{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,31]],"date-time":"2025-10-31T22:10:36Z","timestamp":1761948636844,"version":"3.37.3"},"reference-count":8,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2020,7,31]],"date-time":"2020-07-31T00:00:00Z","timestamp":1596153600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100003725","name":"National Research Foundation of Korea","doi-asserted-by":"publisher","award":["2019R1A2C2002608"],"award-info":[{"award-number":["2019R1A2C2002608"]}],"id":[{"id":"10.13039\/501100003725","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Korean Government"},{"DOI":"10.13039\/501100014188","name":"Ministry of Science and ICT","doi-asserted-by":"crossref","id":[{"id":"10.13039\/501100014188","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/100000002","name":"NIH","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000060","name":"NIAID","doi-asserted-by":"publisher","award":["U19 AI111224-01"],"award-info":[{"award-number":["U19 AI111224-01"]}],"id":[{"id":"10.13039\/100000060","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Creative-Pioneering Researchers Program"},{"DOI":"10.13039\/501100002551","name":"Seoul National University","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100002551","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,4,20]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>Fine-mapping human leukocyte antigen (HLA) genes involved in disease susceptibility to individual alleles or amino acid residues has been challenging. Using information regarding HLA alleles obtained from HLA typing, HLA imputation or HLA inference, our software expands the alleles to amino acid sequences using the most recent IMGT\/HLA database and prepares a dataset suitable for fine-mapping analysis. Our software also provides useful functionalities, such as various association tests, visualization tools and nomenclature conversion.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>https:\/\/github.com\/WansonChoi\/HATK.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaa684","type":"journal-article","created":{"date-parts":[[2020,7,22]],"date-time":"2020-07-22T19:24:53Z","timestamp":1595445893000},"page":"416-418","source":"Crossref","is-referenced-by-count":18,"title":["HATK: HLA analysis toolkit"],"prefix":"10.1093","volume":"37","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-1251-8213","authenticated-orcid":false,"given":"Wanson","family":"Choi","sequence":"first","affiliation":[{"name":"Department of Biomedical Sciences, BK21 Plus Biomedical Science Project, Seoul National University College of Medicine , Seoul 03080, Republic of Korea"}]},{"given":"Yang","family":"Luo","sequence":"additional","affiliation":[{"name":"Division of Genetics, Department of Medicine, Brigham and Women\u2019s Hospital, Harvard Medical School , Boston, MA 02115, USA"},{"name":"Program in Medical and Population Genetics, Broad Institute of MIT and Harvard , Cambridge, MA 02142, USA"},{"name":"Center for Data Sciences, Brigham and Women\u2019s Hospital, Harvard Medical School , Boston, MA 02115, USA"},{"name":"Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women\u2019s Hospital, Harvard Medical School , Boston, MA 02115, USA"},{"name":"Department of Biomedical Informatics, Harvard Medical School , Boston, MA 02115, USA"}]},{"given":"Soumya","family":"Raychaudhuri","sequence":"additional","affiliation":[{"name":"Division of Genetics, Department of Medicine, Brigham and Women\u2019s Hospital, Harvard Medical School , Boston, MA 02115, USA"},{"name":"Program in Medical and Population Genetics, Broad Institute of MIT and Harvard , Cambridge, MA 02142, USA"},{"name":"Center for Data Sciences, Brigham and Women\u2019s Hospital, Harvard Medical School , Boston, MA 02115, USA"},{"name":"Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women\u2019s Hospital, Harvard Medical School , Boston, MA 02115, USA"},{"name":"Department of Biomedical Informatics, Harvard Medical School , Boston, MA 02115, USA"},{"name":"Centre for Genetics and Genomics Versus Arthritis, Manchester Academic Health Science Centre, University of Manchester , Manchester M13 9PL, UK"}]},{"given":"Buhm","family":"Han","sequence":"additional","affiliation":[{"name":"Department of Biomedical Sciences, BK21 Plus Biomedical Science Project, Seoul National University College of Medicine , Seoul 03080, Republic of Korea"}]}],"member":"286","published-online":{"date-parts":[[2020,7,31]]},"reference":[{"key":"2023051603583056700_btaa684-B1","doi-asserted-by":"crossref","first-page":"661","DOI":"10.1038\/nature05911","article-title":"Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls","volume":"447","author":"Burton","year":"2007","journal-title":"Nature"},{"key":"2023051603583056700_btaa684-B2","doi-asserted-by":"crossref","first-page":"968","DOI":"10.1093\/bioinformatics\/btr061","article-title":"HLA*IMP\u2014an integrated framework for imputing classical HLA alleles from SNP genotypes","volume":"27","author":"Dilthey","year":"2011","journal-title":"Bioinformatics"},{"key":"2023051603583056700_btaa684-B3","doi-asserted-by":"crossref","first-page":"e1005151","DOI":"10.1371\/journal.pcbi.1005151","article-title":"High-accuracy HLA type inference from whole-genome sequencing data using population reference graphs","volume":"12","author":"Dilthey","year":"2016","journal-title":"PLoS Comput. Biol"},{"key":"2023051603583056700_btaa684-B4","doi-asserted-by":"crossref","first-page":"e64683","DOI":"10.1371\/journal.pone.0064683","article-title":"Imputing amino acid polymorphisms in human leukocyte antigens","volume":"8","author":"Jia","year":"2013","journal-title":"PLoS One"},{"key":"2023051603583056700_btaa684-B5","doi-asserted-by":"crossref","first-page":"559","DOI":"10.1086\/519795","article-title":"PLINK: a tool set for whole-genome association and population-based linkage analyses","volume":"81","author":"Purcell","year":"2007","journal-title":"Am. J. Hum. Genet"},{"key":"2023051603583056700_btaa684-B6","doi-asserted-by":"crossref","first-page":"233","DOI":"10.1016\/j.humimm.2016.01.020","article-title":"The IPD-IMGT\/HLA database\u2014new developments in reporting HLA variation","volume":"77","author":"Robinson","year":"2016","journal-title":"Hum. Immunol"},{"key":"2023051603583056700_btaa684-B7","doi-asserted-by":"crossref","first-page":"8059","DOI":"10.1073\/pnas.1707945114","article-title":"Fast and accurate HLA typing from short-read next-generation sequence data with xHLA","volume":"114","author":"Xie","year":"2017","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"2023051603583056700_btaa684-B8","doi-asserted-by":"crossref","first-page":"192","DOI":"10.1038\/tpj.2013.18","article-title":"HIBAG\u2014HLA genotype imputation with attribute bagging","volume":"14","author":"Zheng","year":"2014","journal-title":"Pharmacogenomics J"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btaa684\/33694673\/btaa684.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/37\/3\/416\/50326099\/btaa684.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/37\/3\/416\/50326099\/btaa684.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,5,16]],"date-time":"2023-05-16T03:59:20Z","timestamp":1684209560000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/37\/3\/416\/5879278"}},"subtitle":[],"editor":[{"given":"Alfonso","family":"Valencia","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2020,7,31]]},"references-count":8,"journal-issue":{"issue":"3","published-print":{"date-parts":[[2021,4,20]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btaa684","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"type":"print","value":"1367-4803"},{"type":"electronic","value":"1367-4811"}],"subject":[],"published-other":{"date-parts":[[2021,2,1]]},"published":{"date-parts":[[2020,7,31]]}}}