{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,16]],"date-time":"2026-09-16T01:57:53Z","timestamp":1789523873652,"version":"build-2803163510"},"reference-count":48,"publisher":"Wiley","issue":"5","license":[{"start":{"date-parts":[[2026,5,22]],"date-time":"2026-05-22T00:00:00Z","timestamp":1779408000000},"content-version":"vor","delay-in-days":21,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2026,5,1]],"date-time":"2026-05-01T00:00:00Z","timestamp":1777593600000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/doi.wiley.com\/10.1002\/tdm_license_1.1"}],"funder":[{"DOI":"10.13039\/501100000156","name":"Sant\u00e9","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100000156","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["HLA"],"published-print":{"date-parts":[[2026,5]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                  <jats:p>\n                    Genetic colocalisation analyses are frequently conducted to determine if causal signals at a genetic locus are shared between two phenotypes. However, colocalisation is rarely undertaken at the HLA locus, due to its complex linkage disequilibrium (LD) and high polymorphism density. This lack of genetic causal inference method limits our ability to translate HLA associations into therapeutic targets. Here we present a method that uses HLA alleles, instead of nucleotide variants, to perform genetic colocalisation of two traits at HLA genes. The method, which we call HLA\u2010colocalisation, works by controlling for LD using a Bayesian variable selection algorithm (here implemented with SuSiE), then performing Bayesian regression on the resulting posterior inclusion probabilities. We first show through simulation that the method correctly identifies truly colocalising genes. We then test the method in two positive control scenarios, showing colocalisation between hepatitis B and liver disease at HLA\u2010DPB1, and between Epstein\u2013Barr virus and multiple sclerosis at HLA\u2010DRB1 and HLA\u2010DQB1. Finally, we perform a large colocalisation scan between multiple viruses and auto\u2010immune diseases, demonstrating that the method is well calibrated and uncovering multiple biologically plausible novel causal associations, such as cytomegalovirus and ulcerative colitis. To our knowledge, HLA\u2010colocalisation is the first accurate genetic colocalisation method for the HLA locus (github:\n                    <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" xlink:href=\"https:\/\/github.com\/DrGBL\/hlacoloc\">https:\/\/github.com\/DrGBL\/hlacoloc<\/jats:ext-link>\n                    ).\n                  <\/jats:p>","DOI":"10.1111\/tan.70759","type":"journal-article","created":{"date-parts":[[2026,5,23]],"date-time":"2026-05-23T03:01:51Z","timestamp":1779505311000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":2,"title":["An Accurate Genetic Colocalisation Method for the\n                    <scp>HLA<\/scp>\n                    Locus"],"prefix":"10.1111","volume":"107","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-5388-0396","authenticated-orcid":false,"given":"Guillaume","family":"Butler\u2010Laporte","sequence":"first","affiliation":[{"name":"Centre for Human Genetics, University of Oxford  Oxford UK"},{"name":"Lady Davis Institute, Jewish General Hospital, McGill University  Qu\u00e9bec Canada"},{"name":"Division of Infectious Diseases McGill University Health Centre  Qu\u00e9bec Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5664-5698","authenticated-orcid":false,"given":"Tianyuan","family":"Lu","sequence":"additional","affiliation":[{"name":"Department of Statistical Sciences University of Toronto  Toronto Ontario Canada"},{"name":"Department of Biostatistics and Medical Informatics University of Wisconsin\u2013Madison  Madison Wisconsin USA"},{"name":"Department of Population Health Sciences University of Wisconsin\u2013Madison  Madison Wisconsin USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sam","family":"Morris","sequence":"additional","affiliation":[{"name":"Clinical Trial Service Unit and Epidemiological Studies Unit, Nuffield Department of Population Health University of Oxford  Oxford UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wenmin","family":"Zhang","sequence":"additional","affiliation":[{"name":"Montreal Heart Institute  Montreal Quebec Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gavin","family":"Band","sequence":"additional","affiliation":[{"name":"Centre for Human Genetics, University of Oxford  Oxford UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fergus","family":"Hamilton","sequence":"additional","affiliation":[{"name":"MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK; Infection Sciences North Bristol NHS Trust  Bristol UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Amanda","family":"Chong","sequence":"additional","affiliation":[{"name":"Centre for Human Genetics, University of Oxford  Oxford UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kuang","family":"Lin","sequence":"additional","affiliation":[{"name":"Clinical Trial Service Unit and Epidemiological Studies Unit, Nuffield Department of Population Health University of Oxford  Oxford UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ruth","family":"Nanjala","sequence":"additional","affiliation":[{"name":"Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences University of Oxford  Oxford UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"J. Brent","family":"Richards","sequence":"additional","affiliation":[{"name":"Lady Davis Institute, Jewish General Hospital, McGill University  Qu\u00e9bec Canada"},{"name":"Department of Epidemiology Biostatistics and Occupational Health, McGill University  Montr\u00e9al Qu\u00e9bec Canada"},{"name":"Department of Human Genetics McGill University  Montr\u00e9al Qu\u00e9bec Canada"},{"name":"Department of Twin Research King\u2019s College London  London UK"},{"name":"5 Prime Sciences Inc  Montreal Quebec Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mei\u2010Hsuan","family":"Lee","sequence":"additional","affiliation":[{"name":"Institute of Clinical Medicine, National Yang Ming Chiao Tung University  Taipei Taiwan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5750-6588","authenticated-orcid":false,"given":"Ling","family":"Yang","sequence":"additional","affiliation":[{"name":"Clinical Trial Service Unit and Epidemiological Studies Unit, Nuffield Department of Population Health University of Oxford  Oxford UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pang","family":"Yao","sequence":"additional","affiliation":[{"name":"Clinical Trial Service Unit and Epidemiological Studies Unit, Nuffield Department of Population Health University of Oxford  Oxford UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Liming","family":"Li","sequence":"additional","affiliation":[{"name":"Department of Epidemiology &amp; Biostatistics School of Public Health, Peking University  Beijing China"},{"name":"Peking University Center for Public Health and Epidemic Preparedness and Response  Beijing China"},{"name":"Key Laboratory of Epidemiology of Major Diseases (Peking University) Ministry of Education  Beijing China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhengming","family":"Chen","sequence":"additional","affiliation":[{"name":"Clinical Trial Service Unit and Epidemiological Studies Unit, Nuffield Department of Population Health University of Oxford  Oxford UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yang","family":"Luo","sequence":"additional","affiliation":[{"name":"Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences University of Oxford  Oxford UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Iona Y.","family":"Millwood","sequence":"additional","affiliation":[{"name":"Clinical Trial Service Unit and Epidemiological Studies Unit, Nuffield Department of Population Health University of Oxford  Oxford UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Robin G.","family":"Walters","sequence":"additional","affiliation":[{"name":"Clinical Trial Service Unit and Epidemiological Studies Unit, Nuffield Department of Population Health University of Oxford  Oxford UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alexander J.","family":"Mentzer","sequence":"additional","affiliation":[{"name":"Centre for Human Genetics, University of Oxford  Oxford UK"},{"name":"Chinese Academy of Medical Science Oxford Institute, University of Oxford  Oxford UK"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2026,5,22]]},"reference":[{"key":"e_1_2_10_2_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-022-29307-3"},{"key":"e_1_2_10_3_1","doi-asserted-by":"publisher","DOI":"10.1038\/s42003-023-05496-5"},{"key":"e_1_2_10_4_1","doi-asserted-by":"publisher","DOI":"10.1093\/ofid\/ofaa450"},{"key":"e_1_2_10_5_1","doi-asserted-by":"publisher","DOI":"10.3349\/ymj.2007.48.1.11"},{"key":"e_1_2_10_6_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41588\u2010020\u20100682\u20106"},{"key":"e_1_2_10_7_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-018-0579-z"},{"key":"e_1_2_10_8_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.xgen.2023.100361"},{"key":"e_1_2_10_9_1","doi-asserted-by":"publisher","DOI":"10.1038\/ng.348"},{"key":"e_1_2_10_10_1","doi-asserted-by":"publisher","DOI":"10.1093\/hmg\/ddq537"},{"key":"e_1_2_10_11_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-017-00257-5"},{"key":"e_1_2_10_12_1","doi-asserted-by":"publisher","DOI":"10.1038\/ng.694"},{"key":"e_1_2_10_13_1","doi-asserted-by":"publisher","DOI":"10.1038\/nature16549"},{"key":"e_1_2_10_14_1","volume-title":"Autoimmunity: 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