{"entity": "researcher", "timestamp": "2026-07-19T06:09:54.247Z", "family": "Meadows", "given": "Jennifer R S", "initials": "JRS", "orcid": "0000-0002-0850-230X", "affiliations": ["Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden."], "links": {"self": {"href": "https://publications.scilifelab.se/researcher/86acdca0104c4552880d5a7cb5ac6565.json"}, "display": {"href": "https://publications.scilifelab.se/researcher/86acdca0104c4552880d5a7cb5ac6565"}}, "publications": [{"entity": "publication", "iuid": "a0c095fc5e9e48d295cd22a998627f16", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a0c095fc5e9e48d295cd22a998627f16.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a0c095fc5e9e48d295cd22a998627f16"}}, "title": "Interpreting mammalian synonymous site conservation in light of the unwanted transcript hypothesis.", "authors": [{"family": "Christmas", "given": "Matthew J", "initials": "MJ", "orcid": "0000-0002-6355-7581", "researcher": {"href": "https://publications.scilifelab.se/researcher/76e069a0271e4a1fbc31fd3cb440366f.json"}}, {"family": "Dong", "given": "Michael X", "initials": "MX"}, {"family": "Meadows", "given": "Jennifer R S", "initials": "JRS", "orcid": "0000-0002-0850-230X", "researcher": {"href": "https://publications.scilifelab.se/researcher/86acdca0104c4552880d5a7cb5ac6565.json"}}, {"family": "Kozyrev", "given": "Sergey V", "initials": "SV", "orcid": "0000-0001-6209-4100", "researcher": {"href": "https://publications.scilifelab.se/researcher/b6be89ad73a14d66a3b9439efc9c4099.json"}}, {"family": "Lindblad-Toh", "given": "Kerstin", "initials": "K", "orcid": "0000-0001-8338-0253", "researcher": {"href": "https://publications.scilifelab.se/researcher/e0063145f7d6476f80ab42f94833f4cf.json"}}], "type": "journal article", "published": "2025-02-27", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "16", "issue": "1", "pages": "2007", "issn-l": "2041-1723"}, "abstract": "Mammalian genomes are biased towards GC bases at third codon positions, likely due to a GC-biased ancestral genome and the selectively neutral recombination-related process of GC-biased gene conversion. The unwanted transcript hypothesis posits that this high GC content at synonymous sites may be beneficial for protecting against spurious transcripts, particularly in species with low effective population sizes. Utilising a 240 placental mammal genome alignment and single-base resolution conservation scores, we interpret sequence conservation at mammalian four-fold degenerate sites in this context and find evidence in support of the unwanted transcript hypothesis, including a strong GC bias, high conservation at sites relating to exon splicing, less human genetic variation at conserved four-fold degenerate sites, and conservation of sites important for epigenetic regulation of developmental genes. Additionally, we show that high conservation of four-fold degenerate sites in essential developmental genes, including homeobox genes, likely relates to the low mutation rates experienced by these genes.", "doi": "10.1038/s41467-025-57179-w", "pmid": "40011430", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11865589"}, {"db": "pii", "key": "10.1038/s41467-025-57179-w"}], "notes": [], "created": "2025-11-28T10:45:29.590Z", "modified": "2025-11-28T10:45:29.691Z"}, {"entity": "publication", "iuid": "33f838f6e3d2497fa4b6fd9a71cd282a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/33f838f6e3d2497fa4b6fd9a71cd282a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/33f838f6e3d2497fa4b6fd9a71cd282a"}}, "title": "An endothelial regulatory module links blood pressure regulation with elite athletic performance.", "authors": [{"family": "Fegraeus", "given": "Kim", "initials": "K", "orcid": "0000-0002-6428-3420", "researcher": {"href": "https://publications.scilifelab.se/researcher/f232e1deee984344a57c88f550020e61.json"}}, {"family": "Rosengren", "given": "Maria K", "initials": "MK", "orcid": "0000-0003-0144-7034", "researcher": {"href": "https://publications.scilifelab.se/researcher/2b771ed57d3e4c409c2a208173945786.json"}}, {"family": "Naboulsi", "given": "Rakan", "initials": "R", "orcid": "0000-0002-3610-4341", "researcher": {"href": "https://publications.scilifelab.se/researcher/ae740ff060a5499fa477891138e95117.json"}}, {"family": "Orlando", "given": "Ludovic", "initials": "L"}, {"family": "\u00c5brink", "given": "Magnus", "initials": "M", "orcid": "0000-0002-1335-3927", "researcher": {"href": "https://publications.scilifelab.se/researcher/50a91636c1064a0c944f7d794ba6ec72.json"}}, {"family": "Jouni", "given": "Ahmad", "initials": "A"}, {"family": "Velie", "given": "Brandon D", "initials": "BD"}, {"family": "Raine", "given": "Amanda", "initials": "A"}, {"family": "Egner", "given": "Beate", "initials": "B"}, {"family": "Mattsson", "given": "C Mikael", "initials": "CM", "orcid": "0000-0002-0642-4838", "researcher": {"href": "https://publications.scilifelab.se/researcher/2ca360922eb047129f945ec3ca5f59e3.json"}}, {"family": "L\u00e5ng", "given": "Karin", "initials": "K"}, {"family": "Zhigulev", "given": "Artemy", "initials": "A", "orcid": "0000-0001-9251-1059", "researcher": {"href": "https://publications.scilifelab.se/researcher/81a7e8bb937744b5a18ed42d4f2dea5e.json"}}, {"family": "Bj\u00f6rck", "given": "Hanna M", "initials": "HM", "orcid": "0000-0002-9155-3609", "researcher": {"href": "https://publications.scilifelab.se/researcher/3d162f3de0f941e0a91387357892d656.json"}}, {"family": "Franco-Cereceda", "given": "Anders", "initials": "A"}, {"family": "Eriksson", "given": "Per", "initials": "P"}, {"family": "Andersson", "given": "G\u00f6ran", "initials": "G", "orcid": "0000-0001-5131-3144", "researcher": {"href": "https://publications.scilifelab.se/researcher/39ce81c314db47c8ad63c3ed38dffcb3.json"}}, {"family": "Sahl\u00e9n", "given": "Pelin", "initials": "P", "orcid": "0000-0001-6943-9618", "researcher": {"href": "https://publications.scilifelab.se/researcher/d032e807335049b2ac8a5e2398dd48e7.json"}}, {"family": "Meadows", "given": "Jennifer R S", "initials": "JRS", "orcid": "0000-0002-0850-230X", "researcher": {"href": "https://publications.scilifelab.se/researcher/86acdca0104c4552880d5a7cb5ac6565.json"}}, {"family": "Lindgren", "given": "Gabriella", "initials": "G", "orcid": "0000-0001-6046-9669", "researcher": {"href": "https://publications.scilifelab.se/researcher/a050dea8e99c47fabac28c14fe4daabb.json"}}], "type": "journal article", "published": "2024-06-00", "journal": {"title": "PLoS Genet.", "issn": "1553-7404", "volume": "20", "issue": "6", "pages": "e1011285", "issn-l": "1553-7390"}, "abstract": "The control of transcription is crucial for homeostasis in mammals. A previous selective sweep analysis of horse racing performance revealed a 19.6 kb candidate regulatory region 50 kb downstream of the Endothelin3 (EDN3) gene. Here, the region was narrowed to a 5.5 kb span of 14 SNVs, with elite and sub-elite haplotypes analyzed for association to racing performance, blood pressure and plasma levels of EDN3 in Coldblooded trotters and Standardbreds. Comparative analysis of human HiCap data identified the span as an enhancer cluster active in endothelial cells, interacting with genes relevant to blood pressure regulation. Coldblooded trotters with the sub-elite haplotype had significantly higher blood pressure compared to horses with the elite performing haplotype during exercise. Alleles within the elite haplotype were part of the standing variation in pre-domestication horses, and have risen in frequency during the era of breed development and selection. These results advance our understanding of the molecular genetics of athletic performance and vascular traits in both horses and humans.", "doi": "10.1371/journal.pgen.1011285", "pmid": "38885195", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Short read": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11182536"}, {"db": "pii", "key": "PGENETICS-D-23-00898"}], "notes": [], "created": "2024-10-21T11:19:11.160Z", "modified": "2024-11-25T10:31:46.138Z"}, {"entity": "publication", "iuid": "a6e01a3cb4e94b1f8abee9bf3a1dcada", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a6e01a3cb4e94b1f8abee9bf3a1dcada.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a6e01a3cb4e94b1f8abee9bf3a1dcada"}}, "title": "Genome sequencing of 2000 canids by the Dog10K consortium advances the understanding of demography, genome function and architecture.", "authors": [{"family": "Meadows", "given": "Jennifer R S", "initials": "JRS", "orcid": "0000-0002-0850-230X", "researcher": {"href": "https://publications.scilifelab.se/researcher/86acdca0104c4552880d5a7cb5ac6565.json"}}, {"family": "Kidd", "given": "Jeffrey M", "initials": "JM", "orcid": "0000-0002-9631-1465", "researcher": {"href": "https://publications.scilifelab.se/researcher/443559b87cc54118873bf603b40a2859.json"}}, {"family": "Wang", "given": "Guo-Dong", "initials": "G"}, {"family": "Parker", "given": "Heidi G", "initials": "HG", "orcid": "0000-0002-9707-6380", "researcher": {"href": "https://publications.scilifelab.se/researcher/51a8621269234efba8a9db6e56198d34.json"}}, {"family": "Schall", "given": "Peter Z", "initials": "PZ", "orcid": "0000-0003-1016-6998", "researcher": {"href": "https://publications.scilifelab.se/researcher/769dfe26fcfc49ceb8178ef7ae55b304.json"}}, {"family": "Bianchi", "given": "Matteo", "initials": "M", "orcid": "0000-0003-3394-6495", "researcher": {"href": "https://publications.scilifelab.se/researcher/d645ef0e04a245f0ac9e7d7498b2bd69.json"}}, {"family": "Christmas", "given": "Matthew J", "initials": "MJ", "orcid": "0000-0002-6355-7581", "researcher": {"href": "https://publications.scilifelab.se/researcher/76e069a0271e4a1fbc31fd3cb440366f.json"}}, {"family": "Bougiouri", "given": "Katia", "initials": "K", "orcid": "0000-0002-7890-2755", "researcher": {"href": "https://publications.scilifelab.se/researcher/9f3e12cdbe6e4dd5acfc609275595f8b.json"}}, {"family": "Buckley", "given": "Reuben M", "initials": "RM", "orcid": "0000-0001-6334-3906", "researcher": {"href": "https://publications.scilifelab.se/researcher/4f83f4dbc5a847e1aff7e5d0f55971ce.json"}}, {"family": "Hitte", "given": "Christophe", "initials": "C", "orcid": "0000-0003-1714-437X", "researcher": {"href": "https://publications.scilifelab.se/researcher/5d3a7672564d4111a42bcb497355b8c1.json"}}, {"family": "Nguyen", "given": "Anthony K", "initials": "AK", "orcid": "0000-0002-9634-1904", "researcher": {"href": "https://publications.scilifelab.se/researcher/a6352471c5cb492d9ebf3db25d29af47.json"}}, {"family": "Wang", "given": "Chao", "initials": "C", "orcid": "0000-0003-3936-4023", "researcher": {"href": "https://publications.scilifelab.se/researcher/202a8fd115e14824809a362a7cfc5a41.json"}}, {"family": "Jagannathan", "given": "Vidhya", "initials": "V", "orcid": "0000-0002-8155-0041", "researcher": {"href": "https://publications.scilifelab.se/researcher/b49072ce24044ccc8bbb3425be609ec5.json"}}, {"family": "Niskanen", "given": "Julia E", "initials": "JE", "orcid": "0000-0002-2871-6890", "researcher": {"href": "https://publications.scilifelab.se/researcher/6c9070b3a4bb4b9f93f85caf587b2b98.json"}}, {"family": "Frantz", "given": "Laurent A F", "initials": "LAF", "orcid": "0000-0001-8030-3885", "researcher": {"href": "https://publications.scilifelab.se/researcher/76b1179f8ee34ebbbdd466fb977f3ce7.json"}}, {"family": "Arumilli", "given": "Meharji", "initials": "M"}, {"family": "Hundi", "given": "Sruthi", "initials": "S", "orcid": "0000-0002-5803-1841", "researcher": {"href": "https://publications.scilifelab.se/researcher/6874df319b014e4384fb593f2bbeb560.json"}}, {"family": "Lindblad-Toh", "given": "Kerstin", "initials": "K", "orcid": "0000-0001-8338-0253", "researcher": {"href": "https://publications.scilifelab.se/researcher/e0063145f7d6476f80ab42f94833f4cf.json"}}, {"family": "Ginja", "given": "Catarina", "initials": "C", "orcid": "0000-0003-2278-7089", "researcher": {"href": "https://publications.scilifelab.se/researcher/56dfd5da6c504f16bb79196f54f8e833.json"}}, {"family": "Agustina", "given": "Kadek Karang", "initials": "KK", "orcid": "0000-0002-7128-0914", "researcher": {"href": "https://publications.scilifelab.se/researcher/88728c8a24db4794b2b44bc2affc64fe.json"}}, {"family": "Andr\u00e9", "given": "Catherine", "initials": "C"}, {"family": "Boyko", "given": "Adam R", "initials": "AR", "orcid": "0000-0002-9125-6874", "researcher": {"href": "https://publications.scilifelab.se/researcher/7b0d17b0c37c427781065fe542810589.json"}}, {"family": "Davis", "given": "Brian W", "initials": "BW", "orcid": "0000-0002-6121-135X", "researcher": {"href": "https://publications.scilifelab.se/researcher/63981f53ab2e4dc09a4a2a62ae0b7a84.json"}}, {"family": "Dr\u00f6gem\u00fcller", "given": "Michaela", "initials": "M", "orcid": "0000-0001-9378-7903", "researcher": {"href": "https://publications.scilifelab.se/researcher/7f0a8a9e9cd34fa3a633a808bcdad3b4.json"}}, {"family": "Feng", "given": "Xin-Yao", "initials": "X"}, {"family": "Gkagkavouzis", "given": "Konstantinos", "initials": "K"}, {"family": "Iliopoulos", "given": "Giorgos", "initials": "G"}, {"family": "Harris", "given": "Alexander C", "initials": "AC", "orcid": "0000-0002-6868-5363", "researcher": {"href": "https://publications.scilifelab.se/researcher/4c2fbbbe8ed149528f5481f93e867d36.json"}}, {"family": "Hyt\u00f6nen", "given": "Marjo K", "initials": "MK", "orcid": "0000-0003-1976-5874", "researcher": {"href": "https://publications.scilifelab.se/researcher/89e3788ab09f415f918f0bf9ed441fac.json"}}, {"family": "Kalthoff", "given": "Daniela C", "initials": "DC", "orcid": "0000-0003-2439-5484", "researcher": {"href": "https://publications.scilifelab.se/researcher/4c18227dc17f428daca466f6fc7d3888.json"}}, {"family": "Liu", "given": "Yan-Hu", "initials": "Y"}, {"family": "Lymberakis", "given": "Petros", "initials": "P"}, {"family": "Poulakakis", "given": "Nikolaos", "initials": "N"}, {"family": "Pires", "given": "Ana Elisabete", "initials": "AE", "orcid": "0000-0002-1118-8569", "researcher": {"href": "https://publications.scilifelab.se/researcher/b8856555c77443eb8038f5e6c9cead89.json"}}, {"family": "Racimo", "given": "Fernando", "initials": "F", "orcid": "0000-0002-5025-2607", "researcher": {"href": "https://publications.scilifelab.se/researcher/dcd12137b4184a72a81c48d2926c5280.json"}}, {"family": "Ramos-Almodovar", "given": "Fabian", "initials": "F", "orcid": "0000-0001-9094-7895", "researcher": {"href": "https://publications.scilifelab.se/researcher/8ead8fce39844a2d8f9415780d2acdd1.json"}}, {"family": "Savolainen", "given": "Peter", "initials": "P", "orcid": "0000-0002-1495-8338", "researcher": {"href": "https://publications.scilifelab.se/researcher/af5298b9990946b080ac61188cb2b2af.json"}}, {"family": "Venetsani", "given": "Semina", "initials": "S"}, {"family": "Tammen", "given": "Imke", "initials": "I", "orcid": "0000-0002-5520-6597", "researcher": {"href": "https://publications.scilifelab.se/researcher/e5d3f973dfae4a1a914ff8d023e1c5ad.json"}}, {"family": "Triantafyllidis", "given": "Alexandros", "initials": "A", "orcid": "0000-0003-0469-011X", "researcher": {"href": "https://publications.scilifelab.se/researcher/8323f04a414e405380d92113f3628ab8.json"}}, {"family": "vonHoldt", "given": "Bridgett", "initials": "B", "orcid": "0000-0001-6908-1687", "researcher": {"href": "https://publications.scilifelab.se/researcher/b49c5a042db049778ec2d777b985238e.json"}}, {"family": "Wayne", "given": "Robert K", "initials": "RK", "orcid": "0000-0003-3537-2245", "researcher": {"href": "https://publications.scilifelab.se/researcher/641654eaf0d14a2899ce760fda55bc52.json"}}, {"family": "Larson", "given": "Greger", "initials": "G", "orcid": "0000-0002-4092-0392", "researcher": {"href": "https://publications.scilifelab.se/researcher/8313c5d2d5a148349ad14e51deca8ab5.json"}}, {"family": "Nicholas", "given": "Frank W", "initials": "FW", "orcid": "0000-0002-9178-3965", "researcher": {"href": "https://publications.scilifelab.se/researcher/3e6a880495ec4d8da0922ebc94f207db.json"}}, {"family": "Lohi", "given": "Hannes", "initials": "H", "orcid": "0000-0003-1087-5532", "researcher": {"href": "https://publications.scilifelab.se/researcher/903f658d43ea414fb37ef530df3e15e4.json"}}, {"family": "Leeb", "given": "Tosso", "initials": "T", "orcid": "0000-0003-0553-4880", "researcher": {"href": "https://publications.scilifelab.se/researcher/0f3aab15785e4875a06b659c9ded0ddd.json"}}, {"family": "Zhang", "given": "Ya-Ping", "initials": "Y"}, {"family": "Ostrander", "given": "Elaine A", "initials": "EA", "orcid": "0000-0001-6075-9738", "researcher": {"href": "https://publications.scilifelab.se/researcher/2d531414c37d46e987e06cca25f2f9de.json"}}], "type": "journal article", "published": "2023-08-15", "journal": {"title": "Genome Biol.", "issn": "1474-760X", "issn-l": "1474-7596", "volume": "24", "issue": "1", "pages": "187"}, "abstract": "The international Dog10K project aims to sequence and analyze several thousand canine genomes. Incorporating 20 \u00d7 data from 1987 individuals, including 1611 dogs (321 breeds), 309 village dogs, 63 wolves, and four coyotes, we identify genomic variation across the canid family, setting the stage for detailed studies of domestication, behavior, morphology, disease susceptibility, and genome architecture and function.\r\n\r\nWe report the analysis of > 48 M single-nucleotide, indel, and structural variants spanning the autosomes, X chromosome, and mitochondria. We discover more than 75% of variation for 239 sampled breeds. Allele sharing analysis indicates that 94.9% of breeds form monophyletic clusters and 25 major clades. German Shepherd Dogs and related breeds show the highest allele sharing with independent breeds from multiple clades. On average, each breed dog differs from the UU_Cfam_GSD_1.0 reference at 26,960 deletions and 14,034 insertions greater than 50 bp, with wolves having 14% more variants. Discovered variants include retrogene insertions from 926 parent genes. To aid functional prioritization, single-nucleotide variants were annotated with SnpEff and Zoonomia phyloP constraint scores. Constrained positions were negatively correlated with allele frequency. Finally, the utility of the Dog10K data as an imputation reference panel is assessed, generating high-confidence calls across varied genotyping platform densities including for breeds not included in the Dog10K collection.\r\n\r\nWe have developed a dense dataset of 1987 sequenced canids that reveals patterns of allele sharing, identifies likely functional variants, informs breed structure, and enables accurate imputation. Dog10K data are publicly available.", "doi": "10.1186/s13059-023-03023-7", "pmid": "37582787", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10426128"}, {"db": "pii", "key": "10.1186/s13059-023-03023-7"}], "notes": [], "created": "2023-11-27T21:59:43.116Z", "modified": "2024-01-16T13:48:32.480Z"}, {"entity": "publication", "iuid": "6cea0eb350cd40bba54717d8b627da6b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6cea0eb350cd40bba54717d8b627da6b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6cea0eb350cd40bba54717d8b627da6b"}}, "title": "Leveraging base-pair mammalian constraint to understand genetic variation and human disease.", "authors": [{"family": "Sullivan", "given": "Patrick F", "initials": "PF", "orcid": "0000-0002-6619-873X", "researcher": {"href": "https://publications.scilifelab.se/researcher/4d95de0b5ab14586980a6a13c8299346.json"}}, {"family": 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"Steven K", "initials": "SK", "orcid": "0000-0003-3140-1483", "researcher": {"href": "https://publications.scilifelab.se/researcher/0c12bcf707394bb5b9c34075aba19f13.json"}}, {"family": "Hughes", "given": "Graham M", "initials": "GM", "orcid": "0000-0003-3088-345X", "researcher": {"href": "https://publications.scilifelab.se/researcher/800da869332a45b9b4c7bd8fd5522666.json"}}, {"family": "Weng", "given": "Zhiping", "initials": "Z", "orcid": "0000-0002-3032-7966", "researcher": {"href": "https://publications.scilifelab.se/researcher/25ad44250cba4b0cba5250b07f764ba3.json"}}, {"family": "Pollard", "given": "Katherine S", "initials": "KS", "orcid": "0000-0002-9870-6196", "researcher": {"href": "https://publications.scilifelab.se/researcher/bb2a865a28524f55bb5d9df3db79563f.json"}}, {"family": "Pfenning", "given": "Andreas R", "initials": "AR", "orcid": "0000-0002-3447-9801", "researcher": {"href": "https://publications.scilifelab.se/researcher/579e32fe57da4d738b7fbf0a57fb6faf.json"}}, {"family": "Forsberg-Nilsson", "given": "Karin", "initials": "K", "orcid": "0000-0003-0692-6245", "researcher": {"href": "https://publications.scilifelab.se/researcher/5da04859250141a0a7271a69c7da9176.json"}}, {"family": "Karlsson", "given": "Elinor K", "initials": "EK", "orcid": "0000-0002-4343-3776", "researcher": {"href": "https://publications.scilifelab.se/researcher/2bd97378a1cc403db0923895adde15e3.json"}}, {"family": "Lindblad-Toh", "given": "Kerstin", "initials": "K", "orcid": "0000-0001-8338-0253", "researcher": {"href": "https://publications.scilifelab.se/researcher/e0063145f7d6476f80ab42f94833f4cf.json"}}], "type": "journal article", "published": "2023-04-28", "journal": {"title": "Science", "issn": "1095-9203", "issn-l": "0036-8075", "volume": "380", "issue": "6643", "pages": "eabn2937"}, "abstract": "Thousands of genomic regions have been associated with heritable human diseases, but attempts to elucidate biological mechanisms are impeded by an inability to discern which genomic positions are functionally important. Evolutionary constraint is a powerful predictor of function, agnostic to cell type or disease mechanism. Single-base phyloP scores from 240 mammals identified 3.3% of the human genome as significantly constrained and likely functional. We compared phyloP scores to genome annotation, association studies, copy-number variation, clinical genetics findings, and cancer data. Constrained positions are enriched for variants that explain common disease heritability more than other functional annotations. Our results improve variant annotation but also highlight that the regulatory landscape of the human genome still needs to be further explored and linked to disease.", "doi": "10.1126/science.abn2937", "pmid": "37104612", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "mid", "key": "NIHMS1897004"}, {"db": "pmc", "key": "PMC10259825"}], "notes": [], "created": "2023-12-01T08:54:10.456Z", "modified": "2024-01-16T13:48:33.619Z"}, {"entity": "publication", "iuid": "d7e4da3ff4c54966b53e2e1210128441", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d7e4da3ff4c54966b53e2e1210128441.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d7e4da3ff4c54966b53e2e1210128441"}}, "title": "Evolutionary constraint and innovation across hundreds of placental mammals.", "authors": 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"https://publications.scilifelab.se/researcher/74c6c6b31d4e49628a2a74a1f7377ce5.json"}}, {"family": "Supple", "given": "Megan A", "initials": "MA", "orcid": "0000-0002-0204-7852", "researcher": {"href": "https://publications.scilifelab.se/researcher/68aab878c786406da6d8810c1ca6eb04.json"}}, {"family": "Wilder", "given": "Aryn P", "initials": "AP", "orcid": "0000-0003-4970-6891", "researcher": {"href": "https://publications.scilifelab.se/researcher/582a7c9cf0214c8b9063df22f49910d5.json"}}, {"family": "Wirthlin", "given": "Morgan E", "initials": "ME", "orcid": "0000-0001-7967-7070", "researcher": {"href": "https://publications.scilifelab.se/researcher/d37d43eda07f49fa8f44adf0d1f41b5a.json"}}, {"family": "Xue", "given": "James R", "initials": "JR", "orcid": "0000-0002-3332-5747", "researcher": {"href": "https://publications.scilifelab.se/researcher/c910e64598674d5da576b3b5057afb43.json"}}, {"family": "Zoonomia Consortium\u00a7", "given": "", "initials": ""}, {"family": "Birren", "given": "Bruce W", "initials": "BW"}, {"family": "Gazal", "given": "Steven", "initials": "S", "orcid": "0000-0003-4510-5730", "researcher": {"href": "https://publications.scilifelab.se/researcher/fecc8307017145088589536e3c312515.json"}}, {"family": "Hubley", "given": "Robert M", "initials": "RM", "orcid": "0000-0001-9261-3821", "researcher": {"href": "https://publications.scilifelab.se/researcher/76c6f83d0eb34efc9e50811d6af5a0b1.json"}}, {"family": "Koepfli", "given": "Klaus-Peter", "initials": "K"}, {"family": "Marques-Bonet", "given": "Tomas", "initials": "T", "orcid": "0000-0002-5597-3075", "researcher": {"href": "https://publications.scilifelab.se/researcher/b4ea50a4fe3147f3b979ccaa8a2a0de4.json"}}, {"family": "Meyer", "given": "Wynn K", "initials": "WK", "orcid": "0000-0001-7978-3877", "researcher": {"href": "https://publications.scilifelab.se/researcher/d168f23b63994217b3b082c3cd70561b.json"}}, {"family": "Nweeia", "given": "Martin", "initials": "M", "orcid": "0000-0001-7079-4123", "researcher": {"href": "https://publications.scilifelab.se/researcher/32d99c20badf4462b17eb73d543bd766.json"}}, {"family": "Sabeti", "given": "Pardis C", "initials": "PC", "orcid": "0000-0002-9843-1890", "researcher": {"href": "https://publications.scilifelab.se/researcher/7a05c59f83114ac68c7bd1a0930fa0c9.json"}}, {"family": "Shapiro", "given": "Beth", "initials": "B", "orcid": "0000-0002-2733-7776", "researcher": {"href": "https://publications.scilifelab.se/researcher/7e998b6760594d43b00e50c4f6a27d05.json"}}, {"family": "Smit", "given": "Arian F A", "initials": "AFA", "orcid": "0000-0003-2088-3165", "researcher": {"href": "https://publications.scilifelab.se/researcher/34068300dba84e9f80ffde962a8ca49b.json"}}, {"family": "Springer", "given": "Mark S", "initials": "MS", "orcid": "0000-0001-7335-6946", "researcher": {"href": "https://publications.scilifelab.se/researcher/fb2b4f352f9b4e8b9f20da68caa94912.json"}}, {"family": "Teeling", "given": "Emma C", "initials": "EC", "orcid": "0000-0002-3309-1346", "researcher": {"href": "https://publications.scilifelab.se/researcher/50529df15a684ed68e16de6aa981d3aa.json"}}, {"family": "Weng", "given": "Zhiping", "initials": "Z", "orcid": "0000-0002-3032-7966", "researcher": {"href": "https://publications.scilifelab.se/researcher/25ad44250cba4b0cba5250b07f764ba3.json"}}, {"family": "Hiller", "given": "Michael", "initials": "M", "orcid": "0000-0003-3024-1449", "researcher": {"href": "https://publications.scilifelab.se/researcher/c304600adfb24d45a7bd0c94f55d1f5b.json"}}, {"family": "Levesque", "given": "Danielle L", "initials": "DL", "orcid": "0000-0003-0132-8094", "researcher": {"href": "https://publications.scilifelab.se/researcher/c8f6270f0b104f8ba5d216b052d36a0c.json"}}, {"family": "Lewin", "given": "Harris A", "initials": "HA", "orcid": "0000-0002-1043-7287", "researcher": {"href": "https://publications.scilifelab.se/researcher/a2f6f17d3e4b4b7e8f47349bda4c1bb0.json"}}, {"family": "Murphy", "given": "William J", "initials": "WJ", "orcid": "0000-0003-3699-0723", "researcher": {"href": "https://publications.scilifelab.se/researcher/bedfc4bc5b6e421da56cfe2bebfa21f3.json"}}, {"family": "Navarro", "given": "Arcadi", "initials": "A", "orcid": "0000-0003-2162-8246", "researcher": {"href": "https://publications.scilifelab.se/researcher/c541642111d94cb8a682b1ff8bea41ac.json"}}, {"family": "Paten", "given": "Benedict", "initials": "B", "orcid": "0000-0001-8863-3539", "researcher": {"href": "https://publications.scilifelab.se/researcher/956ebe9c0b6e43d7ac2a568519f43431.json"}}, {"family": "Pollard", "given": "Katherine S", "initials": "KS", "orcid": "0000-0002-9870-6196", "researcher": {"href": "https://publications.scilifelab.se/researcher/bb2a865a28524f55bb5d9df3db79563f.json"}}, {"family": "Ray", "given": "David A", "initials": "DA", "orcid": "0000-0002-3340-3987", "researcher": {"href": "https://publications.scilifelab.se/researcher/1637808586b2454190e734d575cf0140.json"}}, {"family": "Ruf", "given": "Irina", "initials": "I", "orcid": "0000-0002-9728-1210", "researcher": {"href": "https://publications.scilifelab.se/researcher/838b4e91f9484f26a6dcc1404051a38a.json"}}, {"family": "Ryder", "given": "Oliver A", "initials": "OA", "orcid": "0000-0003-2427-763X", "researcher": {"href": "https://publications.scilifelab.se/researcher/7a55f8ea442f4168a8426ae4a2c43a46.json"}}, {"family": "Pfenning", "given": "Andreas R", "initials": "AR", "orcid": "0000-0002-3447-9801", "researcher": {"href": "https://publications.scilifelab.se/researcher/579e32fe57da4d738b7fbf0a57fb6faf.json"}}, {"family": "Lindblad-Toh", "given": "Kerstin", "initials": "K", "orcid": "0000-0001-8338-0253", "researcher": {"href": "https://publications.scilifelab.se/researcher/e0063145f7d6476f80ab42f94833f4cf.json"}}, {"family": "Karlsson", "given": "Elinor K", "initials": "EK", "orcid": "0000-0002-4343-3776", "researcher": {"href": "https://publications.scilifelab.se/researcher/2bd97378a1cc403db0923895adde15e3.json"}}], "type": "journal article", "published": "2023-04-28", "journal": {"title": "Science", "issn": "1095-9203", "issn-l": "0036-8075", "volume": "380", "issue": "6643", "pages": "eabn3943"}, "abstract": "Zoonomia is the largest comparative genomics resource for mammals produced to date. By aligning genomes for 240 species, we identify bases that, when mutated, are likely to affect fitness and alter disease risk. At least 332 million bases (~10.7%) in the human genome are unusually conserved across species (evolutionarily constrained) relative to neutrally evolving repeats, and 4552 ultraconserved elements are nearly perfectly conserved. Of 101 million significantly constrained single bases, 80% are outside protein-coding exons and half have no functional annotations in the Encyclopedia of DNA Elements (ENCODE) resource. Changes in genes and regulatory elements are associated with exceptional mammalian traits, such as hibernation, that could inform therapeutic development. Earth's vast and imperiled biodiversity offers distinctive power for identifying genetic variants that affect genome function and organismal phenotypes.", "doi": "10.1126/science.abn3943", "pmid": "37104599", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "mid", "key": "NIHMS1896905"}, {"db": "pmc", "key": "PMC10250106"}], "notes": [], "created": "2023-12-01T08:40:50.036Z", "modified": "2024-01-16T13:48:33.655Z"}, {"entity": "publication", "iuid": "de1b7b013894428fbdf16c8aaaec4514", "links": {"self": {"href": "https://publications.scilifelab.se/publication/de1b7b013894428fbdf16c8aaaec4514.json"}, "display": {"href": "https://publications.scilifelab.se/publication/de1b7b013894428fbdf16c8aaaec4514"}}, "title": "Bayesian model and selection signature analyses reveal risk factors for canine atopic dermatitis.", "authors": [{"family": "Tengvall", "given": "Katarina", "initials": "K", "orcid": "0000-0003-0424-3571", "researcher": {"href": "https://publications.scilifelab.se/researcher/59b02aaaf03b4cd39150c3034888c81d.json"}}, {"family": "Sundstr\u00f6m", "given": "Elisabeth", "initials": "E", "orcid": "0000-0001-9526-8541", "researcher": {"href": "https://publications.scilifelab.se/researcher/20f87b64e71b4a00a9474ec4d898601d.json"}}, {"family": "Wang", "given": "Chao", "initials": "C", "orcid": "0000-0003-3936-4023", "researcher": {"href": "https://publications.scilifelab.se/researcher/202a8fd115e14824809a362a7cfc5a41.json"}}, {"family": "Bergvall", "given": "Kerstin", "initials": "K"}, {"family": "Wallerman", "given": "Ola", "initials": "O"}, {"family": "Pederson", "given": "Eric", "initials": "E"}, {"family": "Karlsson", "given": "\u00c5sa", "initials": "\u00c5"}, {"family": "Harvey", "given": "Naomi D", "initials": "ND"}, {"family": "Blott", "given": "Sarah C", "initials": "SC"}, {"family": "Olby", "given": "Natasha", "initials": "N", "orcid": "0000-0003-1349-3484", "researcher": {"href": "https://publications.scilifelab.se/researcher/99d7ecf8e71a4b92b0da71f6a7c031eb.json"}}, {"family": "Olivry", "given": "Thierry", "initials": "T"}, {"family": "Brander", "given": "Gustaf", "initials": "G", "orcid": "0000-0002-9549-4909", "researcher": {"href": "https://publications.scilifelab.se/researcher/8c4831e82d3643c4b81e2359b6418066.json"}}, {"family": "Meadows", "given": "Jennifer R S", "initials": "JRS", "orcid": "0000-0002-0850-230X", "researcher": {"href": "https://publications.scilifelab.se/researcher/86acdca0104c4552880d5a7cb5ac6565.json"}}, {"family": "Roosje", "given": "Petra", "initials": "P"}, {"family": "Leeb", "given": "Tosso", "initials": "T", "orcid": "0000-0003-0553-4880", "researcher": {"href": "https://publications.scilifelab.se/researcher/0f3aab15785e4875a06b659c9ded0ddd.json"}}, {"family": "Hedhammar", "given": "\u00c5ke", "initials": "\u00c5"}, {"family": "Andersson", "given": "G\u00f6ran", "initials": "G", "orcid": "0000-0001-5131-3144", "researcher": {"href": "https://publications.scilifelab.se/researcher/39ce81c314db47c8ad63c3ed38dffcb3.json"}}, {"family": "Lindblad-Toh", "given": "Kerstin", "initials": "K", "orcid": "0000-0001-8338-0253", "researcher": {"href": "https://publications.scilifelab.se/researcher/e0063145f7d6476f80ab42f94833f4cf.json"}}], "type": "journal article", "published": "2022-12-08", "journal": {"title": "Commun Biol", "issn": "2399-3642", "volume": "5", "issue": "1", "pages": "1348", "issn-l": "2399-3642"}, "abstract": "Canine atopic dermatitis is an inflammatory skin disease with clinical similarities to human atopic dermatitis. Several dog breeds are at increased risk for developing this disease but previous genetic associations are poorly defined. To identify additional genetic risk factors for canine atopic dermatitis, we here apply a Bayesian mixture model adapted for mapping complex traits and a cross-population extended haplotype test to search for disease-associated loci and selective sweeps in four dog breeds at risk for atopic dermatitis. We define 15 associated loci and eight candidate regions under selection by comparing cases with controls. One associated locus is syntenic to the major genetic risk locus (Filaggrin locus) in human atopic dermatitis. One selection signal in common type Labrador retriever cases positions across the TBC1D1 gene (body weight) and one signal of selection in working type German shepherd controls overlaps the LRP1B gene (brain), near the KYNU gene (psoriasis). In conclusion, we identify candidate genes, including genes belonging to the same biological pathways across multiple loci, with potential relevance to the pathogenesis of canine atopic dermatitis. The results show genetic similarities between dog and human atopic dermatitis, and future across-species genetic comparisons are hereby further motivated.", "doi": "10.1038/s42003-022-04279-8", "pmid": "36482174", "labels": {"Bioinformatics Long-term Support WABI": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s42003-022-04279-8"}], "notes": [], "created": "2022-12-09T14:39:22.770Z", "modified": "2022-12-09T14:39:22.914Z"}, {"entity": "publication", "iuid": "28bea3b7207d47f79712b969b987d91b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/28bea3b7207d47f79712b969b987d91b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/28bea3b7207d47f79712b969b987d91b"}}, "title": "Contribution of Rare Genetic Variation to Disease Susceptibility in a Large Scandinavian Myositis Cohort.", "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": "Hultin Rosenberg", "given": "Lina", "initials": "L"}, {"family": "Karlsson", "given": "\u00c5sa", "initials": "\u00c5"}, {"family": "Pucholt", "given": "Pascal", "initials": "P", "orcid": "0000-0003-3342-1373", "researcher": {"href": "https://publications.scilifelab.se/researcher/61a214ff2d494b568cb6da944e858acf.json"}}, {"family": "Rothwell", "given": "Simon", "initials": "S", "orcid": "0000-0003-2123-9902", "researcher": {"href": "https://publications.scilifelab.se/researcher/b39ce853a3d041b68e4d4e82e64e3703.json"}}, {"family": "Alexsson", "given": "Andrei", "initials": "A"}, {"family": "Sandling", "given": "Johanna K", "initials": "JK", "orcid": "0000-0003-1382-2321", "researcher": {"href": "https://publications.scilifelab.se/researcher/9c7bae5a05ac47eeac96547ca7336767.json"}}, {"family": "Andersson", "given": "Helena", "initials": "H"}, {"family": "Cooper", "given": "Robert G", "initials": "RG"}, {"family": "Padyukov", "given": "Leonid", "initials": "L", "orcid": "0000-0003-2950-5670", "researcher": {"href": "https://publications.scilifelab.se/researcher/052dbef663f442f2a72161d634b9ce7d.json"}}, {"family": "Tj\u00e4rnlund", "given": "Anna", "initials": "A"}, {"family": "Dastmalchi", "given": "Maryam", "initials": "M"}, {"family": "ImmunoArray Development Consortium", "given": "", "initials": ""}, {"family": "DISSECT Consortium", "given": "", "initials": ""}, {"family": "Meadows", "given": "Jennifer R S", "initials": "JRS", "orcid": "0000-0002-0850-230X", "researcher": {"href": "https://publications.scilifelab.se/researcher/86acdca0104c4552880d5a7cb5ac6565.json"}}, {"family": "Pyndt Diederichsen", "given": "Louise", "initials": "L"}, {"family": "Molberg", "given": "\u00d8yvind", "initials": "\u00d8"}, {"family": "Chinoy", "given": "Hector", "initials": "H", "orcid": "0000-0001-6492-1288", "researcher": {"href": "https://publications.scilifelab.se/researcher/03b0a1d459104296baba3dedebf10e08.json"}}, {"family": "Lamb", "given": "Janine A", "initials": "JA", "orcid": "0000-0002-7248-0539", "researcher": {"href": "https://publications.scilifelab.se/researcher/290c4b3570124cbea63a99516c294da2.json"}}, {"family": "R\u00f6nnblom", "given": "Lars", "initials": "L", "orcid": "0000-0001-9403-6503", "researcher": {"href": "https://publications.scilifelab.se/researcher/053ed3b657124a1bab3a78dc685556e6.json"}}, {"family": "Lindblad-Toh", "given": "Kerstin", "initials": "K", "orcid": "0000-0001-8338-0253", "researcher": {"href": "https://publications.scilifelab.se/researcher/e0063145f7d6476f80ab42f94833f4cf.json"}}, {"family": "Lundberg", "given": "Ingrid E", "initials": "IE", "orcid": "0000-0002-6068-9212", "researcher": {"href": "https://publications.scilifelab.se/researcher/40f6c8e761a944b78e67f0e04453f78b.json"}}], "type": "journal article", "published": "2022-02-00", "journal": {"title": "Arthritis & rheumatology (Hoboken, N.J.)", "issn": "2326-5205", "volume": "74", "issue": "2", "pages": "342-352", "issn-l": "2326-5191"}, "abstract": "Idiopathic inflammatory myopathies (IIMs) are a heterogeneous group of complex autoimmune conditions characterized by inflammation in skeletal muscle and extramuscular compartments, and interferon (IFN) system activation. We undertook this study to examine the contribution of genetic variation to disease susceptibility and to identify novel avenues for research in IIMs.\n\nTargeted DNA sequencing was used to mine coding and potentially regulatory single nucleotide variants from ~1,900 immune-related genes in a Scandinavian case-control cohort of 454 IIM patients and 1,024 healthy controls. Gene-based aggregate testing, together with rare variant- and gene-level enrichment analyses, was implemented to explore genotype-phenotype relations.\n\nGene-based aggregate tests of all variants, including rare variants, identified IFI35 as a potential genetic risk locus for IIMs, suggesting a genetic signature of type I IFN pathway activation. Functional annotation of the IFI35 locus highlighted a regulatory network linked to the skeletal muscle-specific gene PTGES3L, as a potential candidate for IIM pathogenesis. Aggregate genetic associations with AGER and PSMB8 in the major histocompatibility complex locus were detected in the antisynthetase syndrome subgroup, which also showed a less marked genetic signature of the type I IFN pathway. Enrichment analyses indicated a burden of synonymous and noncoding rare variants in IIM patients, suggesting increased disease predisposition associated with these classes of rare variants.\n\nOur study suggests the contribution of rare genetic variation to disease susceptibility in IIM and specific patient subgroups, and pinpoints genetic associations consistent with previous findings by gene expression profiling. These features highlight genetic profiles that are potentially relevant to disease pathogenesis.", "doi": "10.1002/art.41929", "pmid": "34279065", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2023-11-27T21:41:26.094Z", "modified": "2024-01-16T13:48:37.654Z"}, {"entity": "publication", "iuid": "e5924e2e04a64152ac970d7f2353229e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e5924e2e04a64152ac970d7f2353229e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e5924e2e04a64152ac970d7f2353229e"}}, "title": "A novel canine reference genome resolves genomic architecture and uncovers transcript complexity.", "authors": [{"family": "Wang", "given": "Chao", "initials": "C", "orcid": "0000-0003-3936-4023", "researcher": {"href": "https://publications.scilifelab.se/researcher/202a8fd115e14824809a362a7cfc5a41.json"}}, {"family": "Wallerman", "given": "Ola", "initials": "O"}, {"family": "Arendt", "given": "Maja-Louise", "initials": "ML"}, {"family": "Sundstr\u00f6m", "given": "Elisabeth", "initials": "E", "orcid": "0000-0001-9526-8541", "researcher": {"href": "https://publications.scilifelab.se/researcher/20f87b64e71b4a00a9474ec4d898601d.json"}}, {"family": "Karlsson", "given": "\u00c5sa", "initials": "\u00c5"}, {"family": "Nordin", "given": "Jessika", "initials": "J", "orcid": "0000-0002-8414-2190", "researcher": {"href": "https://publications.scilifelab.se/researcher/2603df7f3ff84e6980605b9e8eef4c2f.json"}}, {"family": "M\u00e4kel\u00e4inen", "given": "Suvi", "initials": "S", "orcid": "0000-0001-7378-4991", "researcher": {"href": "https://publications.scilifelab.se/researcher/1b1f91bf7dcd466a9814effddf67976e.json"}}, {"family": "Pielberg", "given": "Gerli Rosengren", "initials": "GR"}, {"family": "Hanson", "given": "Jeanette", "initials": "J"}, {"family": "Ohlsson", "given": "\u00c5sa", "initials": "\u00c5"}, {"family": "Saellstr\u00f6m", "given": "Sara", "initials": "S", "orcid": "0000-0001-5253-5830", "researcher": {"href": "https://publications.scilifelab.se/researcher/aac98530437d4d6890dffcbd31eabde0.json"}}, {"family": "R\u00f6nnberg", "given": "Henrik", "initials": "H", "orcid": "0000-0001-6098-5364", "researcher": {"href": "https://publications.scilifelab.se/researcher/8f8783f23d664f4b98ef8f6ff03b6693.json"}}, {"family": "Ljungvall", "given": "Ingrid", "initials": "I"}, {"family": "H\u00e4ggstr\u00f6m", "given": "Jens", "initials": "J"}, {"family": "Bergstr\u00f6m", "given": "Tomas F", "initials": "TF", "orcid": "0000-0002-7480-2669", "researcher": {"href": "https://publications.scilifelab.se/researcher/b590797209ee4feab6302920621fc621.json"}}, {"family": "Hedhammar", "given": "\u00c5ke", "initials": "\u00c5"}, {"family": "Meadows", "given": "Jennifer R S", "initials": "JRS", "orcid": "0000-0002-0850-230X", "researcher": {"href": "https://publications.scilifelab.se/researcher/86acdca0104c4552880d5a7cb5ac6565.json"}}, {"family": "Lindblad-Toh", "given": "Kerstin", "initials": "K", "orcid": "0000-0001-8338-0253", "researcher": {"href": "https://publications.scilifelab.se/researcher/e0063145f7d6476f80ab42f94833f4cf.json"}}], "type": "comparative study", "published": "2021-02-10", "journal": {"title": "Commun Biol", "issn": "2399-3642", "issn-l": "2399-3642", "volume": "4", "issue": "1", "pages": "185"}, "abstract": "We present GSD_1.0, a high-quality domestic dog reference genome with chromosome length scaffolds and contiguity increased 55-fold over CanFam3.1. Annotation with generated and existing long and short read RNA-seq, miRNA-seq and ATAC-seq, revealed that 32.1% of lifted over CanFam3.1 gaps harboured previously hidden functional elements, including promoters, genes and miRNAs in GSD_1.0. A catalogue of canine \"dark\" regions was made to facilitate mapping rescue. Alignment in these regions is difficult, but we demonstrate that they harbour trait-associated variation. Key genomic regions were completed, including the Dog Leucocyte Antigen (DLA), T Cell Receptor (TCR) and 366 COSMIC cancer genes. 10x linked-read sequencing of 27 dogs (19 breeds) uncovered 22.1 million SNPs, indels and larger structural variants. Subsequent intersection with protein coding genes showed that 1.4% of these could directly influence gene products, and so provide a source of normal or aberrant phenotypic modifications.", "doi": "10.1038/s42003-021-01698-x", "pmid": "33568770", "labels": {"NGI Uppsala (Uppsala Genome Center)": "Service", "National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s42003-021-01698-x"}, {"db": "pmc", "key": "PMC7875987"}], "notes": [], "created": "2021-02-17T19:15:39.689Z", "modified": "2024-01-16T13:48:40.742Z"}]}