{"entity": "researcher", "timestamp": "2026-08-13T19:20:47.157Z", "family": "Wang", "given": "Chao", "initials": "C", "orcid": "0000-0003-3936-4023", "affiliations": ["Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden. chao.wang@imbim.uu.se."], "links": {"self": {"href": "https://publications.scilifelab.se/researcher/202a8fd115e14824809a362a7cfc5a41.json"}, "display": {"href": "https://publications.scilifelab.se/researcher/202a8fd115e14824809a362a7cfc5a41"}}, "publications": [{"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": "Meadows", "given": "Jennifer R S", "initials": "JRS", "orcid": "0000-0002-0850-230X", "researcher": {"href": "https://publications.scilifelab.se/researcher/86acdca0104c4552880d5a7cb5ac6565.json"}}, {"family": "Gazal", "given": "Steven", "initials": "S", "orcid": "0000-0003-4510-5730", "researcher": {"href": "https://publications.scilifelab.se/researcher/fecc8307017145088589536e3c312515.json"}}, {"family": "Phan", "given": "BaDoi N", "initials": "BN", "orcid": "0000-0001-6331-5980", "researcher": {"href": "https://publications.scilifelab.se/researcher/b9e37df4e5c54204a19ea394e1f7651e.json"}}, {"family": "Li", "given": "Xue", "initials": "X", "orcid": "0000-0002-9126-2692", "researcher": {"href": "https://publications.scilifelab.se/researcher/bfa777bbc9d34c0e9f4920decc7cdcb3.json"}}, {"family": "Genereux", "given": "Diane P", "initials": "DP", "orcid": "0000-0001-5770-0989", "researcher": {"href": "https://publications.scilifelab.se/researcher/0dedda53aab044eabd09ae377084ff9d.json"}}, {"family": "Dong", "given": "Michael X", "initials": "MX", "orcid": "0000-0003-4084-3099", "researcher": {"href": "https://publications.scilifelab.se/researcher/d44d219b319346c481c82d69d5055cd8.json"}}, {"family": "Bianchi", "given": "Matteo", "initials": "M", "orcid": "0000-0003-3394-6495", "researcher": {"href": "https://publications.scilifelab.se/researcher/d645ef0e04a245f0ac9e7d7498b2bd69.json"}}, {"family": "Andrews", "given": "Gregory", "initials": "G", "orcid": "0000-0002-9880-3965", "researcher": {"href": "https://publications.scilifelab.se/researcher/3f84c888473d45ea8d8e97945d508705.json"}}, {"family": "Sakthikumar", "given": "Sharadha", "initials": "S", "orcid": "0000-0002-7746-8264", "researcher": {"href": "https://publications.scilifelab.se/researcher/538c86311b2549d6a5214a5562578cc2.json"}}, {"family": "Nordin", "given": "Jessika", "initials": "J", "orcid": "0000-0002-8414-2190", "researcher": {"href": "https://publications.scilifelab.se/researcher/2603df7f3ff84e6980605b9e8eef4c2f.json"}}, {"family": "Roy", "given": "Ananya", "initials": "A"}, {"family": "Christmas", "given": "Matthew J", "initials": "MJ", "orcid": "0000-0002-6355-7581", "researcher": {"href": "https://publications.scilifelab.se/researcher/76e069a0271e4a1fbc31fd3cb440366f.json"}}, {"family": "Marinescu", "given": "Voichita D", "initials": "VD", "orcid": "0000-0002-4803-4707", "researcher": {"href": "https://publications.scilifelab.se/researcher/087384bb1f8743158b76352c8847d48d.json"}}, {"family": "Wang", "given": "Chao", "initials": "C", "orcid": "0000-0003-3936-4023", "researcher": {"href": "https://publications.scilifelab.se/researcher/202a8fd115e14824809a362a7cfc5a41.json"}}, {"family": "Wallerman", "given": "Ola", "initials": "O", "orcid": "0000-0003-1037-7904", "researcher": {"href": "https://publications.scilifelab.se/researcher/9b32e1cfd3084b10a4c220416a6bc589.json"}}, {"family": "Xue", "given": "James", "initials": "J", "orcid": "0000-0002-3332-5747", "researcher": {"href": "https://publications.scilifelab.se/researcher/c910e64598674d5da576b3b5057afb43.json"}}, {"family": "Yao", "given": "Shuyang", "initials": "S", "orcid": "0000-0001-9669-4470", "researcher": {"href": "https://publications.scilifelab.se/researcher/fcd036ee020e4622ad16d020bfcd7b38.json"}}, {"family": "Sun", "given": "Quan", "initials": "Q", "orcid": "0000-0001-8324-2803", "researcher": {"href": "https://publications.scilifelab.se/researcher/ed5ee3899858449cae82e6be2e6faca6.json"}}, {"family": "Szatkiewicz", "given": "Jin", "initials": "J", "orcid": "0000-0002-4898-7401", "researcher": {"href": "https://publications.scilifelab.se/researcher/eb39edd3c6c14938a47f1e22ecfea080.json"}}, {"family": "Wen", "given": "Jia", "initials": "J"}, {"family": "Huckins", "given": "Laura M", "initials": "LM", "orcid": "0000-0002-5369-6502", "researcher": {"href": "https://publications.scilifelab.se/researcher/aef1cd06be604bc9ac483e888bf2235d.json"}}, {"family": "Lawler", "given": "Alyssa", "initials": "A", "orcid": "0000-0002-2151-5164", "researcher": {"href": "https://publications.scilifelab.se/researcher/9ac870df8d074925b9956e82fba828eb.json"}}, {"family": "Keough", "given": "Kathleen C", "initials": "KC", "orcid": "0000-0002-7481-0511", "researcher": {"href": "https://publications.scilifelab.se/researcher/60254d61d3d64a8e80eee17c1e3d24db.json"}}, {"family": "Zheng", "given": "Zhili", "initials": "Z", "orcid": "0000-0003-2102-221X", "researcher": {"href": "https://publications.scilifelab.se/researcher/d6856724cd504fca8624fc001f9e6381.json"}}, {"family": "Zeng", "given": "Jian", "initials": "J", "orcid": "0000-0001-8801-5220", "researcher": {"href": "https://publications.scilifelab.se/researcher/483f4a2875dd42a68b4f6f4e18c503ec.json"}}, {"family": "Wray", "given": "Naomi R", "initials": "NR", "orcid": "0000-0001-7421-3357", "researcher": {"href": "https://publications.scilifelab.se/researcher/15a175036d9f44f9b4090d7d431f78d7.json"}}, {"family": "Li", "given": "Yun", "initials": "Y", "orcid": "0000-0002-9275-4189", "researcher": {"href": "https://publications.scilifelab.se/researcher/c294ce82ce8946428048b9b4e3e9cad8.json"}}, {"family": "Johnson", "given": "Jessica", "initials": "J", "orcid": "0000-0002-4519-3120", "researcher": {"href": "https://publications.scilifelab.se/researcher/c2cc5da674c44d4cb58c1f98d145043a.json"}}, {"family": "Chen", "given": "Jiawen", "initials": "J", "orcid": "0000-0002-6193-534X", "researcher": {"href": "https://publications.scilifelab.se/researcher/39de15a492f34e4b8e237e748c38524b.json"}}, {"family": "Zoonomia Consortium\u00a7", "given": "", "initials": ""}, {"family": "Paten", "given": "Benedict", "initials": "B", "orcid": "0000-0001-8863-3539", "researcher": {"href": "https://publications.scilifelab.se/researcher/956ebe9c0b6e43d7ac2a568519f43431.json"}}, {"family": "Reilly", "given": "Steven K", "initials": "SK", "orcid": "0000-0003-3140-1483", "researcher": {"href": "https://publications.scilifelab.se/researcher/0c12bcf707394bb5b9c34075aba19f13.json"}}, {"family": "Hughes", "given": "Graham M", "initials": "GM", "orcid": "0000-0003-3088-345X", "researcher": {"href": "https://publications.scilifelab.se/researcher/800da869332a45b9b4c7bd8fd5522666.json"}}, {"family": "Weng", "given": "Zhiping", "initials": "Z", "orcid": "0000-0002-3032-7966", "researcher": {"href": "https://publications.scilifelab.se/researcher/25ad44250cba4b0cba5250b07f764ba3.json"}}, {"family": "Pollard", "given": "Katherine S", "initials": "KS", "orcid": "0000-0002-9870-6196", "researcher": {"href": "https://publications.scilifelab.se/researcher/bb2a865a28524f55bb5d9df3db79563f.json"}}, {"family": "Pfenning", "given": "Andreas R", "initials": "AR", "orcid": "0000-0002-3447-9801", "researcher": {"href": "https://publications.scilifelab.se/researcher/579e32fe57da4d738b7fbf0a57fb6faf.json"}}, {"family": "Forsberg-Nilsson", "given": "Karin", "initials": "K", "orcid": "0000-0003-0692-6245", "researcher": {"href": "https://publications.scilifelab.se/researcher/5da04859250141a0a7271a69c7da9176.json"}}, {"family": "Karlsson", "given": "Elinor K", "initials": "EK", "orcid": "0000-0002-4343-3776", "researcher": {"href": "https://publications.scilifelab.se/researcher/2bd97378a1cc403db0923895adde15e3.json"}}, {"family": "Lindblad-Toh", "given": "Kerstin", "initials": "K", "orcid": "0000-0001-8338-0253", "researcher": {"href": "https://publications.scilifelab.se/researcher/e0063145f7d6476f80ab42f94833f4cf.json"}}], "type": "journal article", "published": "2023-04-28", "journal": {"title": "Science", "issn": "1095-9203", "issn-l": "0036-8075", "volume": "380", "issue": "6643", "pages": "eabn2937"}, "abstract": "Thousands of genomic regions have been associated with heritable human diseases, but attempts to elucidate biological mechanisms are impeded by an inability to discern which genomic positions are functionally important. Evolutionary constraint is a powerful predictor of function, agnostic to cell type or disease mechanism. Single-base phyloP scores from 240 mammals identified 3.3% of the human genome as significantly constrained and likely functional. We compared phyloP scores to genome annotation, association studies, copy-number variation, clinical genetics findings, and cancer data. Constrained positions are enriched for variants that explain common disease heritability more than other functional annotations. Our results improve variant annotation but also highlight that the regulatory landscape of the human genome still needs to be further explored and linked to disease.", "doi": "10.1126/science.abn2937", "pmid": "37104612", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "mid", "key": "NIHMS1897004"}, {"db": "pmc", "key": "PMC10259825"}], "notes": [], "created": "2023-12-01T08:54:10.456Z", "modified": "2024-01-16T13:48:33.619Z"}, {"entity": "publication", "iuid": "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": "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": "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"}]}