{"entity": "researcher", "timestamp": "2026-09-23T15:08:27.140Z", "family": "Bianchi", "given": "Matteo", "initials": "M", "orcid": "0000-0003-3394-6495", "affiliations": ["Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, 751 32 Uppsala, Sweden."], "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/researcher/3183e335a393486f8b6534db17b066d0.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/researcher/3183e335a393486f8b6534db17b066d0"}}, "publications": [{"entity": "publication", "iuid": "f8942a7836cc47c9ac266895832ee8f9", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/f8942a7836cc47c9ac266895832ee8f9.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/f8942a7836cc47c9ac266895832ee8f9"}}, "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-affiliated.scilifelab.se/researcher/3183e335a393486f8b6534db17b066d0.json"}}, {"family": "Kozyrev", "given": "Sergey V", "initials": "SV", "orcid": "0000-0001-6209-4100", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/cef7ddc40d8f47468f3f3dec3caa5de3.json"}}, {"family": "Notarnicola", "given": "Antonella", "initials": "A", "orcid": "0000-0003-0272-2931", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/708cd9cafb384ed29732f2c5fb1a17bd.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-affiliated.scilifelab.se/researcher/a9fcc24622ec440bac6996072cceea0e.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-affiliated.scilifelab.se/researcher/1c8c4d669b3942309a148980c1437b5d.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-affiliated.scilifelab.se/researcher/2c44ebd4f33e46a1862877bce94be05b.json"}}, {"family": "Enocsson", "given": "Helena", "initials": "H", "orcid": "0000-0002-2125-2931", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/174462ef4f7c4f6381aa2fd4cc29569d.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-affiliated.scilifelab.se/researcher/0db5190dbe894a5e9cd961e66ba5c75d.json"}}, {"family": "Nordmark", "given": "Gunnel", "initials": "G", "orcid": "0000-0002-3829-7431", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f618934952594d76a747bcbe2c27bbf2.json"}}, {"family": "Lundberg", "given": "Ingrid E", "initials": "IE", "orcid": "0000-0002-6068-9212", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a2891140c49d446dbd82c96857bcde73.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": [], "xrefs": [{"db": "pmc", "key": "PMC11782108"}], "notes": [], "created": "2026-09-23T12:19:32.987Z", "modified": "2026-09-23T12:19:33.106Z"}, {"entity": "publication", "iuid": "919b592edda54099a0b4b37338ab2000", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/919b592edda54099a0b4b37338ab2000.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/919b592edda54099a0b4b37338ab2000"}}, "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-affiliated.scilifelab.se/researcher/9f363e8d74594ffeb0d68aa6d774b242.json"}}, {"family": "Kidd", "given": "Jeffrey M", "initials": "JM", "orcid": "0000-0002-9631-1465", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/87d00735bd48420896025e5e52aa7298.json"}}, {"family": "Wang", "given": "Guo-Dong", "initials": "GD", "orcid": "0000-0002-9407-4363", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/61a7c21f358b4feea0ec783219f7ac42.json"}}, {"family": "Parker", "given": "Heidi G", "initials": "HG", "orcid": "0000-0002-9707-6380", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8bbe68238e524a85bdf7f2556b61301f.json"}}, {"family": "Schall", "given": "Peter Z", "initials": "PZ", "orcid": "0000-0003-1016-6998", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/81d0ab278ec44c4b83e1180740fa9a26.json"}}, {"family": "Bianchi", "given": "Matteo", "initials": "M", "orcid": "0000-0003-3394-6495", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3183e335a393486f8b6534db17b066d0.json"}}, {"family": "Christmas", "given": "Matthew J", "initials": "MJ", "orcid": "0000-0002-6355-7581", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/997ea196d4ae4c9790a715246dbfac82.json"}}, {"family": "Bougiouri", "given": "Katia", "initials": "K", "orcid": "0000-0002-7890-2755", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/14fbc8f63c084c1f948d7f819c7e4be8.json"}}, {"family": "Buckley", "given": "Reuben M", "initials": "RM", "orcid": "0000-0001-6334-3906", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/52f6dd32f4b9457b82e1f381b36657f8.json"}}, {"family": "Hitte", "given": "Christophe", "initials": "C", "orcid": "0000-0003-1714-437X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b2aec5eba577458badfa5f3e9da2c7e2.json"}}, {"family": "Nguyen", "given": "Anthony K", "initials": "AK", "orcid": "0000-0002-9634-1904", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/19d1cf1c2d5f4529b41628766ccb2cd8.json"}}, {"family": "Wang", "given": "Chao", "initials": "C", "orcid": "0000-0003-3936-4023", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/cfac9dfcdfc04a88b002ffe4ee8a5bb4.json"}}, {"family": "Jagannathan", "given": "Vidhya", "initials": "V", "orcid": "0000-0002-8155-0041", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/61e55b7d7ff44bfa8c602463aff78927.json"}}, {"family": "Niskanen", "given": "Julia E", "initials": "JE", "orcid": "0000-0002-2871-6890", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4fe654ab4f7443a69dd17a6b43c79f47.json"}}, {"family": "Frantz", "given": "Laurent A F", "initials": "LAF", "orcid": "0000-0001-8030-3885", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/268c91b6ad33496da684e340f543862c.json"}}, {"family": "Arumilli", "given": "Meharji", "initials": "M"}, {"family": "Hundi", "given": "Sruthi", "initials": "S", "orcid": "0000-0002-5803-1841", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5637e79b33854d3eb24d9cb1e16786bd.json"}}, {"family": "Lindblad-Toh", "given": "Kerstin", "initials": "K", "orcid": "0000-0001-8338-0253", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/612a779b69494f1ca9b6c5f1d84fd711.json"}}, {"family": "Ginja", "given": "Catarina", "initials": "C", "orcid": "0000-0003-2278-7089", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/fb9e7853817d4232b6bf2c81f2d1f4a9.json"}}, {"family": "Agustina", "given": "Kadek Karang", "initials": "KK", "orcid": "0000-0002-7128-0914", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/82ae61c2ab1e4aa1af4eedae1c5c9fbb.json"}}, {"family": "Andr\u00e9", "given": "Catherine", "initials": "C"}, {"family": "Boyko", "given": "Adam R", "initials": "AR", "orcid": "0000-0002-9125-6874", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/93514d8cc7b945619ed50443e7ca6030.json"}}, {"family": "Davis", "given": "Brian W", "initials": "BW", "orcid": "0000-0002-6121-135X", "researcher": {"href": 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"researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e1389bbb3ba141598a0a896b056dea89.json"}}, {"family": "Kalthoff", "given": "Daniela C", "initials": "DC", "orcid": "0000-0003-2439-5484", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/fbf95ba94cfa41ef8a2ad3e8e34d23cf.json"}}, {"family": "Liu", "given": "Yan-Hu", "initials": "YH", "orcid": "0000-0001-9991-4571", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8fb30cae56ae46528587c81431298e7f.json"}}, {"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-affiliated.scilifelab.se/researcher/0f6a7202e66442a882c5ff8760dc761e.json"}}, {"family": "Racimo", "given": "Fernando", "initials": "F", "orcid": "0000-0002-5025-2607", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ea20be00d9a149568c27a0e5d0f66c9f.json"}}, {"family": "Ramos-Almodovar", "given": "Fabian", "initials": "F", "orcid": "0000-0001-9094-7895", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b43257be391040d8a140a60258987f9c.json"}}, {"family": "Savolainen", "given": "Peter", "initials": "P", "orcid": "0000-0002-1495-8338", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/06353af3236049c4988c0bb038443a96.json"}}, {"family": "Venetsani", "given": "Semina", "initials": "S"}, {"family": "Tammen", "given": "Imke", "initials": "I", "orcid": "0000-0002-5520-6597", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1f46ec5759b447068f4ffbe2731ad9d0.json"}}, {"family": "Triantafyllidis", "given": "Alexandros", "initials": "A", "orcid": "0000-0003-0469-011X", "researcher": {"href": 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"initials": "H", "orcid": "0000-0003-1087-5532", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/eab428714c9f4f5eb0de63ffc7500f25.json"}}, {"family": "Leeb", "given": "Tosso", "initials": "T", "orcid": "0000-0003-0553-4880", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8b9a5b55628740d99bdb37372a1c37b3.json"}}, {"family": "Zhang", "given": "Ya-Ping", "initials": "YP", "orcid": "0000-0002-5401-1114", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/08315abecebf43c0adc5874c44e3cf11.json"}}, {"family": "Ostrander", "given": "Elaine A", "initials": "EA", "orcid": "0000-0001-6075-9738", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/cb08ca2565ce45c9adfa484cf60b2909.json"}}], "type": "journal article", "published": "2023-08-15", "journal": {"title": "Genome Biol.", "issn": "1474-760X", "volume": "24", "issue": "1", "pages": "187", "issn-l": "1474-7596"}, "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.\n\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.\n\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": [], "xrefs": [{"db": "pmc", "key": "PMC10426128"}, {"db": "pii", "key": "10.1186/s13059-023-03023-7"}], "notes": [], "created": "2026-09-23T07:32:42.444Z", "modified": "2026-09-23T07:32:43.598Z"}, {"entity": "publication", "iuid": "399b546bde564b2c882cf3737f1c30f8", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/399b546bde564b2c882cf3737f1c30f8.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/399b546bde564b2c882cf3737f1c30f8"}}, "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-affiliated.scilifelab.se/researcher/0c59458e7834499cbe990b1f9b83236c.json"}}, {"family": "Meadows", "given": "Jennifer R S", 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article", "published": "2023-04-28", "journal": {"title": "Science (New York, N.Y.)", "issn": "1095-9203", "volume": "380", "issue": "6643", "pages": "eabn2937", "issn-l": "0036-8075"}, "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": [], "xrefs": [{"db": "mid", "key": "NIHMS1897004"}, {"db": "pmc", "key": "PMC10259825"}], "notes": [], "created": "2026-09-23T07:35:15.983Z", "modified": "2026-09-23T07:35:16.500Z"}, {"entity": "publication", "iuid": "b9fd8cd4df2f4cfd90ea1c40bf40619e", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/b9fd8cd4df2f4cfd90ea1c40bf40619e.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/b9fd8cd4df2f4cfd90ea1c40bf40619e"}}, "title": "Evolutionary constraint and innovation across hundreds of placental mammals.", "authors": [{"family": "Christmas", "given": "Matthew J", "initials": "MJ", "orcid": "0000-0002-6355-7581", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/997ea196d4ae4c9790a715246dbfac82.json"}}, {"family": "Kaplow", "given": "Irene M", "initials": "IM", "orcid": "0000-0002-8924-8269", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4fc8b6ee363a4ccaaea909392715888a.json"}}, {"family": "Genereux", "given": "Diane P", "initials": "DP", "orcid": "0000-0001-5770-0989", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/352ee25047c544aaa486a69e7e3333fc.json"}}, {"family": "Dong", "given": "Michael X", "initials": "MX", "orcid": "0000-0003-4084-3099", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/acaddec22cd64c8aaec92764cd4adf08.json"}}, {"family": "Hughes", "given": "Graham M", "initials": "GM", "orcid": "0000-0003-3088-345X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9785e94b95a3466dbb70ad8eb9b34ccd.json"}}, {"family": "Li", "given": "Xue", 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"https://publications-affiliated.scilifelab.se/researcher/7b1757207aa24108859d7c116bda19b7.json"}}, {"family": "Xue", "given": "James R", "initials": "JR", "orcid": "0000-0002-3332-5747", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bd4a26d78f1547c7865cab2847ab0d6b.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-affiliated.scilifelab.se/researcher/992edd7528434c7b900b8d531f18b15c.json"}}, {"family": "Hubley", "given": "Robert M", "initials": "RM", "orcid": "0000-0001-9261-3821", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/86b6fe3c9be54bc58dd8c750dda51aa3.json"}}, {"family": "Koepfli", "given": "Klaus-Peter", "initials": "KP"}, {"family": "Marques-Bonet", "given": "Tomas", "initials": "T", "orcid": "0000-0002-5597-3075", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1091cb5bfe394d459969d24bb1c22c66.json"}}, {"family": "Meyer", "given": "Wynn K", "initials": "WK", "orcid": "0000-0001-7978-3877", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4b1fba9de46a4c8c8cbbbec685a9b94c.json"}}, {"family": "Nweeia", "given": "Martin", "initials": "M", "orcid": "0000-0001-7079-4123", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b4846b6d146a4a7288db1543583a0158.json"}}, {"family": "Sabeti", "given": "Pardis C", "initials": "PC", "orcid": "0000-0002-9843-1890", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6848f42df6b146df8fd953c169193eb4.json"}}, {"family": "Shapiro", "given": "Beth", "initials": "B", "orcid": "0000-0002-2733-7776", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8f15a636469944ddb56489a74a75591b.json"}}, {"family": "Smit", "given": "Arian F A", "initials": "AFA", "orcid": "0000-0003-2088-3165", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ddf0080c6ee44cbe830114f0ab126884.json"}}, {"family": "Springer", "given": "Mark S", "initials": "MS", "orcid": "0000-0001-7335-6946", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/93985cf0515345b8b302228258be970e.json"}}, {"family": "Teeling", "given": "Emma C", "initials": "EC", "orcid": "0000-0002-3309-1346", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/28069443db794cb596e58aea060d9dea.json"}}, {"family": "Weng", "given": "Zhiping", "initials": "Z", "orcid": "0000-0002-3032-7966", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/22242b8810024fa6b7c098ced475db12.json"}}, {"family": "Hiller", "given": "Michael", "initials": "M", "orcid": "0000-0003-3024-1449", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1005d0d1f4264b46b1cfe214c7aca246.json"}}, {"family": "Levesque", "given": "Danielle L", "initials": "DL", "orcid": "0000-0003-0132-8094", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/291c0db9f1014708bfe1c52a946e1df7.json"}}, {"family": "Lewin", "given": "Harris A", "initials": "HA", "orcid": "0000-0002-1043-7287", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5059da24204049c696aec45b62526759.json"}}, {"family": "Murphy", "given": "William J", "initials": "WJ", "orcid": "0000-0003-3699-0723", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6a71bcbcd8a6437ea7c32ce512ebd38c.json"}}, {"family": "Navarro", "given": "Arcadi", "initials": "A", "orcid": "0000-0003-2162-8246", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b8360a54a1b447d0b67d85b3f1e40b5a.json"}}, {"family": "Paten", "given": "Benedict", "initials": "B", "orcid": "0000-0001-8863-3539", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c916e24b35f2459480cf87e27bb21ee1.json"}}, {"family": "Pollard", "given": "Katherine S", "initials": "KS", "orcid": "0000-0002-9870-6196", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8d080bc9bff548958f0c161612cdc4cf.json"}}, {"family": "Ray", "given": "David A", "initials": "DA", "orcid": "0000-0002-3340-3987", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d6392a5497414b98999823cbafd67d4b.json"}}, {"family": "Ruf", "given": "Irina", "initials": "I", "orcid": "0000-0002-9728-1210", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/cbc58d9ceb8d490baab61cb6002cecbe.json"}}, {"family": "Ryder", "given": "Oliver A", "initials": "OA", "orcid": "0000-0003-2427-763X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3d18635ed6fa42d4bbcfddadae70e308.json"}}, {"family": "Pfenning", "given": "Andreas R", "initials": "AR", "orcid": "0000-0002-3447-9801", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5f7c2be6e32147d19f03c7ff88fb3f80.json"}}, {"family": "Lindblad-Toh", "given": "Kerstin", "initials": "K", "orcid": "0000-0001-8338-0253", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/612a779b69494f1ca9b6c5f1d84fd711.json"}}, {"family": "Karlsson", "given": "Elinor K", "initials": "EK", "orcid": "0000-0002-4343-3776", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/81b5c82fcb904394b6a6b1d811863fa0.json"}}], "type": "journal article", "published": "2023-04-28", "journal": {"title": "Science (New York, N.Y.)", "issn": "1095-9203", "volume": "380", "issue": "6643", "pages": "eabn3943", "issn-l": "0036-8075"}, "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": [], "xrefs": [{"db": "mid", "key": "NIHMS1896905"}, {"db": "pmc", "key": "PMC10250106"}], "notes": [], "created": "2026-09-23T06:39:33.319Z", "modified": "2026-09-23T06:39:34.893Z"}, {"entity": "publication", "iuid": "e1ece15c11e14b8d8cd0d18214fda961", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/e1ece15c11e14b8d8cd0d18214fda961.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/e1ece15c11e14b8d8cd0d18214fda961"}}, "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-affiliated.scilifelab.se/researcher/3183e335a393486f8b6534db17b066d0.json"}}, {"family": "Kozyrev", "given": "Sergey V", "initials": "SV", "orcid": "0000-0001-6209-4100", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/cef7ddc40d8f47468f3f3dec3caa5de3.json"}}, {"family": "Notarnicola", "given": "Antonella", "initials": "A", "orcid": "0000-0003-0272-2931", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/708cd9cafb384ed29732f2c5fb1a17bd.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-affiliated.scilifelab.se/researcher/b8d564c4e36f451f9b78f563c9e8fa07.json"}}, {"family": "Rothwell", "given": "Simon", "initials": "S", "orcid": "0000-0003-2123-9902", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6e28d139b79e4cf9a76140fd2ae830b3.json"}}, {"family": "Alexsson", "given": "Andrei", "initials": "A"}, {"family": "Sandling", "given": "Johanna K", "initials": "JK", "orcid": "0000-0003-1382-2321", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c5bbdb0cf40c48198ea04ede2fb33377.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-affiliated.scilifelab.se/researcher/336dfd4ed41542338e3aae1e29ce1da2.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-affiliated.scilifelab.se/researcher/9f363e8d74594ffeb0d68aa6d774b242.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-affiliated.scilifelab.se/researcher/d3d7de322dd44925adf4ffdc01365f8f.json"}}, {"family": "Lamb", "given": "Janine A", "initials": "JA", "orcid": "0000-0002-7248-0539", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/07cd7a5b44b54240aa81d5f257743da4.json"}}, {"family": "R\u00f6nnblom", "given": "Lars", "initials": "L", "orcid": "0000-0001-9403-6503", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5f7ec7a7befd44cc988091ba0858d3c0.json"}}, {"family": "Lindblad-Toh", "given": "Kerstin", "initials": "K", "orcid": "0000-0001-8338-0253", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/612a779b69494f1ca9b6c5f1d84fd711.json"}}, {"family": "Lundberg", "given": "Ingrid E", "initials": "IE", "orcid": "0000-0002-6068-9212", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a2891140c49d446dbd82c96857bcde73.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": [], "xrefs": [], "notes": [], "created": "2026-09-23T12:01:09.322Z", "modified": "2026-09-23T12:01:09.576Z"}, {"entity": "publication", "iuid": "f3cc367b842743f2be0b5d19deede9d4", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/f3cc367b842743f2be0b5d19deede9d4.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/f3cc367b842743f2be0b5d19deede9d4"}}, "title": "Whole-genome genotyping and resequencing reveal the association of a deletion in the complex interferon alpha gene cluster with hypothyroidism in dogs.", "authors": [{"family": "Bianchi", "given": "Matteo", "initials": "M", "orcid": "0000-0003-3394-6495", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3183e335a393486f8b6534db17b066d0.json"}}, {"family": "Rafati", "given": "Nima", "initials": "N"}, {"family": "Karlsson", "given": "\u00c5sa", "initials": "\u00c5"}, {"family": "Mur\u00e9n", "given": "Eva", "initials": "E"}, {"family": "Rubin", "given": "Carl-Johan", "initials": "CJ"}, {"family": "Sundberg", "given": "Katarina", "initials": "K"}, {"family": "Andersson", "given": "G\u00f6ran", "initials": "G"}, {"family": "K\u00e4mpe", "given": "Olle", "initials": "O"}, {"family": "Hedhammar", "given": "\u00c5ke", "initials": "\u00c5"}, {"family": "Lindblad-Toh", "given": "Kerstin", "initials": "K"}, {"family": "Rosengren Pielberg", "given": "Gerli", "initials": "G"}], "type": "journal article", "published": "2020-04-16", "journal": {"title": "BMC Genomics", "issn": "1471-2164", "volume": "21", "issue": "1", "pages": "307", "issn-l": "1471-2164"}, "abstract": "Hypothyroidism is a common complex endocrinopathy that typically has an autoimmune etiology, and it affects both humans and dogs. Genetic and environmental factors are both known to play important roles in the disease development. In this study, we sought to identify the genetic risk factors potentially involved in the susceptibility to the disease in the high-risk Giant Schnauzer dog breed.\n\nBy employing genome-wide association followed by fine-mapping (top variant p-value = 5.7 \u00d7 10- 6), integrated with whole-genome resequencing and copy number variation analysis, we detected a ~ 8.9 kbp deletion strongly associated (p-value = 0.0001) with protection against development of hypothyroidism. The deletion is located between two predicted Interferon alpha (IFNA) genes and it may eliminate functional elements potentially involved in the transcriptional regulation of these genes. Remarkably, type I IFNs have been extensively associated to human autoimmune hypothyroidism and general autoimmunity. Nonetheless, the extreme genomic complexity of the associated region on CFA11 warrants further long-read sequencing and annotation efforts in order to ascribe functions to the identified deletion and to characterize the canine IFNA gene cluster in more detail.\n\nOur results expand the current knowledge on genetic determinants of canine hypothyroidism by revealing a significant link with the human counterpart disease, potentially translating into better diagnostic tools across species, and may contribute to improved canine breeding strategies.", "doi": "10.1186/s12864-020-6700-3", "pmid": "32299354", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC7160888"}, {"db": "pii", "key": "10.1186/s12864-020-6700-3"}], "notes": [], "created": "2026-09-23T12:46:59.183Z", "modified": "2026-09-23T12:46:59.218Z"}]}