty-one single-nucleotide polymorphisms were significantly associated with lean body mass either genome wide (p < 5 \u00d7 10 -8) or suggestively genome wide (p < 2.3 \u00d7 10-6). Replication in 63,475 (47,227 of European ancestry) individuals from 33 cohorts for whole body lean body mass and in 45,090 (42,360 of European ancestry) subjects from 25 cohorts for appendicular lean body mass was successful for five single-nucleotide polymorphisms in/near HSD17B11, VCAN, ADAMTSL3, IRS1, and FTO for total lean body mass and for three single-nucleotide polymorphisms in/near VCAN, ADAMTSL3, and IRS1 for appendicular lean body mass. Our findings provide new insight into the genetics of lean body mass.Lean body mass is a highly heritable trait and is associated with various health conditions. Here, Kiel and colleagues perform a meta-analysis of genome-wide association studies for whole body lean body mass and find five novel genetic loci to be significantly associated.", "doi": "10.1038/s41467-017-00031-7", "pmid": "28724990", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-017-00031-7"}, {"db": "pmc", "key": "PMC5517526"}], "notes": [], "created": "2018-01-09T13:55:56.946Z", "modified": "2021-06-21T14:59:44.927Z"}, {"entity": "publication", "iuid": "c3577bba83a74b17857adfd5789c0771", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c3577bba83a74b17857adfd5789c0771.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c3577bba83a74b17857adfd5789c0771"}}, "title": "Transancestral mapping and genetic load in systemic lupus erythematosus.", "authors": [{"family": "Langefeld", "given": "Carl D", "initials": "CD"}, 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"Tushar", "initials": "T"}, {"family": "Oksenberg", "given": "Jorge R", "initials": "JR"}, {"family": "Rioux", "given": "John D", "initials": "JD"}, {"family": "Gregersen", "given": "Peter K", "initials": "PK"}, {"family": "Syv\u00e4nen", "given": "Ann-Christine", "initials": "AC", "orcid": "0000-0002-9681-9146", "researcher": {"href": "https://publications.scilifelab.se/researcher/f7012e35025543379380cb90efd71243.json"}}, {"family": "R\u00f6nnblom", "given": "Lars", "initials": "L"}, {"family": "Criswell", "given": "Lindsey A", "initials": "LA"}, {"family": "Jacob", "given": "Chaim O", "initials": "CO"}, {"family": "Sivils", "given": "Kathy L", "initials": "KL"}, {"family": "Tsao", "given": "Betty P", "initials": "BP"}, {"family": "Schanberg", "given": "Laura E", "initials": "LE"}, {"family": "Behrens", "given": "Timothy W", "initials": "TW"}, {"family": "Silverman", "given": "Earl D", "initials": "ED"}, {"family": "Alarc\u00f3n-Riquelme", "given": "Marta E", "initials": "ME"}, {"family": "Kimberly", "given": "Robert P", "initials": "RP"}, {"family": "Harley", "given": "John B", "initials": "JB"}, {"family": "Wakeland", "given": "Edward K", "initials": "EK"}, {"family": "Graham", "given": "Robert R", "initials": "RR"}, {"family": "Gaffney", "given": "Patrick M", "initials": "PM"}, {"family": "Vyse", "given": "Timothy J", "initials": "TJ"}], "type": "journal article", "published": "2017-07-17", "journal": {"volume": "8", "issn": "2041-1723", "issue": null, "pages": "16021", "title": "Nat Commun", "issn-l": "2041-1723"}, "abstract": "Systemic lupus erythematosus (SLE) is an autoimmune disease with marked gender and ethnic disparities. We report a large transancestral association study of SLE using Immunochip genotype data from 27,574 individuals of European (EA), African (AA) and Hispanic Amerindian (HA) ancestry. We identify 58 distinct non-HLA regions in EA, 9 in AA and 16 in HA (\u223c50% of these regions have multiple independent associations); these include 24 novel SLE regions (P<5 \u00d7 10-8), refined association signals in established regions, extended associations to additional ancestries, and a disentangled complex HLA multigenic effect. The risk allele count (genetic load) exhibits an accelerating pattern of SLE risk, leading us to posit a cumulative hit hypothesis for autoimmune disease. Comparing results across the three ancestries identifies both ancestry-dependent and ancestry-independent contributions to SLE risk. Our results are consistent with the unique and complex histories of the populations sampled, and collectively help clarify the genetic architecture and ethnic disparities in SLE.", "doi": "10.1038/ncomms16021", "pmid": "28714469", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "ncomms16021"}, {"db": "pmc", "key": "PMC5520018"}], "notes": [], "created": "2017-10-25T15:18:21.921Z", "modified": "2024-01-16T13:48:47.734Z"}, {"entity": "publication", "iuid": "486b9a2053714ec0b814295e77d2e76d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/486b9a2053714ec0b814295e77d2e76d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/486b9a2053714ec0b814295e77d2e76d"}}, "title": "Loss of DIP2C in RKO cells stimulates changes in DNA methylation and epithelial-mesenchymal transition.", "authors": [{"family": "Larsson", "given": "Chatarina", "initials": "C"}, {"family": "Ali", "given": "Muhammad Akhtar", "initials": "MA"}, {"family": "Pandzic", "given": "Tatjana", "initials": "T"}, {"family": "Lindroth", "given": "Anders M", "initials": "AM"}, {"family": "He", "given": "Liqun", "initials": "L"}, {"family": "Sj\u00f6blom", "given": "Tobias", "initials": "T"}], "type": "journal article", "published": "2017-07-17", "journal": {"volume": "17", "issn": "1471-2407", "issue": "1", "pages": "487", "title": "BMC Cancer", "issn-l": "1471-2407"}, "abstract": "The disco-interacting protein 2 homolog C (DIP2C) gene is an uncharacterized gene found mutated in a subset of breast and lung cancers. To understand the role of DIP2C in tumour development we studied the gene in human cancer cells.\n\nWe engineered human DIP2C knockout cells by genome editing in cancer cells. The growth properties of the engineered cells were characterised and transcriptome and methylation analyses were carried out to identify pathways deregulated by inactivation of DIP2C. Effects on cell death pathways and epithelial-mesenchymal transition traits were studied based on the results from expression profiling.\n\nKnockout of DIP2C in RKO cells resulted in cell enlargement and growth retardation. Expression profiling revealed 780 genes for which the expression level was affected by the loss of DIP2C, including the tumour-suppressor encoding CDKN2A gene, the epithelial-mesenchymal transition (EMT) regulator-encoding ZEB1, and CD44 and CD24 that encode breast cancer stem cell markers. Analysis of DNA methylation showed more than 30,000 sites affected by differential methylation, the majority of which were hypomethylated following loss of DIP2C. Changes in DNA methylation at promoter regions were strongly correlated to changes in gene expression, and genes involved with EMT and cell death were enriched among the differentially regulated genes. The DIP2C knockout cells had higher wound closing capacity and showed an increase in the proportion of cells positive for cellular senescence markers.\n\nLoss of DIP2C triggers substantial DNA methylation and gene expression changes, cellular senescence and epithelial-mesenchymal transition in cancer cells.", "doi": "10.1186/s12885-017-3472-5", "pmid": "28716088", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1186/s12885-017-3472-5"}, {"db": "pmc", "key": "PMC5513093"}], "notes": [], "created": "2017-10-17T09:31:57.476Z", "modified": "2024-01-16T13:48:47.742Z"}, {"entity": "publication", "iuid": "1c679203ec3d46318d64bb6dce8e0b08", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1c679203ec3d46318d64bb6dce8e0b08.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1c679203ec3d46318d64bb6dce8e0b08"}}, "title": "Association analyses based on false discovery rate implicate new loci for coronary artery disease", "authors": [{"family": "Nelson", "given": "Christopher P", "initials": "CP"}, {"family": "Goel", "given": "Anuj", "initials": "A"}, {"family": "Butterworth", "given": "Adam S", "initials": "AS"}, {"family": "Kanoni", "given": "Stavroula", "initials": "S"}, {"family": "Webb", "given": "Tom R", "initials": "TR"}, {"family": "Marouli", "given": "Eirini", "initials": "E"}, {"family": "Zeng", "given": "Lingyao", "initials": "L"}, {"family": "Ntalla", "given": "Ioanna", "initials": "I"}, {"family": "Lai", "given": "Florence Y", "initials": "FY"}, {"family": "Hopewell", "given": "Jemma C", "initials": "JC"}, {"family": "Giannakopoulou", "given": "Olga", "initials": "O"}, {"family": "Jiang", "given": "Tao", "initials": "T"}, {"family": "Hamby", "given": "Stephen E", "initials": "SE"}, {"family": "Di Angelantonio", "given": "Emanuele", "initials": "E"}, {"family": "Assimes", "given": "Themistocles L", "initials": "TL"}, {"family": "Bottinger", "given": "Erwin P", "initials": "EP"}, {"family": "Chambers", "given": "John C", "initials": "JC"}, {"family": "Clarke", "given": "Robert", "initials": "R"}, {"family": "Palmer", "given": "Colin N A", "initials": "CNA"}, {"family": "Cubbon", "given": "Richard M", "initials": "RM"}, {"family": "Ellinor", "given": "Patrick", "initials": "P"}, {"family": "Ermel", "given": "Raili", "initials": "R"}, {"family": "Evangelou", "given": "Evangelos", "initials": "E"}, {"family": "Franks", "given": "Paul W", "initials": "PW"}, {"family": "Grace", "given": "Christopher", "initials": "C"}, {"family": "Gu", "given": "Dongfeng", "initials": "D"}, {"family": "Hingorani", "given": "Aroon D", "initials": "AD"}, {"family": "Howson", "given": "Joanna M M", "initials": "JMM"}, {"family": "Ingelsson", "given": "Erik", "initials": "E"}, {"family": "Kastrati", "given": "Adnan", "initials": "A"}, {"family": "Kessler", "given": "Thorsten", "initials": "T"}, {"family": "Kyriakou", "given": "Theodosios", "initials": "T"}, {"family": "Lehtim\u00e4ki", "given": "Terho", "initials": "T"}, {"family": "Lu", "given": "Xiangfeng", "initials": "X"}, {"family": "Lu", "given": "Yingchang", "initials": "Y"}, {"family": "M\u00e4rz", "given": "Winfried", "initials": "W"}, {"family": "McPherson", "given": "Ruth", "initials": "R"}, {"family": "Metspalu", "given": "Andres", "initials": "A"}, {"family": "Pujades-Rodriguez", "given": "Mar", "initials": "M"}, {"family": "Ruusalepp", "given": "Arno", "initials": "A"}, {"family": "Schadt", "given": "Eric E", "initials": "EE"}, {"family": "Schmidt", "given": "Amand F", "initials": "AF"}, {"family": "Sweeting", "given": "Michael J", "initials": "MJ"}, {"family": "Zalloua", "given": "Pierre A", "initials": "PA"}, {"family": "AlGhalayini", "given": "Kamal", "initials": "K"}, {"family": "Keavney", "given": "Bernard D", "initials": "BD"}, {"family": "Kooner", "given": "Jaspal S", "initials": "JS"}, {"family": "Loos", "given": "Ruth J F", "initials": "RJF"}, {"family": "Patel", "given": "Riyaz S", "initials": "RS"}, {"family": "Rutter", "given": "Martin K", "initials": "MK"}, {"family": "Tomaszewski", "given": "Maciej", "initials": "M"}, {"family": "Tzoulaki", "given": "Ioanna", "initials": "I"}, {"family": "Zeggini", "given": "Eleftheria", "initials": "E"}, {"family": "Erdmann", "given": "Jeanette", "initials": "J"}, {"family": "Dedoussis", "given": "George", "initials": "G"}, {"family": "Bj\u00f6rkegren", "given": "Johan L M", "initials": "JLM"}, {"family": "Schunkert", "given": "Heribert", "initials": "H"}, {"family": "Farrall", "given": "Martin", "initials": "M"}, {"family": "Danesh", "given": "John", "initials": "J"}, {"family": "Samani", "given": "Nilesh J", "initials": "NJ"}, {"family": "Watkins", "given": "Hugh", "initials": "H"}, {"family": "Deloukas", "given": "Panos", "initials": "P"}], "type": "journal-article", "published": "2017-07-17", "journal": {"volume": "49", "issn": "1061-4036", "issue": "9", "pages": "1385-1391", "title": "Nat Genet", "issn-l": "1061-4036"}, "abstract": null, "doi": "10.1038/ng.3913", "pmid": "28714975", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [], "notes": [], "created": "2018-01-09T13:58:07.831Z", "modified": "2020-01-21T13:56:11.833Z"}, {"entity": "publication", "iuid": "fbc51120b36048ecaa8ce43eb420a46b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/fbc51120b36048ecaa8ce43eb420a46b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/fbc51120b36048ecaa8ce43eb420a46b"}}, "title": "Genotype\u2013covariate interaction effects and the heritability of adult body mass index", "authors": [{"family": "Robinson", "given": "Matthew R", "initials": "MR"}, {"family": "English", "given": "Geoffrey", "initials": "G"}, {"family": "Moser", "given": "Gerhard", "initials": "G"}, {"family": "Lloyd-Jones", "given": "Luke R", "initials": "LR"}, {"family": "Triplett", "given": "Marcus A", "initials": "MA"}, {"family": "Zhu", "given": "Zhihong", "initials": "Z"}, {"family": "Nolte", "given": "Ilja M", "initials": "IM"}, {"family": "van Vliet-Ostaptchouk", "given": "Jana V", "initials": "JV"}, {"family": "Snieder", "given": "Harold", "initials": "H"}, {"family": "Esko", "given": "Tonu", "initials": "T"}, {"family": "Milani", "given": "Lili", "initials": "L"}, {"family": "M\u00e4gi", "given": "Reedik", "initials": "R"}, {"family": "Metspalu", "given": "Andres", "initials": "A"}, {"family": "Magnusson", "given": "Patrik K E", "initials": "PKE"}, {"family": "Pedersen", "given": "Nancy L", "initials": "NL"}, {"family": "Ingelsson", "given": "Erik", "initials": "E"}, {"family": "Johannesson", "given": "Magnus", "initials": "M"}, {"family": "Yang", "given": "Jian", "initials": "J"}, {"family": "Cesarini", "given": "David", "initials": "D"}, {"family": "Visscher", "given": "Peter M", "initials": "PM"}], "type": "journal-article", "published": "2017-07-10", "journal": {"volume": "49", "issn": "1061-4036", "issue": "8", "pages": "1174-1181", "title": "Nat Genet", "issn-l": "1061-4036"}, "abstract": null, "doi": "10.1038/ng.3912", "pmid": "28692066", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [], "notes": [], "created": "2018-01-09T13:58:08.920Z", "modified": "2020-01-21T13:56:11.819Z"}, {"entity": "publication", "iuid": "7531a3c092394bef971ba96e83bd5466", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7531a3c092394bef971ba96e83bd5466.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7531a3c092394bef971ba96e83bd5466"}}, "title": "Genetics of phenotypic plasticity and biomass traits in hybrid willows across contrasting environments and years", "authors": [{"family": "Berlin", "given": "Sofia", "initials": "S"}, {"family": "Hallingb\u00e4ck", "given": "Henrik R", "initials": "HR"}, {"family": "Beyer", "given": "Friderike", "initials": "F"}, {"family": "Nordh", "given": "Nils Erik", "initials": "NE"}, {"family": "Weih", "given": "Martin", "initials": "M"}, {"family": "R\u00f6nnberg-W\u00e4stljung", "given": "Ann Christin", "initials": "AC"}], "type": "journal-article", "published": "2017-07-01", "journal": {"volume": "120", "issn": "0305-7364", "issue": "1", "pages": "87-100", "title": "", "issn-l": null}, "abstract": null, "doi": "10.1093/aob/mcx029", "pmid": "28449073", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [], "notes": [], "created": "2018-01-09T14:01:32.552Z", "modified": "2020-01-21T13:56:11.809Z"}, {"entity": "publication", "iuid": "685e135330d64bf8b825df7e44a76180", "links": {"self": {"href": "https://publications.scilifelab.se/publication/685e135330d64bf8b825df7e44a76180.json"}, "display": {"href": "https://publications.scilifelab.se/publication/685e135330d64bf8b825df7e44a76180"}}, "title": "Relations between lipoprotein(a) concentrations, LPA genetic variants, and the risk of mortality in patients with established coronary heart disease: a molecular and genetic association study", "authors": [{"family": "Zewinger", "given": "Stephen", "initials": "S"}, {"family": "Kleber", "given": "Marcus E", "initials": "ME"}, {"family": "Tragante", "given": "Vinicius", "initials": "V"}, {"family": "McCubrey", "given": "Raymond O", "initials": "RO"}, {"family": "Schmidt", "given": "Amand F", "initials": "AF"}, {"family": "Direk", "given": "Kenan", "initials": "K"}, {"family": "Laufs", "given": "Ulrich", "initials": "U"}, {"family": "Werner", "given": "Christian", "initials": "C"}, {"family": "Koenig", "given": "Wolfgang", "initials": "W"}, {"family": "Rothenbacher", "given": "Dietrich", "initials": "D"}, {"family": "Mons", "given": "Ute", "initials": "U"}, {"family": "Breitling", "given": "Lutz P", "initials": "LP"}, {"family": "Brenner", "given": "Herrmann", "initials": "H"}, {"family": "Jennings", "given": "Richard T", "initials": "RT"}, {"family": "Petrakis", "given": "Ioannis", "initials": "I"}, {"family": "Triem", "given": "Sarah", "initials": "S"}, {"family": "Klug", "given": "Mira", "initials": "M"}, {"family": "Filips", "given": "Alexandra", "initials": "A"}, {"family": "Blankenberg", "given": "Stefan", "initials": "S"}, {"family": "Waldeyer", "given": "Christoph", "initials": "C"}, {"family": "Sinning", "given": "Christoph", "initials": "C"}, {"family": "Schnabel", "given": "Renate B", "initials": "RB"}, {"family": "Lackner", "given": "Karl J", "initials": "KJ"}, {"family": "Vlachopoulou", "given": "Efthymia", "initials": "E"}, {"family": "Nyg\u00e5rd", "given": "Ottar", "initials": "O"}, {"family": "Svingen", "given": "Gard Frodahl Tveitev\u00e5g", "initials": "GFT"}, {"family": "Pedersen", "given": "Eva Ringdal", "initials": "ER"}, {"family": "Tell", "given": "Grethe S", "initials": "GS"}, {"family": "Sinisalo", "given": "Juha", "initials": "J"}, {"family": "Nieminen", "given": "Markku S", "initials": "MS"}, {"family": "Laaksonen", "given": "Reijo", "initials": "R"}, {"family": "Trompet", "given": "Stella", "initials": "S"}, {"family": "Smit", "given": "Roelof A J", "initials": "RAJ"}, {"family": "Sattar", "given": "Naveed", "initials": "N"}, {"family": "Jukema", "given": "J Wouter", "initials": "JW"}, {"family": "Groesdonk", "given": "Heinrich V", "initials": "HV"}, {"family": "Delgado", "given": "Graciela", "initials": "G"}, {"family": "Stojakovic", "given": "Tatjana", "initials": "T"}, {"family": "Pilbrow", "given": "Anna P", "initials": "AP"}, {"family": "Cameron", "given": "Vicky A", "initials": "VA"}, {"family": "Richards", "given": "A Mark", "initials": "AM"}, {"family": "Doughty", "given": "Robert N", "initials": "RN"}, {"family": "Gong", "given": "Yan", "initials": "Y"}, {"family": "Cooper-DeHoff", "given": "Rhonda", "initials": "R"}, {"family": "Johnson", "given": "Julie", "initials": "J"}, {"family": "Scholz", "given": "Markus", "initials": "M"}, {"family": "Beutner", "given": "Frank", "initials": "F"}, {"family": "Thiery", "given": "Joachim", "initials": "J"}, {"family": "Smith", "given": "J Gustav", "initials": "JG"}, {"family": "Vilmundarson", "given": "Ragnar O", "initials": "RO"}, {"family": "McPherson", "given": "Ruth", "initials": "R"}, {"family": "Stewart", "given": "Alexandre F R", "initials": "AFR"}, {"family": "Cresci", "given": "Sharon", "initials": "S"}, {"family": "Lenzini", "given": "Petra A", "initials": "PA"}, {"family": "Spertus", "given": "John A", "initials": "JA"}, {"family": "Olivieri", "given": "Oliviero", "initials": "O"}, {"family": "Girelli", "given": "Domenico", "initials": "D"}, {"family": "Martinelli", "given": "Nicola I", "initials": "NI"}, {"family": "Leiherer", "given": "Andreas", "initials": "A"}, {"family": "Saely", "given": "Christoph H", "initials": "CH"}, {"family": "Drexel", "given": "Heinz", "initials": "H"}, {"family": "M\u00fcndlein", "given": "Axel", "initials": "A"}, {"family": "Braund", "given": "Peter S", "initials": "PS"}, {"family": "Nelson", "given": "Christopher P", "initials": "CP"}, {"family": "Samani", "given": "Nilesh J", "initials": "NJ"}, {"family": "Kofink", "given": "Daniel", "initials": "D"}, {"family": "Hoefer", "given": "Imo E", "initials": "IE"}, {"family": "Pasterkamp", "given": "Gerard", "initials": "G"}, {"family": "Quyyumi", "given": "Arshed A", "initials": "AA"}, {"family": "Ko", "given": "Yi An", "initials": "YA"}, {"family": "Hartiala", "given": "Jaana A", "initials": "JA"}, {"family": "Allayee", "given": "Hooman", "initials": "H"}, {"family": "Tang", "given": "W H Wilson", "initials": "WHW"}, {"family": "Hazen", "given": "Stanley L", "initials": "SL"}, {"family": "Eriksson", "given": "Niclas", "initials": "N"}, {"family": "Held", "given": "Claes", "initials": "C"}, {"family": "Hagstr\u00f6m", "given": "Emil", "initials": "E"}, {"family": "Wallentin", "given": "Lars", "initials": "L"}, {"family": "\u00c5kerblom", "given": "Axel", "initials": "A"}, {"family": "Siegbahn", "given": "Agneta", "initials": "A"}, {"family": "Karp", "given": "Igor", "initials": "I"}, {"family": "Labos", "given": "Christopher", "initials": "C"}, {"family": "Pilote", "given": "Louise", "initials": "L"}, {"family": "Engert", "given": "James C", "initials": "JC"}, {"family": "Brophy", "given": "James M", "initials": "JM"}, {"family": "Thanassoulis", "given": "George", "initials": "G"}, {"family": "Bogaty", "given": "Peter", "initials": "P"}, {"family": "Szczeklik", "given": "Wojciech", "initials": "W"}, {"family": "Kaczor", "given": "Marcin", "initials": "M"}, {"family": "Sanak", "given": "Marek", "initials": "M"}, {"family": "Virani", "given": "Salim S", "initials": "SS"}, {"family": "Ballantyne", "given": "Christie M", "initials": "CM"}, {"family": "Lee", "given": "Vei Vei", "initials": "VV"}, {"family": "Boerwinkle", "given": "Eric", "initials": "E"}, {"family": "Holmes", "given": "Michael V", "initials": "MV"}, {"family": "Horne", "given": "Benjamin D", "initials": "BD"}, {"family": "Hingorani", "given": "Aroon", "initials": "A"}, {"family": "Asselbergs", "given": "Folkert W", "initials": "FW"}, {"family": "Patel", "given": "Riyaz S", "initials": "RS"}, {"family": "Kr\u00e4mer", "given": "Bernhard K", "initials": "BK"}, {"family": "Scharnagl", "given": "Hubert", "initials": "H"}, {"family": "Fliser", "given": "Danilo", "initials": "D"}, {"family": "M\u00e4rz", "given": "Winfried", "initials": "W"}, {"family": "Speer", "given": "Thimoteus", "initials": "T"}], "type": "journal-article", "published": "2017-07-00", "journal": {"volume": "5", "issn": "2213-8587", "issue": "7", "pages": "534-543", "title": "The Lancet Diabetes & Endocrinology", "issn-l": "2213-8587"}, "abstract": "Lipoprotein(a) concentrations in plasma are associated with cardiovascular risk in the general population. Whether lipoprotein(a) concentrations or LPA genetic variants predict long-term mortality in patients with established coronary heart disease remains less clear.\n\nWe obtained data from 3313 patients with established coronary heart disease in the Ludwigshafen Risk and Cardiovascular Health (LURIC) study. We tested associations of tertiles of lipoprotein(a) concentration in plasma and two LPA single-nucleotide polymorphisms ([SNPs] rs10455872 and rs3798220) with all-cause mortality and cardiovascular mortality by Cox regression analysis and with severity of disease by generalised linear modelling, with and without adjustment for age, sex, diabetes diagnosis, systolic blood pressure, BMI, smoking status, estimated glomerular filtration rate, LDL-cholesterol concentration, and use of lipid-lowering therapy. Results for plasma lipoprotein(a) concentrations were validated in five independent studies involving 10 195 patients with established coronary heart disease. Results for genetic associations were replicated through large-scale collaborative analysis in the GENIUS-CHD consortium, comprising 106 353 patients with established coronary heart disease and 19 332 deaths in 22 studies or cohorts.\n\nThe median follow-up was 9\u00b79 years. Increased severity of coronary heart disease was associated with lipoprotein(a) concentrations in plasma in the highest tertile (adjusted hazard radio [HR] 1\u00b744, 95% CI 1\u00b714-1\u00b783) and the presence of either LPA SNP (1\u00b788, 1\u00b740-2\u00b753). No associations were found in LURIC with all-cause mortality (highest tertile of lipoprotein(a) concentration in plasma 0\u00b795, 0\u00b781-1\u00b711 and either LPA SNP 1\u00b710, 0\u00b792-1\u00b731) or cardiovascular mortality (0\u00b799, 0\u00b781-1\u00b72 and 1\u00b713, 0\u00b790-1\u00b740, respectively) or in the validation studies.\n\nIn patients with prevalent coronary heart disease, lipoprotein(a) concentrations and genetic variants showed no associations with mortality. We conclude that these variables are not useful risk factors to measure to predict progression to death after coronary heart disease is established.\n\nSeventh Framework Programme for Research and Technical Development (AtheroRemo and RiskyCAD), INTERREG IV Oberrhein Programme, Deutsche Nierenstiftung, Else-Kroener Fresenius Foundation, Deutsche Stiftung f\u00fcr Herzforschung, Deutsche Forschungsgemeinschaft, Saarland University, German Federal Ministry of Education and Research, Willy Robert Pitzer Foundation, and Waldburg-Zeil Clinics Isny.", "doi": "10.1016/s2213-8587(17)30096-7", "pmid": "28566218", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "mid", "key": "NIHMS909985"}, {"db": "pmc", "key": "PMC5651679"}, {"db": "pii", "key": "S2213-8587(17)30096-7"}], "notes": [], "created": "2018-01-09T13:58:11.019Z", "modified": "2023-06-19T11:44:07.841Z"}, {"entity": "publication", "iuid": "e1ee87b50807452bbdaa71bc517f10ca", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e1ee87b50807452bbdaa71bc517f10ca.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e1ee87b50807452bbdaa71bc517f10ca"}}, "title": "Genomewide analysis of admixture and adaptation in the Africanized honeybee.", "authors": [{"family": "Nelson", "given": "Ronald M", "initials": "RM"}, {"family": "Wallberg", "given": "Andreas", "initials": "A"}, {"family": "Sim\u00f5es", "given": "Zil\u00e1 Luz Paulino", "initials": "ZLP"}, {"family": "Lawson", "given": "Daniel J", "initials": "DJ"}, {"family": "Webster", "given": "Matthew T", "initials": "MT"}], "type": "journal article", "published": "2017-07-00", "journal": {"volume": "26", "issn": "1365-294X", "issue": "14", "pages": "3603-3617", "title": "Mol. Ecol.", "issn-l": "0962-1083"}, "abstract": "Genetic exchange by hybridization or admixture can make an important contribution to evolution, and introgression of favourable alleles can facilitate adaptation to new environments. A small number of honeybees (Apis mellifera) with African ancestry were introduced to Brazil ~60\u00a0years ago, which dispersed and hybridized with existing managed populations of European origin, quickly spreading across much of the Americas in an example of a massive biological invasion. Here, we analyse whole-genome sequences of 32 Africanized honeybees sampled from throughout Brazil to study the effect of this process on genome diversity. By comparison with ancestral populations from Europe and Africa, we infer that these samples have 84% African ancestry, with the remainder from western European populations. However, this proportion varies across the genome and we identify signals of positive selection in regions with high European ancestry proportions. These observations are largely driven by one large gene-rich 1.4-Mbp segment on chromosome 11 where European haplotypes are present at a significantly elevated frequency and likely confer an adaptive advantage in the Africanized honeybee population. This region has previously been implicated in reproductive traits and foraging behaviour in worker bees. Finally, by analysing the distribution of ancestry tract lengths in the context of the known time of the admixture event, we are able to infer an average generation time of 2.0\u00a0years. Our analysis highlights the processes by which populations of mixed genetic ancestry form and adapt to new environments.", "doi": "10.1111/mec.14122", "pmid": "28378497", "labels": {"NGI Stockholm (Genomics Production)": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "BioProject", "description": "Population-scale sequencing of Apis mellifera and Apis cerana", "key": "PRJNA236426"}, {"db": "BioProject", "description": "Africanized honeybee (Apis mellifera) sequencing", "key": "PRJNA350769"}], "notes": [], "created": "2017-11-02T13:51:52.946Z", "modified": "2024-01-16T13:48:47.796Z"}, {"entity": "publication", "iuid": "5cf4730cf1b146878c93fd28bd5b83ec", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5cf4730cf1b146878c93fd28bd5b83ec.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5cf4730cf1b146878c93fd28bd5b83ec"}}, "title": "Genome-wide association meta-analysis of 78,308 individuals identifies new loci and genes influencing human intelligence.", "authors": [{"family": "Sniekers", "given": "Suzanne", "initials": "S"}, {"family": "Stringer", "given": "Sven", "initials": "S", "orcid": "0000-0003-3115-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/f7e6ae56d0474688b3722f58d33f385d.json"}}, {"family": "Watanabe", "given": "Kyoko", "initials": "K"}, {"family": "Jansen", "given": "Philip R", "initials": "PR"}, {"family": "Coleman", "given": "Jonathan R I", "initials": "JRI"}, {"family": "Krapohl", "given": "Eva", "initials": "E"}, {"family": "Taskesen", "given": "Erdogan", "initials": "E"}, {"family": "Hammerschlag", "given": "Anke R", "initials": "AR", "orcid": "0000-0003-4847-4814", "researcher": {"href": "https://publications.scilifelab.se/researcher/cf251c46945046c79447bcdb7d3f28da.json"}}, {"family": "Okbay", "given": "Aysu", "initials": "A"}, {"family": "Zabaneh", "given": "Delilah", "initials": "D"}, {"family": "Amin", "given": "Najaf", "initials": "N"}, {"family": "Breen", "given": "Gerome", "initials": "G"}, {"family": "Cesarini", "given": "David", "initials": "D"}, {"family": "Chabris", "given": "Christopher F", "initials": "CF"}, {"family": "Iacono", "given": "William G", "initials": "WG"}, {"family": "Ikram", "given": "M Arfan", "initials": "MA", "orcid": "0000-0003-0372-8585", "researcher": {"href": "https://publications.scilifelab.se/researcher/2ec81571f4a94af682b4e23526f87385.json"}}, {"family": "Johannesson", "given": "Magnus", "initials": "M", "orcid": "0000-0001-8759-6393", "researcher": {"href": "https://publications.scilifelab.se/researcher/164991d6c183431d8245e08bd876f400.json"}}, {"family": "Koellinger", "given": "Philipp", "initials": "P"}, {"family": "Lee", "given": "James J", "initials": "JJ", "orcid": "0000-0001-6547-5128", "researcher": {"href": "https://publications.scilifelab.se/researcher/a62c02dc148145f78d711190c246a59e.json"}}, {"family": "Magnusson", "given": "Patrik K E", "initials": "PKE"}, {"family": "McGue", "given": "Matt", "initials": "M"}, {"family": "Miller", "given": "Mike B", "initials": "MB"}, {"family": "Ollier", "given": "William E R", "initials": "WER"}, {"family": "Payton", "given": "Antony", "initials": "A"}, {"family": "Pendleton", "given": "Neil", "initials": "N"}, {"family": "Plomin", "given": "Robert", "initials": "R"}, {"family": "Rietveld", "given": "Cornelius A", "initials": "CA"}, {"family": "Tiemeier", "given": "Henning", "initials": "H"}, {"family": "van Duijn", "given": "Cornelia M", "initials": "CM"}, {"family": "Posthuma", "given": "Danielle", "initials": "D", "orcid": "0000-0001-7582-2365", "researcher": {"href": "https://publications.scilifelab.se/researcher/406e98180d174e8ca087f50074c025c9.json"}}], "type": "journal article", "published": "2017-07-00", "journal": {"volume": "49", "issn": "1546-1718", "issue": "7", "pages": "1107-1112", "title": "Nat. Genet.", "issn-l": "1061-4036"}, "abstract": "Intelligence is associated with important economic and health-related life outcomes. Despite intelligence having substantial heritability (0.54) and a confirmed polygenic nature, initial genetic studies were mostly underpowered. Here we report a meta-analysis for intelligence of 78,308 individuals. We identify 336 associated SNPs (METAL P < 5 \u00d7 10 -8) in 18 genomic loci, of which 15 are new. Around half of the SNPs are located inside a gene, implicating 22 genes, of which 11 are new findings. Gene-based analyses identified an additional 30 genes (MAGMA P < 2.73 \u00d7 10-6), of which all but one had not been implicated previously. We show that the identified genes are predominantly expressed in brain tissue, and pathway analysis indicates the involvement of genes regulating cell development (MAGMA competitive P = 3.5 \u00d7 10-6). Despite the well-known difference in twin-based heritability for intelligence in childhood (0.45) and adulthood (0.80), we show substantial genetic correlation (rg = 0.89, LD score regression P = 5.4 \u00d7 10-29). These findings provide new insight into the genetic architecture of intelligence.", "doi": "10.1038/ng.3869", "pmid": "28530673", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "ng.3869"}, {"db": "pmc", "key": "PMC5665562"}, {"db": "mid", "key": "NIHMS871043"}], "notes": [], "created": "2018-01-09T14:01:32.174Z", "modified": "2021-06-21T15:38:03.122Z"}, {"entity": "publication", "iuid": "50bf4910f1e345aeb3712d65fa4662dd", "links": {"self": {"href": "https://publications.scilifelab.se/publication/50bf4910f1e345aeb3712d65fa4662dd.json"}, "display": {"href": "https://publications.scilifelab.se/publication/50bf4910f1e345aeb3712d65fa4662dd"}}, "title": "EGR2 mutations define a new clinically aggressive subgroup of chronic lymphocytic leukemia", "authors": [{"family": "Young", "given": "E", "initials": "E"}, {"family": "Noerenberg", "given": "D", "initials": "D"}, {"family": "Mansouri", "given": "L", "initials": "L"}, {"family": "Ljungstr\u00f6m", "given": "V", "initials": "V"}, {"family": "Frick", "given": "M", "initials": "M"}, {"family": "Sutton", "given": "L A", "initials": "LA"}, {"family": "Blakemore", "given": "S J", "initials": "SJ"}, {"family": "Galan-Sousa", "given": "J", "initials": "J"}, {"family": "Plevova", "given": "K", "initials": "K"}, {"family": "Baliakas", "given": "P", "initials": "P"}, {"family": "Rossi", "given": "D", "initials": "D"}, {"family": "Clifford", "given": "R", "initials": "R"}, {"family": "Roos-Weil", "given": "D", "initials": "D"}, {"family": "Navrkalova", "given": "V", "initials": "V"}, {"family": "D\u00f6rken", "given": "B", "initials": "B"}, {"family": "Schmitt", "given": "C A", "initials": "CA"}, {"family": "Smedby", "given": "K E", "initials": "KE"}, {"family": "Juliusson", "given": "G", "initials": "G"}, {"family": "Giacopelli", "given": "B", "initials": "B"}, {"family": "Blachly", "given": "J S", "initials": "JS"}, {"family": "Belessi", "given": "C", "initials": "C"}, {"family": "Panagiotidis", "given": "P", "initials": "P"}, {"family": "Chiorazzi", "given": "N", "initials": "N"}, {"family": "Davi", "given": "F", "initials": "F"}, {"family": "Langerak", "given": "A W", "initials": "AW"}, {"family": "Oscier", "given": "D", "initials": "D"}, {"family": "Schuh", "given": "A", "initials": "A"}, {"family": "Gaidano", "given": "G", "initials": "G"}, {"family": "Ghia", "given": "P", "initials": "P"}, {"family": "Xu", "given": "W", "initials": "W"}, {"family": "Fan", "given": "L", "initials": "L"}, {"family": "Bernard", "given": "O A", "initials": "OA"}, {"family": "Nguyen-Khac", "given": "F", "initials": "F"}, {"family": "Rassenti", "given": "L", "initials": "L"}, {"family": "Li", "given": "J", "initials": "J"}, {"family": "Kipps", "given": "T J", "initials": "TJ"}, {"family": "Stamatopoulos", "given": "K", "initials": "K"}, {"family": "Pospisilova", "given": "S", "initials": "S"}, {"family": "Zenz", "given": "T", "initials": "T"}, {"family": "Oakes", "given": "C C", "initials": "CC"}, {"family": "Strefford", "given": "J C", "initials": "JC"}, {"family": "Rosenquist", "given": "R", "initials": "R"}, {"family": "Damm", "given": "F", "initials": "F"}], "type": "journal-article", "published": "2017-07-00", "journal": {"volume": "31", "issn": "1476-5551", "issue": "7", "pages": "1547-1554", "title": "Leukemia", "issn-l": "0887-6924"}, "abstract": null, "doi": "10.1038/leu.2016.359", "pmid": "27890934", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2017-10-30T09:30:04.162Z", "modified": "2024-01-16T13:48:47.805Z"}, {"entity": "publication", "iuid": "74bdc77a2a8a4d918aeb02299ccac60b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/74bdc77a2a8a4d918aeb02299ccac60b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/74bdc77a2a8a4d918aeb02299ccac60b"}}, "title": "Blood transcriptomes and de novo identification of candidate loci for mating success in lekking great snipe (Gallinago media)", "authors": [{"family": "H\u00f6glund", "given": "Jacob", "initials": "J"}, {"family": "Wang", "given": "Biao", "initials": "B"}, {"family": "Saether", "given": "Stein Are", "initials": "SA"}, {"family": "Blom", "given": "Mozes Pil Kyu", "initials": "MPK"}, {"family": "Fiske", "given": "Peder", "initials": "P"}, {"family": "Halvarsson", "given": "Peter", "initials": "P"}, {"family": "Horsburgh", "given": "Gavin J", "initials": "GJ"}, {"family": "Burke", "given": "Terry", "initials": "T"}, {"family": "K\u00e5l\u00e5s", "given": "John Atle", "initials": "JA"}, {"family": "Ekblom", "given": "Robert", "initials": "R"}], "type": "journal-article", "published": "2017-07-00", "journal": {"volume": "26", "issn": "0962-1083", "issue": "13", "pages": "3458-3471", "title": "Mol Ecol", "issn-l": "0962-1083"}, "abstract": "We assembled the great snipe blood transcriptome using data from fourteen lekking males, in order to de novo identify candidate genes related to sexual selection, and determined the expression profiles in relation to mating success. The three most highly transcribed genes were encoding different haemoglobin subunits. All tended to be overexpressed in males with high mating success. We also called single nucleotide polymorphisms (SNPs) from the transcriptome data and found considerable genetic variation for many genes expressed during lekking. Among these, we identified 14 polymorphic candidate SNPs that had a significant genotypic association with mating success (number of females mated with) and/or mating status (mated or not). Four of the candidate SNPs were found in HBAA (encoding the haemoglobin \u03b1-chain). Heterozygotes for one of these and one SNP in the gene PABPC1 appeared to enjoy higher mating success compared to males homozygous for either of the alleles. In a larger data set of individuals, we genotyped 38 of the identified SNPs but found low support for consistent selection as only one of the zygosities of previously identified candidate SNPs and none of their genotypes were associated with mating status. However, candidate SNPs generally showed lower levels of spatial genetic structure compared to noncandidate markers. We also scored the prevalence of avian malaria in a subsample of birds. Males infected with avian malaria parasites had lower mating success in the year of sampling than noninfected males. Parasite infection and its interaction with specific genes may thus affect performance on the lek.", "doi": "10.1111/mec.14118", "pmid": "28345264", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [], "notes": [], "created": "2018-01-09T20:48:44.020Z", "modified": "2020-01-21T13:56:11.928Z"}, {"entity": "publication", "iuid": "11cec8cacdd44603bc2ae2054cc21468", "links": {"self": {"href": "https://publications.scilifelab.se/publication/11cec8cacdd44603bc2ae2054cc21468.json"}, "display": {"href": "https://publications.scilifelab.se/publication/11cec8cacdd44603bc2ae2054cc21468"}}, "title": "A Low-Frequency Inactivating AKT2 Variant Enriched in the Finnish Population Is Associated With Fasting Insulin Levels and Type 2 Diabetes Risk.", "authors": [{"family": "Manning", "given": "Alisa", "initials": "A"}, {"family": "Highland", "given": "Heather M", "initials": "HM"}, {"family": "Gasser", "given": "Jessica", "initials": "J"}, {"family": "Sim", "given": "Xueling", "initials": "X"}, {"family": "Tukiainen", "given": "Taru", "initials": "T"}, {"family": "Fontanillas", "given": "Pierre", "initials": "P"}, {"family": "Grarup", "given": "Niels", "initials": "N"}, {"family": "Rivas", "given": "Manuel A", "initials": "MA"}, {"family": "Mahajan", "given": "Anubha", "initials": "A"}, {"family": "Locke", "given": "Adam E", "initials": "AE"}, {"family": "Cingolani", "given": "Pablo", "initials": "P"}, {"family": "Pers", "given": "Tune H", "initials": "TH"}, {"family": "Vi\u00f1uela", "given": "Ana", "initials": "A"}, {"family": "Brown", "given": "Andrew A", "initials": "AA"}, {"family": "Wu", "given": "Ying", "initials": "Y"}, {"family": "Flannick", "given": "Jason", "initials": "J"}, {"family": "Fuchsberger", "given": "Christian", "initials": "C"}, {"family": "Gamazon", "given": "Eric R", "initials": "ER"}, {"family": "Gaulton", "given": "Kyle J", "initials": "KJ"}, {"family": "Im", "given": "Hae Kyung", "initials": "HK"}, {"family": "Teslovich", "given": "Tanya M", "initials": "TM"}, {"family": "Blackwell", "given": "Thomas W", "initials": "TW"}, {"family": "Bork-Jensen", "given": "Jette", "initials": "J"}, {"family": "Burtt", "given": "No\u00ebl P", "initials": "NP"}, {"family": "Chen", "given": "Yuhui", "initials": "Y"}, {"family": "Green", "given": "Todd", "initials": "T"}, {"family": "Hartl", "given": "Christopher", "initials": "C"}, {"family": "Kang", "given": "Hyun Min", "initials": "HM"}, {"family": "Kumar", "given": "Ashish", "initials": "A"}, {"family": "Ladenvall", "given": "Claes", "initials": "C"}, {"family": "Ma", "given": "Clement", "initials": "C"}, {"family": "Moutsianas", "given": "Loukas", "initials": "L"}, {"family": "Pearson", "given": "Richard D", "initials": "RD"}, {"family": "Perry", "given": "John R B", "initials": "JRB"}, {"family": "Rayner", "given": "N William", "initials": "NW"}, {"family": "Robertson", "given": "Neil R", "initials": "NR"}, {"family": "Scott", "given": "Laura J", "initials": "LJ"}, {"family": "van de Bunt", "given": "Martijn", "initials": "M"}, {"family": "Eriksson", "given": "Johan G", "initials": "JG"}, {"family": "Jula", "given": "Antti", "initials": "A"}, {"family": "Koskinen", "given": "Seppo", "initials": "S"}, {"family": "Lehtim\u00e4ki", "given": "Terho", "initials": "T"}, {"family": "Palotie", "given": "Aarno", "initials": "A"}, {"family": "Raitakari", "given": "Olli T", "initials": "OT"}, {"family": "Jacobs", "given": "Suzanne B R", "initials": "SBR"}, {"family": "Wessel", "given": "Jennifer", "initials": "J"}, {"family": "Chu", "given": "Audrey Y", "initials": "AY"}, {"family": "Scott", "given": "Robert A", "initials": "RA"}, {"family": "Goodarzi", "given": "Mark O", "initials": "MO"}, {"family": "Blancher", "given": "Christine", "initials": "C"}, {"family": "Buck", "given": "Gemma", "initials": "G"}, {"family": "Buck", "given": "David", "initials": "D"}, {"family": "Chines", "given": "Peter S", "initials": "PS"}, {"family": "Gabriel", "given": "Stacey", "initials": "S"}, {"family": "Gjesing", "given": "Anette P", "initials": "AP"}, {"family": "Groves", "given": "Christopher J", "initials": "CJ"}, {"family": "Hollensted", "given": "Mette", "initials": "M"}, {"family": "Huyghe", "given": "Jeroen R", "initials": "JR"}, {"family": "Jackson", "given": "Anne U", "initials": "AU"}, {"family": "Jun", "given": "Goo", "initials": "G"}, {"family": "Justesen", "given": "Johanne Marie", "initials": "JM"}, {"family": "Mangino", "given": "Massimo", "initials": "M"}, {"family": "Murphy", "given": "Jacquelyn", "initials": "J"}, {"family": "Neville", "given": "Matt", "initials": "M"}, {"family": "Onofrio", "given": "Robert", "initials": "R"}, {"family": "Small", "given": "Kerrin S", "initials": "KS"}, {"family": "Stringham", "given": "Heather M", "initials": "HM"}, {"family": "Trakalo", "given": "Joseph", "initials": "J"}, {"family": "Banks", "given": "Eric", "initials": "E"}, {"family": "Carey", "given": "Jason", "initials": "J"}, {"family": "Carneiro", "given": "Mauricio O", "initials": "MO"}, {"family": "DePristo", "given": "Mark", "initials": "M"}, {"family": "Farjoun", "given": "Yossi", "initials": "Y"}, {"family": "Fennell", "given": "Timothy", "initials": "T"}, {"family": "Goldstein", "given": "Jacqueline I", "initials": "JI"}, {"family": "Grant", "given": "George", "initials": "G"}, {"family": "Hrab\u00e9 de Angelis", "given": "Martin", "initials": "M"}, {"family": "Maguire", "given": "Jared", "initials": "J"}, {"family": "Neale", "given": "Benjamin M", "initials": "BM"}, {"family": "Poplin", "given": "Ryan", "initials": "R"}, {"family": "Purcell", "given": "Shaun", "initials": "S"}, {"family": "Schwarzmayr", "given": "Thomas", "initials": "T"}, {"family": "Shakir", "given": "Khalid", "initials": "K"}, {"family": "Smith", "given": "Joshua D", "initials": "JD"}, {"family": "Strom", "given": "Tim M", "initials": "TM"}, {"family": "Wieland", "given": "Thomas", 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"Nancy J", "initials": "NJ"}, {"family": "Duggirala", "given": "Ravindranath", "initials": "R"}, {"family": "Seielstad", "given": "Mark", "initials": "M"}, {"family": "Wilson", "given": "James G", "initials": "JG"}, {"family": "Dupuis", "given": "Josee", "initials": "J"}, {"family": "Ripatti", "given": "Samuli", "initials": "S"}, {"family": "Hanis", "given": "Craig L", "initials": "CL"}, {"family": "Florez", "given": "Jose C", "initials": "JC"}, {"family": "Mohlke", "given": "Karen L", "initials": "KL"}, {"family": "Meigs", "given": "James B", "initials": "JB"}, {"family": "Laakso", "given": "Markku", "initials": "M"}, {"family": "Morris", "given": "Andrew P", "initials": "AP"}, {"family": "Boehnke", "given": "Michael", "initials": "M"}, {"family": "Altshuler", "given": "David", "initials": "D"}, {"family": "McCarthy", "given": "Mark I", "initials": "MI"}, {"family": "Gloyn", "given": "Anna L", "initials": "AL"}, {"family": "Lindgren", "given": "Cecilia M", "initials": "CM"}], "type": "journal article", "published": "2017-07-00", "journal": {"volume": "66", "issn": "1939-327X", "issue": "7", "pages": "2019-2032", "title": "Diabetes", "issn-l": "0012-1797"}, "abstract": "To identify novel coding association signals and facilitate characterization of mechanisms influencing glycemic traits and type 2 diabetes risk, we analyzed 109,215 variants derived from exome array genotyping together with an additional 390,225 variants from exome sequence in up to 39,339 normoglycemic individuals from five ancestry groups. We identified a novel association between the coding variant (p.Pro50Thr) in AKT2 and fasting plasma insulin (FI), a gene in which rare fully penetrant mutations are causal for monogenic glycemic disorders. The low-frequency allele is associated with a 12% increase in FI levels. This variant is present at 1.1% frequency in Finns but virtually absent in individuals from other ancestries. Carriers of the FI-increasing allele had increased 2-h insulin values, decreased insulin sensitivity, and increased risk of type 2 diabetes (odds ratio 1.05). In cellular studies, the AKT2-Thr50 protein exhibited a partial loss of function. We extend the allelic spectrum for coding variants in AKT2 associated with disorders of glucose homeostasis and demonstrate bidirectional effects of variants within the pleckstrin homology domain of AKT2.", "doi": "10.2337/db16-1329", "pmid": "28341696", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "db16-1329"}, {"db": "pmc", "key": "PMC5482074"}, {"db": "mid", "key": "EMS72347"}], "notes": [], "created": "2017-10-25T15:18:19.643Z", "modified": "2024-01-16T13:48:47.816Z"}, {"entity": "publication", "iuid": "64f09ccd0fe64bf093e9d17de685ef9c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/64f09ccd0fe64bf093e9d17de685ef9c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/64f09ccd0fe64bf093e9d17de685ef9c"}}, "title": "Moderate nucleotide diversity in the Atlantic herring 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"given": "Cecilia", "initials": "C"}, {"family": "Magnusson", "given": "Patrik K E", "initials": "PKE"}, {"family": "Pedersen", "given": "Nancy L", "initials": "NL"}, {"family": "Hallmans", "given": "G\u00f6ran", "initials": "G"}, {"family": "Chu", "given": "Audrey Y", "initials": "AY"}, {"family": "Justice", "given": "Anne E", "initials": "AE"}, {"family": "Graff", "given": "Mariaelisa", "initials": "M"}, {"family": "Winkler", "given": "Thomas W", "initials": "TW"}, {"family": "Rose", "given": "Lynda M", "initials": "LM"}, {"family": "Langenberg", "given": "Claudia", "initials": "C"}, {"family": "Cupples", "given": "L Adrienne", "initials": "LA"}, {"family": "Ridker", "given": "Paul M", "initials": "PM"}, {"family": "Wareham", "given": "Nicholas J", "initials": "NJ"}, {"family": "Ong", "given": "Ken K", "initials": "KK"}, {"family": "Loos", "given": "Ruth J F", "initials": "RJF"}, {"family": "Chasman", "given": "Daniel I", "initials": "DI"}, {"family": "Ingelsson", "given": "Erik", "initials": "E"}, {"family": "Kilpel\u00e4inen", "given": "Tuomas O", "initials": "TO"}, {"family": "Scott", "given": "Robert A", "initials": "RA"}, {"family": "M\u00e4gi", "given": "Reedik", "initials": "R"}, {"family": "Par\u00e9", "given": "Guillaume", "initials": "G"}, {"family": "Franks", "given": "Paul W", "initials": "PW"}, {"family": null, "given": "", "initials": ""}], "type": "journal-article", "published": "2017-06-14", "journal": {"volume": "13", "issn": "1553-7404", "issue": "6", "pages": "e1006812", "title": "PLoS Genet.", "issn-l": "1553-7390"}, "abstract": null, "doi": "10.1371/journal.pgen.1006812", "pmid": "28614350", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [], "notes": [], "created": "2018-01-09T13:58:09.716Z", "modified": "2020-01-21T13:56:11.781Z"}, {"entity": "publication", "iuid": "88adbd607a954e539fe5a35a01aba19a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/88adbd607a954e539fe5a35a01aba19a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/88adbd607a954e539fe5a35a01aba19a"}}, "title": "Genetic loci associated with heart rate variability and their effects on cardiac disease risk.", "authors": [{"family": "Nolte", "given": "Ilja M", "initials": "IM", "orcid": "0000-0001-5047-4077", "researcher": {"href": "https://publications.scilifelab.se/researcher/abd76becaa8a4df284103c3e20261f10.json"}}, {"family": "Munoz", "given": "M Loretto", "initials": "ML"}, {"family": "Tragante", "given": "Vinicius", "initials": "V"}, {"family": "Amare", "given": "Azmeraw T", "initials": "AT", "orcid": "0000-0002-7940-0335", "researcher": {"href": "https://publications.scilifelab.se/researcher/028fd1a615ef4dc1a71067d82f094c9c.json"}}, {"family": "Jansen", "given": "Rick", "initials": "R", "orcid": "0000-0002-3333-6737", "researcher": {"href": "https://publications.scilifelab.se/researcher/bcd392c9b9784ebe8c8730e05463377a.json"}}, {"family": "Vaez", "given": "Ahmad", "initials": "A", "orcid": "0000-0001-9048-3795", "researcher": {"href": "https://publications.scilifelab.se/researcher/34a09aa88bc74e1285ddd71655dbddc3.json"}}, {"family": "von der Heyde", "given": "Benedikt", "initials": "B"}, {"family": "Avery", "given": "Christy L", "initials": "CL"}, {"family": "Bis", "given": "Joshua C", "initials": "JC"}, {"family": "Dierckx", "given": "Bram", "initials": "B"}, {"family": "van Dongen", "given": "Jenny", "initials": "J"}, {"family": "Gogarten", "given": "Stephanie M", "initials": "SM"}, {"family": "Goyette", "given": "Philippe", "initials": "P"}, {"family": "Hernesniemi", "given": "Jussi", "initials": "J"}, {"family": "Huikari", "given": "Ville", "initials": "V"}, {"family": "Hwang", "given": "Shih-Jen", "initials": "SJ"}, {"family": "Jaju", "given": "Deepali", "initials": "D"}, {"family": "Kerr", "given": "Kathleen F", "initials": "KF"}, {"family": "Kluttig", "given": "Alexander", "initials": "A"}, {"family": "Krijthe", "given": "Bouwe P", "initials": "BP"}, {"family": "Kumar", "given": "Jitender", "initials": "J"}, {"family": "van der Laan", "given": "Sander W", "initials": "SW", "orcid": "0000-0001-6888-1404", "researcher": {"href": "https://publications.scilifelab.se/researcher/9bd54ab413974b9096ff3d924f8b8eb6.json"}}, {"family": "Lyytik\u00e4inen", "given": "Leo-Pekka", "initials": "LP"}, {"family": "Maihofer", "given": "Adam X", "initials": "AX"}, {"family": "Minassian", "given": "Arpi", "initials": "A"}, {"family": "van der Most", "given": "Peter J", "initials": "PJ", "orcid": "0000-0001-8450-3518", "researcher": {"href": "https://publications.scilifelab.se/researcher/17cd11842111490ba5460f3093a366f3.json"}}, {"family": "M\u00fcller-Nurasyid", "given": "Martina", "initials": "M"}, {"family": "Nivard", "given": "Michel", "initials": "M", "orcid": "0000-0003-2015-1888", "researcher": {"href": "https://publications.scilifelab.se/researcher/0d65d2277e7344a3a13f0d2193c6813b.json"}}, {"family": "Salvi", "given": "Erika", "initials": "E", "orcid": "0000-0002-2724-2291", "researcher": {"href": "https://publications.scilifelab.se/researcher/c5119a5a894746dc92bb484e0d5cc4a3.json"}}, {"family": "Stewart", "given": "James D", "initials": "JD"}, {"family": "Thayer", "given": "Julian F", "initials": "JF"}, {"family": "Verweij", "given": "Niek", "initials": "N", "orcid": "0000-0002-4303-7685", "researcher": {"href": "https://publications.scilifelab.se/researcher/7306319d42a640a483b937de588a17a4.json"}}, {"family": "Wong", "given": "Andrew", "initials": "A", "orcid": "0000-0003-2079-4779", "researcher": {"href": "https://publications.scilifelab.se/researcher/d4e71c13d81a4ec5a496737a5657c97e.json"}}, {"family": "Zabaneh", "given": "Delilah", "initials": "D"}, {"family": "Zafarmand", "given": "Mohammad H", "initials": "MH"}, {"family": "Abdellaoui", "given": "Abdel", "initials": "A"}, 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"initials": "H"}, {"family": "Hutri-K\u00e4h\u00f6nen", "given": "Nina", "initials": "N"}, {"family": "Jouven", "given": "Xavier", "initials": "X"}, {"family": "Junttila", "given": "Juhani", "initials": "J"}, {"family": "Juonala", "given": "Markus", "initials": "M"}, {"family": "Kiviniemi", "given": "Antti M", "initials": "AM", "orcid": "0000-0002-1160-493X", "researcher": {"href": "https://publications.scilifelab.se/researcher/583df0b19f724b0395d90fd9f8785e50.json"}}, {"family": "Kors", "given": "Jan A", "initials": "JA"}, {"family": "Kumari", "given": "Meena", "initials": "M"}, {"family": "Kuznetsova", "given": "Tatiana", "initials": "T"}, {"family": "Laurie", "given": "Cathy C", "initials": "CC"}, {"family": "Lefrandt", "given": "Joop D", "initials": "JD"}, {"family": "Li", "given": "Yong", "initials": "Y"}, {"family": "Li", "given": "Yun", "initials": "Y"}, {"family": "Liao", "given": "Duanping", "initials": "D"}, {"family": "Limacher", "given": "Marian C", "initials": "MC"}, {"family": "Lin", "given": "Henry J", "initials": "HJ"}, {"family": "Lindgren", "given": "Cecilia M", "initials": "CM"}, {"family": "Lubitz", "given": "Steven A", "initials": "SA"}, {"family": "Mahajan", "given": "Anubha", "initials": "A"}, {"family": "McKnight", "given": "Barbara", "initials": "B"}, {"family": "Zu Schwabedissen", "given": "Henriette Meyer", "initials": "HM"}, {"family": "Milaneschi", "given": "Yuri", "initials": "Y"}, {"family": "Mononen", "given": "Nina", "initials": "N"}, {"family": "Morris", "given": "Andrew P", "initials": "AP"}, {"family": "Nalls", "given": "Mike A", "initials": "MA"}, {"family": "Navis", "given": "Gerjan", "initials": "G"}, {"family": "Neijts", "given": "Melanie", "initials": "M"}, {"family": "Nikus", "given": "Kjell", "initials": "K"}, {"family": "North", "given": "Kari E", "initials": "KE"}, {"family": "O'Connor", "given": "Daniel T", "initials": "DT"}, {"family": "Ormel", "given": "Johan", "initials": "J"}, {"family": "Perz", "given": "Siegfried", "initials": "S"}, {"family": "Peters", "given": "Annette", "initials": "A"}, {"family": "Psaty", "given": "Bruce M", "initials": "BM"}, {"family": "Raitakari", "given": "Olli T", "initials": "OT"}, {"family": "Risbrough", "given": "Victoria B", "initials": "VB"}, {"family": "Sinner", "given": "Moritz F", "initials": "MF"}, {"family": "Siscovick", "given": "David", "initials": "D"}, {"family": "Smit", "given": "Johannes H", "initials": "JH"}, {"family": "Smith", "given": "Nicholas L", "initials": "NL"}, {"family": "Soliman", "given": "Elsayed Z", "initials": "EZ", "orcid": "0000-0001-5632-8150", "researcher": {"href": "https://publications.scilifelab.se/researcher/96e79156ff664c509217e8834a728c79.json"}}, {"family": "Sotoodehnia", "given": "Nona", "initials": "N"}, {"family": "Staessen", "given": "Jan A", "initials": "JA"}, {"family": "Stein", "given": "Phyllis K", "initials": "PK"}, {"family": "Stilp", "given": "Adrienne M", "initials": "AM"}, {"family": "Stolarz-Skrzypek", "given": "Katarzyna", "initials": "K"}, {"family": "Strauch", "given": "Konstantin", "initials": "K"}, {"family": "Sundstr\u00f6m", "given": "Johan", "initials": "J"}, {"family": "Swenne", "given": "Cees A", "initials": "CA"}, {"family": "Syv\u00e4nen", "given": "Ann-Christine", "initials": "AC", "orcid": "0000-0002-9681-9146", "researcher": {"href": "https://publications.scilifelab.se/researcher/f7012e35025543379380cb90efd71243.json"}}, {"family": "Tardif", "given": "Jean-Claude", "initials": "JC"}, {"family": "Taylor", "given": "Kent D", "initials": "KD"}, {"family": "Teumer", "given": "Alexander", "initials": "A", "orcid": "0000-0002-8309-094X", "researcher": {"href": "https://publications.scilifelab.se/researcher/dc9c2667a55b47a6a08aea764fab0946.json"}}, {"family": "Thornton", "given": "Timothy A", "initials": "TA"}, {"family": "Tinker", "given": "Lesley E", "initials": "LE"}, {"family": "Uitterlinden", "given": "Andr\u00e9 G", "initials": "AG"}, {"family": "van Setten", "given": "Jessica", "initials": "J", "orcid": "0000-0002-4934-7510", "researcher": {"href": "https://publications.scilifelab.se/researcher/4be6dce84e8a4f46bf15f4de178f70ba.json"}}, {"family": "Voss", "given": "Andreas", "initials": "A"}, {"family": "Waldenberger", "given": "Melanie", "initials": "M"}, {"family": "Wilhelmsen", "given": "Kirk C", "initials": "KC"}, {"family": "Willemsen", "given": "Gonneke", "initials": "G"}, {"family": "Wong", "given": "Quenna", "initials": "Q"}, {"family": "Zhang", "given": "Zhu-Ming", "initials": "ZM"}, {"family": "Zonderman", "given": "Alan B", "initials": "AB"}, {"family": "Cusi", "given": "Daniele", "initials": "D"}, {"family": "Evans", "given": "Michele K", "initials": "MK"}, {"family": "Greiser", "given": "Halina K", "initials": "HK"}, {"family": "van der Harst", "given": "Pim", "initials": "P"}, {"family": "Hassan", "given": "Mohammad", "initials": "M"}, {"family": "Ingelsson", "given": "Erik", "initials": "E"}, {"family": "J\u00e4rvelin", "given": "Marjo-Riitta", "initials": "MR"}, {"family": "K\u00e4\u00e4b", "given": "Stefan", "initials": "S"}, {"family": "K\u00e4h\u00f6nen", "given": "Mika", "initials": "M"}, {"family": "Kivimaki", "given": "Mika", "initials": "M", "orcid": "0000-0002-4699-5627", "researcher": {"href": "https://publications.scilifelab.se/researcher/6f81f2fb70b14197829de8cd819ceaa6.json"}}, {"family": "Kooperberg", "given": "Charles", "initials": "C"}, {"family": "Kuh", "given": "Diana", "initials": "D"}, {"family": "Lehtim\u00e4ki", "given": "Terho", "initials": "T"}, {"family": "Lind", "given": "Lars", "initials": "L"}, {"family": "Nievergelt", "given": "Caroline M", "initials": "CM"}, {"family": "O'Donnell", "given": "Chris J", "initials": "CJ"}, {"family": "Oldehinkel", "given": "Albertine J", "initials": "AJ"}, {"family": "Penninx", "given": "Brenda", "initials": "B"}, {"family": "Reiner", "given": "Alexander P", "initials": "AP"}, {"family": "Riese", "given": "Harri\u00ebtte", "initials": "H"}, {"family": "van Roon", "given": "Arie M", "initials": "AM"}, {"family": "Rioux", "given": "John D", "initials": "JD"}, {"family": "Rotter", "given": "Jerome I", "initials": "JI"}, {"family": "Sofer", "given": "Tamar", "initials": "T"}, {"family": "Stricker", "given": "Bruno H", "initials": "BH"}, {"family": "Tiemeier", "given": "Henning", "initials": "H", "orcid": "0000-0002-4395-1397", "researcher": {"href": "https://publications.scilifelab.se/researcher/73e05bd74af344ba8d963463f49bb242.json"}}, {"family": "Vrijkotte", "given": "Tanja G M", "initials": "TGM"}, {"family": "Asselbergs", "given": "Folkert W", "initials": "FW", "orcid": "0000-0002-1692-8669", "researcher": {"href": "https://publications.scilifelab.se/researcher/7037429ef1304bdaabd837d242b1e6f5.json"}}, {"family": "Brundel", "given": "Bianca J J M", "initials": "BJJM"}, {"family": "Heckbert", "given": "Susan R", "initials": "SR"}, {"family": "Whitsel", "given": "Eric A", "initials": "EA"}, {"family": "den Hoed", "given": "Marcel", "initials": "M"}, {"family": "Snieder", "given": "Harold", "initials": "H"}, {"family": "de Geus", "given": "Eco J C", "initials": "EJC"}], "type": "journal article", "published": "2017-06-14", "journal": {"volume": "8", "issn": "2041-1723", "issue": null, "pages": "15805", "title": "Nat Commun", "issn-l": "2041-1723"}, "abstract": "Reduced cardiac vagal control reflected in low heart rate variability (HRV) is associated with greater risks for cardiac morbidity and mortality. In two-stage meta-analyses of genome-wide association studies for three HRV traits in up to 53,174 individuals of European ancestry, we detect 17 genome-wide significant SNPs in eight loci. HRV SNPs tag non-synonymous SNPs (in NDUFA11 and KIAA1755), expression quantitative trait loci (eQTLs) (influencing GNG11, RGS6 and NEO1), or are located in genes preferentially expressed in the sinoatrial node (GNG11, RGS6 and HCN4). Genetic risk scores account for 0.9 to 2.6% of the HRV variance. Significant genetic correlation is found for HRV with heart rate (-0.74<rg<-0.55) and blood pressure (-0.35<rg<-0.20). These findings provide clinically relevant biological insight into heritable variation in vagal heart rhythm regulation, with a key role for genetic variants (GNG11, RGS6) that influence G-protein heterotrimer action in GIRK-channel induced pacemaker membrane hyperpolarization.", "doi": "10.1038/ncomms15805", "pmid": "28613276", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "ncomms15805"}, {"db": "pmc", "key": "PMC5474732"}], "notes": [], "created": "2017-10-25T15:27:47.158Z", "modified": "2024-01-16T13:48:47.870Z"}, {"entity": "publication", "iuid": "11b11d52ef8f47d8b685c7a4eccadc9a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/11b11d52ef8f47d8b685c7a4eccadc9a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/11b11d52ef8f47d8b685c7a4eccadc9a"}}, "title": "Functional and Compositional Stability of Bacterial Metacommunities in Response to Salinity Changes", "authors": [{"family": "Berga", "given": "Merc\u00e8", "initials": "M"}, {"family": "Zha", "given": "Yinghua", "initials": "Y"}, {"family": "Sz\u00e9kely", "given": "Anna J", "initials": "AJ"}, {"family": "Langenheder", "given": "Silke", "initials": "S"}], "type": "journal-article", "published": "2017-06-08", "journal": {"volume": "8", "issn": "1664-302X", "issue": null, "pages": null, "title": "Front Microbiol", "issn-l": "1664-302X"}, "abstract": null, "doi": "10.3389/fmicb.2017.00948", "pmid": "28642735", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [], "notes": [], "created": "2018-01-09T20:49:54.874Z", "modified": "2020-01-21T13:56:11.774Z"}, {"entity": "publication", "iuid": "b95add923913483c89ea2e12850ab207", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b95add923913483c89ea2e12850ab207.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b95add923913483c89ea2e12850ab207"}}, "title": "Fast and general tests of genetic interaction for genome-wide association studies", "authors": [{"family": "Fr\u00e5nberg", "given": "Mattias", "initials": "M"}, {"family": "Strawbridge", "given": "Rona J", "initials": "RJ"}, {"family": "Hamsten", "given": "Anders", "initials": "A"}, {"family": "de Faire", "given": "Ulf", "initials": "U"}, {"family": "Lagergren", "given": "Jens", "initials": "J"}, {"family": "Sennblad", "given": "Bengt", "initials": "B"}, {"family": null, "given": "", "initials": ""}], "type": "journal-article", "published": "2017-06-06", "journal": {"volume": "13", "issn": "1553-7358", "issue": "6", "pages": "e1005556", "title": "PLoS Comput. Biol.", "issn-l": "1553-734X"}, "abstract": null, "doi": "10.1371/journal.pcbi.1005556", "pmid": "28586362", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [], "notes": [], "created": "2018-01-09T13:58:10.227Z", "modified": "2020-01-21T13:56:11.767Z"}, {"entity": "publication", "iuid": "8d30f96d3ed34e76b303cfeab798e8e9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8d30f96d3ed34e76b303cfeab798e8e9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8d30f96d3ed34e76b303cfeab798e8e9"}}, "title": "Large-Scale Identification of Common Trait and Disease Variants Affecting Gene Expression.", "authors": [{"family": "Hauberg", "given": "Mads Engel", "initials": "ME"}, {"family": "Zhang", "given": "Wen", "initials": "W"}, {"family": "Giambartolomei", "given": "Claudia", "initials": "C"}, {"family": "Franz\u00e9n", "given": "Oscar", "initials": "O"}, {"family": "Morris", "given": "David L", "initials": "DL"}, {"family": "Vyse", "given": "Timothy J", "initials": "TJ"}, {"family": "Ruusalepp", "given": "Arno", "initials": "A"}, {"family": "CommonMind Consortium", "given": "", "initials": ""}, {"family": "Sklar", "given": "Pamela", "initials": "P"}, {"family": "Schadt", "given": "Eric E", "initials": "EE"}, {"family": "Bj\u00f6rkegren", "given": "Johan L M", "initials": "JLM"}, {"family": "Roussos", "given": "Panos", "initials": "P"}], "type": "journal article", "published": "2017-06-01", "journal": {"volume": "100", "issn": "1537-6605", "issue": "6", "pages": "885-894", "title": "Am. J. Hum. Genet.", "issn-l": "0002-9297"}, "abstract": "Genome-wide association studies (GWASs) have identified a multitude of genetic loci involved with traits and diseases. However, it is often unclear which genes are affected in such loci and whether the associated genetic variants lead to increased or decreased gene function. To mitigate this, we integrated associations of common genetic variants in 57 GWASs with 24 studies of expression quantitative trait loci (eQTLs) from a broad range of tissues by using a Mendelian randomization approach. We discovered a total of 3,484 instances of gene-trait-associated changes in expression at a false-discovery rate < 0.05. These genes were often not closest to the genetic variant and were primarily identified in eQTLs derived from pathophysiologically relevant tissues. For instance, genes with expression changes associated with lipid traits were mostly identified in the liver, and those associated with cardiovascular disease were identified in arterial tissue. The affected genes additionally point to biological processes implicated in the interrogated traits, such as the interleukin-27 pathway in rheumatoid arthritis. Further, comparing trait-associated gene expression changes across traits suggests that pleiotropy is a widespread phenomenon and points to specific instances of both agonistic and antagonistic pleiotropy. For instance, expression of SNX19 and ABCB9 is positively correlated with both the risk of schizophrenia and educational attainment. To facilitate interpretation, we provide this lexicon of how common trait-associated genetic variants alter gene expression in various tissues as the online database GWAS2Genes.", "doi": "10.1016/j.ajhg.2017.04.016", "pmid": "28552197", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "S0002-9297(17)30161-1"}, {"db": "pmc", "key": "PMC5474225"}], "notes": [], "created": "2017-10-27T06:59:34.187Z", "modified": "2021-06-21T15:36:46.748Z"}, {"entity": "publication", "iuid": "7026633507fa4c85bac58c1c8537bb10", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7026633507fa4c85bac58c1c8537bb10.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7026633507fa4c85bac58c1c8537bb10"}}, "title": "No evidence for MHC class II-based non-random mating at the gametic haplotype in Atlantic salmon", "authors": [{"family": "Promerov\u00e1", "given": "M", "initials": "M"}, {"family": "Alavioon", "given": "G", "initials": "G"}, {"family": "Tusso", "given": "S", "initials": "S"}, {"family": "Burri", "given": "R", "initials": "R"}, {"family": "Immler", "given": "S", "initials": "S"}], "type": "journal-article", "published": "2017-06-00", "journal": {"volume": "118", "issn": "0018-067X", "issue": "6", "pages": "563-567", "title": "Heredity", "issn-l": "0018-067X"}, "abstract": null, "doi": "10.1038/hdy.2016.129", "pmid": "28098849", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [], "notes": [], "created": "2018-01-09T20:54:58.636Z", "modified": "2020-01-21T13:56:11.744Z"}, {"entity": "publication", "iuid": "0e86b0163ab8494386109ae3f51cb69e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0e86b0163ab8494386109ae3f51cb69e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0e86b0163ab8494386109ae3f51cb69e"}}, "title": "Methylation of HPA axis related genes in men with hypersexual disorder", "authors": [{"family": "Jokinen", "given": "Jussi", "initials": "J"}, {"family": "Bostr\u00f6m", "given": "Adrian E", "initials": "AE"}, {"family": "Chatzittofis", "given": "Andreas", "initials": "A"}, {"family": "Ciuculete", "given": "Diana M", "initials": "DM"}, {"family": "\u00d6berg", "given": "Katarina G\u00f6rts", "initials": "KG"}, {"family": "Flanagan", "given": "John N", "initials": "JN"}, {"family": "Arver", "given": "Stefan", "initials": "S"}, {"family": "Schi\u00f6th", "given": "Helgi B", "initials": "HB"}], "type": "journal-article", "published": "2017-06-00", "journal": {"volume": "80", "issn": "0306-4530", "issue": null, "pages": "67-73", "title": "Psychoneuroendocrinology", "issn-l": null}, "abstract": null, "doi": "10.1016/j.psyneuen.2017.03.007", "pmid": "28319850", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [], "notes": [], "created": "2017-10-25T15:15:16.501Z", "modified": "2020-01-21T13:56:10.087Z"}, {"entity": "publication", "iuid": "0c580009d54b4df1bc620037c8ee9093", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0c580009d54b4df1bc620037c8ee9093.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0c580009d54b4df1bc620037c8ee9093"}}, "title": "Large-scale analyses of common and rare variants identify 12 new loci associated with atrial fibrillation.", "authors": [{"family": "Christophersen", "given": "Ingrid E", "initials": "IE", "orcid": "0000-0002-6141-4712", "researcher": {"href": "https://publications.scilifelab.se/researcher/6430b9a129c1433a8e883a16a174b7a1.json"}}, {"family": "Rienstra", "given": "Michiel", "initials": "M"}, {"family": "Roselli", "given": "Carolina", "initials": "C"}, {"family": "Yin", "given": "Xiaoyan", "initials": "X"}, {"family": "Geelhoed", "given": "Bastiaan", "initials": "B"}, {"family": "Barnard", "given": "John", "initials": "J", "orcid": "0000-0003-2403-8268", "researcher": {"href": "https://publications.scilifelab.se/researcher/93c6ec0bcbe54cc6b139f96adc40d4f4.json"}}, {"family": "Lin", "given": "Honghuang", "initials": "H", "orcid": "0000-0003-3043-3942", "researcher": {"href": "https://publications.scilifelab.se/researcher/9bc2f1e6bb1140dfa054376eac685d5e.json"}}, {"family": "Arking", "given": "Dan E", "initials": "DE"}, {"family": "Smith", "given": "Albert V", "initials": "AV", "orcid": "0000-0003-1942-5845", "researcher": {"href": "https://publications.scilifelab.se/researcher/7b28739aa7d746718d670363d7c18a40.json"}}, {"family": "Albert", "given": "Christine M", "initials": "CM"}, {"family": "Chaffin", "given": "Mark", "initials": "M"}, {"family": "Tucker", "given": "Nathan R", "initials": "NR", "orcid": "0000-0002-5071-4218", "researcher": {"href": "https://publications.scilifelab.se/researcher/f89b1366ff014dc6a9cc5fe4bd37becf.json"}}, {"family": "Li", "given": "Molong", "initials": "M", "orcid": "0000-0002-3839-0281", "researcher": {"href": "https://publications.scilifelab.se/researcher/42c39506589c43b783f9e00c32882045.json"}}, {"family": "Klarin", "given": "Derek", "initials": "D"}, {"family": "Bihlmeyer", "given": "Nathan A", "initials": "NA", "orcid": "0000-0002-4415-7419", "researcher": {"href": "https://publications.scilifelab.se/researcher/bf23138a475f4dfbbacdb95ea9f70baa.json"}}, {"family": "Low", "given": "Siew-Kee", "initials": "SK"}, {"family": "Weeke", "given": "Peter E", "initials": "PE"}, {"family": "M\u00fcller-Nurasyid", "given": "Martina", "initials": "M"}, {"family": "Smith", "given": "J Gustav", "initials": "JG"}, {"family": "Brody", "given": "Jennifer A", "initials": "JA", "orcid": "0000-0001-8509-148X", "researcher": {"href": "https://publications.scilifelab.se/researcher/7e137fc0192e4fa295a88589d57e3498.json"}}, {"family": "Niemeijer", "given": "Maartje N", "initials": "MN"}, {"family": "D\u00f6rr", "given": "Marcus", "initials": "M"}, {"family": "Trompet", "given": "Stella", "initials": "S"}, {"family": "Huffman", "given": "Jennifer", "initials": "J", "orcid": "0000-0002-9672-2491", "researcher": {"href": "https://publications.scilifelab.se/researcher/cfa4efb5afae47528265d8be0d5e67fd.json"}}, {"family": "Gustafsson", "given": "Stefan", "initials": "S", "orcid": "0000-0001-5894-0351", "researcher": {"href": "https://publications.scilifelab.se/researcher/9a0552f8a6514baa9bdb6809148aaddc.json"}}, {"family": "Schurmann", "given": "Claudia", "initials": "C"}, {"family": "Kleber", "given": "Marcus E", "initials": "ME", "orcid": "0000-0003-0663-7275", "researcher": {"href": "https://publications.scilifelab.se/researcher/a51175112cfb4721b8c9fbfdc71c4307.json"}}, {"family": "Lyytik\u00e4inen", "given": "Leo-Pekka", "initials": "LP", "orcid": "0000-0002-7200-5455", "researcher": {"href": "https://publications.scilifelab.se/researcher/9fbbacc538e648368607d08b91f955bc.json"}}, {"family": 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"M"}, {"family": "Risch", "given": "Lorenz", "initials": "L"}, {"family": "Mansur", "given": "Alfredo J", "initials": "AJ"}, {"family": "Peters", "given": "Annette", "initials": "A"}, {"family": "Smith", "given": "Blair H", "initials": "BH", "orcid": "0000-0002-5362-9430", "researcher": {"href": "https://publications.scilifelab.se/researcher/ed343544e1324911931517689ad9ba6b.json"}}, {"family": "Lind", "given": "Lars", "initials": "L"}, {"family": "Scott", "given": "Stuart A", "initials": "SA", "orcid": "0000-0001-5720-1864", "researcher": {"href": "https://publications.scilifelab.se/researcher/2cb1efe5da074b6885f59ba4d80cbcd5.json"}}, {"family": "Lu", "given": "Yingchang", "initials": "Y"}, {"family": "Bottinger", "given": "Erwin B", "initials": "EB"}, {"family": "Hernesniemi", "given": "Jussi", "initials": "J"}, {"family": "Lindgren", "given": "Cecilia M", "initials": "CM"}, {"family": "Wong", "given": "Jorge A", "initials": "JA"}, {"family": "Huang", "given": "Jie", "initials": "J"}, 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"Kent D", "initials": "KD"}, {"family": "Campbell", "given": "Archie", "initials": "A", "orcid": "0000-0003-0198-5078", "researcher": {"href": "https://publications.scilifelab.se/researcher/89d6b9cb975246e5aa97c60035e2fdcc.json"}}, {"family": "Magnusson", "given": "Patrik K", "initials": "PK"}, {"family": "Porteous", "given": "David", "initials": "D"}, {"family": "Hocking", "given": "Lynne J", "initials": "LJ"}, {"family": "Vlachopoulou", "given": "Efthymia", "initials": "E"}, {"family": "Pedersen", "given": "Nancy L", "initials": "NL"}, {"family": "Nikus", "given": "Kjell", "initials": "K"}, {"family": "Orho-Melander", "given": "Marju", "initials": "M"}, {"family": "Hamsten", "given": "Anders", "initials": "A"}, {"family": "Heeringa", "given": "Jan", "initials": "J"}, {"family": "Denny", "given": "Joshua C", "initials": "JC"}, {"family": "Kriebel", "given": "Jennifer", "initials": "J", "orcid": "0000-0003-4270-018X", "researcher": {"href": 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"V\u00f6lker", "given": "Uwe", "initials": "U"}, {"family": "J\u00f6ckel", "given": "Karl-Heinz", "initials": "KH"}, {"family": "Sinner", "given": "Moritz F", "initials": "MF"}, {"family": "Lin", "given": "Henry J", "initials": "HJ"}, {"family": "Guo", "given": "Xiuqing", "initials": "X"}, {"family": "METASTROKE Consortium of the ISGC", "given": "", "initials": ""}, {"family": "Neurology Working Group of the CHARGE Consortium", "given": "", "initials": ""}, {"family": "Dichgans", "given": "Martin", "initials": "M"}, {"family": "Ingelsson", "given": "Erik", "initials": "E"}, {"family": "Kooperberg", "given": "Charles", "initials": "C"}, {"family": "Melander", "given": "Olle", "initials": "O"}, {"family": "Loos", "given": "Ruth J F", "initials": "RJF"}, {"family": "Laurikka", "given": "Jari", "initials": "J"}, {"family": "Conen", "given": "David", "initials": "D"}, {"family": "Rosand", "given": "Jonathan", "initials": "J"}, {"family": "van der Harst", "given": "Pim", "initials": "P"}, {"family": "Lokki", "given": "Marja-Liisa", "initials": "ML"}, {"family": "Kathiresan", "given": "Sekar", "initials": "S"}, {"family": "Pereira", "given": "Alexandre", "initials": "A"}, {"family": "Jukema", "given": "J Wouter", "initials": "JW", "orcid": "0000-0002-3246-8359", "researcher": {"href": "https://publications.scilifelab.se/researcher/0479b794031d4df7bed96340b3470c19.json"}}, {"family": "Hayward", "given": "Caroline", "initials": "C"}, {"family": "Rotter", "given": "Jerome I", "initials": "JI"}, {"family": "M\u00e4rz", "given": "Winfried", "initials": "W"}, {"family": "Lehtim\u00e4ki", "given": "Terho", "initials": "T"}, {"family": "Stricker", "given": "Bruno H", "initials": "BH"}, {"family": "Chung", "given": "Mina K", "initials": "MK"}, {"family": "Felix", "given": "Stephan B", "initials": "SB"}, {"family": "Gudnason", "given": "Vilmundur", "initials": "V"}, {"family": "Alonso", "given": "Alvaro", "initials": "A"}, {"family": "Roden", "given": "Dan M", "initials": "DM"}, {"family": "K\u00e4\u00e4b", "given": "Stefan", "initials": "S"}, {"family": "Chasman", "given": "Daniel I", "initials": "DI"}, {"family": "Heckbert", "given": "Susan R", "initials": "SR"}, {"family": "Benjamin", "given": "Emelia J", "initials": "EJ", "orcid": "0000-0003-4076-2336", "researcher": {"href": "https://publications.scilifelab.se/researcher/31c69bdf118d4b36ad65a6c4f780bab2.json"}}, {"family": "Tanaka", "given": "Toshihiro", "initials": "T", "orcid": "0000-0001-6201-9784", "researcher": {"href": "https://publications.scilifelab.se/researcher/021685ef890444bbb2870298ca2399d1.json"}}, {"family": "Lunetta", "given": "Kathryn L", "initials": "KL"}, {"family": "Lubitz", "given": "Steven A", "initials": "SA"}, {"family": "Ellinor", "given": "Patrick T", "initials": "PT", "orcid": "0000-0002-2067-0533", "researcher": {"href": "https://publications.scilifelab.se/researcher/dd513dc49e0945bc8298f72d1244648d.json"}}, {"family": "AFGen Consortium", "given": "", "initials": ""}], "type": "journal article", "published": "2017-06-00", "journal": {"volume": "49", "issn": "1546-1718", "issue": "6", "pages": "946-952", "title": "Nat. Genet.", "issn-l": "1061-4036"}, "abstract": "Atrial fibrillation affects more than 33 million people worldwide and increases the risk of stroke, heart failure, and death. Fourteen genetic loci have been associated with atrial fibrillation in European and Asian ancestry groups. To further define the genetic basis of atrial fibrillation, we performed large-scale, trans-ancestry meta-analyses of common and rare variant association studies. The genome-wide association studies (GWAS) included 17,931 individuals with atrial fibrillation and 115,142 referents; the exome-wide association studies (ExWAS) and rare variant association studies (RVAS) involved 22,346 cases and 132,086 referents. We identified 12 new genetic loci that exceeded genome-wide significance, implicating genes involved in cardiac electrical and structural remodeling. Our results nearly double the number of known genetic loci for atrial fibrillation, provide insights into the molecular basis of atrial fibrillation, and may facilitate the identification of new potential targets for drug discovery.", "doi": "10.1038/ng.3843", "pmid": "28416818", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "ng.3843"}, {"db": "pmc", "key": "PMC5585859"}, {"db": "mid", "key": "NIHMS901319"}], "notes": [], "created": "2018-01-09T14:01:34.761Z", "modified": "2021-06-21T15:40:01.019Z"}, {"entity": "publication", "iuid": "8bd2429d596e4fb8bac36780cb81deed", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8bd2429d596e4fb8bac36780cb81deed.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8bd2429d596e4fb8bac36780cb81deed"}}, "title": "Gene flow, ancient polymorphism, and ecological adaptation shape the genomic landscape of divergence among Darwin's finches", "authors": [{"family": "Han", "given": "Fan", "initials": "F"}, {"family": "Lamichhaney", "given": "Sangeet", "initials": "S"}, {"family": "Grant", "given": "B Rosemary", "initials": "BR"}, {"family": "Grant", "given": "Peter R", "initials": "PR"}, {"family": "Andersson", "given": "Leif", "initials": "L"}, {"family": "Webster", "given": "Matthew T", "initials": "MT"}], "type": "journal-article", "published": "2017-06-00", "journal": {"volume": "27", "issn": "1549-5469", "issue": "6", "pages": "1004-1015", "title": "Genome Res.", "issn-l": "1088-9051"}, "abstract": null, "doi": "10.1101/gr.212522.116", "pmid": "28442558", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2017-10-30T09:25:53.822Z", "modified": "2024-01-16T13:48:47.908Z"}, {"entity": "publication", "iuid": "fefb85a3d39a4972a4f6d33401fe4909", "links": {"self": {"href": "https://publications.scilifelab.se/publication/fefb85a3d39a4972a4f6d33401fe4909.json"}, "display": {"href": "https://publications.scilifelab.se/publication/fefb85a3d39a4972a4f6d33401fe4909"}}, "title": "Contribution of different bacterial dispersal sources to lakes: Population and community effects in different seasons", "authors": [{"family": "Comte", "given": "J\u00e9r\u00f4me", "initials": "J"}, {"family": "Berga", "given": "Merc\u00e8", "initials": "M"}, {"family": "Severin", "given": "Ina", "initials": "I"}, {"family": "Logue", "given": "J\u00fcrg Brendan", "initials": "JB"}, {"family": "Lindstr\u00f6m", "given": "Eva S", "initials": "ES"}], "type": "journal-article", "published": "2017-06-00", "journal": {"volume": "19", "issn": "1462-2912", "issue": "6", "pages": "2391-2404", "title": "Environ Microbiol", "issn-l": "1462-2912"}, "abstract": null, "doi": "10.1111/1462-2920.13749", "pmid": "28401636", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [], "notes": [], "created": "2017-10-19T20:16:45.696Z", "modified": "2020-01-21T13:56:10.121Z"}, {"entity": "publication", "iuid": "6993e12273c44e0ea535c85e7bfc107d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6993e12273c44e0ea535c85e7bfc107d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6993e12273c44e0ea535c85e7bfc107d"}}, "title": "A DNA methylation site within the KLF13 gene is associated with orexigenic processes based on neural responses and ghrelin levels.", "authors": [{"family": "Wiemerslage", "given": "L", "initials": "L"}, {"family": "Islam", "given": "R", "initials": "R"}, {"family": "van der Kamp", "given": "C", "initials": "C"}, {"family": "Cao", "given": "H", "initials": "H"}, {"family": "Olivo", "given": "G", "initials": "G"}, {"family": "Ence-Eriksson", "given": "F", "initials": "F"}, {"family": "Castillo", "given": "S", "initials": "S"}, {"family": "Larsen", "given": "A L", "initials": "AL"}, {"family": "Bandstein", "given": "M", "initials": "M"}, {"family": "Dahlberg", "given": "L S", "initials": "LS"}, {"family": "Perland", "given": "E", "initials": "E"}, {"family": "Gustavsson", "given": "V", "initials": "V"}, {"family": "Nilsson", "given": "J", "initials": "J"}, {"family": "Vogel", "given": "H", "initials": "H"}, {"family": "Sch\u00fcrmann", "given": "A", "initials": "A"}, {"family": "Larsson", "given": "E-M", "initials": "EM"}, {"family": "Rask-Andersen", "given": "M", "initials": "M"}, {"family": "Benedict", "given": "C", "initials": "C"}, {"family": "Schi\u00f6th", "given": "H B", "initials": "HB"}], "type": "journal article", "published": "2017-06-00", "journal": {"volume": "41", "issn": "1476-5497", "issue": "6", "pages": "990-994", "title": "Int J Obes (Lond)", "issn-l": "0307-0565"}, "abstract": "We investigated five methylation markers recently linked to body mass index, for their role in the neuropathology of obesity. In neuroimaging experiments, our analysis involving 23 participants showed that methylation levels for the cg07814318 site, which lies within the KLF13 gene, correlated with brain activity in the claustrum, putamen, cingulate gyrus and frontal gyri, some of which have been previously associated to food signaling, obesity or reward. Methylation levels at cg07814318 also positively correlated with ghrelin levels. Moreover, expression of KLF13 was augmented in the brains of obese and starved mice. Our results suggest the cg07814318 site could be involved in orexigenic processes, and also implicate KLF13 in obesity. Our findings are the first to associate methylation levels in blood with brain activity in obesity-related regions, and further support previous findings between ghrelin, brain activity and genetic differences.", "doi": "10.1038/ijo.2017.43", "pmid": "28194012", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "ijo201743"}], "notes": [], "created": "2017-10-25T15:27:46.412Z", "modified": "2024-01-16T13:48:47.929Z"}, {"entity": "publication", "iuid": "1d8f9559700447cb85c24a82a88e4d3d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1d8f9559700447cb85c24a82a88e4d3d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1d8f9559700447cb85c24a82a88e4d3d"}}, "title": "Genetic susceptibility to cardiovascular disease and risk of dementia.", "authors": [{"family": "Karlsson", "given": "I K", "initials": "IK"}, {"family": "Ploner", "given": "A", "initials": "A"}, {"family": "Song", "given": "C", "initials": "C"}, {"family": "Gatz", "given": "M", "initials": "M"}, {"family": "Pedersen", "given": "N L", "initials": "NL"}, {"family": "H\u00e4gg", "given": "S", "initials": "S"}], "type": "journal article", "published": "2017-05-30", "journal": {"volume": "7", "issn": "2158-3188", "issue": "5", "pages": "e1142", "title": "Transl Psychiatry", "issn-l": "2158-3188"}, "abstract": "Several studies have shown cardiovascular disease (CVD) to be associated with dementia, but it is not clear whether CVD per se increases the risk of dementia or whether the association is due to shared risk factors. We tested how a genetic risk score (GRS) for coronary artery disease (CAD) affects dementia risk after CVD in 13 231 Swedish twins. We also utilized summarized genome-wide association data to study genetic overlap between CAD and Alzheimer\u00b4s disease (AD), and additionally between shared risk factors and each disease. There was no direct effect of a CAD GRS on dementia (hazard ratio 0.99, 95% confidence interval (CI): 0.98-1.01). However, the GRS for CAD modified the association between CVD and dementia within 3 years of CVD diagnosis, ranging from a hazard ratio of 1.59 (95% CI: 1.05-2.41) in the first GRS quartile to 1.91 (95% CI: 1.28-2.86) in the fourth GRS quartile. Using summary statistics, we found no genetic overlap between CAD and AD. We did, however, find that both AD and CAD share a significant genetic overlap with lipids, but that the overlap arose from clearly distinct gene clusters. In conclusion, genetic susceptibility to CAD was found to modify the association between CVD and dementia, most likely through associations with shared risk factors.", "doi": "10.1038/tp.2017.110", "pmid": "28556832", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "tp2017110"}, {"db": "pmc", "key": "PMC5534941"}], "notes": [], "created": "2018-01-09T13:58:11.467Z", "modified": "2021-06-21T15:37:39.117Z"}, {"entity": "publication", "iuid": "a2e1d3ebe2ba437f93cd653482788ae5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a2e1d3ebe2ba437f93cd653482788ae5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a2e1d3ebe2ba437f93cd653482788ae5"}}, "title": "QTL mapping of stress related gene expression in a cross between domesticated chickens and ancestral red junglefowl.", "authors": [{"family": "Fallahsharoudi", "given": "Amir", "initials": "A", "orcid": "0000-0001-8820-0098", "researcher": {"href": "https://publications.scilifelab.se/researcher/3254f702d33342ed8e40e90dd9e72823.json"}}, {"family": "de Kock", "given": "Neil", "initials": "N", "orcid": "0000-0002-7167-5473", "researcher": {"href": "https://publications.scilifelab.se/researcher/81ad05a2eb494c5eb3a7a1f7d0a66b9c.json"}}, {"family": "Johnsson", "given": "Martin", "initials": "M", "orcid": "0000-0003-1262-4585", "researcher": {"href": "https://publications.scilifelab.se/researcher/02b768197c08422aaad526f35c526eaf.json"}}, {"family": "Bektic", "given": "Lejla", "initials": "L", "orcid": "0000-0003-1590-0653", "researcher": {"href": "https://publications.scilifelab.se/researcher/ebc866f430e34e5a9af55ecc227047e6.json"}}, {"family": "Ubhayasekera", "given": "S J Kumari A", "initials": "SJ"}, {"family": "Bergquist", "given": "Jonas", "initials": "J"}, {"family": "Wright", "given": "Dominic", "initials": "D"}, {"family": "Jensen", "given": "Per", "initials": "P"}], "type": "journal article", "published": "2017-05-05", "journal": {"volume": "446", "issn": "1872-8057", "issue": null, "pages": "52-58", "title": "Mol. Cell. Endocrinol.", "issn-l": "0303-7207"}, "abstract": "Domestication of animals is associated with numerous alterations in physiology, morphology, and behavior. Lower reactivity of the hypothalamic-pituitary-adrenal (HPA) axis and reduced fearfulness is seen in most studied domesticates, including chickens. Previously we have shown that the physiological stress response as well as expression levels of hundreds of genes in the hypothalamus and adrenal glands are different between domesticated White Leghorn and the progenitor of modern chickens, the Red Junglefowl. To map genetic loci associated with the transcription levels of genes involved in the physiological stress response, we conducted an eQTL analysis in the F 12 generation of an inter-cross between White Leghorn and Red Junglefowl. We selected genes for further studies based on their known function in the regulation of the HPA axis or sympathoadrenal (SA) system, and measured their expression levels in the hypothalamus and the adrenal glands after a brief stress exposure (physical restraint). The expression values were treated as quantitative traits for the eQTL mapping. The plasma levels of corticosterone were also assessed. We analyzed the correlation between gene expression and corticosterone levels and mapped eQTL and their potential effects on corticosterone levels. The effects on gene transcription of a previously found QTL for corticosterone response were also investigated. The expression levels of the glucocorticoid receptor (GR) in the hypothalamus and several genes in the adrenal glands were correlated with the post-stress levels of corticosterone in plasma. We found several cis- and trans-acting eQTL for stress-related genes in both hypothalamus and adrenal. In the hypothalamus, one eQTL for c-FOS and one QTL for expression of GR were found. In the adrenal tissue, we identified eQTL for the genes NR0B1, RGS4, DBH, MAOA, GRIN1, GABRB2, GABRB3, and HSF1. None of the found eQTL were significant predictors of corticosterone levels. The previously found QTL for corticosterone was associated with GR expression in hypothalamus. Our data suggests that domestication related modification in the stress response is driven by changes in the transcription levels of several modulators of the HPA and SA systems in hypothalamus and adrenal glands and not by changes in the expression of the steroidogenic genes. The presence of eQTL for GR in hypothalamus combined with the negative correlation between GR expression and corticosterone response suggests GR as a candidate for further functional studies regarding modification of stress response during chicken domestication.", "doi": "10.1016/j.mce.2017.02.010", "pmid": "28189567", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "S0303-7207(17)30090-4"}], "notes": [], "created": "2018-01-09T14:03:02.813Z", "modified": "2021-06-21T15:38:58.284Z"}, {"entity": "publication", "iuid": "181c30fb74a842d1b820ac8da5faf40c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/181c30fb74a842d1b820ac8da5faf40c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/181c30fb74a842d1b820ac8da5faf40c"}}, "title": "Two extended haplotype blocks are associated with adaptation to high altitude habitats in East African honey bees.", "authors": [{"family": "Wallberg", "given": "Andreas", "initials": "A"}, {"family": "Sch\u00f6ning", "given": "Caspar", "initials": "C"}, {"family": "Webster", "given": "Matthew T", "initials": "MT"}, {"family": "Hasselmann", "given": "Martin", "initials": "M"}], "type": "journal article", "published": "2017-05-00", "journal": {"volume": "13", "issn": "1553-7404", "issue": "5", "pages": "e1006792", "title": "PLoS Genet.", "issn-l": "1553-7390"}, "abstract": "Understanding the genetic basis of adaption is a central task in biology. Populations of the honey bee Apis mellifera that inhabit the mountain forests of East Africa differ in behavior and morphology from those inhabiting the surrounding lowland savannahs, which likely reflects adaptation to these habitats. We performed whole genome sequencing on 39 samples of highland and lowland bees from two pairs of populations to determine their evolutionary affinities and identify the genetic basis of these putative adaptations. We find that in general, levels of genetic differentiation between highland and lowland populations are very low, consistent with them being a single panmictic population. However, we identify two loci on chromosomes 7 and 9, each several hundred kilobases in length, which exhibit near fixation for different haplotypes between highland and lowland populations. The highland haplotypes at these loci are extremely rare in samples from the rest of the world. Patterns of segregation of genetic variants suggest that recombination between haplotypes at each locus is suppressed, indicating that they comprise independent structural variants. The haplotype on chromosome 7 harbors nearly all octopamine receptor genes in the honey bee genome. These have a role in learning and foraging behavior in honey bees and are strong candidates for adaptation to highland habitats. Molecular analysis of a putative breakpoint indicates that it may disrupt the coding sequence of one of these genes. Divergence between the highland and lowland haplotypes at both loci is extremely high suggesting that they are ancient balanced polymorphisms that greatly predate divergence between the extant honey bee subspecies.", "doi": "10.1371/journal.pgen.1006792", "pmid": "28542163", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "PGENETICS-D-17-00165"}, {"db": "pmc", "key": "PMC5444601"}, {"db": "BioProject", "description": "Population-scale sequencing of Apis mellifera monticola and scutellata from Kenya", "key": "PRJNA357367"}, {"db": "Dryad", "description": "Data from: Two extended haplotype blocks are associated with adaptation to high altitude habitats in East African honey bees", "key": "https://doi.org/10.5061/dryad.jn630"}], "notes": [], "created": "2017-10-27T06:59:44.233Z", "modified": "2024-01-16T13:48:48.005Z"}, {"entity": "publication", "iuid": "f6741ded19a843938682cf6b4a642326", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f6741ded19a843938682cf6b4a642326.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f6741ded19a843938682cf6b4a642326"}}, "title": "Loss of chromosome Y (LOY) in blood cells is associated with increased risk for disease and mortality in aging men", "authors": [{"family": "Forsberg", "given": "Lars A", "initials": "LA"}], "type": "journal-article", "published": "2017-05-00", "journal": {"volume": "136", "issn": "0340-6717", "issue": "5", "pages": "657-663", "title": "Hum Genet", "issn-l": "0340-6717"}, "abstract": null, "doi": "10.1007/s00439-017-1799-2", "pmid": "28424864", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [], "notes": [], "created": "2018-01-09T14:01:34.236Z", "modified": "2020-01-21T13:56:11.730Z"}, {"entity": "publication", "iuid": "8fdeb5a6200148f7b6db35cc74332911", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8fdeb5a6200148f7b6db35cc74332911.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8fdeb5a6200148f7b6db35cc74332911"}}, "title": "Combination of short-read, long-read, and optical mapping assemblies reveals large-scale tandem repeat arrays with population genetic implications.", "authors": [{"family": "Weissensteiner", "given": "Matthias H", "initials": "MH"}, {"family": "Pang", "given": "Andy W C", "initials": "AWC"}, {"family": "Bunikis", "given": "Ignas", "initials": "I"}, {"family": "H\u00f6ijer", "given": "Ida", "initials": "I"}, {"family": "Vinnere-Petterson", "given": "Olga", "initials": "O"}, {"family": "Suh", "given": "Alexander", "initials": "A"}, {"family": "Wolf", "given": "Jochen B W", "initials": "JBW"}], "type": "journal article", "published": "2017-05-00", "journal": {"volume": "27", "issn": "1549-5469", "issue": "5", "pages": "697-708", "title": "Genome Res.", "issn-l": "1088-9051"}, "abstract": "Accurate and contiguous genome assembly is key to a comprehensive understanding of the processes shaping genomic diversity and evolution. Yet, it is frequently constrained by constitutive heterochromatin, usually characterized by highly repetitive DNA. As a key feature of genome architecture associated with centromeric and subtelomeric regions, it locally influences meiotic recombination. In this study, we assess the impact of large tandem repeat arrays on the recombination rate landscape in an avian speciation model, the Eurasian crow. We assembled two high-quality genome references using single-molecule real-time sequencing (long-read assembly [LR]) and single-molecule optical maps (optical map assembly [OM]). A three-way comparison including the published short-read assembly (SR) constructed for the same individual allowed assessing assembly properties and pinpointing misassemblies. By combining information from all three assemblies, we characterized 36 previously unidentified large repetitive regions in the proximity of sequence assembly breakpoints, the majority of which contained complex arrays of a 14-kb satellite repeat or its 1.2-kb subunit. Using whole-genome population resequencing data, we estimated the population-scaled recombination rate (\u03c1) and found it to be significantly reduced in these regions. These findings are consistent with an effect of low recombination in regions adjacent to centromeric or subtelomeric heterochromatin and add to our understanding of the processes generating widespread heterogeneity in genetic diversity and differentiation along the genome. By combining three different technologies, our results highlight the importance of adding a layer of information on genome structure that is inaccessible to each approach independently.", "doi": "10.1101/gr.215095.116", "pmid": "28360231", "labels": {"NGI Stockholm (Genomics Production)": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Uppsala (Uppsala Genome Center)": "Collaborative", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "gr.215095.116"}, {"db": "pmc", "key": "PMC5411765"}], "notes": [], "created": "2017-10-17T09:42:42.055Z", "modified": "2024-01-16T13:48:48.069Z"}, {"entity": "publication", "iuid": "728551f2381b43668a2a2516d07437aa", "links": {"self": {"href": "https://publications.scilifelab.se/publication/728551f2381b43668a2a2516d07437aa.json"}, "display": {"href": "https://publications.scilifelab.se/publication/728551f2381b43668a2a2516d07437aa"}}, "title": "Bayesian Inference of Allele-Specific Gene Expression Indicates Abundant Cis-Regulatory Variation in Natural Flycatcher Populations", "authors": [{"family": "Wang", "given": "Mi", "initials": "M"}, {"family": "Uebbing", "given": "Severin", "initials": "S"}, {"family": "Ellegren", "given": "Hans", "initials": "H"}], "type": "journal-article", "published": "2017-05-00", "journal": {"volume": "9", "issn": "1759-6653", "issue": "5", "pages": "1266-1279", "title": "Genome Biol Evol", "issn-l": "1759-6653"}, "abstract": null, "doi": "10.1093/gbe/evx080", "pmid": "28453623", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [], "notes": [], "created": "2018-01-09T20:57:46.835Z", "modified": "2020-01-21T13:56:11.723Z"}, {"entity": "publication", "iuid": "9405f119832b4231a5f50c1dff6cd6c5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9405f119832b4231a5f50c1dff6cd6c5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9405f119832b4231a5f50c1dff6cd6c5"}}, "title": "Does the sex of one's co-twin affect height and BMI in adulthood? A study of dizygotic adult twins from 31 cohorts.", "authors": [{"family": "Bogl", "given": "Leonie H", "initials": "LH"}, {"family": "Jelenkovic", "given": "Aline", "initials": "A"}, {"family": "Vuoksimaa", "given": "Eero", "initials": "E"}, {"family": "Ahrenfeldt", "given": "Linda", "initials": "L"}, {"family": "Pietil\u00e4inen", "given": "Kirsi H", "initials": "KH"}, {"family": "Stazi", "given": "Maria A", "initials": "MA"}, {"family": "Fagnani", "given": "Corrado", "initials": "C"}, {"family": "D'Ippolito", "given": "Cristina", "initials": "C"}, {"family": "Hur", "given": "Yoon-Mi", "initials": "YM"}, {"family": "Jeong", "given": "Hoe-Uk", "initials": "HU"}, {"family": "Silberg", "given": "Judy L", "initials": "JL"}, {"family": "Eaves", "given": "Lindon J", "initials": "LJ"}, {"family": "Maes", "given": "Hermine H", "initials": "HH"}, {"family": "Bayasgalan", "given": "Gombojav", "initials": "G"}, {"family": "Narandalai", "given": "Danshiitsoodol", "initials": "D"}, {"family": "Cutler", "given": "Tessa L", "initials": "TL"}, {"family": "Kandler", "given": "Christian", "initials": "C"}, {"family": "Jang", "given": "Kerry L", "initials": "KL"}, {"family": "Christensen", "given": "Kaare", "initials": "K"}, {"family": "Skytthe", "given": "Axel", "initials": "A"}, {"family": "Kyvik", "given": "Kirsten O", "initials": "KO"}, {"family": "Cozen", "given": "Wendy", "initials": "W"}, {"family": "Hwang", "given": "Amie E", "initials": "AE"}, {"family": "Mack", "given": "Thomas M", "initials": "TM"}, {"family": "Derom", "given": "Catherine A", "initials": "CA"}, {"family": "Vlietinck", "given": "Robert F", "initials": "RF"}, {"family": "Nelson", "given": "Tracy L", "initials": "TL"}, {"family": "Whitfield", "given": "Keith E", "initials": "KE"}, {"family": "Corley", "given": "Robin P", "initials": "RP"}, {"family": "Huibregtse", "given": "Brooke M", "initials": "BM"}, {"family": "McAdams", "given": "Tom A", "initials": "TA"}, {"family": "Eley", "given": "Thalia C", "initials": "TC"}, {"family": "Gregory", "given": "Alice M", "initials": "AM"}, {"family": "Krueger", "given": "Robert F", "initials": "RF"}, {"family": "McGue", "given": "Matt", "initials": "M"}, {"family": "Pahlen", "given": "Shandell", "initials": "S"}, {"family": "Willemsen", "given": "Gonneke", "initials": "G"}, {"family": "Bartels", "given": "Meike", "initials": "M"}, {"family": "van Beijsterveldt", "given": "Toos C E M", "initials": "TCEM"}, {"family": "Pang", "given": "Zengchang", "initials": "Z"}, {"family": "Tan", "given": "Qihua", "initials": "Q"}, {"family": "Zhang", "given": "Dongfeng", "initials": "D"}, {"family": "Martin", "given": "Nicholas G", "initials": "NG"}, {"family": "Medland", "given": "Sarah E", "initials": "SE"}, {"family": "Montgomery", "given": "Grant W", "initials": "GW"}, {"family": "Hjelmborg", "given": "Jacob V B", "initials": "JVB"}, {"family": "Rebato", "given": "Esther", "initials": "E"}, {"family": "Swan", "given": "Gary E", "initials": "GE"}, {"family": "Krasnow", "given": "Ruth", "initials": "R"}, {"family": "Busjahn", "given": "Andreas", "initials": "A"}, {"family": "Lichtenstein", "given": "Paul", "initials": "P"}, {"family": "\u00d6ncel", "given": "Sevgi Y", "initials": "SY"}, {"family": "Aliev", "given": "Fazil", "initials": "F"}, {"family": "Baker", "given": "Laura A", "initials": "LA"}, {"family": "Tuvblad", "given": "Catherine", "initials": "C"}, {"family": "Siribaddana", "given": "Sisira H", "initials": "SH"}, {"family": "Hotopf", "given": "Matthew", "initials": "M"}, {"family": "Sumathipala", "given": "Athula", "initials": "A"}, {"family": "Rijsdijk", "given": "Fruhling", "initials": "F"}, {"family": "Magnusson", "given": "Patrik K E", "initials": "PKE"}, {"family": "Pedersen", "given": "Nancy L", "initials": "NL"}, {"family": "Aslan", "given": "Anna K Dahl", "initials": "AKD"}, {"family": "Ordo\u00f1ana", "given": "Juan R", "initials": "JR"}, {"family": "S\u00e1nchez-Romera", "given": "Juan F", "initials": "JF"}, {"family": "Colodro-Conde", "given": "Lucia", "initials": "L"}, {"family": "Duncan", "given": "Glen E", "initials": "GE"}, {"family": "Buchwald", "given": "Dedra", "initials": "D"}, {"family": "Tarnoki", "given": "Adam D", "initials": "AD"}, {"family": "Tarnoki", "given": "David L", "initials": "DL"}, {"family": "Yokoyama", "given": "Yoshie", "initials": "Y"}, {"family": "Hopper", "given": "John L", "initials": "JL"}, {"family": "Loos", "given": "Ruth J F", "initials": "RJF"}, {"family": "Boomsma", "given": "Dorret I", "initials": "DI"}, {"family": "S\u00f8rensen", "given": "Thorkild I A", "initials": "TIA"}, {"family": "Silventoinen", "given": "Karri", "initials": "K"}, {"family": "Kaprio", "given": "Jaakko", "initials": "J"}], "type": "journal article", "published": "2017-04-27", "journal": {"volume": "8", "issn": "2042-6410", "issue": null, "pages": "14", "title": "Biol Sex Differ", "issn-l": "2042-6410"}, "abstract": "The comparison of traits in twins from opposite-sex (OS) and same-sex (SS) dizygotic twin pairs is considered a proxy measure of prenatal hormone exposure. To examine possible prenatal hormonal influences on anthropometric traits, we compared mean height, body mass index (BMI), and the prevalence of being overweight or obese between men and women from OS and SS dizygotic twin pairs.\n\nThe data were derived from the COllaborative project of Development of Anthropometrical measures in Twins (CODATwins) database, and included 68,494 SS and 53,808 OS dizygotic twin individuals above the age of 20\u00a0years from 31 twin cohorts representing 19 countries. Zygosity was determined by questionnaires or DNA genotyping depending on the study. Multiple regression and logistic regression models adjusted for cohort, age, and birth year with the twin type as a predictor were carried out to compare height and BMI in twins from OS pairs with those from SS pairs and to calculate the adjusted odds ratios and 95% confidence intervals for being overweight or obese.\n\nOS females were, on average, 0.31\u00a0cm (95% confidence interval (CI) 0.20, 0.41) taller than SS females. OS males were also, on average, taller than SS males, but this difference was only 0.14\u00a0cm (95% CI 0.02, 0.27). Mean BMI and the prevalence of overweight or obesity did not differ between males and females from SS and OS twin pairs. The statistically significant differences between OS and SS twins for height were small and appeared to reflect our large sample size rather than meaningful differences of public health relevance.\n\nWe found no evidence to support the hypothesis that prenatal hormonal exposure or postnatal socialization (i.e., having grown up with a twin of the opposite sex) has a major impact on height and BMI in adulthood.", "doi": "10.1186/s13293-017-0134-x", "pmid": "28465822", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "134"}, {"db": "pmc", "key": "PMC5408365"}], "notes": [], "created": "2017-10-25T15:27:45.038Z", "modified": "2024-01-16T13:48:48.078Z"}, {"entity": "publication", "iuid": "307148582507404896332168f5379674", "links": {"self": {"href": "https://publications.scilifelab.se/publication/307148582507404896332168f5379674.json"}, "display": {"href": "https://publications.scilifelab.se/publication/307148582507404896332168f5379674"}}, "title": "Genome-wide meta-analysis of 241,258 adults accounting for smoking behaviour identifies novel loci for obesity traits", "authors": [{"family": "Justice", "given": "Anne E", "initials": "AE"}, {"family": "Winkler", "given": "Thomas W", "initials": "TW"}, {"family": "Feitosa", "given": "Mary F", "initials": "MF"}, {"family": "Graff", "given": "Misa", "initials": "M"}, {"family": "Fisher", "given": "Virginia A", "initials": "VA"}, {"family": "Young", "given": "Kristin", "initials": "K"}, {"family": "Barata", "given": "Llilda", "initials": "L"}, {"family": "Deng", "given": "Xuan", "initials": "X"}, {"family": "Czajkowski", "given": "Jacek", "initials": "J"}, {"family": "Hadley", "given": "David", "initials": "D"}, {"family": "Ngwa", "given": "Julius S", "initials": "JS"}, {"family": "Ahluwalia", "given": "Tarunveer S", "initials": "TS"}, {"family": "Chu", "given": "Audrey Y", "initials": "AY"}, {"family": "Heard-Costa", "given": "Nancy L", "initials": "NL"}, {"family": "Lim", "given": "Elise", "initials": "E"}, {"family": "Perez", "given": "Jeremiah", "initials": "J"}, {"family": "Eicher", "given": "John D", "initials": "JD"}, {"family": "Kutalik", "given": "Zolt\u00e1n", "initials": "Z"}, {"family": "Xue", "given": "Luting", "initials": "L"}, {"family": "Mahajan", "given": "Anubha", "initials": "A"}, {"family": "Renstr\u00f6m", "given": "Frida", "initials": "F"}, {"family": "Wu", "given": "Joseph", "initials": "J"}, {"family": "Qi", "given": "Qibin", "initials": "Q"}, {"family": "Ahmad", "given": "Shafqat", "initials": "S"}, {"family": "Alfred", "given": "Tamuno", "initials": "T"}, {"family": "Amin", "given": "Najaf", "initials": "N"}, {"family": "Bielak", "given": "Lawrence F", "initials": "LF"}, {"family": "Bonnefond", "given": "Amelie", "initials": "A"}, {"family": "Bragg", "given": "Jennifer", "initials": "J"}, {"family": "Cadby", "given": "Gemma", "initials": "G"}, {"family": "Chittani", "given": "Martina", "initials": "M"}, {"family": "Coggeshall", "given": "Scott", "initials": "S"}, {"family": "Corre", "given": "Tanguy", "initials": "T"}, {"family": "Direk", "given": "Nese", "initials": "N"}, {"family": "Eriksson", "given": "Joel", "initials": "J"}, {"family": "Fischer", "given": "Krista", "initials": "K"}, {"family": "Gorski", "given": "Mathias", "initials": "M"}, {"family": "Neergaard Harder", "given": "Marie", "initials": "M"}, {"family": "Horikoshi", "given": "Momoko", "initials": "M"}, {"family": "Huang", "given": "Tao", "initials": "T"}, {"family": "Huffman", "given": "Jennifer E", "initials": "JE"}, {"family": "Jackson", "given": "Anne U", "initials": "AU"}, {"family": "Justesen", "given": "Johanne Marie", "initials": "JM"}, {"family": "Kanoni", "given": "Stavroula", "initials": "S"}, {"family": "Kinnunen", "given": "Leena", "initials": "L"}, {"family": "Kleber", "given": "Marcus E", "initials": "ME"}, {"family": "Komulainen", "given": "Pirjo", "initials": "P"}, {"family": "Kumari", "given": "Meena", "initials": "M"}, {"family": "Lim", "given": "Unhee", "initials": "U"}, {"family": "Luan", "given": "Jian'an", "initials": "J"}, {"family": "Lyytik\u00e4inen", "given": "Leo Pekka", "initials": "LP"}, {"family": "Mangino", "given": "Massimo", "initials": "M"}, {"family": "Manichaikul", "given": "Ani", "initials": "A"}, {"family": "Marten", "given": "Jonathan", "initials": "J"}, {"family": "Middelberg", "given": "Rita P S", "initials": "RPS"}, {"family": "M\u00fcller-Nurasyid", "given": "Martina", "initials": "M"}, {"family": "Navarro", "given": "Pau", "initials": "P"}, {"family": "P\u00e9russe", "given": "Louis", "initials": "L"}, {"family": "Pervjakova", "given": "Natalia", "initials": "N"}, {"family": "Sarti", "given": "Cinzia", "initials": "C"}, {"family": "Smith", "given": "Albert Vernon", "initials": "AV"}, {"family": "Smith", "given": "Jennifer A", "initials": "JA"}, {"family": "Stan\u010d\u00e1kov\u00e1", "given": "Alena", "initials": "A"}, {"family": "Strawbridge", "given": "Rona J", "initials": "RJ"}, {"family": "Stringham", "given": "Heather M", "initials": "HM"}, {"family": "Sung", "given": "Yun Ju", "initials": "YJ"}, {"family": "Tanaka", "given": "Toshiko", "initials": "T"}, {"family": "Teumer", "given": "Alexander", "initials": "A"}, {"family": "Trompet", "given": "Stella", "initials": "S"}, {"family": "van der Laan", "given": "Sander W", "initials": "SW"}, {"family": "van der Most", "given": "Peter J", "initials": "PJ"}, {"family": "Van Vliet-Ostaptchouk", "given": "Jana V", "initials": "JV"}, {"family": "Vedantam", "given": "Sailaja L", "initials": "SL"}, {"family": "Verweij", "given": "Niek", "initials": "N"}, {"family": "Vink", "given": "Jacqueline M", "initials": "JM"}, {"family": "Vitart", "given": "Veronique", "initials": "V"}, {"family": "Wu", "given": "Ying", "initials": "Y"}, {"family": "Yengo", "given": "Loic", "initials": "L"}, {"family": "Zhang", "given": "Weihua", "initials": "W"}, {"family": "Hua Zhao", "given": "Jing", "initials": "J"}, {"family": "Zimmermann", "given": "Martina E", "initials": "ME"}, {"family": "Zubair", "given": "Niha", "initials": "N"}, {"family": "Abecasis", "given": "Gon\u00e7alo R", "initials": "GR"}, {"family": "Adair", "given": "Linda S", "initials": "LS"}, {"family": "Afaq", "given": "Saima", "initials": "S"}, {"family": "Afzal", "given": "Uzma", "initials": "U"}, {"family": "Bakker", "given": "Stephan J L", "initials": "SJL"}, {"family": "Bartz", "given": "Traci M", "initials": "TM"}, {"family": "Beilby", "given": "John", "initials": "J"}, {"family": "Bergman", "given": "Richard N", "initials": "RN"}, {"family": "Bergmann", "given": "Sven", "initials": "S"}, {"family": "Biffar", "given": "Reiner", "initials": "R"}, {"family": "Blangero", "given": "John", "initials": "J"}, {"family": "Boerwinkle", "given": "Eric", "initials": "E"}, {"family": "Bonnycastle", "given": "Lori L", "initials": "LL"}, {"family": "Bottinger", "given": "Erwin", "initials": "E"}, {"family": "Braga", "given": "Daniele", "initials": "D"}, {"family": "Buckley", "given": "Brendan M", "initials": "BM"}, {"family": "Buyske", "given": "Steve", "initials": "S"}, {"family": "Campbell", "given": "Harry", "initials": "H"}, {"family": "Chambers", "given": "John C", "initials": "JC"}, {"family": "Collins", "given": "Francis S", "initials": "FS"}, {"family": "Curran", "given": "Joanne E", "initials": "JE"}, {"family": "de Borst", "given": "Gert J", "initials": "GJ"}, {"family": "de Craen", "given": "Anton J M", "initials": "AJM"}, {"family": "de Geus", "given": "Eco J C", "initials": "EJC"}, {"family": "Dedoussis", "given": "George", "initials": "G"}, {"family": "Delgado", "given": "Graciela E", "initials": "GE"}, {"family": "den Ruijter", "given": "Hester M", "initials": "HM"}, {"family": "Eiriksdottir", "given": "Gudny", "initials": "G"}, {"family": "Eriksson", "given": "Anna L", "initials": "AL"}, {"family": "Esko", "given": "T\u00f5nu", "initials": "T"}, {"family": "Faul", "given": "Jessica D", "initials": "JD"}, {"family": "Ford", "given": "Ian", "initials": "I"}, {"family": "Forrester", "given": "Terrence", "initials": "T"}, {"family": "Gertow", "given": "Karl", "initials": "K"}, {"family": "Gigante", "given": "Bruna", "initials": "B"}, {"family": "Glorioso", "given": "Nicola", "initials": "N"}, {"family": "Gong", "given": "Jian", "initials": "J"}, {"family": "Grallert", "given": "Harald", "initials": "H"}, {"family": "Grammer", "given": "Tanja B", "initials": "TB"}, {"family": "Grarup", "given": "Niels", "initials": "N"}, {"family": "Haitjema", "given": "Saskia", "initials": "S"}, {"family": "Hallmans", "given": "G\u00f6ran", "initials": "G"}, {"family": "Hamsten", "given": "Anders", "initials": "A"}, {"family": "Hansen", "given": "Torben", "initials": "T"}, {"family": "Harris", "given": "Tamara B", "initials": "TB"}, {"family": "Hartman", "given": "Catharina A", "initials": "CA"}, {"family": "Hassinen", "given": "Maija", "initials": "M"}, {"family": "Hastie", "given": "Nicholas D", "initials": "ND"}, {"family": "Heath", "given": "Andrew C", "initials": "AC"}, {"family": "Hernandez", "given": "Dena", "initials": "D"}, {"family": "Hindorff", "given": "Lucia", "initials": "L"}, {"family": "Hocking", "given": "Lynne J", "initials": "LJ"}, {"family": "Hollensted", "given": "Mette", "initials": "M"}, {"family": "Holmen", "given": "Oddgeir L", "initials": "OL"}, {"family": "Homuth", "given": "Georg", "initials": "G"}, {"family": "Jan Hottenga", "given": "Jouke", "initials": "J"}, {"family": "Huang", "given": "Jie", "initials": "J"}, {"family": "Hung", "given": "Joseph", "initials": "J"}, {"family": "Hutri-K\u00e4h\u00f6nen", "given": "Nina", "initials": "N"}, {"family": "Ingelsson", "given": "Erik", "initials": "E"}, {"family": "James", "given": "Alan L", "initials": "AL"}, {"family": "Jansson", "given": "John Olov", "initials": "JO"}, {"family": "Jarvelin", "given": "Marjo Riitta", "initials": "MR"}, {"family": "Jhun", "given": "Min A", "initials": "MA"}, {"family": "J\u00f8rgensen", "given": "Marit E", "initials": "ME"}, {"family": "Juonala", "given": "Markus", "initials": "M"}, {"family": "K\u00e4h\u00f6nen", "given": "Mika", "initials": "M"}, {"family": "Karlsson", "given": "Magnus", "initials": "M"}, {"family": "Koistinen", "given": "Heikki A", "initials": "HA"}, {"family": "Kolcic", "given": "Ivana", "initials": "I"}, {"family": "Kolovou", "given": "Genovefa", "initials": "G"}, {"family": "Kooperberg", "given": "Charles", "initials": "C"}, {"family": "Kr\u00e4mer", "given": "Bernhard K", "initials": "BK"}, {"family": "Kuusisto", "given": "Johanna", "initials": "J"}, {"family": "Kval\u00f8y", "given": "Kirsti", "initials": "K"}, {"family": "Lakka", "given": "Timo A", "initials": "TA"}, {"family": "Langenberg", "given": "Claudia", "initials": "C"}, {"family": "Launer", "given": "Lenore J", "initials": "LJ"}, {"family": "Leander", "given": "Karin", "initials": "K"}, {"family": "Lee", "given": "Nanette R", "initials": "NR"}, {"family": "Lind", "given": "Lars", "initials": "L"}, {"family": "Lindgren", "given": "Cecilia M", "initials": "CM"}, {"family": "Linneberg", "given": "Allan", "initials": "A"}, {"family": "Lobbens", "given": "Stephane", "initials": "S"}, {"family": "Loh", "given": "Marie", "initials": "M"}, {"family": "Lorentzon", "given": "Mattias", "initials": "M"}, {"family": "Luben", "given": "Robert", "initials": "R"}, {"family": "Lubke", "given": "Gitta", "initials": "G"}, {"family": "Ludolph-Donislawski", "given": "Anja", "initials": "A"}, {"family": "Lupoli", "given": "Sara", "initials": "S"}, {"family": "Madden", "given": "Pamela A F", "initials": "PAF"}, {"family": "M\u00e4nnikk\u00f6", "given": "Reija", "initials": "R"}, {"family": "Marques-Vidal", "given": "Pedro", "initials": "P"}, {"family": "Martin", "given": "Nicholas G", "initials": "NG"}, {"family": "McKenzie", "given": "Colin A", "initials": "CA"}, {"family": "McKnight", "given": "Barbara", "initials": "B"}, {"family": "Mellstr\u00f6m", "given": "Dan", "initials": "D"}, {"family": "Menni", "given": "Cristina", "initials": "C"}, {"family": "Montgomery", "given": "Grant W", "initials": "GW"}, {"family": "Musk", "given": "AW (Bill)", "initials": "A("}, {"family": "Narisu", "given": "Narisu", "initials": "N"}, {"family": "Nauck", "given": "Matthias", "initials": "M"}, {"family": "Nolte", "given": "Ilja M", "initials": "IM"}, {"family": "Oldehinkel", "given": "Albertine J", "initials": "AJ"}, {"family": "Olden", "given": "Matthias", "initials": "M"}, {"family": "Ong", "given": "Ken K", "initials": "KK"}, {"family": "Padmanabhan", "given": "Sandosh", "initials": "S"}, {"family": "Peyser", "given": "Patricia A", "initials": "PA"}, {"family": "Pisinger", "given": "Charlotta", "initials": "C"}, {"family": "Porteous", "given": "David J", "initials": "DJ"}, {"family": "Raitakari", "given": "Olli T", "initials": "OT"}, {"family": "Rankinen", "given": "Tuomo", "initials": "T"}, {"family": "Rao", "given": "D C", "initials": "DC"}, {"family": "Rasmussen-Torvik", "given": "Laura J", "initials": "LJ"}, {"family": "Rawal", "given": "Rajesh", "initials": "R"}, {"family": "Rice", "given": "Treva", "initials": "T"}, {"family": "Ridker", "given": "Paul M", "initials": "PM"}, {"family": "Rose", "given": "Lynda M", "initials": "LM"}, {"family": "Bien", "given": "Stephanie A", "initials": "SA"}, {"family": "Rudan", "given": "Igor", "initials": "I"}, {"family": "Sanna", "given": "Serena", "initials": "S"}, {"family": "Sarzynski", "given": "Mark A", "initials": "MA"}, {"family": "Sattar", "given": "Naveed", "initials": "N"}, {"family": "Savonen", "given": "Kai", "initials": "K"}, {"family": "Schlessinger", "given": "David", "initials": "D"}, {"family": "Scholtens", "given": "Salome", "initials": "S"}, {"family": "Schurmann", "given": 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"given": "Alkes L", "initials": "AL"}, {"family": "Ridker", "given": "Paul M", "initials": "PM"}, {"family": "Snieder", "given": "Harold", "initials": "H"}, {"family": "Spector", "given": "Tim D", "initials": "TD"}, {"family": "St\u00f6ckl", "given": "Doris", "initials": "D"}, {"family": "Toniolo", "given": "Daniela", "initials": "D"}, {"family": "Ulivi", "given": "Sheila", "initials": "S"}, {"family": "Visser", "given": "Jenny A", "initials": "JA"}, {"family": "V\u00f6lzke", "given": "Henry", "initials": "H"}, {"family": "Wareham", "given": "Nicholas J", "initials": "NJ"}, {"family": "Wilson", "given": "James F", "initials": "JF"}, {"family": "Spurdle", "given": "Amanda B", "initials": "AB"}, {"family": "Thorsteindottir", "given": "Unnur", "initials": "U"}, {"family": "Pollard", "given": "Katherine S", "initials": "KS"}, {"family": "Easton", "given": "Douglas F", "initials": "DF"}, {"family": "Tung", "given": "Joyce Y", "initials": "JY"}, {"family": "Chang-Claude", "given": "Jenny", "initials": "J"}, {"family": "Hinds", "given": "David", "initials": "D"}, {"family": "Murray", "given": "Anna", "initials": "A"}, {"family": "Murabito", "given": "Joanne M", "initials": "JM"}, {"family": "Stefansson", "given": "Kari", "initials": "K"}, {"family": "Ong", "given": "Ken K", "initials": "KK"}, {"family": "Perry", "given": "John R B", "initials": "JRB"}], "type": "journal-article", "published": "2017-04-24", "journal": {"volume": "49", "issn": "1061-4036", "issue": "6", "pages": "834-841", "title": "Nat Genet", "issn-l": "1061-4036"}, "abstract": null, "doi": "10.1038/ng.3841", "pmid": "28436984", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [], "notes": [], "created": "2018-01-09T14:01:33.659Z", "modified": "2020-01-21T13:56:11.689Z"}, {"entity": "publication", "iuid": "d07f80e9ae9c420d82d3a29d34c31f42", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d07f80e9ae9c420d82d3a29d34c31f42.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d07f80e9ae9c420d82d3a29d34c31f42"}}, "title": "Gain-of-function SAMD9L mutations cause a syndrome of cytopenia, immunodeficiency, MDS, and neurological symptoms.", "authors": [{"family": "Tesi", "given": "Bianca", "initials": "B"}, {"family": "Davidsson", "given": "Josef", "initials": "J"}, {"family": "Voss", "given": "Matthias", "initials": "M"}, {"family": "Rahikkala", "given": "Elisa", "initials": "E"}, {"family": "Holmes", "given": "Tim D", "initials": "TD"}, {"family": "Chiang", "given": "Samuel C C", "initials": "SCC"}, {"family": "Komulainen-Ebrahim", "given": "Jonna", "initials": "J"}, {"family": "Gorcenco", "given": "Sorina", "initials": "S"}, {"family": "Rundberg Nilsson", "given": "Alexandra", "initials": "A"}, {"family": "Ripperger", "given": "Tim", "initials": "T"}, {"family": "Kokkonen", "given": "Hannaleena", "initials": "H"}, {"family": "Bryder", "given": "David", "initials": "D"}, {"family": "Fioretos", "given": "Thoas", "initials": "T", "orcid": "0000-0002-3235-6154", "researcher": {"href": "https://publications.scilifelab.se/researcher/35a5c1b6023345c6b1317c590bf80680.json"}}, {"family": "Henter", "given": "Jan-Inge", "initials": "JI"}, {"family": "M\u00f6tt\u00f6nen", "given": "Merja", "initials": "M"}, {"family": "Niinim\u00e4ki", "given": "Riitta", "initials": "R"}, {"family": "Nilsson", "given": "Lars", "initials": "L"}, {"family": "Pronk", "given": "Cornelis Jan", "initials": "CJ"}, {"family": "Puschmann", "given": "Andreas", "initials": "A"}, {"family": "Qian", "given": "Hong", "initials": "H"}, {"family": "Uusimaa", "given": "Johanna", "initials": "J"}, {"family": "Moilanen", "given": "Jukka", "initials": "J"}, {"family": "Tedg\u00e5rd", "given": "Ulf", "initials": "U"}, {"family": "Cammenga", "given": "J\u00f6rg", "initials": "J"}, {"family": "Bryceson", "given": "Yenan T", "initials": "YT"}], "type": "journal article", "published": "2017-04-20", "journal": {"volume": "129", "issn": "1528-0020", "issue": "16", "pages": "2266-2279", "title": "Blood", "issn-l": "0006-4971"}, "abstract": "Several monogenic causes of familial myelodysplastic syndrome (MDS) have recently been identified. We studied 2 families with cytopenia, predisposition to MDS with chromosome 7 aberrations, immunodeficiency, and progressive cerebellar dysfunction. Genetic studies uncovered heterozygous missense mutations in SAMD9L, a tumor suppressor gene located on chromosome arm 7q. Consistent with a gain-of-function effect, ectopic expression of the 2 identified SAMD9L mutants decreased cell proliferation relative to wild-type protein. Of the 10 individuals identified who were heterozygous for either SAMD9L mutation, 3 developed MDS upon loss of the mutated SAMD9L allele following intracellular infections associated with myeloid, B-, and natural killer (NK)-cell deficiency. Five other individuals, 3 with spontaneously resolved cytopenic episodes in infancy, harbored hematopoietic revertant mosaicism by uniparental disomy of 7q, with loss of the mutated allele or additional in cisSAMD9L truncating mutations. Examination of 1 individual indicated that somatic reversions were postnatally selected. Somatic mutations were tracked to CD34+ hematopoietic progenitor cell populations, being further enriched in B and NK cells. Stimulation of these cell types with interferon (IFN)-\u03b1 or IFN-\u03b3 induced SAMD9L expression. Clinically, revertant mosaicism was associated with milder disease, yet neurological manifestations persisted in 3 individuals. Two carriers also harbored a rare, in trans germ line SAMD9L missense loss-of-function variant, potentially counteracting the SAMD9L mutation. Our results demonstrate that gain-of-function mutations in the tumor suppressor SAMD9L cause cytopenia, immunodeficiency, variable neurological presentation, and predisposition to MDS with -7/del(7q), whereas hematopoietic revertant mosaicism commonly ameliorated clinical manifestations. The findings suggest a role for SAMD9L in regulating IFN-driven, demand-adapted hematopoiesis.", "doi": "10.1182/blood-2016-10-743302", "pmid": "28202457", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Clinical Genomics Stockholm": "Service", "Clinical Genomics": "Service"}, "xrefs": [{"db": "pii", "key": "S0006-4971(20)33461-3"}, {"db": "pmc", "key": "PMC5399482"}], "notes": [], "created": "2017-10-13T14:45:25.923Z", "modified": "2021-07-06T15:41:35.342Z"}, {"entity": "publication", "iuid": "b065ba93cc264109a62c401b02ac7cd9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b065ba93cc264109a62c401b02ac7cd9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b065ba93cc264109a62c401b02ac7cd9"}}, "title": "Adaptation to infectious disease exposure in indigenous Southern African populations.", "authors": [{"family": "Owers", "given": "Katharine A", "initials": "KA", "orcid": "0000-0002-5323-5079", "researcher": {"href": "https://publications.scilifelab.se/researcher/e4357c52141940a1a68b6a241f4aa100.json"}}, {"family": "Sj\u00f6din", "given": "Per", "initials": "P"}, {"family": "Schlebusch", "given": "Carina M", "initials": "CM", "orcid": "0000-0002-8160-9621", "researcher": {"href": "https://publications.scilifelab.se/researcher/682f10853c1145649b8c76680605dd9b.json"}}, {"family": "Skoglund", "given": "Pontus", "initials": "P", "orcid": "0000-0002-3021-5913", "researcher": {"href": "https://publications.scilifelab.se/researcher/338a5f8f37fb48b3887230dfd81786d3.json"}}, {"family": "Soodyall", "given": "Himla", "initials": "H"}, {"family": "Jakobsson", "given": "Mattias", "initials": "M", "orcid": "0000-0001-7840-7853", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a4abe0fcb20492d9ec849c9fbf58a71.json"}}], "type": "journal article", "published": "2017-04-12", "journal": {"volume": "284", "issn": "1471-2954", "issue": "1852", "pages": "20170226", "title": "Proc. Biol. Sci.", "issn-l": "0962-8452"}, "abstract": "Genetic analyses can provide information about human evolutionary history that cannot always be gleaned from other sources. We evaluated evidence of selective pressure due to introduced infectious diseases in the genomes of two indigenous southern African San groups-the \u2021Khomani who had abundant contact with other people migrating into the region and the more isolated Ju|'hoansi. We used a dual approach to test for increased selection on immune genes compared with the rest of the genome in these groups. First, we calculated summary values of statistics that measure genomic signatures of adaptation to contrast selection signatures in immune genes and all genes. Second, we located regions of the genome with extreme values of three selection statistics and examined these regions for enrichment of immune genes. We found stronger and more abundant signals of selection in immune genes in the \u2021Khomani than in the Ju|'hoansi. We confirm this finding within each population to avoid effects of different demographic histories of the two populations. We identified eight immune genes that have potentially been targets of strong selection in the \u2021Khomani, whereas in the Ju|'hoansi, no immune genes were found in the genomic regions with the strongest signals of selection. We suggest that the more abundant signatures of selection at immune genes in the \u2021Khomani could be explained by their more frequent contact with immigrant groups, which likely led to increased exposure and adaptation to introduced infectious diseases.", "doi": "10.1098/rspb.2017.0226", "pmid": "28381615", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "rspb.2017.0226"}, {"db": "pmc", "key": "PMC5394675"}], "notes": [], "created": "2018-01-09T14:01:35.720Z", "modified": "2021-07-07T10:32:33.473Z"}, {"entity": "publication", "iuid": "4e03b1140bb94f24a5dfc579a2902505", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4e03b1140bb94f24a5dfc579a2902505.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4e03b1140bb94f24a5dfc579a2902505"}}, "title": "Large-scale genome-wide analysis identifies genetic variants associated with cardiac structure and function", "authors": [{"family": "Wild", "given": "Philipp S", "initials": "PS"}, {"family": "Felix", "given": "Janine F", "initials": "JF"}, {"family": "Schillert", "given": "Arne", "initials": "A"}, {"family": "Teumer", "given": "Alexander", "initials": "A"}, {"family": "Chen", "given": "Ming Huei", "initials": "MH"}, {"family": "Leening", "given": "Maarten J G", "initials": "MJG"}, {"family": "V\u00f6lker", "given": "Uwe", "initials": "U"}, {"family": "Gro\u00dfmann", "given": "Vera", "initials": "V"}, {"family": "Brody", "given": "Jennifer A", "initials": "JA"}, {"family": "Irvin", "given": "Marguerite R", "initials": "MR"}, {"family": "Shah", "given": "Sanjiv J", "initials": "SJ"}, {"family": "Pramana", "given": "Setia", "initials": "S"}, {"family": "Lieb", "given": "Wolfgang", "initials": "W"}, {"family": "Schmidt", "given": "Reinhold", "initials": "R"}, {"family": "Stanton", "given": "Alice V", "initials": "AV"}, {"family": "Malzahn", "given": "D\u00f6rthe", "initials": "D"}, {"family": "Smith", "given": "Albert Vernon", "initials": "AV"}, {"family": "Sundstr\u00f6m", "given": "Johan", "initials": "J"}, {"family": "Minelli", "given": "Cosetta", "initials": "C"}, {"family": "Ruggiero", "given": "Daniela", "initials": "D"}, {"family": "Lyytik\u00e4inen", "given": "Leo Pekka", "initials": "LP"}, {"family": "Tiller", "given": "Daniel", "initials": "D"}, {"family": "Smith", "given": "J Gustav", "initials": "JG"}, {"family": "Monnereau", "given": "Claire", "initials": "C"}, {"family": "Di Tullio", "given": "Marco R", "initials": "MR"}, {"family": "Musani", "given": "Solomon K", "initials": "SK"}, {"family": "Morrison", "given": "Alanna C", "initials": "AC"}, {"family": "Pers", "given": "Tune H", "initials": "TH"}, {"family": "Morley", "given": "Michael", "initials": "M"}, {"family": "Kleber", "given": "Marcus E", "initials": "ME"}, {"family": "Aragam", "given": "Jayashri", "initials": "J"}, {"family": "Benjamin", "given": "Emelia J", "initials": "EJ"}, {"family": "Bis", "given": "Joshua C", "initials": "JC"}, {"family": "Bisping", "given": "Egbert", "initials": "E"}, {"family": "Broeckel", "given": "Ulrich", "initials": "U"}, {"family": "Cheng", "given": "Susan", "initials": "S"}, {"family": "Deckers", "given": "Jaap W", "initials": "JW"}, {"family": "Del Greco M", "given": "Fabiola", "initials": "F"}, {"family": "Edelmann", "given": "Frank", "initials": "F"}, {"family": "Fornage", "given": "Myriam", "initials": "M"}, {"family": "Franke", "given": "Lude", "initials": "L"}, {"family": "Friedrich", "given": "Nele", "initials": "N"}, {"family": "Harris", "given": "Tamara B", "initials": "TB"}, {"family": "Hofer", "given": "Edith", "initials": "E"}, {"family": "Hofman", "given": "Albert", "initials": "A"}, {"family": "Huang", "given": "Jie", "initials": "J"}, {"family": "Hughes", "given": "Alun D", "initials": "AD"}, {"family": "K\u00e4h\u00f6nen", "given": "Mika", "initials": "M"}, {"family": "investigators", "given": "KNHI", "initials": "K"}, {"family": "Kruppa", "given": "Jochen", "initials": "J"}, {"family": "Lackner", "given": "Karl J", "initials": "KJ"}, {"family": "Lannfelt", "given": "Lars", "initials": "L"}, {"family": "Laskowski", "given": "Rafael", "initials": "R"}, {"family": "Launer", "given": "Lenore J", "initials": "LJ"}, {"family": "Leosdottir", "given": "Margr\u00e9t", "initials": "M"}, {"family": "Lin", "given": "Honghuang", "initials": "H"}, {"family": "Lindgren", "given": "Cecilia M", "initials": "CM"}, {"family": "Loley", "given": "Christina", "initials": "C"}, {"family": "MacRae", "given": "Calum A", "initials": "CA"}, {"family": "Mascalzoni", "given": "Deborah", "initials": "D"}, {"family": "Mayet", "given": "Jamil", "initials": "J"}, {"family": "Medenwald", "given": "Daniel", "initials": "D"}, {"family": "Morris", "given": "Andrew P", "initials": "AP"}, {"family": "M\u00fcller", "given": "Christian", "initials": "C"}, {"family": "M\u00fcller-Nurasyid", "given": "Martina", "initials": "M"}, {"family": "Nappo", "given": "Stefania", "initials": "S"}, {"family": "Nilsson", "given": "Peter M", "initials": "PM", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}, {"family": "Nuding", "given": "Sebastian", "initials": "S"}, {"family": "Nutile", "given": "Teresa", "initials": "T"}, {"family": "Peters", "given": "Annette", "initials": "A"}, {"family": "Pfeufer", "given": "Arne", "initials": "A"}, {"family": "Pietzner", "given": "Diana", "initials": "D"}, {"family": "Pramstaller", "given": "Peter P", "initials": "PP"}, {"family": "Raitakari", "given": "Olli T", "initials": "OT"}, {"family": "Rice", "given": "Kenneth M", "initials": "KM"}, {"family": "Rivadeneira", "given": "Fernando", "initials": "F"}, {"family": "Rotter", "given": "Jerome I", "initials": "JI"}, {"family": "Ruohonen", "given": "Saku T", "initials": "ST"}, {"family": "Sacco", "given": "Ralph L", "initials": "RL"}, {"family": "Samdarshi", "given": "Tandaw E", "initials": "TE"}, {"family": "Schmidt", "given": "Helena", "initials": "H"}, {"family": "Sharp", "given": "Andrew S P", "initials": "ASP"}, {"family": "Shields", "given": "Denis C", "initials": "DC"}, {"family": "Sorice", "given": "Rossella", "initials": "R"}, {"family": "Sotoodehnia", "given": "Nona", "initials": "N"}, {"family": "Stricker", "given": "Bruno H", "initials": "BH"}, {"family": "Surendran", "given": "Praveen", "initials": "P"}, {"family": "Thom", "given": "Simon", "initials": "S"}, {"family": "T\u00f6glhofer", "given": "Anna M", "initials": "AM"}, {"family": "Uitterlinden", "given": "Andr\u00e9 G", "initials": "AG"}, {"family": "Wachter", "given": "Rolf", "initials": "R"}, {"family": "V\u00f6lzke", "given": "Henry", "initials": "H"}, {"family": "Ziegler", "given": "Andreas", "initials": "A"}, {"family": "M\u00fcnzel", "given": "Thomas", "initials": "T"}, {"family": "M\u00e4rz", "given": "Winfried", "initials": "W"}, {"family": "Cappola", "given": "Thomas P", "initials": "TP"}, {"family": "Hirschhorn", "given": "Joel N", "initials": "JN"}, {"family": "Mitchell", "given": "Gary F", "initials": "GF"}, {"family": "Smith", "given": "Nicholas L", "initials": "NL"}, {"family": "Fox", "given": "Ervin R", "initials": "ER"}, {"family": "Dueker", "given": "Nicole D", "initials": "ND"}, {"family": "Jaddoe", "given": "Vincent W V", "initials": "VWV"}, {"family": "Melander", "given": "Olle", "initials": "O"}, {"family": "Russ", "given": "Martin", "initials": "M"}, {"family": "Lehtim\u00e4ki", "given": "Terho", "initials": "T"}, {"family": "Ciullo", "given": "Marina", "initials": "M"}, {"family": "Hicks", "given": "Andrew A", "initials": "AA"}, {"family": "Lind", "given": "Lars", "initials": "L"}, {"family": "Gudnason", "given": "Vilmundur", "initials": "V"}, {"family": "Pieske", "given": "Burkert", "initials": "B"}, {"family": "Barron", "given": "Anthony J", "initials": "AJ"}, {"family": "Zweiker", "given": "Robert", "initials": "R"}, {"family": "Schunkert", "given": "Heribert", "initials": "H"}, {"family": "Ingelsson", "given": "Erik", "initials": "E"}, {"family": "Liu", "given": "Kiang", "initials": "K"}, {"family": "Arnett", "given": "Donna K", "initials": "DK"}, {"family": "Psaty", "given": "Bruce M", "initials": "BM"}, {"family": "Blankenberg", "given": "Stefan", "initials": "S"}, {"family": "Larson", "given": "Martin G", "initials": "MG"}, {"family": "Felix", "given": "Stephan B", "initials": "SB"}, {"family": "Franco", "given": "Oscar H", "initials": "OH"}, {"family": "Zeller", "given": "Tanja", "initials": "T"}, {"family": "Vasan", "given": "Ramachandran S", "initials": "RS"}, {"family": "D\u00f6rr", "given": "Marcus", "initials": "M"}], "type": "journal-article", "published": "2017-04-10", "journal": {"volume": "127", "issn": "0021-9738", "issue": "5", "pages": "1798-1812", "title": "J Clin Invest.", "issn-l": null}, "abstract": null, "doi": "10.1172/jci84840", "pmid": "28394258", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [], "notes": [], "created": "2018-01-09T14:01:35.302Z", "modified": "2021-07-07T15:50:03.445Z"}, {"entity": "publication", "iuid": "f6ff44cbb6cb43d4ad682c875c41495c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f6ff44cbb6cb43d4ad682c875c41495c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f6ff44cbb6cb43d4ad682c875c41495c"}}, "title": "SPlinted Ligation Adapter Tagging (SPLAT), a novel library preparation method for whole genome bisulphite sequencing.", "authors": [{"family": "Raine", "given": "Amanda", "initials": "A"}, {"family": "Manlig", "given": "Erika", "initials": "E"}, {"family": "Wahlberg", "given": "Per", "initials": "P"}, {"family": "Syv\u00e4nen", "given": "Ann-Christine", "initials": "AC", "orcid": "0000-0002-9681-9146", "researcher": {"href": "https://publications.scilifelab.se/researcher/f7012e35025543379380cb90efd71243.json"}}, {"family": "Nordlund", "given": "Jessica", "initials": "J", "orcid": "0000-0001-8699-9959", "researcher": {"href": "https://publications.scilifelab.se/researcher/ddf48c9262134821bcc6ce1180049753.json"}}], "type": "journal article", "published": "2017-04-07", "journal": {"volume": "45", "issn": "1362-4962", "issue": "6", "pages": "e36", "title": "Nucleic Acids Res.", "issn-l": "0305-1048"}, "abstract": "Sodium bisulphite treatment of DNA combined with next generation sequencing (NGS) is a powerful combination for the interrogation of genome-wide DNA methylation profiles. Library preparation for whole genome bisulphite sequencing (WGBS) is challenging due to side effects of the bisulphite treatment, which leads to extensive DNA damage. Recently, a new generation of methods for bisulphite sequencing library preparation have been devised. They are based on initial bisulphite treatment of the DNA, followed by adaptor tagging of single stranded DNA fragments, and enable WGBS using low quantities of input DNA. In this study, we present a novel approach for quick and cost effective WGBS library preparation that is based on splinted adaptor tagging (SPLAT) of bisulphite-converted single-stranded DNA. Moreover, we validate SPLAT against three commercially available WGBS library preparation techniques, two of which are based on bisulphite treatment prior to adaptor tagging and one is a conventional WGBS method.", "doi": "10.1093/nar/gkw1110", "pmid": "27899585", "labels": {"National Genomics Infrastructure": "Technology development", "NGI Uppsala (SNP&SEQ Technology Platform)": "Technology development", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "gkw1110"}, {"db": "pmc", "key": "PMC5389478"}], "notes": [], "created": "2017-10-30T09:31:42.942Z", "modified": "2024-01-16T13:48:48.095Z"}, {"entity": "publication", "iuid": "8315872149d64774893689fec33af1a5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8315872149d64774893689fec33af1a5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8315872149d64774893689fec33af1a5"}}, "title": "Interactions of Freshwater Cyanobacteria with Bacterial Antagonists", "authors": [{"family": "Osman", "given": "Omneya Ahmed", "initials": "OA"}, {"family": "Beier", "given": "Sara", "initials": "S"}, {"family": "Grabherr", "given": "Manfred", "initials": "M"}, {"family": "Bertilsson", "given": "Stefan", "initials": "S"}], "type": "journal-article", "published": "2017-04-01", "journal": {"volume": "83", "issn": "1098-5336", "issue": "7", "pages": "e02634-16", "title": "Appl. Environ. Microbiol.", "issn-l": "0099-2240"}, "abstract": null, "doi": "10.1128/aem.02634-16", "pmid": "28115385", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2017-10-19T20:28:59.730Z", "modified": "2024-01-16T13:48:48.128Z"}, {"entity": "publication", "iuid": "805eaa34c87f47998780736a864788c7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/805eaa34c87f47998780736a864788c7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/805eaa34c87f47998780736a864788c7"}}, "title": "Whole-Genome Bisulfite Sequencing of Human Pancreatic Islets Reveals Novel Differentially Methylated Regions in Type 2 Diabetes Pathogenesis", "authors": [{"family": "Volkov", "given": "Petr", "initials": "P"}, {"family": "Bacos", "given": "Karl", "initials": "K"}, {"family": "Ofori", "given": "Jones K", "initials": "JK"}, {"family": "Esguerra", "given": "Jonathan Lou S", "initials": "JLS"}, {"family": "Eliasson", "given": "Lena", "initials": "L"}, {"family": "R\u00f6nn", "given": "Tina", "initials": "T"}, {"family": "Ling", "given": "Charlotte", "initials": "C"}], "type": "journal-article", "published": "2017-04-00", "journal": {"volume": "66", "issn": "1939-327X", "issue": "4", "pages": "1074-1085", "title": "Diabetes", "issn-l": "0012-1797"}, "abstract": null, "doi": "10.2337/db16-0996", "pmid": "28052964", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2017-10-19T20:37:34.478Z", "modified": "2024-01-16T13:48:48.141Z"}, {"entity": "publication", "iuid": "3833bdb907964e41b9acfb00520e1629", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3833bdb907964e41b9acfb00520e1629.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3833bdb907964e41b9acfb00520e1629"}}, "title": "Mapping of 79 loci for 83 plasma protein biomarkers in cardiovascular disease.", "authors": [{"family": "Folkersen", "given": "Lasse", "initials": "L", "orcid": "0000-0003-0708-9530", "researcher": {"href": "https://publications.scilifelab.se/researcher/7202a83ff6484d5c9d77f448f93c6520.json"}}, {"family": "Fauman", "given": "Eric", "initials": "E", "orcid": "0000-0002-9739-0249", "researcher": {"href": "https://publications.scilifelab.se/researcher/33640d6d585f4715ad0754af256954fd.json"}}, {"family": "Sabater-Lleal", "given": "Maria", "initials": "M", "orcid": "0000-0002-0128-379X", "researcher": {"href": "https://publications.scilifelab.se/researcher/588239fdbde94de0b5de738fd9c7a8a9.json"}}, {"family": "Strawbridge", "given": "Rona J", "initials": "RJ"}, {"family": "Fr\u00e5nberg", "given": "Mattias", "initials": "M"}, {"family": "Sennblad", "given": "Bengt", "initials": "B"}, {"family": "Baldassarre", "given": "Damiano", "initials": "D", "orcid": "0000-0002-2766-8882", "researcher": {"href": "https://publications.scilifelab.se/researcher/0c131cad5784434eb16cf720f7964ecb.json"}}, {"family": "Veglia", "given": "Fabrizio", "initials": "F"}, {"family": "Humphries", "given": "Steve E", "initials": "SE", "orcid": "0000-0002-8221-6547", "researcher": {"href": "https://publications.scilifelab.se/researcher/7669b620701f4ebd97f91594c9a4989e.json"}}, {"family": "Rauramaa", "given": "Rainer", "initials": "R"}, {"family": "de Faire", "given": "Ulf", "initials": "U"}, {"family": "Smit", "given": "Andries J", "initials": "AJ"}, {"family": "Giral", "given": "Philippe", "initials": "P"}, {"family": "Kurl", "given": "Sudhir", "initials": "S"}, {"family": "Mannarino", "given": "Elmo", "initials": "E"}, {"family": "Enroth", "given": "Stefan", "initials": "S", "orcid": "0000-0002-5056-9137", "researcher": {"href": "https://publications.scilifelab.se/researcher/16bb97ef16ee49f3ae0c7ea0495fd971.json"}}, {"family": "Johansson", "given": "\u00c5sa", "initials": "\u00c5", "orcid": "0000-0002-2915-4498", "researcher": {"href": "https://publications.scilifelab.se/researcher/76265c54961046e99bdb0439f9ae1d34.json"}}, {"family": "Enroth", "given": "Sofia Bosdotter", "initials": "SB"}, {"family": "Gustafsson", "given": "Stefan", "initials": "S"}, {"family": "Lind", "given": "Lars", "initials": "L"}, {"family": "Lindgren", "given": "Cecilia", "initials": "C"}, {"family": "Morris", "given": "Andrew P", "initials": "AP"}, {"family": "Giedraitis", "given": "Vilmantas", "initials": "V"}, {"family": "Silveira", "given": "Angela", "initials": "A"}, {"family": "Franco-Cereceda", "given": "Anders", "initials": "A"}, {"family": "Tremoli", "given": "Elena", "initials": "E"}, {"family": "IMPROVE study group", "given": "", "initials": ""}, {"family": "Gyllensten", "given": "Ulf", "initials": "U"}, {"family": "Ingelsson", "given": "Erik", "initials": "E"}, {"family": "Brunak", "given": "S\u00f8ren", "initials": "S"}, {"family": "Eriksson", "given": "Per", "initials": "P", "orcid": "0000-0002-5635-2692", "researcher": {"href": "https://publications.scilifelab.se/researcher/247b26c7360d4032b9cecc81bfac3ed0.json"}}, {"family": "Ziemek", "given": "Daniel", "initials": "D"}, {"family": "Hamsten", "given": "Anders", "initials": "A"}, {"family": "M\u00e4larstig", "given": "Anders", "initials": "A", "orcid": "0000-0003-2608-1358", "researcher": {"href": "https://publications.scilifelab.se/researcher/e70c845d32264b448e0b4631b826be6d.json"}}], "type": "journal article", "published": "2017-04-00", "journal": {"title": "PLoS Genet.", "issn": "1553-7404", "issn-l": "1553-7390", "volume": "13", "issue": "4", "pages": "e1006706"}, "abstract": "Recent advances in highly multiplexed immunoassays have allowed systematic large-scale measurement of hundreds of plasma proteins in large cohort studies. In combination with genotyping, such studies offer the prospect to 1) identify mechanisms involved with regulation of protein expression in plasma, and 2) determine whether the plasma proteins are likely to be causally implicated in disease. We report here the results of genome-wide association (GWA) studies of 83 proteins considered relevant to cardiovascular disease (CVD), measured in 3,394 individuals with multiple CVD risk factors. We identified 79 genome-wide significant (p<5e-8) association signals, 55 of which replicated at P<0.0007 in separate validation studies (n = 2,639 individuals). Using automated text mining, manual curation, and network-based methods incorporating information on expression quantitative trait loci (eQTL), we propose plausible causal mechanisms for 25 trans-acting loci, including a potential post-translational regulation of stem cell factor by matrix metalloproteinase 9 and receptor-ligand pairs such as RANK-RANK ligand. Using public GWA study data, we further evaluate all 79 loci for their causal effect on coronary artery disease, and highlight several potentially causal associations. Overall, a majority of the plasma proteins studied showed evidence of regulation at the genetic level. Our results enable future studies of the causal architecture of human disease, which in turn should aid discovery of new drug targets.", "doi": "10.1371/journal.pgen.1006706", "pmid": "28369058", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Clinical Biomarkers": "Service", "PLA and Single Cell Proteomics": "Service", "Affinity Proteomics Uppsala": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "PGENETICS-D-16-01965"}, {"db": "pmc", "key": "PMC5393901"}], "notes": [], "created": "2017-10-25T15:18:21.171Z", "modified": "2024-01-16T13:48:48.159Z"}, {"entity": "publication", "iuid": "033b5a0bde204450b47ca9e89437b1fe", "links": {"self": {"href": "https://publications.scilifelab.se/publication/033b5a0bde204450b47ca9e89437b1fe.json"}, "display": {"href": "https://publications.scilifelab.se/publication/033b5a0bde204450b47ca9e89437b1fe"}}, "title": "Epigenome-wide DNA methylation study of IgE concentration in relation to self-reported allergies.", "authors": [{"family": "Ek", "given": "Weronica E", "initials": "WE"}, {"family": "Ahsan", "given": "Muhammad", "initials": "M"}, {"family": "Rask-Andersen", "given": "Mathias", "initials": "M"}, {"family": "Liang", "given": "Liming", "initials": "L"}, {"family": "Moffatt", "given": "Miriam F", "initials": "MF"}, {"family": "Gyllensten", "given": "Ulf", "initials": "U"}, {"family": "Johansson", "given": "\u00c5sa", "initials": "\u00c5"}], "type": "journal article", "published": "2017-04-00", "journal": {"volume": "9", "issn": "1750-192X", "issue": "4", "pages": "407-418", "title": "Epigenomics", "issn-l": null}, "abstract": "Epigenetic mechanisms are critical for normal immune development and epigenetic alterations might therefore be possible contributors to immune diseases. To investigate if DNA methylation in whole blood is associated with total and allergen-specific IgE levels.\n\nWe performed an epigenome-wide association study to investigate the association between DNA methylation and IgE level, allergen-specific IgE and self-reported immune diseases and allergies in 728 individuals.\n\nWe identified and replicated 15 CpG sites associated with IgE, mapping to biologically relevant genes, including ACOT7, ILR5A, KCNH2, PRG2 and EPX. A total of 331 loci were associated with allergen-specific IgE, but none of these CpG sites were associated with self-reported allergies and immune diseases.\n\nThis study shows that IgE levels are associated with DNA methylation levels at numerous CpG sites, which might provide new leads for investigating the links between IgE and allergic inflammation.", "doi": "10.2217/epi-2016-0158", "pmid": "28322575", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2017-10-25T15:18:20.445Z", "modified": "2024-01-16T13:48:48.187Z"}, {"entity": "publication", "iuid": "6ba3241f53fa4f55aa4eec0a4f518f18", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6ba3241f53fa4f55aa4eec0a4f518f18.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6ba3241f53fa4f55aa4eec0a4f518f18"}}, "title": "PATZ1 down-regulates FADS1 by binding to rs174557 and is opposed by SP1/SREBP1c.", "authors": [{"family": "Pan", "given": "Gang", "initials": "G"}, {"family": "Ameur", "given": "Adam", "initials": "A", "orcid": "0000-0001-6085-6749", "researcher": {"href": "https://publications.scilifelab.se/researcher/e960811513664a78b2804a00ee70f7c3.json"}}, {"family": "Enroth", "given": "Stefan", "initials": "S"}, {"family": "Bysani", "given": "Madhusudhan", "initials": "M"}, {"family": "Nord", "given": "Helena", "initials": "H"}, {"family": "Cavalli", "given": "Marco", "initials": "M"}, {"family": "Essand", "given": "Magnus", "initials": "M"}, {"family": "Gyllensten", "given": "Ulf", "initials": "U"}, {"family": "Wadelius", "given": "Claes", "initials": "C"}], "type": "journal article", "published": "2017-03-17", "journal": {"volume": "45", "issn": "1362-4962", "issue": "5", "pages": "2408-2422", "title": "Nucleic Acids Res.", "issn-l": "0305-1048"}, "abstract": "The FADS1 and FADS2 genes in the FADS cluster encode the rate-limiting enzymes in the synthesis of long-chain polyunsaturated fatty acids (LC-PUFAs). Genetic variation in this region has been associated with a large number of diseases and traits many of them correlated to differences in metabolism of PUFAs. However, the causative variants leading to these associations have not been identified. Here we find that the multiallelic rs174557 located in an AluYe5 element in intron 1 of FADS1 is functional and lies within a PATZ1 binding site. The derived allele of rs174557, which is the common variant in most populations, diminishes binding of PATZ1, a transcription factor conferring allele-specific downregulation of FADS1. The PATZ1 binding site overlaps with a SP1 site. The competitive binding between the suppressive PATZ1 and the activating complex of SP1 and SREBP1c determines the enhancer activity of this region, which regulates expression of FADS1.", "doi": "10.1093/nar/gkw1186", "pmid": "27932482", "labels": {"National Genomics Infrastructure": "Technology development", "NGI Uppsala (SNP&SEQ Technology Platform)": "Technology development", "NGI Uppsala (Uppsala Genome Center)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "gkw1186"}, {"db": "pmc", "key": "PMC5389558"}], "notes": [], "created": "2017-05-03T13:01:46.011Z", "modified": "2024-01-16T13:48:48.278Z"}, {"entity": "publication", "iuid": "3ab189fbee87422abd559ff87c88dd32", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3ab189fbee87422abd559ff87c88dd32.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3ab189fbee87422abd559ff87c88dd32"}}, "title": "Microbial community assembly and evolution in subseafloor sediment", "authors": [{"family": "Starnawski", "given": "Piotr", "initials": "P"}, {"family": "Bataillon", "given": "Thomas", "initials": "T"}, {"family": "Ettema", "given": "Thijs J G", "initials": "TJG"}, {"family": "Jochum", "given": "Lara M", "initials": "LM"}, {"family": "Schreiber", "given": "Lars", "initials": "L"}, {"family": "Chen", "given": "Xihan", "initials": "X"}, {"family": "Lever", "given": "Mark A", "initials": "MA"}, {"family": "Polz", "given": "Martin F", "initials": "MF"}, {"family": "J\u00f8rgensen", "given": "Bo B", "initials": "BB"}, {"family": "Schramm", "given": "Andreas", "initials": "A"}, {"family": "Kjeldsen", "given": "Kasper U", "initials": "KU"}], "type": "journal-article", "published": "2017-03-14", "journal": {"volume": "114", "issn": "0027-8424", "issue": "11", "pages": "2940-2945", "title": "Proc Natl Acad Sci USA", "issn-l": "0027-8424"}, "abstract": null, "doi": "10.1073/pnas.1614190114", "pmid": "28242677", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "BioProject", "description": "Marine sediment amplicon Targeted loci environmental", "key": "PRJNA308429"}, {"db": "BioProject", "description": "Marine sediment communities", "key": "PRJNA305566"}, {"db": "img.jgi.doe.gov", "description": "2606217225, 2626541591, 2606217224, 2609459604, 2606217227, 2606217228, 2609459605, 2626541542, 2626541544, 2626541633, 2626541550, 2626541552, 2626541551, 2609459610, 2609459611, 2609459606, 2609459607, 2626541553, 2615840654 and 2615840655", "key": "https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=TaxonDetail&page=taxonDetail&taxon_oid=2615840655"}], "notes": [], "created": "2017-10-19T20:12:08.593Z", "modified": "2024-01-16T13:48:48.315Z"}, {"entity": "publication", "iuid": "725b691fbefb457a9acd5f5fd689c118", "links": {"self": {"href": "https://publications.scilifelab.se/publication/725b691fbefb457a9acd5f5fd689c118.json"}, "display": {"href": "https://publications.scilifelab.se/publication/725b691fbefb457a9acd5f5fd689c118"}}, "title": "Inferring Individual Inbreeding and Demographic History from Segments of Identity by Descent in Ficedula Flycatcher Genome Sequences", "authors": [{"family": "Kardos", "given": "Marty", "initials": "M"}, {"family": "Qvarnstr\u00f6m", "given": "Anna", "initials": "A"}, {"family": "Ellegren", "given": "Hans", "initials": "H"}], "type": "journal-article", "published": "2017-03-00", "journal": {"volume": "205", "issn": "1943-2631", "issue": "3", "pages": "1319-1334", "title": "Genetics", "issn-l": "0016-6731"}, "abstract": null, "doi": "10.1534/genetics.116.198861", "pmid": "28100590", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "BioProject", "description": "Genetic variation in Ficedula flycatchers", "key": "PRJEB7359"}, {"db": "BioProject", "description": "Detecting QTL in natural populations", "key": "PRJEB11502"}], "notes": [], "created": "2017-10-19T20:22:23.226Z", "modified": "2024-01-16T13:48:48.342Z"}, {"entity": "publication", "iuid": "3174c50b7f7444a1bf2978b567b3a401", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3174c50b7f7444a1bf2978b567b3a401.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3174c50b7f7444a1bf2978b567b3a401"}}, "title": "Damaged reward areas in human alcoholics: neuronal proportion decline and astrocyte activation.", "authors": [{"family": "Sarkisyan", "given": "Daniil", "initials": "D"}, {"family": "Bazov", "given": "Igor", "initials": "I"}, {"family": "Watanabe", "given": "Hiroyuki", "initials": "H"}, {"family": "Kononenko", "given": "Olga", "initials": "O"}, {"family": "Syv\u00e4nen", "given": "Ann-Christine", "initials": "AC", "orcid": "0000-0002-9681-9146", "researcher": {"href": "https://publications.scilifelab.se/researcher/f7012e35025543379380cb90efd71243.json"}}, {"family": "Schumann", "given": "Gunter", "initials": "G"}, {"family": "Yakovleva", "given": "Tatiana", "initials": "T"}, {"family": "Bakalkin", "given": "Georgy", "initials": "G"}], "type": "letter", "published": "2017-03-00", "journal": {"volume": "133", "issn": "1432-0533", "issue": "3", "pages": "485-487", "title": "Acta Neuropathol.", "issn-l": "0001-6322"}, "abstract": null, "doi": "10.1007/s00401-017-1675-0", "pmid": "28097436", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1007/s00401-017-1675-0"}], "notes": [], "created": "2017-10-25T15:54:12.769Z", "modified": "2024-01-16T13:48:48.352Z"}, {"entity": "publication", "iuid": "46c57c089f404bc792706ca3baa9d9be", "links": {"self": {"href": "https://publications.scilifelab.se/publication/46c57c089f404bc792706ca3baa9d9be.json"}, "display": {"href": "https://publications.scilifelab.se/publication/46c57c089f404bc792706ca3baa9d9be"}}, "title": "DNA methylation profiling of pediatric B-cell lymphoblastic leukemia with KMT2A rearrangement identifies hypomethylation at enhancer sites.", "authors": [{"family": "Bergmann", "given": "Anke K", "initials": "AK"}, {"family": "Castellano", "given": "Giancarlo", "initials": "G"}, {"family": "Alten", "given": "Julia", "initials": "J"}, {"family": "Ammerpohl", "given": "Ole", "initials": "O"}, {"family": "Kolarova", "given": "Julia", "initials": "J"}, {"family": "Nordlund", "given": "Jessica", "initials": "J", "orcid": "0000-0001-8699-9959", "researcher": {"href": "https://publications.scilifelab.se/researcher/ddf48c9262134821bcc6ce1180049753.json"}}, {"family": "Martin-Subero", "given": "Jose Ignacio", "initials": "JI"}, {"family": "Schrappe", "given": "Martin", "initials": "M"}, {"family": "Siebert", "given": "Reiner", "initials": "R"}], "type": "comparative study", "published": "2017-03-00", "journal": {"volume": "64", "issn": "1545-5017", "issue": "3", "title": "Pediatr Blood Cancer", "issn-l": "1545-5009"}, "abstract": "Deregulation of the epigenome is an important pathogenetic mechanism in acute lymphoblastic leukemia (ALL) with lysine (K)-specific methyltransferase 2A rearrangement (KMT2Ar). We performed array-based DNA methylation profiling of KMT2Ar ALL cells from 26 children in comparison to normal B-cell precursors. Significant changes in DNA methylation in KMT2Ar ALL were identified in 2,545 CpG loci, influenced by age and the translocation partners AFF1 and MLLT1. In KMT2Ar ALL, DNA methylation loss was enriched at enhancers and for certain transcription factor binding sites such as BCL11A, EBF, and MEF2A. In summary, DNA methylation changes in KMT2Ar ALL target enhancers, genes involved in leukemogenesis and normal hematopoiesis, as well as transcription factor networks.", "doi": "10.1002/pbc.26251", "pmid": "27786413", "labels": {"National Genomics Infrastructure": "Technology development", "NGI Uppsala (SNP&SEQ Technology Platform)": "Technology development", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2017-05-03T12:59:45.837Z", "modified": "2024-01-16T13:48:48.363Z"}, {"entity": "publication", "iuid": "6306f0bfadd949feaecbcd33e05f999b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6306f0bfadd949feaecbcd33e05f999b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6306f0bfadd949feaecbcd33e05f999b"}}, "title": "A genetic risk score is significantly associated with statin therapy response in the elderly population.", "authors": [{"family": "Ciuculete", "given": "D M", "initials": "DM"}, {"family": "Bandstein", "given": "M", "initials": "M"}, {"family": "Benedict", "given": "C", "initials": "C"}, {"family": "Waeber", "given": "G", "initials": "G"}, {"family": "Vollenweider", "given": "P", "initials": "P"}, {"family": "Lind", "given": "L", "initials": "L"}, {"family": "Schi\u00f6th", "given": "H B", "initials": "HB"}, {"family": "Mwinyi", "given": "J", "initials": "J"}], "type": "journal article", "published": "2017-03-00", "journal": {"volume": "91", "issn": "1399-0004", "issue": "3", "pages": "379-385", "title": "Clin. Genet.", "issn-l": "0009-9163"}, "abstract": "The ability of statins to strongly reduce low-density lipoprotein cholesterol (LDL-C) varies interindividually and is partially influenced by genetic variants. Based on a comprehensive analysis of 23 single nucleotide polymorphisms (SNPs) known to be associated with pharmacokinetics and dynamics of statins, we developed a genetic risk score to study its impact on the therapy outcome in elderly individuals under at least 5 years statin therapy. The study was performed in a population-based cohort of 1016 elderly individuals, which comprised 168 statin users investigated at age 75 and 80. Using random forest models, the major variants influencing LDL-C levels were summarized in a weighted GRS (wGRS). The wGRS was tested with lipid and glucose outcomes and validated in an independent population-based cohort including 221 statin users. Four SNPs within the APOE cluster (rs7412, rs4420638), ABCC2 (rs2002042) and CELSR/SORT1/PSRC1 (rs646776), displayed a major impact on statin efficacy. The wGRS was significantly associated with lower LDL-C at age 75 and 80. This association was replicated displaying similar results. GRS analysis is a powerful tool to evaluate the additive effects of genetic variants on statin response and to estimate the magnitude of LDL-C reduction to a considerable extent in the older population.", "doi": "10.1111/cge.12890", "pmid": "27943270", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2017-05-03T12:58:53.688Z", "modified": "2024-01-16T13:48:48.381Z"}, {"entity": "publication", "iuid": "c6f37a4cb0494adab40df449aa3f4707", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c6f37a4cb0494adab40df449aa3f4707.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c6f37a4cb0494adab40df449aa3f4707"}}, "title": "Covariation in levels of nucleotide diversity in homologous regions of the avian genome long after completion of lineage sorting", "authors": [{"family": "Dutoit", "given": "Ludovic", "initials": "L"}, {"family": "Vijay", "given": "Nagarjun", "initials": "N"}, {"family": "Mugal", "given": "Carina F", "initials": "CF"}, {"family": "Bossu", "given": "Christen M", "initials": "CM"}, {"family": "Burri", "given": "Reto", "initials": "R"}, {"family": "Wolf", "given": "Jochen", "initials": "J"}, {"family": "Ellegren", "given": "Hans", "initials": "H"}], "type": "journal-article", "published": "2017-02-22", "journal": {"volume": "284", "issn": "0962-8452", "issue": "1849", "pages": "20162756", "title": "Proc. R. Soc. B", "issn-l": "0962-8452"}, "abstract": null, "doi": "10.1098/rspb.2016.2756", "pmid": "28202815", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2017-10-30T09:24:44.458Z", "modified": "2024-01-16T13:48:48.388Z"}, {"entity": "publication", "iuid": "49e5872c79664d88937a1adc92d80dc4", "links": {"self": {"href": "https://publications.scilifelab.se/publication/49e5872c79664d88937a1adc92d80dc4.json"}, "display": {"href": "https://publications.scilifelab.se/publication/49e5872c79664d88937a1adc92d80dc4"}}, "title": "Genome-wide Association for Major Depression Through Age at Onset Stratification: Major Depressive Disorder Working Group of the Psychiatric Genomics Consortium.", "authors": [{"family": "Power", "given": "Robert A", "initials": "RA"}, {"family": "Tansey", "given": "Katherine E", "initials": "KE"}, {"family": "Buttensch\u00f8n", "given": "Henriette N\u00f8rm\u00f8lle", "initials": "HN"}, {"family": "Cohen-Woods", "given": "Sarah", "initials": "S"}, {"family": "Bigdeli", "given": "Tim", "initials": "T"}, {"family": "Hall", "given": "Lynsey S", "initials": "LS"}, {"family": "Kutalik", "given": "Zolt\u00e1n", "initials": "Z"}, {"family": "Lee", "given": "S Hong", "initials": "SH"}, {"family": "Ripke", "given": "Stephan", "initials": "S"}, {"family": "Steinberg", "given": "Stacy", "initials": "S"}, {"family": "Teumer", "given": "Alexander", "initials": "A"}, {"family": "Viktorin", "given": "Alexander", "initials": "A"}, {"family": "Wray", "given": "Naomi R", "initials": "NR"}, {"family": "Arolt", "given": "Volker", "initials": "V"}, {"family": "Baune", "given": "Bernard T", "initials": "BT"}, {"family": "Boomsma", "given": "Dorret I", "initials": "DI"}, {"family": "B\u00f8rglum", "given": "Anders D", "initials": "AD"}, {"family": "Byrne", "given": "Enda M", "initials": "EM"}, {"family": "Castelao", "given": "Enrique", "initials": "E"}, {"family": "Craddock", "given": "Nick", "initials": "N"}, {"family": "Craig", "given": "Ian W", "initials": "IW"}, {"family": "Dannlowski", "given": "Udo", "initials": "U"}, {"family": "Deary", "given": "Ian J", "initials": "IJ"}, {"family": "Degenhardt", "given": "Franziska", "initials": "F"}, {"family": "Forstner", "given": "Andreas J", "initials": "AJ"}, {"family": "Gordon", "given": "Scott D", "initials": "SD"}, {"family": "Grabe", "given": "Hans J", "initials": "HJ"}, {"family": "Grove", "given": "Jakob", "initials": "J"}, {"family": "Hamilton", "given": "Steven P", "initials": "SP"}, {"family": "Hayward", "given": "Caroline", "initials": "C"}, {"family": "Heath", "given": "Andrew C", "initials": "AC"}, {"family": "Hocking", "given": "Lynne J", "initials": "LJ"}, {"family": "Homuth", "given": "Georg", "initials": "G"}, {"family": "Hottenga", "given": "Jouke J", "initials": "JJ"}, {"family": "Kloiber", "given": "Stefan", "initials": "S"}, {"family": "Krogh", "given": "Jesper", "initials": "J"}, {"family": "Land\u00e9n", "given": "Mikael", "initials": "M"}, {"family": "Lang", "given": "Maren", "initials": "M"}, {"family": "Levinson", "given": "Douglas F", "initials": "DF"}, {"family": "Lichtenstein", "given": "Paul", "initials": "P"}, {"family": "Lucae", "given": "Susanne", "initials": "S"}, {"family": "MacIntyre", "given": "Donald J", "initials": "DJ"}, {"family": "Madden", "given": "Pamela", "initials": "P"}, {"family": "Magnusson", "given": "Patrik K E", "initials": "PK"}, {"family": "Martin", "given": "Nicholas G", "initials": "NG"}, {"family": "McIntosh", "given": "Andrew M", "initials": "AM"}, {"family": "Middeldorp", "given": "Christel M", "initials": "CM"}, {"family": "Milaneschi", "given": "Yuri", "initials": "Y"}, {"family": "Montgomery", "given": "Grant W", "initials": "GW"}, {"family": "Mors", "given": "Ole", "initials": "O"}, {"family": "M\u00fcller-Myhsok", "given": "Bertram", "initials": "B"}, {"family": "Nyholt", "given": "Dale R", "initials": "DR"}, {"family": "Oskarsson", "given": "Hogni", "initials": "H"}, {"family": "Owen", "given": "Michael J", "initials": "MJ"}, {"family": "Padmanabhan", "given": "Sandosh", "initials": "S"}, {"family": "Penninx", "given": "Brenda W J H", "initials": "BW"}, {"family": "Pergadia", "given": "Michele L", "initials": "ML"}, {"family": "Porteous", "given": "David J", "initials": "DJ"}, {"family": "Potash", "given": "James B", "initials": "JB"}, {"family": "Preisig", "given": "Martin", "initials": "M"}, {"family": "Rivera", "given": "Margarita", "initials": "M"}, {"family": "Shi", "given": "Jianxin", "initials": "J"}, {"family": "Shyn", "given": "Stanley I", "initials": "SI"}, {"family": "Sigurdsson", "given": "Engilbert", "initials": "E"}, {"family": "Smit", "given": "Johannes H", "initials": "JH"}, {"family": "Smith", "given": "Blair H", "initials": "BH"}, {"family": "Stefansson", "given": "Hreinn", "initials": "H"}, {"family": "Stefansson", "given": "Kari", "initials": "K"}, {"family": "Strohmaier", "given": "Jana", "initials": "J"}, {"family": "Sullivan", "given": "Patrick F", "initials": "PF"}, {"family": "Thomson", "given": "Pippa", "initials": "P"}, {"family": "Thorgeirsson", "given": "Thorgeir E", "initials": "TE"}, {"family": "Van der Auwera", "given": "Sandra", "initials": "S"}, {"family": "Weissman", "given": "Myrna M", "initials": "MM"}, {"family": "CONVERGE Consortium, CARDIoGRAM Consortium, GERAD1 Consortium", "given": null, "initials": null}, {"family": "Breen", "given": "Gerome", "initials": "G"}, {"family": "Lewis", "given": "Cathryn M", "initials": "CM"}], "type": "journal article", "published": "2017-02-15", "journal": {"volume": "81", "issn": "1873-2402", "issue": "4", "pages": "325-335", "title": "Biol. Psychiatry", "issn-l": "0006-3223"}, "abstract": "Major depressive disorder (MDD) is a disabling mood disorder, and despite a known heritable component, a large meta-analysis of genome-wide association studies revealed no replicable genetic risk variants. Given prior evidence of heterogeneity by age at onset in MDD, we tested whether genome-wide significant risk variants for MDD could be identified in cases subdivided by age at onset.\n\nDiscovery case-control genome-wide association studies were performed where cases were stratified using increasing/decreasing age-at-onset cutoffs; significant single nucleotide polymorphisms were tested in nine independent replication samples, giving a total sample of 22,158 cases and 133,749 control subjects for subsetting. Polygenic score analysis was used to examine whether differences in shared genetic risk exists between earlier and adult-onset MDD with commonly comorbid disorders of schizophrenia, bipolar disorder, Alzheimer's disease, and coronary artery disease.\n\nWe identified one replicated genome-wide significant locus associated with adult-onset (>27 years) MDD (rs7647854, odds ratio: 1.16, 95% confidence interval: 1.11-1.21, p = 5.2 \u00d7 10(-11)). Using polygenic score analyses, we show that earlier-onset MDD is genetically more similar to schizophrenia and bipolar disorder than adult-onset MDD.\n\nWe demonstrate that using additional phenotype data previously collected by genetic studies to tackle phenotypic heterogeneity in MDD can successfully lead to the discovery of genetic risk factor despite reduced sample size. Furthermore, our results suggest that the genetic susceptibility to MDD differs between adult- and earlier-onset MDD, with earlier-onset cases having a greater genetic overlap with schizophrenia and bipolar disorder.", "doi": "10.1016/j.biopsych.2016.05.010", "pmid": "27519822", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "S0006-3223(16)32386-1"}, {"db": "pmc", "key": "PMC5262436"}], "notes": [], "created": "2017-05-03T12:59:49.338Z", "modified": "2024-01-16T13:48:48.438Z"}, {"entity": "publication", "iuid": "760b105c4c974b08bbf488f12adb4fcf", "links": {"self": {"href": "https://publications.scilifelab.se/publication/760b105c4c974b08bbf488f12adb4fcf.json"}, "display": {"href": "https://publications.scilifelab.se/publication/760b105c4c974b08bbf488f12adb4fcf"}}, "title": "Distinct Anaerobic Bacterial Consumers of Cellobiose-Derived Carbon in Boreal Fens with Different CO2/CH4 Production Ratios", "authors": [{"family": "Juottonen", "given": "Heli", "initials": "H"}, {"family": "Eiler", "given": "Alexander", "initials": "A"}, {"family": "Biasi", "given": "Christina", "initials": "C"}, {"family": "Tuittila", "given": "Eeva Stiina", "initials": "ES"}, {"family": "Yrj\u00e4l\u00e4", "given": "Kim", "initials": "K"}, {"family": "Fritze", "given": "Hannu", "initials": "H"}], "type": "journal-article", "published": "2017-02-15", "journal": {"volume": "83", "issn": "1098-5336", "issue": "4", "pages": "e02533-16", "title": "Appl. Environ. Microbiol.", "issn-l": "0099-2240"}, "abstract": "Northern peatlands in general have high methane (CH\n                4) emissions, but individual peatlands show considerable variation as CH4 sources. Particularly in nutrient-poor peatlands, CH4 production can be low and exceeded by carbon dioxide (CO2) production from unresolved anaerobic processes. To clarify the role anaerobic bacterial degraders play in this variation, we compared consumers of cellobiose-derived carbon in two fens differing in nutrient status and the ratio of CO2 to CH4 produced. After [13C]cellobiose amendment, the mesotrophic fen produced equal amounts of CH4 and CO2 The oligotrophic fen had lower CH4 production but produced 3 to 59 times more CO2 than CH4 RNA stable-isotope probing revealed that in the mesotrophic fen with higher CH4 production, cellobiose-derived carbon was mainly assimilated by various recognized fermenters of Firmicutes and by Proteobacteria The oligotrophic peat with excess CO2 production revealed a wider variety of cellobiose-C consumers, including Firmicutes and Proteobacteria, but also more unconventional degraders, such as Telmatobacter-related Acidobacteria and subphylum 3 of Verrucomicrobia Prominent and potentially fermentative Planctomycetes and Chloroflexi did not appear to process cellobiose-C. Our results show that anaerobic degradation resulting in different levels of CH4 production can involve distinct sets of bacterial degraders. By distinguishing cellobiose degraders from the total community, this study contributes to defining anaerobic bacteria that process cellulose-derived carbon in peat. Several of the identified degraders, particularly fermenters and potential Fe(III) or humic substance reducers in the oligotrophic peat, represent promising candidates for resolving the origin of excess CO2 production in peatlands.\n\nPeatlands are major sources of the greenhouse gas methane (CH\n                4), yet in many peatlands, CO2 production from unresolved anaerobic processes exceeds CH4 production. Anaerobic degradation produces the precursors of CH4 production but also represents competing processes. We show that anaerobic degradation leading to high or low CH4 production involved distinct sets of bacteria. Well-known fermenters dominated in a peatland with high CH4 production, while novel and unconventional degraders could be identified in a site where CO2 production greatly exceeds CH4 production. Our results help identify and assign functions to uncharacterized bacteria that promote or inhibit CH4 production and reveal bacteria potentially producing the excess CO2 in acidic peat. This study contributes to understanding the microbiological basis for different levels of CH4 emission from peatlands.", "doi": "10.1128/aem.02533-16", "pmid": "27913414", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "SRA", "description": null, "key": "SRP075161"}], "notes": [], "created": "2017-05-03T13:00:16.242Z", "modified": "2024-01-16T13:48:48.453Z"}, {"entity": "publication", "iuid": "52aeeba6f0b143fcbf6610d898639cbe", "links": {"self": {"href": "https://publications.scilifelab.se/publication/52aeeba6f0b143fcbf6610d898639cbe.json"}, "display": {"href": "https://publications.scilifelab.se/publication/52aeeba6f0b143fcbf6610d898639cbe"}}, "title": "Genetic and Functional Study of L-Type Amino Acid Transporter 1 in Schizophrenia.", "authors": [{"family": "Comasco", "given": "Erika", "initials": "E"}, {"family": "Vumma", "given": "Ravi", "initials": "R"}, {"family": "Toffoletto", "given": "Simone", "initials": "S"}, {"family": "Johansson", "given": "Jessica", "initials": "J"}, {"family": "Flyckt", "given": "Lena", "initials": "L"}, {"family": "Lewander", "given": "Tommy", "initials": "T"}, {"family": "Oreland", "given": "Lars", "initials": "L"}, {"family": "Bjerkenstedt", "given": "Lars", "initials": "L"}, {"family": "Andreou", "given": "Dimitrios", "initials": "D"}, {"family": "S\u00f6derman", "given": "Erik", "initials": "E"}, {"family": "Terenius", "given": "Lars", "initials": "L"}, {"family": "Agartz", "given": "Ingrid", "initials": "I"}, {"family": "J\u00f6nsson", "given": "Erik G", "initials": "EG"}, {"family": "Venizelos", "given": "Nikolaos", "initials": "N"}], "type": "journal article", "published": "2017-02-11", "journal": {"volume": "74", "issn": "1423-0224", "issue": "2", "pages": "96-103", "title": "Neuropsychobiology", "issn-l": "0302-282X"}, "abstract": "Schizophrenia involves neural catecholaminergic dysregulation. Tyrosine is the precursor of catecholamines, and its major transporter, according to studies on fibroblasts, in the brain is the L-type amino acid transporter 1 (LAT1). The present study assessed haplotype tag single-nucleotide polymorphisms (SNPs) of the SLC7A5/LAT1 gene in 315 patients with psychosis within the schizophrenia spectrum and 233 healthy controls to investigate genetic vulnerability to the disorder as well as genetic relationships to homovanillic acid (HVA) and 3-methoxy-4-hydroxyphenylglycol (MHPG), the major catecholamine metabolites in the cerebrospinal fluid (CSF). Moreover, the involvement of the different isoforms of the system L in tyrosine uptake and LAT1 tyrosine kinetics were studied in fibroblast cell lines of 10 patients with schizophrenia and 10 healthy controls. The results provide suggestive evidence of individual vulnerability to schizophrenia related to the LAT1 SNP rs9936204 genotype. A number of SNPs were nominally associated with CSF HVA and MHPG concentrations but did not survive correction for multiple testing. The LAT1 isoform was confirmed as the major tyrosine transporter in patients with schizophrenia. However, the kinetic parameters (maximal transport capacity, affinity of the binding sites, and diffusion constant of tyrosine transport through the LAT1 isoform) did not differ between patients with schizophrenia and controls. The present genetic findings call for independent replication in larger samples, while the functional study seems to exclude a role of LAT1 in the aberrant transport of tyrosine in fibroblasts of patients with schizophrenia.", "doi": "10.1159/000455234", "pmid": "28190014", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "000455234"}], "notes": [], "created": "2018-01-09T14:07:15.547Z", "modified": "2021-06-22T11:34:21.312Z"}, {"entity": "publication", "iuid": "fbc5fb6308f74c049a6285b5b4849133", "links": {"self": {"href": "https://publications.scilifelab.se/publication/fbc5fb6308f74c049a6285b5b4849133.json"}, "display": {"href": "https://publications.scilifelab.se/publication/fbc5fb6308f74c049a6285b5b4849133"}}, "title": "Detection of Somatic Mutations in Gastroenteropancreatic Neuroendocrine Tumors Using Targeted Deep Sequencing", "authors": [{"family": "BACKMAN", "given": "SAMUEL", "initials": "S"}, {"family": "NORL\u00c9N", "given": "OLOV", "initials": "O"}, {"family": "ERIKSSON", "given": "BARBRO", "initials": "B"}, {"family": "SKOGSEID", "given": "BRITT", "initials": "B"}, {"family": "ST\u00c5LBERG", "given": "PETER", "initials": "P"}, {"family": "CRONA", "given": "JOAKIM", "initials": "J"}], "type": "journal-article", "published": "2017-02-10", "journal": {"volume": "37", "issn": "0250-7005", "issue": "2", "pages": "705-712", "title": "AR", "issn-l": "0250-7005"}, "abstract": null, "doi": "10.21873/anticanres.11367", "pmid": "28179320", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [], "notes": [], "created": "2017-10-19T20:36:20.548Z", "modified": "2020-01-21T13:56:10.041Z"}, {"entity": "publication", "iuid": "e16b1a021a0e42aea2eb4a9ed9d95719", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e16b1a021a0e42aea2eb4a9ed9d95719.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e16b1a021a0e42aea2eb4a9ed9d95719"}}, "title": "Rare and low-frequency coding variants alter human adult height.", "authors": [{"family": "Marouli", "given": "Eirini", "initials": "E"}, {"family": "Graff", "given": "Mariaelisa", "initials": "M"}, {"family": "Medina-Gomez", "given": "Carolina", "initials": "C"}, {"family": "Lo", "given": "Ken Sin", "initials": "KS"}, {"family": "Wood", "given": "Andrew R", "initials": "AR"}, {"family": "Kjaer", "given": "Troels R", "initials": "TR"}, {"family": "Fine", "given": "Rebecca S", "initials": "RS"}, {"family": "Lu", "given": "Yingchang", "initials": "Y"}, {"family": "Schurmann", "given": "Claudia", "initials": "C"}, {"family": "Highland", "given": "Heather M", "initials": "HM"}, {"family": "R\u00fceger", "given": "Sina", "initials": "S"}, {"family": "Thorleifsson", "given": "Gudmar", "initials": "G"}, {"family": "Justice", "given": "Anne E", "initials": "AE"}, {"family": "Lamparter", "given": 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"initials": ""}, {"family": "Global Lipids Genetics Consortium", "given": "", "initials": ""}, {"family": "ReproGen Consortium", "given": "", "initials": ""}, {"family": "MAGIC Investigators", "given": "", "initials": ""}, {"family": "Rotter", "given": "Jerome I", "initials": "JI"}, {"family": "Boehnke", "given": "Michael", "initials": "M"}, {"family": "Kathiresan", "given": "Sekar", "initials": "S"}, {"family": "McCarthy", "given": "Mark I", "initials": "MI"}, {"family": "Willer", "given": "Cristen J", "initials": "CJ"}, {"family": "Stefansson", "given": "Kari", "initials": "K"}, {"family": "Borecki", "given": "Ingrid B", "initials": "IB"}, {"family": "Liu", "given": "Dajiang J", "initials": "DJ"}, {"family": "North", "given": "Kari E", "initials": "KE"}, {"family": "Heard-Costa", "given": "Nancy L", "initials": "NL"}, {"family": "Pers", "given": "Tune H", "initials": "TH"}, {"family": "Lindgren", "given": "Cecilia M", "initials": "CM"}, {"family": "Oxvig", "given": "Claus", "initials": "C"}, {"family": "Kutalik", "given": "Zolt\u00e1n", "initials": "Z"}, {"family": "Rivadeneira", "given": "Fernando", "initials": "F"}, {"family": "Loos", "given": "Ruth J F", "initials": "RJ"}, {"family": "Frayling", "given": "Timothy M", "initials": "TM"}, {"family": "Hirschhorn", "given": "Joel N", "initials": "JN"}, {"family": "Deloukas", "given": "Panos", "initials": "P"}, {"family": "Lettre", "given": "Guillaume", "initials": "G"}], "type": "journal article", "published": "2017-02-09", "journal": {"volume": "542", "issn": "1476-4687", "issue": "7640", "pages": "186-190", "title": "Nature", "issn-l": "0028-0836"}, "abstract": "Height is a highly heritable, classic polygenic trait with approximately 700 common associated variants identified through genome-wide association studies so far. Here, we report 83 height-associated coding variants with lower minor-allele frequencies (in the range of 0.1-4.8%) and effects of up to 2\u2009centimetres per allele (such as those in IHH, STC2, AR and CRISPLD2), greater than ten times the average effect of common variants. In functional follow-up studies, rare height-increasing alleles of STC2 (giving an increase of 1-2\u2009centimetres per allele) compromised proteolytic inhibition of PAPP-A and increased cleavage of IGFBP-4 in vitro, resulting in higher bioavailability of insulin-like growth factors. These 83 height-associated variants overlap genes that are mutated in monogenic growth disorders and highlight new biological candidates (such as ADAMTS3, IL11RA and NOX4) and pathways (such as proteoglycan and glycosaminoglycan synthesis) involved in growth. Our results demonstrate that sufficiently large sample sizes can uncover rare and low-frequency variants of moderate-to-large effect associated with polygenic human phenotypes, and that these variants implicate relevant genes and pathways.", "doi": "10.1038/nature21039", "pmid": "28146470", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "nature21039"}, {"db": "pmc", "key": "PMC5302847"}, {"db": "mid", "key": "NIHMS834200"}], "notes": [], "created": "2017-10-25T15:54:16.444Z", "modified": "2024-01-16T13:48:48.470Z"}, {"entity": "publication", "iuid": "c50b3617005b4f488783938e7540a7d5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c50b3617005b4f488783938e7540a7d5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c50b3617005b4f488783938e7540a7d5"}}, "title": "Posttranscriptional Regulation in Adenovirus Infected Cells.", "authors": [{"family": "Zhao", "given": "Hongxing", "initials": "H"}, {"family": "Konzer", "given": "Anne", "initials": "A"}, {"family": "Mi", "given": "Jia", "initials": "J"}, {"family": "Chen", "given": "Moashan", "initials": "M"}, {"family": "Pettersson", "given": "Ulf", "initials": "U"}, {"family": "Lind", "given": "Sara Bergstr\u00f6m", "initials": "SB", "orcid": "0000-0002-9510-3816", "researcher": {"href": "https://publications.scilifelab.se/researcher/2c2549b838d7416ea5823767aff3ef30.json"}}], "type": "journal article", "published": "2017-02-03", "journal": {"volume": "16", "issn": "1535-3907", "issue": "2", "pages": "872-888", "title": "J. Proteome Res.", "issn-l": "1535-3893"}, "abstract": "A deeper understanding of how viruses reprogram their hosts for production of progeny is needed to combat infections. Most knowledge on the regulation of cellular gene expression during adenovirus infection is derived from mRNA studies. Here, we investigated the changes in protein expression during the late phase of adenovirus type 2 (Ad2) infection of the IMR-90 cell line by stable isotope labeling in cell culture with subsequent liquid chromatography-high resolution tandem mass spectrometric analysis. Two biological replicates of samples collected at 24 and 36 h post-infection (hpi) were investigated using swapped labeling. In total, 2648 and 2394 proteins were quantified at 24 and 36 hpi, respectively. Among them, 659 and 645 were deregulated >1.6-fold at the two time points. The protein expression was compared with RNA expression using cDNA sequencing data. The correlation was surprisingly low (r = 0.3), and several examples of posttranscriptional regulation were observed; e.g., proteins related to carbohydrate metabolism were up-regulated at the protein level but unchanged at the RNA level, whereas histone proteins were down-regulated at the protein level but up-regulated at the RNA level. The deregulation of cellular gene expression by adenovirus is mediated at multiple levels and more complex than hitherto believed.", "doi": "10.1021/acs.jproteome.6b00834", "pmid": "27959563", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2017-10-30T09:25:19.054Z", "modified": "2024-01-16T13:48:48.490Z"}, {"entity": "publication", "iuid": "ffb4e02791ba47ac883a6415b0338549", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ffb4e02791ba47ac883a6415b0338549.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ffb4e02791ba47ac883a6415b0338549"}}, "title": "Genome-wide association study with additional genetic and post-transcriptional analyses reveals novel regulators of plasma factor XI levels.", "authors": [{"family": "Sennblad", "given": "Bengt", "initials": "B", "orcid": "0000-0002-4360-8003", "researcher": {"href": "https://publications.scilifelab.se/researcher/1c991150beec46ba8886379193d6037b.json"}}, {"family": "Basu", "given": "Saonli", "initials": "S"}, {"family": "Mazur", "given": "Johanna", "initials": "J"}, {"family": "Suchon", "given": "Pierre", "initials": "P"}, {"family": "Martinez-Perez", "given": "Angel", "initials": "A"}, {"family": "van Hylckama Vlieg", "given": "Astrid", "initials": "A"}, {"family": "Truong", "given": "Vinh", "initials": "V"}, {"family": "Li", "given": "Yuhuang", "initials": "Y"}, {"family": "G\u00e5din", "given": "Jesper R", "initials": "JR"}, {"family": "Tang", "given": "Weihong", "initials": "W"}, {"family": "Grossman", "given": "Vera", "initials": "V"}, {"family": "de Haan", "given": "Hugoline G", "initials": "HG"}, {"family": "Handin", "given": "Niklas", "initials": "N"}, {"family": "Silveira", "given": "Angela", "initials": "A"}, {"family": "Souto", "given": "Juan Carlos", "initials": "JC"}, {"family": "Franco-Cereceda", "given": "Anders", "initials": "A"}, {"family": "Morange", "given": "Pierre-Emmanuel", "initials": "PE"}, {"family": "Gagnon", "given": "France", "initials": "F"}, {"family": "Soria", "given": "Jose Manuel", "initials": "JM"}, {"family": "Eriksson", "given": "Per", "initials": "P"}, {"family": "Hamsten", "given": "Anders", "initials": "A"}, {"family": "Maegdefessel", "given": "Lars", "initials": "L", "orcid": "0000-0001-5228-2634", "researcher": {"href": "https://publications.scilifelab.se/researcher/79bb494450154c51a70281d20fb07f81.json"}}, {"family": "Rosendaal", "given": "Frits R", "initials": "FR"}, {"family": "Wild", "given": "Philipp", "initials": "P"}, {"family": "Folsom", "given": "Aaron R", "initials": "AR"}, {"family": "Tr\u00e9gou\u00ebt", "given": "David-Alexandre", "initials": "DA", "orcid": "0000-0001-9084-7800", "researcher": {"href": "https://publications.scilifelab.se/researcher/adb3fe1a732b41d79a4a165a64c322d1.json"}}, {"family": "Sabater-Lleal", "given": "Maria", "initials": "M", "orcid": "0000-0002-0128-379X", "researcher": {"href": "https://publications.scilifelab.se/researcher/588239fdbde94de0b5de738fd9c7a8a9.json"}}], "type": "journal article", "published": "2017-02-01", "journal": {"volume": "26", "issn": "1460-2083", "issue": "3", "pages": "637-649", "title": "Hum. Mol. Genet.", "issn-l": "0964-6906"}, "abstract": "Coagulation factor XI (FXI) has become increasingly interesting for its role in pathogenesis of thrombosis. While elevated plasma levels of FXI have been associated with