{"entity": "label", "iuid": "04fb075a770d49b6b6e0c2fb80e85de0", "timestamp": "2026-08-12T15:10:58.400Z", "links": {"self": {"href": "https://publications.scilifelab.se/label/NGI%20SNP%20genotyping.json"}, "display": {"href": "https://publications.scilifelab.se/label/NGI%20SNP%20genotyping"}}, "value": "NGI SNP genotyping", "started": null, "ended": null, "created": "2022-03-11T11:46:05.963Z", "modified": "2022-03-11T11:46:05.974Z", "accounts": [{"entity": "account", "iuid": "0b6af06fa3ac476cbccbab4f1491db42", "timestamp": "2026-08-12T15:10:58.400Z", "links": {"self": {"href": "https://publications.scilifelab.se/account/susanne.kerje%40igp.uu.se.json"}, "display": {"href": "https://publications.scilifelab.se/account/susanne.kerje%40igp.uu.se"}}, "email": "susanne.kerje@igp.uu.se", "name": "Susanne Hellstedt Kerje", "orcid": null, "role": "curator", "status": "enabled", "login": "2025-11-18T10:08:17.635Z", "created": "2021-11-30T13:26:28.982Z", "modified": "2025-11-18T10:08:17.635Z"}, {"entity": "account", "iuid": "2f6a790641494ea3b821ab973dca82db", "timestamp": "2026-08-12T15:10:58.400Z", "links": {"self": {"href": "https://publications.scilifelab.se/account/renuka.kudva%40scilifelab.se.json"}, "display": {"href": "https://publications.scilifelab.se/account/renuka.kudva%40scilifelab.se"}}, "email": "renuka.kudva@scilifelab.se", "name": "Renuka Kudva", "orcid": "", "role": "curator", "status": "enabled", "login": "2026-07-14T17:33:20.266Z", "created": "2022-12-21T17:28:59.690Z", "modified": "2026-07-14T17:33:20.266Z"}, {"entity": "account", "iuid": "32a436398938412b93e7ddcef018c708", "timestamp": "2026-08-12T15:10:58.400Z", "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": "37e4b07800c74e69bfa28dfe0798597b", "timestamp": "2026-08-12T15:10:58.400Z", "links": {"self": {"href": "https://publications.scilifelab.se/account/adam.ameur%40igp.uu.se.json"}, "display": {"href": "https://publications.scilifelab.se/account/adam.ameur%40igp.uu.se"}}, "email": "adam.ameur@igp.uu.se", "name": "Adam Ameur", "orcid": null, "role": "curator", "status": "enabled", "login": "2026-08-12T14:58:16.491Z", "created": "2018-11-08T11:29:34.221Z", "modified": "2026-08-12T14:58:16.491Z"}, {"entity": "account", "iuid": "3a0653fc055b4bebbab6c164f3ac10e4", "timestamp": "2026-08-12T15:10:58.400Z", "links": {"self": {"href": "https://publications.scilifelab.se/account/mattias.ormestad%40scilifelab.se.json"}, "display": {"href": "https://publications.scilifelab.se/account/mattias.ormestad%40scilifelab.se"}}, "email": "mattias.ormestad@scilifelab.se", "name": "Mattias Ormestad", "orcid": "", "role": "curator", "status": "enabled", "login": "2025-11-20T13:16:54.441Z", "created": "2017-05-02T12:10:08.095Z", "modified": "2025-11-20T13:16:54.441Z"}, {"entity": "account", "iuid": "63525022c5204321b7c5dacabd6a5367", "timestamp": "2026-08-12T15:10:58.400Z", "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": "2026-06-24T14:02:02.333Z", "created": "2017-09-18T13:38:27.959Z", "modified": "2026-06-24T14:02:02.333Z"}, {"entity": "account", "iuid": "66178c433a274c59915e7e0a4a79b0dc", "timestamp": "2026-08-12T15:10:58.400Z", "links": {"self": {"href": "https://publications.scilifelab.se/account/johanna.lagensjo%40medsci.uu.se.json"}, "display": {"href": "https://publications.scilifelab.se/account/johanna.lagensjo%40medsci.uu.se"}}, "email": "johanna.lagensjo@medsci.uu.se", "name": "Johanna Lagensj\u00f6", "orcid": null, "role": "curator", "status": "enabled", "login": "2026-05-27T11:36:52.266Z", "created": "2020-12-10T14:55:09.702Z", "modified": "2026-05-27T11:36:52.266Z"}, {"entity": "account", "iuid": "6a38350bd21f4fb6aeeb1530037a99ae", "timestamp": "2026-08-12T15:10:58.400Z", "links": {"self": {"href": "https://publications.scilifelab.se/account/sune.joubert%40scilifelab.uu.se.json"}, "display": {"href": "https://publications.scilifelab.se/account/sune.joubert%40scilifelab.uu.se"}}, "email": "sune.joubert@scilifelab.uu.se", "name": "Sun\u00e9 Joubert", "orcid": "", "role": "curator", "status": "enabled", "login": "2025-10-31T11:15:37.113Z", "created": "2024-08-16T10:01:02.800Z", "modified": "2025-10-31T11:15:37.113Z"}, {"entity": "account", "iuid": "8f582b032455492883c2946527a6e043", "timestamp": "2026-08-12T15:10:58.400Z", "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": "b68b03ae2bcb43febbfa33e1e675efc3", "timestamp": "2026-08-12T15:10:58.400Z", "links": {"self": {"href": "https://publications.scilifelab.se/account/elisabet.einarsdottir%40scilifelab.se.json"}, "display": {"href": "https://publications.scilifelab.se/account/elisabet.einarsdottir%40scilifelab.se"}}, "email": "elisabet.einarsdottir@scilifelab.se", "name": "El\u00edsabet Einarsd\u00f3ttir", "orcid": "", "role": "curator", "status": "enabled", "login": "2023-02-22T16:10:22.529Z", "created": "2021-10-04T07:44:19.507Z", "modified": "2023-02-22T16:10:22.529Z"}, {"entity": "account", "iuid": "c272b0c5c4534a319678418310e37cc1", "timestamp": "2026-08-12T15:10:58.400Z", "links": {"self": {"href": "https://publications.scilifelab.se/account/ellen.sherwood%40scilifelab.se.json"}, "display": {"href": "https://publications.scilifelab.se/account/ellen.sherwood%40scilifelab.se"}}, "email": "ellen.sherwood@scilifelab.se", "name": "Ellen Sherwood", "orcid": null, "role": "curator", "status": "enabled", "login": null, "created": "2017-05-03T12:52:04.270Z", "modified": "2022-03-11T12:51:25.579Z"}, {"entity": "account", "iuid": "eaba3ceb6c484b64be969a9c1f11fb21", "timestamp": "2026-08-12T15:10:58.400Z", "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"}, {"entity": "account", "iuid": "f7089b2e9faf487bba80d04b6c7af324", "timestamp": "2026-08-12T15:10:58.400Z", "links": {"self": {"href": "https://publications.scilifelab.se/account/olga.pettersson%40igp.uu.se.json"}, "display": {"href": "https://publications.scilifelab.se/account/olga.pettersson%40igp.uu.se"}}, "email": "olga.pettersson@igp.uu.se", "name": "Olga Pettersson", "orcid": null, "role": "curator", "status": "enabled", "login": "2025-11-11T12:42:00.105Z", "created": "2017-05-03T12:52:08.490Z", "modified": "2025-11-11T12:42:00.105Z"}], "publications_count": 125, "publications": [{"entity": "publication", "iuid": "2d4022b436484360aa5abc58c422de2b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2d4022b436484360aa5abc58c422de2b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2d4022b436484360aa5abc58c422de2b"}}, "title": "When the proteome meets the metabolome observational and Mendelian randomization analyses.", "authors": [{"family": "Zheng", "given": "Rui", "initials": "R"}, {"family": "Delgado-Velandia", "given": "Mario", "initials": "M"}, {"family": "\u00c4rnl\u00f6v", "given": "Johan", "initials": "J"}, {"family": "Sundstr\u00f6m", "given": "Johan", "initials": "J"}, {"family": "Engstr\u00f6m", "given": "Gunnar", "initials": "G"}, {"family": "Smith", "given": "J Gustav", "initials": "JG"}, {"family": "Dekkers", "given": "Koen F", "initials": "KF"}, {"family": "Lundmark", "given": "Per", "initials": "P"}, {"family": "Fall", "given": "Tove", "initials": "T"}, {"family": "Lind", "given": "Lars", "initials": "L"}], "type": "journal article", "published": "2026-07-00", "journal": {"title": "Metabolism", "issn": "1532-8600", "volume": "180", "pages": "156602", "issn-l": "0026-0495"}, "abstract": "The basis for protein synthesis is the genetic code. Many of these proteins will affect intermediary metabolites by acting as enzymes, hormones, or by other actions. The aim of the present study was to assess the relationships of a large number of proteins with endogenous metabolites.\n\nPlasma protein levels were measured by the proximity extension assay (PEA) and metabolites by mass spectrometry. Cross-sectional relationships of 242 proteins and 790 metabolites were evaluated in the EpiHealth and POEM studies using a discovery/validation approach. Genetic instruments identified in UK Biobank for protein levels (n = 1621) and genetics for metabolite levels (n = 777) in SCAPIS and EpiHealth were employed for Mendelian randomization (MR) analysis regarding putative causal associations.\n\nIn the observational analyses, 20% of the evaluated pairwise protein-metabolite associations were found significant in both the discovery and validation samples. We could however only find support for causal effects in the MR analysis for <0.1% of the pairwise associations, representing 326 unique proteins. The R2 for the relationship between the MR and observational estimates was only 0.05. 37 protein-metabolite relationships that were significant in a congruent fashion in both the observational and MR analyses were identified. A searchable online protein vs metabolite atlas was created for the scientific community to use these results. We also give some examples where metabolites were used to enhance protein findings in cardiovascular epidemiological research.\n\nThis study provides a comprehensive assessment of a large number of protein- metabolite relationships using both observational and MR analyses, highlighting how these results could be used to enhance clinical research.", "doi": "10.1016/j.metabol.2026.156602", "pmid": "41962653", "labels": {"NGI SNP genotyping": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pii", "key": "S0026-0495(26)00112-5"}], "notes": [], "created": "2026-06-01T08:45:40.108Z", "modified": "2026-06-01T08:45:40.112Z"}, {"entity": "publication", "iuid": "89ccc379a277435ca0979bc67c55ad04", "links": {"self": {"href": "https://publications.scilifelab.se/publication/89ccc379a277435ca0979bc67c55ad04.json"}, "display": {"href": "https://publications.scilifelab.se/publication/89ccc379a277435ca0979bc67c55ad04"}}, "title": "Environmental factors rather than genetics likely drive vitamin D deficiency in idiopathic scoliosis.", "authors": [{"family": "Georgopoulos", "given": "Ioannis", "initials": "I"}, {"family": "Cheng", "given": "Tian", "initials": "T"}, {"family": "Fell", "given": "Daniel", "initials": "D"}, {"family": "Simony", "given": "Ane", "initials": "A"}, {"family": "Andersen", "given": "Mikkel O", "initials": "MO"}, {"family": "Einarsdottir", "given": "El\u00edsabet", "initials": "E"}, {"family": "Karlsson", "given": "Magnus K", "initials": "MK"}, {"family": "Bergstr\u00f6m", "given": "Ingrid", "initials": "I"}, {"family": "Diarbakerli", "given": "Elias", "initials": "E"}, {"family": "Schizas", "given": "Nikos", "initials": "N"}, {"family": "Gerdhem", "given": "Paul", "initials": "P"}], "type": "journal article", "published": "2026-04-23", "journal": {"title": "Spine J", "issn": "1878-1632", "issn-l": "1529-9430"}, "abstract": "Low vitamin D levels in individuals with idiopathic scoliosis (IS) have been reported and suggested as a potential contributor to IS. Bone density has also been shown to be lower in individuals with IS.\n\nTo investigate serum levels of vitamin D, parathyroid hormone (PTH), markers of bone metabolism, and the genetic variation associated with vitamin D levels and bone density in individuals with IS and healthy controls.\n\nCase-control study combining Scandinavian serum cohorts and genetic cohorts.\n\nSerum analyses: 174 individuals with IS and 153 nonscoliotic controls.\n\nA total of 1,394 individuals with IS and 11,108 controls.\n\nSerum 25-hydroxyvitamin D (25OHD), PTH, C-terminal telopeptide (CTX), osteocalcin, calcium, phosphate, creatinine, albumin, alkaline phosphatase, and leptin. Polygenic risk scores (PRS) for 25OHD and bone mineral density (BMD).\n\nSerum samples were analyzed using validated clinical laboratory methods. PRS for 25OHD and BMD were calculated based on previous literature. Statistical analyses were performed using Mann-Whitney U tests, logistic, and linear regression. Mendelian randomization was analyzed using logistic regression and the inverse-variance weighted method.\n\nIn the serum cohort, median 25OHD levels were 54.4 nmol/L in individuals with IS and 67.0 nmol/L in controls. Corresponding PTH levels were 4.0 and 3.2 pmol/L. No statistically significant differences were found in CTX, osteocalcin, alkaline phosphatase, or leptin. PRS for 25OHD was associated with serum 25OHD levels. PRS in individuals with IS and controls were nonsignificant for 25OHD, BMD femoral neck, and BMD lumbar spine. A tendency for lower values for estimated BMD heel was seen in individuals with scoliosis compared to controls.\n\nOur findings indicate altered regulation of the vitamin D-PTH axis in IS, likely driven by environmental rather than genetic factors. Bone turnover markers were comparable between groups; no clear genetically mediated BMD differences could be observed.", "doi": "10.1016/j.spinee.2026.04.026", "pmid": "42034124", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI SNP genotyping": "Service"}, "xrefs": [{"db": "pii", "key": "S1529-9430(26)00132-4"}], "notes": [], "created": "2026-05-27T11:40:51.749Z", "modified": "2026-05-27T11:40:51.753Z"}, {"entity": "publication", "iuid": "03ccd31f0e5144dc8037a73d69d8ba57", "links": {"self": {"href": "https://publications.scilifelab.se/publication/03ccd31f0e5144dc8037a73d69d8ba57.json"}, "display": {"href": "https://publications.scilifelab.se/publication/03ccd31f0e5144dc8037a73d69d8ba57"}}, "title": "Genetic and environmental influences on data missingness in developmental cognitive neuroscience.", "authors": [{"family": "Bussu", "given": "G", "initials": "G", "orcid": "0000-0002-6071-3964", "researcher": {"href": "https://publications.scilifelab.se/researcher/c203efb6eec84df2abe07ff811cc9309.json"}}, {"family": "Portugal", "given": "A M", "initials": "AM", "orcid": "0000-0002-3627-0753", "researcher": {"href": "https://publications.scilifelab.se/researcher/1a54163213cc46f88ba1a6d31ac9dc66.json"}}, {"family": "Viktorsson", "given": "C", "initials": "C", "orcid": "0000-0003-2727-2957", "researcher": {"href": "https://publications.scilifelab.se/researcher/465e2969410c4109aaa466735d26002b.json"}}, {"family": "Hardiansyah", "given": "I", "initials": "I"}, {"family": "Falck-Ytter", "given": "T", "initials": "T", "orcid": "0000-0001-9714-0197", "researcher": {"href": "https://publications.scilifelab.se/researcher/ead33894d8054f2291e0be7cbb47e015.json"}}], "type": "journal article", "published": "2026-04-22", "journal": {"title": "Commun Psychol", "issn": "2731-9121", "volume": "4", "issue": "1", "issn-l": null}, "abstract": "Missing data are common in social and clinical sciences and understanding the causes and patterns of missing data is important for selecting analysis approach and for the interpretation of the remaining data. Yet, knowledge about the factors influencing data loss is limited. Here, we assessed the contribution of genes and environments to data missingness across three experiments of infant brain and behavioural development. The sample consisted of 594 infant twins (330 monozygotic, 152 female, 178 male infants; 264 dizygotic, 132 female, 132 male infants) who were assessed with electroencephalography (EEG), pupillometry, and gaze tracking technologies at 5 months of age. Substantial familial factors (additive genetics and/or shared environment) for data missingness were found across all experiments. The amount of missing data showed only a low correlation across the experiments, suggesting a high degree of specificity in the factors contributing to missingness. The results underscore the need to adopt and improve procedural and analytical strategies that minimise data loss and its negative impacts on study conclusions.", "doi": "10.1038/s44271-026-00457-0", "pmid": "42020721", "labels": {"NGI SNP genotyping": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC13102918"}, {"db": "pii", "key": "10.1038/s44271-026-00457-0"}], "notes": [], "created": "2026-06-01T08:45:47.729Z", "modified": "2026-06-01T08:45:47.914Z"}, {"entity": "publication", "iuid": "51ab6bef0c294812a1af87272c18bba2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/51ab6bef0c294812a1af87272c18bba2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/51ab6bef0c294812a1af87272c18bba2"}}, "title": "Genetic predisposition to coffee consumption and the association with the early risk of atherosclerosis.", "authors": [{"family": "Qiao", "given": "Xiangyu", "initials": "X"}, {"family": "Toma", "given": "Vanessa William", "initials": "VW"}, {"family": "Wang", "given": "Jing", "initials": "J"}, {"family": "Herraiz-Adillo", "given": "\u00c1ngel", "initials": "\u00c1"}, {"family": "S\u00f6derholm", "given": "Simon", "initials": "S"}, {"family": "Berglind", "given": "Daniel", "initials": "D"}, {"family": "Calling", "given": "Susanna", "initials": "S"}, {"family": "Daka", "given": "Bledar", "initials": "B"}, {"family": "Martinell", "given": "Mats", "initials": "M"}, {"family": "Bergman", "given": "Frida", "initials": "F"}, {"family": "Henriksson", "given": "Pontus", "initials": "P"}, {"family": "Ghafouri", "given": "Bijar", "initials": "B"}, {"family": "Ulander", "given": "Martin", "initials": "M"}, {"family": "\u00d6stgren", "given": "Carl Johan", "initials": "CJ"}, {"family": "Cant\u00f9", "given": "Claudio", "initials": "C"}, {"family": "Zhong", "given": "Wen", "initials": "W"}, {"family": "Iredahl", "given": "Fredrik", "initials": "F"}], "type": "journal article", "published": "2026-03-22", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "16", "issue": "1", "issn-l": "2045-2322"}, "abstract": "The cardiovascular effects of coffee consumption remain debated, particularly regarding early-stage subclinical atherosclerosis. This study investigated the association between coffee intake, genetic predisposition, and the risk of subclinical coronary and carotid atherosclerosis in 24,835 participants from the Swedish CArdioPulmonary bioImage Study (SCAPIS). Coffee intake was assessed via self-reported questionnaires. Atherosclerosis was assessed via segment involvement score (SIS), coronary artery calcium score (CACS) and carotid plaque. Observational analysis showed no significant association between coffee consumption and SIS, CACS, or carotid plaques. However, both one-sample and two-sample (SCAPIS and UK Biobank) Mendelian randomization (MR) analyses showed an association between genetic predisposition to higher coffee consumption and increased SIS. Stratification analyses further explored differences in genetic associations across varying coffee consumption levels. Among individuals consuming coffee more than twice daily, two coffee consumption-associated single nucleotide polymorphisms (SNPs) in AHR and CYP1A1/CYP1A2 were correlated with SIS. Integrative metabolomics and proteomics analyses identified lipid-related metabolites (triglycerides, phospholipids, free cholesterol) and inflammation-related proteins (DLK1, IL1RL2, CCL17) associated with the genetic proxy of coffee consumption. These findings suggest that genetically influenced coffee consumption may be associated with coronary atherosclerosis risk in frequent coffee drinkers, although the underlying biological basis remains to be clarified.", "doi": "10.1038/s41598-026-44122-2", "pmid": "41865070", "labels": {"NGI SNP genotyping": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC13009213"}, {"db": "pii", "key": "10.1038/s41598-026-44122-2"}], "notes": [], "created": "2026-06-01T08:45:44.894Z", "modified": "2026-06-01T08:45:44.897Z"}, {"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": "b7284178e7704139b443a0f9e1f75614", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b7284178e7704139b443a0f9e1f75614.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b7284178e7704139b443a0f9e1f75614"}}, "title": "Homologous recombination deficiency in primary ER-positive and HER2-negative breast cancer.", "authors": [{"family": "Davies", "given": "Helen R", "initials": "HR", "orcid": "0000-0001-6381-3664", "researcher": {"href": "https://publications.scilifelab.se/researcher/e02b6738c9e140858456e24cef5d6b42.json"}}, {"family": "Black", "given": "Daniella", "initials": "D"}, {"family": "Kvist", "given": "Anders", "initials": "A", "orcid": "0000-0002-1358-0695", "researcher": {"href": "https://publications.scilifelab.se/researcher/3e6b39bdc00c442f94caed782772a278.json"}}, {"family": "Sigurj\u00f3nsd\u00f3ttir", "given": "Krist\u00edn", "initials": "K"}, {"family": "Bosch", "given": "Ana", "initials": "A"}, {"family": "Bowden", "given": "Ramsay", "initials": "R", "orcid": "0000-0003-1138-4452", "researcher": {"href": "https://publications.scilifelab.se/researcher/0b6effa9663145dabd83b3ced199385c.json"}}, {"family": "Memari", "given": "Yasin", "initials": "Y"}, {"family": "Chen", "given": "Ziqian", "initials": "Z"}, {"family": "Rinaldi", "given": "Giuseppe", "initials": "G", "orcid": "0000-0002-5650-6049", "researcher": {"href": "https://publications.scilifelab.se/researcher/da7f30b3dfa5489ba61afa7840bc34c7.json"}}, {"family": "Rosengren", "given": "Frida", "initials": "F"}, {"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": "Hohmann", "given": "Lennart", "initials": "L", "orcid": "0000-0002-0281-7140", "researcher": {"href": "https://publications.scilifelab.se/researcher/b605a3b893a24a238b5bb6eddd27b672.json"}}, {"family": "Nordborg", "given": "Nicklas", "initials": "N"}, {"family": "H\u00e4kkinen", "given": "Jari", "initials": "J", "orcid": "0000-0002-8466-9179", "researcher": {"href": "https://publications.scilifelab.se/researcher/9b8605b9a7c74b20986146f020cf4b8f.json"}}, {"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": "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": "2026-02-16", "journal": {"title": "Commun Med (Lond)", "issn": "2730-664X", "volume": "6", "issue": "1", "pages": "118", "issn-l": null}, "abstract": "Homologous recombination deficiency (HRD) originating from inactivation of genes like BRCA1/BRCA2 is a targetable abnormality common in triple-negative breast cancer (TNBC). In estrogen-receptor (ER)-positive HER2-negative (ERpHER2n) breast cancer (BC), HRD prevalence and clinical impact are unclear.\n\nWe analyzed 502 ERpHER2n tumors from patients recruited via the population-representative Swedish SCAN-B study by whole genome sequencing (WGS), defining mutational signatures-based HRD, as well as matched transcriptional, DNA methylation, clinicopathological, adjuvant treatment, and outcome data.\n\nWe show that HRD is much less frequent in ERpHER2n BC (8.4%) compared to TNBC, though induced by similar genetic/epigenetic mechanisms acting on mainly BRCA1/BRCA2/RAD51C/PALB2 together, providing a plausible HR-inactivation mechanism for 71.4% of HRD tumors. Our modelled estimate of HRD in Western European/Nordic BC is ~10-13%. HRD tumors were observed across all PAM50 gene expression subtypes with the exception of Luminal A tumors ( < 1%) and did not exhibit a unique, defining transcriptional or DNA methylation profile. While HRD status was not statistically associated with differences in patient outcome for patients treated with combined chemotherapy and endocrine therapy, a nonsignificant trend of poorer outcome for patients with HRD tumors was observed for patients treated with adjuvant endocrine therapy only.\n\nERpHER2n HRD tumors show features of aggressive disease, but do not display a distinct transcriptional or DNA methylation profile that clearly differentiates them from HR-proficient tumors. Though numbers are limited, we present early evidence that HRD stratification by WGS could impact therapeutic strategies, as HRD BCs trended to poorer outcomes when not treated with chemotherapy.", "doi": "10.1038/s43856-026-01385-0", "pmid": "41699108", "labels": {"NGI SNP genotyping": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12909304"}, {"db": "pii", "key": "10.1038/s43856-026-01385-0"}], "notes": [], "created": "2026-06-01T11:12:58.568Z", "modified": "2026-06-01T11:12:58.707Z"}, {"entity": "publication", "iuid": "43f86786cbb24b618ae7f2e4aff2b849", "links": {"self": {"href": "https://publications.scilifelab.se/publication/43f86786cbb24b618ae7f2e4aff2b849.json"}, "display": {"href": "https://publications.scilifelab.se/publication/43f86786cbb24b618ae7f2e4aff2b849"}}, "title": "Multiomics assessment of lung adenocarcinoma subtypes defined through tumor purity-adjusted DNA methylation.", "authors": [{"family": "Nacer", "given": "Deborah F", "initials": "DF"}, {"family": "Arbajian", "given": "Elsa", "initials": "E"}, {"family": "Veerla", "given": "Srinivas", "initials": "S"}, {"family": "Aine", "given": "Mattias", "initials": "M"}, {"family": "J\u00f6nsson", "given": "Mats", "initials": "M"}, {"family": "Rosengren", "given": "Frida", "initials": "F"}, {"family": "Karlsson", "given": "Anna", "initials": "A"}, {"family": "Salomonsson", "given": "Annette", "initials": "A"}, {"family": "Isaksson", "given": "Sofi", "initials": "S"}, {"family": "Planck", "given": "Maria", "initials": "M"}, {"family": "Staaf", "given": "Johan", "initials": "J"}], "type": "journal article", "published": "2026-02-14", "journal": {"title": "Genome Med", "issn": "1756-994X", "volume": "18", "issue": "1", "issn-l": "1756-994X"}, "abstract": "Molecular subtypes of lung adenocarcinoma (LUAD) with varying prognosis and characteristics have been proposed based on one or two-dimensional studies but are not yet implemented into clinical routine. Epigenetic modifications in cancer cells are independent of sequence variants, directly linked to gene and genome regulation, and thus provide important information to guide subclassification efforts.\n\nWe performed in-depth epigenomic profiling of 95 primary LUAD samples from a Swedish discovery cohort with comprehensive clinicopathological, epigenomic, genomic, transcriptomic, proteomic, and metabolomic data. Additionally, we estimated pure tumor cell methylomes using a computational approach. We subdivided the discovery cohort into four epigenetic subtypes, the epitypes, reflecting distinct tumor cell methylation states. Resulting epitypes were contrasted based on clinicopathological and molecular features, and our main findings were validated in two additional primary tumor cohorts totaling over 700 samples.\n\nOf the four DNA methylation epitypes, M1-M4, M1 and M4 were associated with the previously proposed mRNA subtypes Terminal Respiratory Unit and Proximal Proliferative, respectively. Epitypes M2 and M3 showed similar mRNA/protein subtype composition but differed with respect to e.g., higher expression of the LUAD histology-associated NAPSA/surfactant metabolism expression metagene in M3. Genes included in this metagene showed lower DNA methylation in M3, counter to a global tendency towards promoter hypermethylation in this epitype. To further delineate tumor intrinsic links between the epigenomic and expression phenotypes, 62 LUAD cell lines classified into the four epitypes were investigated and recapitulated several characteristics from the tumor epitypes, such as methylation and expression pattens of NAPSA/surfactant genes, highlighting epigenetic states as likely drivers or maintainers of broad tumor phenotypes and differentiation states.\n\nDissecting LUAD based on combined biological characteristics using multiomics data has deepened our understanding of the heterogeneity in this complex disease and the mechanisms underlying phenotype formation and maintenance. There remains a critical need for large, publicly accessible, well-annotated multiomic LUAD cohorts to support rigorous subtype discovery and validation, particularly those linked to targeted therapy trial outcomes.\n\nThe online version contains supplementary material available at 10.1186/s13073-026-01609-x.", "doi": "10.1186/s13073-026-01609-x", "pmid": "41691315", "labels": {"NGI SNP genotyping": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12927254"}, {"db": "pii", "key": "10.1186/s13073-026-01609-x"}], "notes": [], "created": "2026-06-01T11:12:56.465Z", "modified": "2026-06-01T11:12:56.469Z"}, {"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": "62aeb5e95c7f40e5b971a1dd1f521f6e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/62aeb5e95c7f40e5b971a1dd1f521f6e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/62aeb5e95c7f40e5b971a1dd1f521f6e"}}, "title": "Genetic risk factors and clinical manifestations of systemic lupus erythematosus: Large-scale analysis of genetic predisposition and disease subtypes.", "authors": [{"family": "Reid", "given": "Sarah", "initials": "S"}, {"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"}, {"family": "Sayadi", "given": "Ahmed", "initials": "A"}, {"family": "Frodlund", "given": "Martina", "initials": "M"}, {"family": "Lerang", "given": "Karoline", "initials": "K"}, {"family": "Gunnarsson", "given": "Iva", "initials": "I"}, {"family": "J\u00f6nsen", "given": "Andreas", "initials": "A"}, {"family": "Syv\u00e4nen", "given": "Ann-Christine", "initials": "AC"}, {"family": "Molberg", "given": "\u00d8yvind", "initials": "\u00d8"}, {"family": "Rantap\u00e4\u00e4-Dahlqvist", "given": "Solbritt", "initials": "S", "orcid": "0000-0001-8259-3863", "researcher": {"href": "https://publications.scilifelab.se/researcher/dfca4bfdcf3946fda64397d3b7debc59.json"}}, {"family": "Rudin", "given": "Anna", "initials": "A", "orcid": "0000-0002-4137-1276", "researcher": {"href": "https://publications.scilifelab.se/researcher/fa2b87964bc0472b88fa4267ee23c483.json"}}, {"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": "Bengtsson", "given": "Anders A", "initials": "AA"}, {"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": "2026-01-00", "journal": {"title": "J. Intern. Med.", "issn": "1365-2796", "volume": "299", "issue": "1", "pages": "95-108", "issn-l": "0954-6820"}, "abstract": "Systemic lupus erythematosus (SLE) is an autoimmune disease with a heterogenous clinical picture. This study aimed to link genetic SLE predisposition with relevant clinical manifestations.\n\nDatasets best corresponding to the 11 American College of Rheumatology 1982 (ACR-82) classification criteria for SLE in a large, public database (FinnGen consortium, >218,000 individuals) were identified. Mendelian randomization analysis was conducted to evaluate the effect of a high genetic SLE predisposition on each manifestation. Next, validation was conducted in a clinical SLE cohort comprising 1487 genotyped Scandinavian patients with detailed clinical data. Based on the public datasets, genetic risk scores (GRSs) for each relevant manifestation were constructed for each patient. Associations between each GRS and the corresponding ACR-82 criterion were evaluated using logistic regression.\n\nIn the FinnGen biobank, the cumulative effect of the 57 SLE risk SNPs was associated with an increased risk of rosacea, OR 1.09 (1.03-1.16), polyarthropathies, OR 1.10 (1.06-1.14), pleural effusions, OR 1.09 (1.04-1.14), and hemolytic anemia, OR 1.32 (1.10-1.58). In the clinical cohort, 5 of the 11 GRSs generated from the public datasets were associated with their corresponding ACR-82 criterion: arthritis, OR 1.15 (1.02-1.31), renal disorder, OR 1.15 (1.04-1.29), neurologic disorder, OR 1.24 (1.04-1.47), hematologic disorder, OR 1.12 (1.00-1.24), and immunologic disorder, OR 1.37 (1.22-1.56).\n\nThe findings demonstrate that known SLE risk gene variants play a role in the development of at least half of the ACR-82 criteria for SLE, indicating a future possibility of using genetics to predict a variety of disease sub-phenotypes in SLE.", "doi": "10.1111/joim.70040", "pmid": "41200769", "labels": {"NGI SNP genotyping": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12678220"}], "notes": [], "created": "2026-06-01T08:45:42.226Z", "modified": "2026-06-01T08:45:42.343Z"}, {"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": "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": "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": "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": "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": "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": "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": "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": "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": "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": "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": "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": "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": "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": "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": "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": "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": "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": "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": "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": "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": "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": "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": "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": "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": "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": "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": "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": "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": "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": "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": "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": "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": "7e532fb85545426880d8fb6fec942f51", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7e532fb85545426880d8fb6fec942f51.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7e532fb85545426880d8fb6fec942f51"}}, "title": "Epigenome-wide analysis of frailty: Results from two European twin cohorts.", "authors": [{"family": "Mak", "given": "Jonathan K L", "initials": "JKL", "orcid": "0000-0003-4454-8580", "researcher": {"href": "https://publications.scilifelab.se/researcher/4994e82ef4784f06aff8017a9cf9ad1c.json"}}, {"family": "Skovgaard", "given": "Asmus Cosmos", "initials": "AC"}, {"family": "Nygaard", "given": "Marianne", "initials": "M"}, {"family": "Kananen", "given": "Laura", "initials": "L", "orcid": "0000-0003-3742-8927", "researcher": {"href": "https://publications.scilifelab.se/researcher/b95c9eeb27214482bbbca978d69d79c7.json"}}, {"family": "Reynolds", "given": "Chandra A", "initials": "CA"}, {"family": "Wang", "given": "Yunzhang", "initials": "Y"}, {"family": "Kuja-Halkola", "given": "Ralf", "initials": "R"}, {"family": "Karlsson", "given": "Ida K", "initials": "IK", "orcid": "0000-0003-3605-7829", "researcher": {"href": "https://publications.scilifelab.se/researcher/b2c87ada82ae43df9753a891305ddb40.json"}}, {"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": "Soerensen", "given": "Mette", "initials": "M"}, {"family": "Jylh\u00e4v\u00e4", "given": "Juulia", "initials": "J"}], "type": "journal article", "published": "2024-02-27", "journal": {"title": "Aging Cell", "issn": "1474-9726", "pages": "e14135", "issn-l": "1474-9718"}, "abstract": "Epigenetics plays an important role in the aging process, but it is unclear whether epigenetic factors also influence frailty, an age-related state of physiological decline. In this study, we performed a meta-analysis of epigenome-wide association studies in four samples drawn from the Swedish Adoption/Twin Study of Aging (SATSA) and the Longitudinal Study of Aging Danish Twins (LSADT) to explore the association between DNA methylation and frailty. Frailty was defined using the frailty index (FI), and DNA methylation levels were measured in whole blood using Illumina's Infinium HumanMethylation450K and MethylationEPIC arrays. In the meta-analysis consisting of a total of 829 participants, we identified 589 CpG sites that were statistically significantly associated with either the continuous or categorical FI (false discovery rate <0.05). Many of these CpGs have previously been associated with age and age-related diseases. The identified sites were also largely directionally consistent in a longitudinal analysis using mixed-effects models in SATSA, where the participants were followed up to a maximum of 20 years. Moreover, we identified three differentially methylated regions within the MGRN1, MIR596, and TAPBP genes that have been linked to neuronal aging, tumor growth, and immune functions. Furthermore, our meta-analysis results replicated 34 of the 77 previously reported frailty-associated CpGs at p < 0.05. In conclusion, our findings demonstrate robust associations between frailty and DNA methylation levels in 589 novel CpGs, previously unidentified for frailty, and strengthen the role of neuronal/brain pathways in frailty.", "doi": "10.1111/acel.14135", "pmid": "38414347", "labels": {"NGI Short read": "Service", "NGI SNP genotyping": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [], "notes": [], "created": "2024-03-21T08:58:19.904Z", "modified": "2024-03-21T08:58:20.068Z"}, {"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": "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": "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": "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": "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": "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": "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": "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": "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": "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": "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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"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": "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": "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": "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": "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": "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": "https://publications.scilifelab.se/researcher/141e2930df474ea29c7db131171e95d9.json"}}, {"family": "Clausen", "given": "Tine D", "initials": "TD"}, {"family": "Damm", "given": "Peter", "initials": "P", "orcid": "0000-0002-2067-5246", "researcher": {"href": "https://publications.scilifelab.se/researcher/503b981d3bd942bfa1bff62b55d842b6.json"}}, {"family": "Delgado", "given": "Graciela E", "initials": "GE"}, {"family": "de Mello", "given": "Vanessa D", "initials": "VD"}, {"family": "Dupuis", "given": "Jos\u00e9e", "initials": "J", "orcid": "0000-0003-2871-3603", "researcher": {"href": "https://publications.scilifelab.se/researcher/c9edfafda7364890866115f5343a9583.json"}}, {"family": "Dwivedi", "given": "Om P", "initials": "OP", "orcid": "0000-0001-8670-7717", "researcher": {"href": "https://publications.scilifelab.se/researcher/c93f2a3e88d94bf1b569e0c7adf7f417.json"}}, {"family": "Erdos", "given": "Michael R", "initials": "MR", "orcid": "0000-0002-6603-1833", "researcher": {"href": "https://publications.scilifelab.se/researcher/8da7ddefc23c4a008a0bbe625fab8475.json"}}, {"family": "Fernandes Silva", "given": "Lilian", "initials": "L", "orcid": "0000-0003-0225-842X", "researcher": {"href": "https://publications.scilifelab.se/researcher/cfb1cff42d9e47acafc02cc9c7d0cd69.json"}}, {"family": "Frayling", "given": "Timothy M", "initials": "TM", "orcid": "0000-0001-8362-2603", "researcher": {"href": "https://publications.scilifelab.se/researcher/9722f7f6f1d546ebb8deaddfc21cdb10.json"}}, {"family": "Gieger", "given": "Christian", "initials": "C", "orcid": "0000-0001-6986-9554", "researcher": {"href": "https://publications.scilifelab.se/researcher/86f44e76061c403fadd97b768e2a7e62.json"}}, {"family": "Goodarzi", "given": "Mark O", "initials": "MO", "orcid": "0000-0001-6364-5103", "researcher": {"href": "https://publications.scilifelab.se/researcher/2887097dc8ca4c6e8c22ca7fd6a92b0d.json"}}, {"family": "Guo", "given": "Xiuqing", "initials": "X", "orcid": "0000-0002-5264-5068", "researcher": {"href": "https://publications.scilifelab.se/researcher/a3b59a379da5424ba5c5072e40eb63f5.json"}}, {"family": "Gustafsson", "given": "Stefan", "initials": "S", "orcid": "0000-0001-5894-0351", "researcher": {"href": "https://publications.scilifelab.se/researcher/9a0552f8a6514baa9bdb6809148aaddc.json"}}, {"family": "Hakaste", "given": "Liisa", "initials": "L"}, {"family": "Hammar", "given": "Ulf", "initials": "U"}, {"family": "Hatem", "given": "Gad", "initials": "G"}, {"family": "Herrmann", "given": "Sandra", "initials": "S"}, {"family": "H\u00f8jlund", "given": "Kurt", "initials": "K"}, {"family": "Horn", "given": "Katrin", "initials": "K", "orcid": "0000-0002-5307-6936", "researcher": {"href": "https://publications.scilifelab.se/researcher/8f6e8158e9a3474584921abcff96cf11.json"}}, {"family": "Hsueh", "given": "Willa A", "initials": "WA"}, {"family": "Hung", "given": "Yi-Jen", "initials": "YJ"}, {"family": "Hwu", "given": "Chii-Min", "initials": "CM", "orcid": "0000-0002-8209-9627", "researcher": {"href": "https://publications.scilifelab.se/researcher/8cf87a1ff22b4723b31310c84d402b35.json"}}, {"family": "Jonsson", "given": "Anna", "initials": "A"}, {"family": "K\u00e5rhus", "given": "Line L", "initials": "LL"}, {"family": "Kleber", "given": "Marcus E", "initials": "ME", "orcid": "0000-0003-0663-7275", "researcher": {"href": "https://publications.scilifelab.se/researcher/a51175112cfb4721b8c9fbfdc71c4307.json"}}, {"family": "Kovacs", "given": "Peter", "initials": "P", "orcid": "0000-0002-0290-5423", "researcher": {"href": "https://publications.scilifelab.se/researcher/d37e874ec6804b20a1264a86c9b62eab.json"}}, {"family": "Lakka", "given": "Timo A", "initials": "TA", "orcid": "0000-0002-9199-2871", "researcher": {"href": "https://publications.scilifelab.se/researcher/bf0d612e609d4b4caeab4dfd8fa503e6.json"}}, {"family": "Lauzon", "given": "Marie", "initials": "M"}, {"family": "Lee", "given": "I-Te", "initials": "IT"}, {"family": "Lindgren", "given": "Cecilia M", "initials": "CM"}, {"family": "Lindstr\u00f6m", "given": "Jaana", "initials": "J"}, {"family": "Linneberg", "given": "Allan", "initials": "A", "orcid": "0000-0002-0994-0184", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a314ef72d874c98afce22cd6454ddb8.json"}}, {"family": "Liu", "given": "Ching-Ti", "initials": "CT", "orcid": "0000-0002-0703-0742", "researcher": {"href": "https://publications.scilifelab.se/researcher/c4c4c9c0dd0f49f0a60386ea7052fba2.json"}}, {"family": "Luan", "given": "Jian'an", "initials": "J", "orcid": "0000-0003-3137-6337", "researcher": {"href": "https://publications.scilifelab.se/researcher/7f0ea409f1a2462dbb1b266db8fcc33a.json"}}, {"family": "Aly", "given": "Dina Mansour", "initials": "DM"}, {"family": "Mathiesen", "given": "Elisabeth", "initials": "E"}, {"family": "Moissl", "given": "Angela P", "initials": "AP", "orcid": "0000-0003-0302-2136", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ee94245508c4fe8a777cfcb313be625.json"}}, {"family": "Morris", "given": "Andrew P", "initials": "AP", "orcid": "0000-0002-6805-6014", "researcher": {"href": "https://publications.scilifelab.se/researcher/991fd686a4a040a1a197c1f32d5b731b.json"}}, {"family": "Narisu", "given": "Narisu", "initials": "N", "orcid": "0000-0002-8483-1156", "researcher": {"href": "https://publications.scilifelab.se/researcher/62005ec80b624bf0bd3aeed13fd79542.json"}}, {"family": "Perakakis", "given": "Nikolaos", "initials": "N"}, {"family": "Peters", "given": "Annette", "initials": "A", "orcid": "0000-0001-6645-0985", "researcher": {"href": "https://publications.scilifelab.se/researcher/05465e52a0f6412e81752d2249af30de.json"}}, {"family": "Prasad", "given": "Rashmi B", "initials": "RB", "orcid": "0000-0002-4400-6741", "researcher": {"href": "https://publications.scilifelab.se/researcher/313aa9ded0c946c3b986e856a62ae85a.json"}}, {"family": "Rodionov", "given": "Roman N", "initials": "RN"}, {"family": "Roll", "given": "Kathryn", "initials": "K"}, {"family": "Rundsten", "given": "Carsten F", "initials": "CF"}, {"family": "Sarnowski", "given": "Chlo\u00e9", "initials": "C", "orcid": "0000-0002-6090-7099", "researcher": {"href": "https://publications.scilifelab.se/researcher/f9e9101648db4d398a01ddf83d8e9132.json"}}, {"family": "Savonen", "given": "Kai", "initials": "K"}, {"family": "Scholz", "given": "Markus", "initials": "M", "orcid": "0000-0002-4059-1779", "researcher": {"href": "https://publications.scilifelab.se/researcher/53d7b0e2dcdb4361b54016cb1550c5fe.json"}}, {"family": "Sharma", "given": "Sapna", "initials": "S"}, {"family": "Stinson", "given": "Sara E", "initials": "SE"}, {"family": "Suleman", "given": "Sufyan", "initials": "S"}, {"family": "Tan", "given": "Jingyi", "initials": "J"}, {"family": "Taylor", "given": "Kent D", "initials": "KD"}, {"family": "Uusitupa", "given": "Matti", "initials": "M"}, {"family": "Vistisen", "given": "Dorte", "initials": "D"}, {"family": "Witte", "given": "Daniel R", "initials": "DR"}, {"family": "Walther", "given": "Romy", "initials": "R"}, {"family": "Wu", "given": "Peitao", "initials": "P"}, {"family": "Xiang", "given": "Anny H", "initials": "AH"}, {"family": "Zethelius", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Meta-Analysis of Glucose and Insulin-related Traits Consortium (MAGIC)", "given": "", "initials": ""}, {"family": "Ahlqvist", "given": "Emma", "initials": "E", "orcid": "0000-0002-6513-2384", "researcher": {"href": "https://publications.scilifelab.se/researcher/415b737a7da04f13ab0fd104c375b097.json"}}, {"family": "Bergman", "given": "Richard N", "initials": "RN"}, {"family": "Chen", "given": "Yii-Der Ida", "initials": "YI"}, {"family": "Collins", "given": "Francis S", "initials": "FS", "orcid": "0000-0002-1023-7410", "researcher": {"href": "https://publications.scilifelab.se/researcher/10628a7a84cb4c7dbd6c161a8723ccbb.json"}}, {"family": "Fall", "given": "Tove", "initials": "T", "orcid": "0000-0003-2071-5866", "researcher": {"href": "https://publications.scilifelab.se/researcher/4ed3f066719f43b291743a8bdaf3d2a0.json"}}, {"family": "Florez", "given": "Jose C", "initials": "JC"}, {"family": "Fritsche", "given": "Andreas", "initials": "A"}, {"family": "Grallert", "given": "Harald", "initials": "H"}, {"family": "Groop", "given": "Leif", "initials": "L", "orcid": "0000-0002-0187-3263", "researcher": {"href": "https://publications.scilifelab.se/researcher/8e1c35ae04cd4e9e9525fbc844d15e14.json"}}, {"family": "Hansen", "given": "Torben", "initials": "T", "orcid": "0000-0001-8748-3831", "researcher": {"href": "https://publications.scilifelab.se/researcher/da403496660346079fc41975cae418d9.json"}}, {"family": "Koistinen", "given": "Heikki A", "initials": "HA", "orcid": "0000-0001-7870-070X", "researcher": {"href": "https://publications.scilifelab.se/researcher/c57dc904034d47a8b43d6cae1b1bd6f4.json"}}, {"family": "Komulainen", "given": "Pirjo", "initials": "P"}, {"family": "Laakso", "given": "Markku", "initials": "M", "orcid": "0000-0002-3394-7749", "researcher": {"href": "https://publications.scilifelab.se/researcher/13d8518be25141a296d7f2df5cccb4ee.json"}}, {"family": "Lind", "given": "Lars", "initials": "L"}, {"family": "Loeffler", "given": "Markus", "initials": "M"}, {"family": "M\u00e4rz", "given": "Winfried", "initials": "W"}, {"family": "Meigs", "given": "James B", "initials": "JB"}, {"family": "Raffel", "given": "Leslie J", "initials": "LJ"}, {"family": "Rauramaa", "given": "Rainer", "initials": "R"}, {"family": "Rotter", "given": "Jerome I", "initials": "JI"}, {"family": "Schwarz", "given": "Peter E H", "initials": "PEH", "orcid": "0000-0001-6317-7880", "researcher": {"href": "https://publications.scilifelab.se/researcher/6181d1a3da134b198d0bfd2fcd714561.json"}}, {"family": "Stumvoll", "given": "Michael", "initials": "M", "orcid": "0000-0001-6225-8240", "researcher": {"href": "https://publications.scilifelab.se/researcher/35306e7a97d1401e8d6953223dc0e949.json"}}, {"family": "Sundstr\u00f6m", "given": "Johan", "initials": "J", "orcid": "0000-0003-2247-8454", "researcher": {"href": "https://publications.scilifelab.se/researcher/91a40d3c138d43f2b0d38f66be4b71c7.json"}}, {"family": "T\u00f6njes", "given": "Anke", "initials": "A"}, {"family": "Tuomi", "given": "Tiinamaija", "initials": "T", "orcid": "0000-0002-8306-6202", "researcher": {"href": "https://publications.scilifelab.se/researcher/19f5ce9936ca454c85f0af966acac5c0.json"}}, {"family": "Tuomilehto", "given": "Jaakko", "initials": "J"}, {"family": "Wagner", "given": "Robert", "initials": "R", "orcid": "0000-0002-6120-0191", "researcher": {"href": "https://publications.scilifelab.se/researcher/26361c8c7fc24433832ae95bb52c55ff.json"}}, {"family": "Barroso", "given": "In\u00eas", "initials": "I", "orcid": "0000-0001-5800-4520", "researcher": {"href": "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": "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": "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": "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": "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": "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": "https://publications.scilifelab.se/researcher/2ec81571f4a94af682b4e23526f87385.json"}}, {"family": "Jansen", "given": "Rick", "initials": "R", "orcid": "0000-0002-3333-6737", "researcher": {"href": "https://publications.scilifelab.se/researcher/bcd392c9b9784ebe8c8730e05463377a.json"}}, {"family": "Johannesson", "given": "Magnus", "initials": "M", "orcid": "0000-0001-8759-6393", "researcher": {"href": "https://publications.scilifelab.se/researcher/164991d6c183431d8245e08bd876f400.json"}}, {"family": "Kamali", "given": "Zoha", "initials": "Z", "orcid": "0000-0001-6492-5887", "researcher": {"href": "https://publications.scilifelab.se/researcher/45f4bf1fefc7449a9b6555e0f3f96f58.json"}}, {"family": "Kardia", "given": "Sharon L R", "initials": "SLR"}, {"family": "Kavousi", "given": "Maryam", "initials": "M", "orcid": "0000-0001-5976-6519", "researcher": {"href": "https://publications.scilifelab.se/researcher/bac8aa6fbf1645d0bd2c8954a50456bf.json"}}, {"family": "Kifley", "given": "Annette", "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", "initials": "PA", "orcid": "0000-0002-3887-2598", "researcher": {"href": "https://publications.scilifelab.se/researcher/bded773851d7467f884b1ec628fe73f7.json"}}, {"family": "Luan", "given": "Jian'an", "initials": "J", "orcid": "0000-0003-3137-6337", "researcher": {"href": "https://publications.scilifelab.se/researcher/7f0ea409f1a2462dbb1b266db8fcc33a.json"}}, {"family": "M\u00e4gi", "given": "Reedik", "initials": "R"}, {"family": "Magnusson", "given": "Patrik K E", "initials": "PKE", "orcid": "0000-0002-7315-7899", "researcher": {"href": "https://publications.scilifelab.se/researcher/b277b6387de142bbab91fad82d9eff09.json"}}, {"family": "Mahajan", "given": "Anubha", "initials": "A", "orcid": "0000-0001-5585-3420", "researcher": {"href": "https://publications.scilifelab.se/researcher/194be8a851164e2ea4d004dd2febc9be.json"}}, {"family": "Martin", "given": "Nicholas G", "initials": "NG"}, {"family": "Mbarek", "given": "Hamdi", "initials": "H", "orcid": "0000-0002-1108-0371", "researcher": {"href": "https://publications.scilifelab.se/researcher/a50439a056e94688a64751e2bdc7c502.json"}}, {"family": "McCarthy", "given": "Mark I", "initials": "MI"}, {"family": "McMahon", "given": "George", "initials": "G"}, {"family": "Medland", "given": "Sarah E", "initials": "SE"}, {"family": "Meitinger", "given": "Thomas", "initials": "T"}, {"family": "Metspalu", "given": "Andres", "initials": "A", "orcid": "0000-0002-3718-796X", "researcher": {"href": "https://publications.scilifelab.se/researcher/fd553a77a5a54258b4a4701f0e70a3f8.json"}}, {"family": "Mihailov", "given": "Evelin", "initials": "E"}, {"family": "Milani", "given": "Lili", "initials": "L", "orcid": "0000-0002-5323-3102", "researcher": {"href": "https://publications.scilifelab.se/researcher/dec8d00c4b9d43458c5c895b164695d5.json"}}, {"family": "Missmer", "given": "Stacey A", "initials": "SA"}, {"family": "Mitchell", "given": "Paul", "initials": "P"}, {"family": "M\u00f8llegaard", "given": "Stine", "initials": "S", "orcid": "0000-0001-5676-2248", "researcher": {"href": "https://publications.scilifelab.se/researcher/9b778ebe2b5242f2b1fc55e028cea3c1.json"}}, {"family": "Mook-Kanamori", "given": "Dennis O", "initials": "DO"}, {"family": "Morgan", "given": "Anna", "initials": "A", "orcid": "0000-0001-6290-445X", "researcher": {"href": "https://publications.scilifelab.se/researcher/d11d02b386e64ed1ae1cc109c0b97d9a.json"}}, {"family": "van der Most", "given": "Peter J", "initials": "PJ", "orcid": "0000-0001-8450-3518", "researcher": {"href": "https://publications.scilifelab.se/researcher/17cd11842111490ba5460f3093a366f3.json"}}, {"family": "de Mutsert", "given": "Ren\u00e9e", "initials": "R"}, {"family": "Nauck", "given": "Matthias", "initials": "M", "orcid": "0000-0002-6678-7964", "researcher": {"href": "https://publications.scilifelab.se/researcher/c4b3ce009b2641eda8ad26665e7183f7.json"}}, {"family": "Nolte", "given": "Ilja M", "initials": "IM", "orcid": "0000-0001-5047-4077", "researcher": {"href": "https://publications.scilifelab.se/researcher/abd76becaa8a4df284103c3e20261f10.json"}}, {"family": "Noordam", "given": "Raymond", "initials": "R", "orcid": "0000-0001-7801-809X", "researcher": {"href": "https://publications.scilifelab.se/researcher/6eb07bec2aa54b5a9a661b8b6c431e7a.json"}}, {"family": "Penninx", "given": "Brenda W J H", "initials": "BWJH"}, {"family": "Peters", "given": "Annette", "initials": "A", "orcid": "0000-0001-6645-0985", "researcher": {"href": "https://publications.scilifelab.se/researcher/05465e52a0f6412e81752d2249af30de.json"}}, {"family": "Peyser", "given": "Patricia A", "initials": "PA", "orcid": "0000-0002-9717-8459", "researcher": {"href": "https://publications.scilifelab.se/researcher/3ceeb9094357401e8a8702cb3dc53493.json"}}, {"family": "Pola\u0161ek", "given": "Ozren", "initials": "O"}, {"family": "Power", "given": "Chris", "initials": "C"}, {"family": "Pribisalic", "given": "Ajka", "initials": "A", "orcid": "0000-0002-3725-3728", "researcher": {"href": 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"https://publications.scilifelab.se/researcher/311c7381092b4143bcd2e4ef93250526.json"}}, {"family": "Stankovic", "given": "Stasa", "initials": "S", "orcid": "0000-0002-6602-1379", "researcher": {"href": "https://publications.scilifelab.se/researcher/821b1c3dcb0f42d5b8c285cbc024dda1.json"}}, {"family": "Stef\u00e1nsson", "given": "K\u00e1ri", "initials": "K"}, {"family": "St\u00f6ckl", "given": "Doris", "initials": "D"}, {"family": "Strauch", "given": "Konstantin", "initials": "K"}, {"family": "Swertz", "given": "Morris A", "initials": "MA"}, {"family": "Teumer", "given": "Alexander", "initials": "A", "orcid": "0000-0002-8309-094X", "researcher": {"href": "https://publications.scilifelab.se/researcher/dc9c2667a55b47a6a08aea764fab0946.json"}}, {"family": "Thorleifsson", "given": "Gudmar", "initials": "G"}, {"family": "Thorsteinsdottir", "given": "Unnur", "initials": "U"}, {"family": "Thurik", "given": "A Roy", "initials": "AR", "orcid": "0000-0002-0242-6908", "researcher": {"href": "https://publications.scilifelab.se/researcher/15065c6808d949458295f136422a84dd.json"}}, {"family": "Timpson", "given": "Nicholas J", "initials": "NJ", "orcid": "0000-0002-7141-9189", "researcher": {"href": "https://publications.scilifelab.se/researcher/764ab7a82db24557a5de0fad97bf53f3.json"}}, {"family": "Turman", "given": "Constance", "initials": "C"}, {"family": "Uitterlinden", "given": "Andr\u00e9 G", "initials": "AG", "orcid": "0000-0002-7276-3387", "researcher": {"href": "https://publications.scilifelab.se/researcher/273577b238854023a9dffe34dabc3551.json"}}, {"family": "Waldenberger", "given": "Melanie", "initials": "M", "orcid": "0000-0003-0583-5093", "researcher": {"href": "https://publications.scilifelab.se/researcher/c8de22214f2448c6a7f86fc1040d0104.json"}}, {"family": "Wareham", "given": "Nicholas J", "initials": "NJ", "orcid": "0000-0003-1422-2993", "researcher": {"href": "https://publications.scilifelab.se/researcher/176d8605b9ac4ecbbd5c197335769814.json"}}, {"family": "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", "initials": "NN"}, {"family": "Pozarickij", "given": "Alfred", "initials": "A"}, {"family": "Lin", "given": "Kuang", "initials": "K"}, {"family": "Millwood", "given": "Iona Y", "initials": "IY"}, {"family": "Chen", "given": "Zhengming", "initials": "Z", "orcid": "0000-0001-6423-105X", "researcher": {"href": "https://publications.scilifelab.se/researcher/2bf7c7a02e2c4259b06821d341a7efdf.json"}}, {"family": "Li", "given": "Liming", "initials": "L", "orcid": "0000-0001-5873-7089", "researcher": {"href": "https://publications.scilifelab.se/researcher/64b8d82dbe2c421d95c952b584fbdedf.json"}}, {"family": "China Kadoorie Biobank Collaborative Group", "given": "", "initials": ""}, {"family": "Wijnant", "given": "Sara R A", "initials": "SRA"}, {"family": "Lahousse", "given": "Lies", "initials": "L", "orcid": "0000-0002-3494-4363", "researcher": {"href": "https://publications.scilifelab.se/researcher/62757e242e414fa8badfe29ef9b13091.json"}}, {"family": "Brusselle", "given": "Guy", "initials": "G"}, {"family": "Uitterlinden", "given": "Andre G", "initials": "AG", "orcid": "0000-0002-7276-3387", "researcher": {"href": "https://publications.scilifelab.se/researcher/273577b238854023a9dffe34dabc3551.json"}}, {"family": "Manichaikul", "given": "Ani", "initials": "A"}, {"family": "Oelsner", "given": "Elizabeth C", "initials": "EC", "orcid": "0000-0002-7481-9671", "researcher": {"href": "https://publications.scilifelab.se/researcher/afb61a7c022d4d24890446aa80c447b3.json"}}, {"family": "Rich", "given": "Stephen S", "initials": "SS", "orcid": "0000-0003-3872-7793", "researcher": {"href": "https://publications.scilifelab.se/researcher/e84ce87e45e74e58a095469b311aa4ab.json"}}, {"family": "Barr", "given": "R Graham", "initials": "RG"}, {"family": "Kerr", "given": "Shona M", "initials": "SM", "orcid": "0000-0002-4137-1495", "researcher": {"href": "https://publications.scilifelab.se/researcher/128c14504019419c8b1d6668319569a1.json"}}, {"family": "Vitart", "given": "Veronique", "initials": 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"initials": "B"}, {"family": "Lim", "given": "Elise", "initials": "E", "orcid": "0000-0001-8967-8464", "researcher": {"href": "https://publications.scilifelab.se/researcher/07d8f2f5c30b4f7b9eb409c4969ee283.json"}}, {"family": "Xu", "given": "Hanfei", "initials": "H"}, {"family": "O'Connor", "given": "George T", "initials": "GT"}, {"family": "Thareja", "given": "Gaurav", "initials": "G", "orcid": "0000-0003-2277-6400", "researcher": {"href": "https://publications.scilifelab.se/researcher/eab32eea954347048dc91bd571124f78.json"}}, {"family": "Albagha", "given": "Omar M E", "initials": "OME", "orcid": "0000-0001-5916-5983", "researcher": {"href": "https://publications.scilifelab.se/researcher/df46b95a77e745eab0cd6fadb7e060e3.json"}}, {"family": "Qatar Genome Program Research (QGPR) Consortium", "given": "", "initials": ""}, {"family": "Suhre", "given": "Karsten", "initials": "K", "orcid": "0000-0001-9638-3912", "researcher": {"href": 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{"family": "Patasova", "given": "Karina", "initials": "K"}, {"family": "Hysi", "given": "Pirro", "initials": "P", "orcid": "0000-0001-5752-2510", "researcher": {"href": "https://publications.scilifelab.se/researcher/8d756a9f3294490fa137e2308ccb353e.json"}}, {"family": "Koskela", "given": "Jukka T", "initials": "JT", "orcid": "0000-0002-0154-7222", "researcher": {"href": "https://publications.scilifelab.se/researcher/e6d9979f343e439ab0675d0d515ecbff.json"}}, {"family": "Wyss", "given": "Annah B", "initials": "AB"}, {"family": "Jin", "given": "Jianping", "initials": "J", "orcid": "0000-0002-3774-1609", "researcher": {"href": "https://publications.scilifelab.se/researcher/ed488bfe2c024a6b874b3b964ce80b97.json"}}, {"family": "Sikdar", "given": "Sinjini", "initials": "S", "orcid": "0000-0003-1230-5162", "researcher": {"href": "https://publications.scilifelab.se/researcher/8904ab61ecd4446480954598906b8fc3.json"}}, {"family": "Lee", "given": "Mikyeong", "initials": "M", "orcid": "0000-0002-3036-3684", "researcher": {"href": "https://publications.scilifelab.se/researcher/218e142cd94d4fbcbce40ceaf20193f2.json"}}, {"family": "May-Wilson", "given": "Sebastian", "initials": "S", "orcid": "0000-0003-2668-5717", "researcher": {"href": "https://publications.scilifelab.se/researcher/127b9e9589cd460c8271cb1e82c57870.json"}}, {"family": "Pirastu", "given": "Nicola", "initials": "N"}, {"family": "Kentistou", "given": "Katherine A", "initials": "KA"}, {"family": "Joshi", "given": "Peter K", "initials": "PK", "orcid": "0000-0002-6361-5059", "researcher": {"href": "https://publications.scilifelab.se/researcher/46050ddec8f64054b3bab46c5016aebf.json"}}, {"family": "Timmers", "given": "Paul R H J", "initials": "PRHJ", "orcid": "0000-0002-5197-1267", "researcher": {"href": "https://publications.scilifelab.se/researcher/735ad29e71ad4e748041039f6d249d0e.json"}}, {"family": "Williams", "given": "Alexander T", "initials": "AT"}, {"family": "Free", "given": "Robert C", "initials": "RC"}, {"family": "Wang", "given": "Xueyang", "initials": "X"}, {"family": "Morrison", "given": "John L", "initials": "JL"}, {"family": "Gilliland", "given": "Frank D", "initials": "FD", "orcid": "0000-0002-9033-7269", "researcher": {"href": "https://publications.scilifelab.se/researcher/419c7e14fb884a859a17447794bba965.json"}}, {"family": "Chen", "given": "Zhanghua", "initials": "Z"}, {"family": "Wang", "given": "Carol A", "initials": "CA", "orcid": "0000-0002-4301-3974", "researcher": {"href": "https://publications.scilifelab.se/researcher/bf99a43c27034a68976e978b104a91d7.json"}}, {"family": "Foong", "given": "Rachel E", "initials": "RE"}, {"family": "Harris", "given": "Sarah E", "initials": "SE", "orcid": "0000-0002-4941-5106", "researcher": {"href": "https://publications.scilifelab.se/researcher/1bbd06383e594035ab80af3bcdb29f91.json"}}, {"family": "Taylor", "given": "Adele", "initials": "A"}, {"family": "Redmond", "given": "Paul", "initials": "P"}, {"family": "Cook", "given": "James P", "initials": "JP"}, {"family": "Mahajan", "given": "Anubha", "initials": "A", "orcid": "0000-0001-5585-3420", "researcher": {"href": "https://publications.scilifelab.se/researcher/194be8a851164e2ea4d004dd2febc9be.json"}}, {"family": "Lind", "given": "Lars", "initials": "L"}, {"family": "Palviainen", "given": "Teemu", "initials": "T", "orcid": "0000-0002-7847-8384", "researcher": {"href": "https://publications.scilifelab.se/researcher/bcbc4c92052b4819b5d7d821c0c421b0.json"}}, {"family": "Lehtim\u00e4ki", "given": "Terho", "initials": "T"}, {"family": "Raitakari", "given": "Olli T", "initials": "OT"}, {"family": "Kaprio", "given": "Jaakko", "initials": "J", "orcid": "0000-0002-3716-2455", "researcher": {"href": "https://publications.scilifelab.se/researcher/814d362333844b72a70cba9ebcf61e6f.json"}}, {"family": "Rantanen", "given": "Taina", "initials": "T"}, {"family": "Pietil\u00e4inen", "given": "Kirsi H", "initials": "KH", "orcid": "0000-0002-8522-1288", "researcher": {"href": "https://publications.scilifelab.se/researcher/a4fcc8535d2f42d99e83f8146734ae8b.json"}}, {"family": "Cox", "given": "Simon R", "initials": "SR", "orcid": "0000-0003-4036-3642", "researcher": {"href": "https://publications.scilifelab.se/researcher/52416a98fd6e44bcb8092baa8837ff04.json"}}, {"family": "Pennell", "given": "Craig E", "initials": "CE", "orcid": "0000-0002-0937-6165", "researcher": {"href": "https://publications.scilifelab.se/researcher/9e35a98141ce4350b6775593f87e40a5.json"}}, {"family": "Hall", "given": "Graham L", "initials": "GL"}, {"family": "Gauderman", "given": "W James", "initials": "WJ"}, {"family": "Brightling", "given": "Chris", "initials": "C"}, {"family": "Wilson", "given": "James F", "initials": "JF", "orcid": "0000-0001-5751-9178", "researcher": {"href": "https://publications.scilifelab.se/researcher/b39e6e0f7210494cb4f80be0f7413b6f.json"}}, {"family": "Vasankari", "given": "Tuula", "initials": "T", "orcid": "0000-0002-1413-8970", "researcher": {"href": "https://publications.scilifelab.se/researcher/faac905e8b7e44aba291681629cd26a7.json"}}, {"family": "Laitinen", "given": "Tarja", "initials": "T"}, {"family": "Salomaa", "given": "Veikko", "initials": "V", "orcid": "0000-0001-7563-5324", "researcher": {"href": "https://publications.scilifelab.se/researcher/f2396c578c254e39b66538c3033c9ce9.json"}}, {"family": "Mook-Kanamori", "given": "Dennis O", "initials": "DO"}, {"family": "Timpson", "given": "Nicholas J", "initials": "NJ", "orcid": "0000-0002-7141-9189", "researcher": {"href": "https://publications.scilifelab.se/researcher/764ab7a82db24557a5de0fad97bf53f3.json"}}, {"family": "Zeggini", "given": "Eleftheria", "initials": "E"}, {"family": "Dupuis", "given": "Jos\u00e9e", "initials": "J", "orcid": "0000-0003-2871-3603", "researcher": {"href": "https://publications.scilifelab.se/researcher/c9edfafda7364890866115f5343a9583.json"}}, {"family": "Hayward", "given": "Caroline", "initials": "C"}, {"family": "Brumpton", "given": "Ben", "initials": "B", "orcid": "0000-0002-3058-1059", "researcher": {"href": "https://publications.scilifelab.se/researcher/da9d23aaf1dc4d18a0a13e4847ea9955.json"}}, {"family": "Langenberg", "given": "Claudia", "initials": "C", "orcid": "0000-0002-5017-7344", "researcher": {"href": "https://publications.scilifelab.se/researcher/ca19370bb4d6437aa9df3905db9d3dd2.json"}}, {"family": "Weiss", "given": "Stefan", "initials": "S", "orcid": "0000-0002-3553-4315", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a7c021b692c4fc1b2468c63fd0b2c43.json"}}, {"family": "Homuth", "given": "Georg", "initials": "G", "orcid": "0000-0001-6839-0605", "researcher": {"href": "https://publications.scilifelab.se/researcher/3ff9df166c2a4643990b250c74c5dad3.json"}}, {"family": "Schmidt", "given": "Carsten Oliver", "initials": "CO"}, {"family": "Probst-Hensch", "given": "Nicole", "initials": "N"}, {"family": "Jarvelin", "given": "Marjo-Riitta", "initials": "MR", "orcid": "0000-0002-2149-0630", "researcher": {"href": "https://publications.scilifelab.se/researcher/a7d00b649d284101b0501e2024fb651a.json"}}, {"family": "Morrison", "given": "Alanna C", "initials": "AC", "orcid": "0000-0001-6381-4296", "researcher": {"href": "https://publications.scilifelab.se/researcher/336512e8a711459a9a5c391ffa8bb7b3.json"}}, {"family": "Polasek", "given": "Ozren", "initials": "O"}, {"family": "Rudan", "given": "Igor", "initials": "I", "orcid": "0000-0001-6993-6884", "researcher": {"href": "https://publications.scilifelab.se/researcher/d50e1ca836e841f8a7a748ae93b59d75.json"}}, {"family": "Lee", "given": "Joo-Hyeon", "initials": "JH", "orcid": "0000-0002-7364-6422", "researcher": {"href": "https://publications.scilifelab.se/researcher/00c9d0fac7db4cb1a545df7910c42825.json"}}, {"family": "Sayers", "given": "Ian", "initials": "I", "orcid": "0000-0001-5601-5410", "researcher": {"href": "https://publications.scilifelab.se/researcher/9e07233de8cc402db12839f3dd3c7080.json"}}, {"family": "Rawlins", "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": "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": "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": "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": "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", "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": "Frank", "given": "Mirjam", "initials": "M"}, {"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", "given": "Valeriya", "initials": "V"}, {"family": "Nongmaithem", "given": "Suraj S", "initials": "SS"}, {"family": "Bayyana", "given": "Swati", "initials": "S"}, {"family": "Stringham", "given": "Heather M", "initials": "HM"}, {"family": "Irvin", "given": "Marguerite R", "initials": "MR"}, {"family": "Oldmeadow", "given": "Christopher", "initials": "C"}, {"family": "Kim", "given": "Han Na", "initials": "HN"}, {"family": "Ryu", "given": "Seungho", "initials": "S"}, {"family": "Timmers", "given": "Paul R H J", "initials": "PRHJ"}, {"family": "Arbeeva", "given": "Liubov", "initials": "L"}, {"family": "Dorajoo", "given": "Rajkumar", "initials": "R"}, {"family": "Lange", "given": "Leslie A", "initials": "LA"}, {"family": "Prasad", "given": "Gauri", "initials": "G"}, {"family": "Lor\u00e9s-Motta", "given": "Laura", "initials": "L"}, {"family": "Pauper", "given": "Marc", "initials": "M"}, {"family": "Long", "given": "Jirong", "initials": "J"}, {"family": "Li", "given": "Xiaohui", "initials": "X"}, 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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": "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": "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": "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": "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": "https://publications.scilifelab.se/researcher/ce268fc4b3564f5d91472994c6997f1b.json"}}, {"family": "Koido", "given": "Masaru", "initials": "M", "orcid": "0000-0002-0348-0666", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a043341b935440ba16475b158cbf147.json"}}, {"family": "Le Grand", "given": "Quentin", "initials": "Q", "orcid": "0000-0002-9299-0747", "researcher": {"href": "https://publications.scilifelab.se/researcher/641c0fa6e2fe482ea31e8d3172e657eb.json"}}, {"family": "Shi", "given": "Mingyang", "initials": "M"}, {"family": "He", "given": "Yunye", "initials": "Y", "orcid": "0000-0001-8581-7826", "researcher": {"href": "https://publications.scilifelab.se/researcher/3a824b5e411941a8974f3d4ed2454286.json"}}, {"family": "Georgakis", "given": "Marios K", "initials": "MK", "orcid": "0000-0003-3507-3659", "researcher": {"href": "https://publications.scilifelab.se/researcher/dcdd76c54f4c4fccbc927967d4ec7fa8.json"}}, {"family": "Caro", "given": "Ilana", "initials": "I", "orcid": "0000-0003-3075-4682", "researcher": {"href": "https://publications.scilifelab.se/researcher/8058124982514661a5f2d96e16389e8a.json"}}, {"family": "Krebs", "given": "Kristi", "initials": "K", "orcid": "0000-0003-0494-2751", "researcher": {"href": "https://publications.scilifelab.se/researcher/4b74550db5d04a6bbdb7359669edbec0.json"}}, {"family": "Liaw", "given": "Yi-Ching", "initials": "YC", "orcid": "0000-0002-4973-2777", "researcher": {"href": "https://publications.scilifelab.se/researcher/e03f5dae51a049f186c5f15fb9da4279.json"}}, {"family": "Vaura", "given": "Felix C", "initials": "FC", "orcid": "0000-0002-6036-889X", "researcher": {"href": "https://publications.scilifelab.se/researcher/0f0d0f3f301449b7ac23539d83f7274d.json"}}, {"family": "Lin", "given": "Kuang", "initials": "K"}, {"family": "Winsvold", "given": "Bendik Slagsvold", "initials": "BS", "orcid": "0000-0003-4171-8919", "researcher": {"href": 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"https://publications.scilifelab.se/researcher/e1c36e13b3d54a6085b8c26ce33169c2.json"}}, {"family": "Jee", "given": "Yon Ho", "initials": "YH"}, {"family": "Thomassen", "given": "Jesper Qvist", "initials": "JQ", "orcid": "0000-0003-3484-9531", "researcher": {"href": "https://publications.scilifelab.se/researcher/adf6fc2d75364b328dd93849256eef2b.json"}}, {"family": "Abedi", "given": "Vida", "initials": "V", "orcid": "0000-0001-7689-933X", "researcher": {"href": "https://publications.scilifelab.se/researcher/c86b40236a7e4cc187e152f765867168.json"}}, {"family": "C\u00e1rcel-M\u00e1rquez", "given": "Jara", "initials": "J"}, {"family": "Nygaard", "given": "Marianne", "initials": "M", "orcid": "0000-0003-0703-2665", "researcher": {"href": "https://publications.scilifelab.se/researcher/1d68eda16735460d81993dc39006d5a5.json"}}, {"family": "Leonard", "given": "Hampton L", "initials": "HL", "orcid": "0000-0003-2390-8110", "researcher": {"href": 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"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": "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": "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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"given": "Charumathi", "initials": "C"}, {"family": "Saleheen", "given": "Danish", "initials": "D"}, {"family": "Salomaa", "given": "Veikko", "initials": "V"}, {"family": "Samani", "given": "Nilesh J", "initials": "NJ"}, {"family": "Sanghera", "given": "Dharambir K", "initials": "DK"}, {"family": "Sattar", "given": "Naveed", "initials": "N"}, {"family": "Schmidt", "given": "B\u00f6rge", "initials": "B"}, {"family": "Schmidt", "given": "Helena", "initials": "H"}, {"family": "Schmidt", "given": "Reinhold", "initials": "R"}, {"family": "Schulze", "given": "Matthias B", "initials": "MB"}, {"family": "Schunkert", "given": "Heribert", "initials": "H"}, {"family": "Scott", "given": "Laura J", "initials": "LJ"}, {"family": "Scott", "given": "Rodney J", "initials": "RJ"}, {"family": "Sever", "given": "Peter", "initials": "P"}, {"family": "Shiroma", "given": "Eric J", "initials": "EJ"}, {"family": "Shoemaker", "given": "M Benjamin", "initials": "MB"}, {"family": "Shu", "given": "Xiao-Ou", "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": "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": "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": "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", "given": "Valeriya", "initials": "V"}, {"family": "Nongmaithem", "given": "Suraj S", "initials": "SS"}, {"family": "Sankareswaran", "given": "Alagu", "initials": "A"}, {"family": "Irvin", "given": "Marguerite R", "initials": "MR"}, {"family": "Oldmeadow", "given": "Christopher", "initials": "C"}, {"family": "Kim", "given": "Han Na", "initials": "HN"}, {"family": "Ryu", "given": "Seungho", "initials": "S"}, {"family": "Timmers", "given": "Paul R H J", "initials": "PRHJ"}, {"family": "Arbeeva", "given": "Liubov", "initials": "L"}, {"family": "Dorajoo", "given": "Rajkumar", "initials": "R"}, {"family": "Lange", "given": "Leslie A", "initials": "LA"}, {"family": "Prasad", "given": "Gauri", "initials": "G"}, {"family": "Lor\u00e9s-Motta", "given": "Laura", "initials": "L"}, {"family": "Pauper", "given": "Marc", "initials": "M"}, {"family": "Long", "given": "Jirong", "initials": "J"}, {"family": "Li", "given": "Xiaohui", "initials": "X"}, {"family": "Theusch", "given": "Elizabeth", "initials": "E"}, {"family": "Takeuchi", "given": "Fumihiko", "initials": "F"}, {"family": "Spracklen", "given": "Cassandra N", "initials": "CN"}, {"family": "Loukola", "given": "Anu", "initials": "A"}, {"family": "Bollepalli", "given": "Sailalitha", "initials": "S"}, {"family": "Warner", "given": "Sophie C", "initials": "SC"}, {"family": "Wang", "given": "Ya Xing", "initials": "YX"}, {"family": "Wei", "given": "Wen B", "initials": "WB"}, {"family": "Nutile", "given": "Teresa", "initials": "T"}, {"family": "Ruggiero", "given": "Daniela", "initials": "D"}, {"family": "Sung", "given": "Yun Ju", "initials": "YJ"}, {"family": "Chen", "given": "Shufeng", "initials": "S"}, {"family": "Liu", "given": "Fangchao", "initials": "F"}, {"family": "Yang", "given": "Jingyun", "initials": "J"}, {"family": "Kentistou", "given": "Katherine A", "initials": "KA"}, {"family": "Banas", "given": "Bernhard", "initials": "B"}, {"family": "Morgan", "given": "Anna", "initials": "A"}, {"family": "Meidtner", "given": "Karina", "initials": "K"}, {"family": "Bielak", "given": "Lawrence F", "initials": "LF"}, {"family": "Smith", "given": "Jennifer A", "initials": "JA"}, {"family": "Hebbar", "given": "Prashantha", "initials": "P"}, {"family": "Farmaki", "given": "Aliki Eleni", "initials": "AE"}, {"family": "Hofer", "given": "Edith", "initials": "E"}, {"family": "Lin", "given": "Maoxuan", "initials": "M"}, {"family": "Concas", "given": "Maria Pina", "initials": "MP"}, {"family": "Vaccargiu", "given": "Simona", "initials": "S"}, {"family": "van der Most", "given": "Peter J", "initials": "PJ"}, {"family": "Pitk\u00e4nen", "given": "Niina", "initials": "N"}, {"family": "Cade", "given": "Brian E", "initials": "BE"}, {"family": "van der Laan", "given": "Sander W", "initials": "SW"}, {"family": "Chitrala", "given": "Kumaraswamy Naidu", "initials": "KN"}, {"family": "Weiss", "given": "Stefan", "initials": "S"}, {"family": "Bentley", "given": "Amy R", "initials": "AR"}, {"family": "Doumatey", "given": "Ayo P", "initials": "AP"}, {"family": "Adeyemo", "given": "Adebowale A", "initials": "AA"}, {"family": "Lee", "given": "Jong Young", "initials": "JY"}, {"family": "Petersen", "given": "Eva R B", "initials": "ERB"}, {"family": "Nielsen", "given": "Aneta A", "initials": "AA"}, {"family": "Choi", "given": "Hyeok Sun", "initials": "HS"}, {"family": "Nethander", "given": "Maria", "initials": "M"}, {"family": "Freitag-Wolf", "given": "Sandra", "initials": "S"}, {"family": "Southam", "given": "Lorraine", "initials": "L"}, {"family": "Rayner", "given": "Nigel W", "initials": "NW"}, {"family": "Wang", "given": "Carol A", "initials": "CA"}, {"family": "Lin", "given": "Shih Yi", "initials": "SY"}, {"family": "Wang", "given": "Jun Sing", "initials": "JS"}, {"family": "Couture", "given": "Christian", "initials": "C"}, {"family": "Lyytik\u00e4inen", "given": "Leo Pekka", "initials": "LP"}, {"family": "Nikus", "given": "Kjell", "initials": "K"}, {"family": "Cuellar-Partida", "given": "Gabriel", "initials": "G"}, {"family": "Vestergaard", "given": "Henrik", "initials": "H"}, {"family": "Hidalgo", "given": "Bertha", "initials": "B"}, {"family": "Giannakopoulou", "given": "Olga", "initials": "O"}, {"family": "Cai", "given": "Qiuyin", "initials": "Q"}, {"family": "Obura", "given": "Morgan O", "initials": "MO"}, {"family": "van Setten", "given": "Jessica", "initials": "J"}, {"family": "He", "given": "Karen Y", "initials": "KY"}, {"family": "Tang", "given": "Hua", "initials": "H"}, {"family": "Terzikhan", "given": "Natalie", "initials": "N"}, {"family": "Shin", "given": "Jae 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"Haretsugu", "initials": "H"}, {"family": "Lin", "given": "Xu", "initials": "X"}, {"family": "M\u00e4rz", "given": "Winfried", "initials": "W"}, {"family": "Gudnason", "given": "Vilmundur", "initials": "V"}, {"family": "Tardif", "given": "Jean Claude", "initials": "JC"}, {"family": "Lettre", "given": "Guillaume", "initials": "G"}, {"family": "t Hart", "given": "Leen M", "initials": "LM"}, {"family": "Elders", "given": "Petra J M", "initials": "PJM"}, {"family": "Rader", "given": "Daniel J", "initials": "DJ"}, {"family": "Damrauer", "given": "Scott M", "initials": "SM"}, {"family": "Kumari", "given": "Meena", "initials": "M"}, {"family": "Kivimaki", "given": "Mika", "initials": "M"}, {"family": "van der Harst", "given": "Pim", "initials": "P"}, {"family": "Spector", "given": "Tim D", "initials": "TD"}, {"family": "Loos", "given": "Ruth J F", "initials": "RJF"}, {"family": "Province", "given": "Michael A", "initials": "MA"}, {"family": "Parra", "given": "Esteban J", "initials": "EJ"}, 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"Schunkert", "given": "Heribert", "initials": "H"}, {"family": "Franks", "given": "Paul W", "initials": "PW"}, {"family": "Linneberg", "given": "Allan", "initials": "A"}, {"family": "Jukema", "given": "J Wouter", "initials": "JW"}, {"family": "Khera", "given": "Amit V", "initials": "AV"}, {"family": "M\u00e4nnikk\u00f6", "given": "Minna", "initials": "M"}, {"family": "Jarvelin", "given": "Marjo Riitta", "initials": "MR"}, {"family": "Kutalik", "given": "Zoltan", "initials": "Z"}, {"family": "Francesco", "given": "Cucca", "initials": "C"}, {"family": "Mook-Kanamori", "given": "Dennis O", "initials": "DO"}, {"family": "Willems van Dijk", "given": "Ko", "initials": "K"}, {"family": "Watkins", "given": "Hugh", "initials": "H"}, {"family": "Strachan", "given": "David P", "initials": "DP"}, {"family": "Grarup", "given": "Niels", "initials": "N"}, {"family": "Sever", "given": "Peter", "initials": "P"}, {"family": "Poulter", "given": "Neil", "initials": "N"}, {"family": "Huey-Herng Sheu", 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I", "initials": "DI"}, {"family": "de Geus", "given": "Eco J C", "initials": "EJC"}, {"family": "Cupples", "given": "L Adrienne", "initials": "LA"}, {"family": "van Meurs", "given": "Joyce B J", "initials": "JBJ"}, {"family": "Ikram", "given": "Arfan", "initials": "A"}, {"family": "Ghanbari", "given": "Mohsen", "initials": "M"}, {"family": "Gordon-Larsen", "given": "Penny", "initials": "P"}, {"family": "Huang", "given": "Wei", "initials": "W"}, {"family": "Kim", "given": "Young Jin", "initials": "YJ"}, {"family": "Tabara", "given": "Yasuharu", "initials": "Y"}, {"family": "Wareham", "given": "Nicholas J", "initials": "NJ"}, {"family": "Langenberg", "given": "Claudia", "initials": "C"}, {"family": "Zeggini", "given": "Eleftheria", "initials": "E"}, {"family": "Tuomilehto", "given": "Jaakko", "initials": "J"}, {"family": "Kuusisto", "given": "Johanna", "initials": "J"}, {"family": "Laakso", "given": "Markku", "initials": "M"}, {"family": "Ingelsson", "given": "Erik", "initials": "E"}, {"family": "Abecasis", "given": "Goncalo", "initials": "G"}, {"family": "Chambers", "given": "John C", "initials": "JC"}, {"family": "Kooner", "given": "Jaspal S", "initials": "JS"}, {"family": "de Vries", "given": "Paul S", "initials": "PS"}, {"family": "Morrison", "given": "Alanna C", "initials": "AC"}, {"family": "Hazelhurst", "given": "Scott", "initials": "S"}, {"family": "Ramsay", "given": "Mich\u00e8le", "initials": "M"}, {"family": "North", "given": "Kari E", "initials": "KE"}, {"family": "Daviglus", "given": "Martha", "initials": "M"}, {"family": "Kraft", "given": "Peter", "initials": "P"}, {"family": "Martin", "given": "Nicholas G", "initials": "NG"}, {"family": "Whitfield", "given": "John B", "initials": "JB"}, {"family": "Abbas", "given": "Shahid", "initials": "S"}, {"family": "Saleheen", "given": "Danish", "initials": "D"}, {"family": "Walters", "given": "Robin G", "initials": "RG"}, {"family": "Holmes", "given": "Michael V", "initials": "MV"}, {"family": "Black", "given": "Corri", "initials": "C"}, {"family": "Smith", "given": "Blair H", "initials": "BH"}, {"family": "Baras", "given": "Aris", "initials": "A"}, {"family": "Justice", "given": "Anne E", "initials": "AE"}, {"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": "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": "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": "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": "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", 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"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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{"family": "Thorsteinsdottir", "given": "Unnur", "initials": "U"}, {"family": "V\u00f6lker", "given": "Uwe", "initials": "U", "orcid": "0000-0002-5689-3448", "researcher": {"href": "https://publications.scilifelab.se/researcher/e529a40052644d83bdef588a3e4f4e99.json"}}, {"family": "Foo", "given": "Valencia Hui Xian", "initials": "VHX"}, {"family": "Salomaa", "given": "Veikko", "initials": "V", "orcid": "0000-0001-7563-5324", "researcher": {"href": "https://publications.scilifelab.se/researcher/f2396c578c254e39b66538c3033c9ce9.json"}}, {"family": "Vitart", "given": "Veronique", "initials": "V", "orcid": "0000-0002-4991-3797", "researcher": {"href": "https://publications.scilifelab.se/researcher/0ca9835a494849af861673bf7989b523.json"}}, {"family": "Giedraitis", "given": "Vilmantas", "initials": "V"}, {"family": "Gudnason", "given": "Vilmundur", "initials": "V", "orcid": "0000-0001-5696-0084", "researcher": {"href": "https://publications.scilifelab.se/researcher/d18327939c1541acba054b2340ac174f.json"}}, {"family": "Jaddoe", "given": "Vincent W V", "initials": "VWV", "orcid": "0000-0003-2939-0041", "researcher": {"href": "https://publications.scilifelab.se/researcher/d738994d1bcc4accadeed32b57e1bc9c.json"}}, {"family": "Huang", "given": "Wei", "initials": "W"}, {"family": "Zhang", "given": "Weihua", "initials": "W", "orcid": "0000-0001-8279-3611", "researcher": {"href": "https://publications.scilifelab.se/researcher/b8e84add58dd48989b281b735a6b2bd0.json"}}, {"family": "Wei", "given": "Wen Bin", "initials": "WB"}, {"family": "Kiess", "given": "Wieland", "initials": "W"}, {"family": "M\u00e4rz", "given": "Winfried", "initials": "W"}, {"family": "Koenig", "given": "Wolfgang", "initials": "W", "orcid": "0000-0002-2064-9603", "researcher": {"href": "https://publications.scilifelab.se/researcher/b358f3d797814a07a05a63364ae37d27.json"}}, {"family": "Lieb", "given": "Wolfgang", "initials": "W", "orcid": "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": "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": "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": "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": "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": "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": "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": "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": "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": "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": "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"}]}