{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,7]],"date-time":"2026-04-07T20:14:36Z","timestamp":1775592876262,"version":"3.50.1"},"reference-count":31,"publisher":"Oxford University Press (OUP)","issue":"7","license":[{"start":{"date-parts":[[2019,11,21]],"date-time":"2019-11-21T00:00:00Z","timestamp":1574294400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"name":"Labex IGO","award":["ANR-11-LABX-0016-01"],"award-info":[{"award-number":["ANR-11-LABX-0016-01"]}]},{"name":"IHU-CESTI"},{"name":"European Union\u2019s Horizon 2020"},{"name":"Sk\u0142odowska-Curie","award":["846520"],"award-info":[{"award-number":["846520"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,4,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>The HLA system plays a pivotal role in both clinical applications and immunology research. Typing HLA genes in patient and donor is indeed required in hematopoietic stem cell and solid-organ transplantation, and the histocompatibility complex region exhibits countless genetic associations with immune-related pathologies. Since the discovery of HLA antigens, the HLA system nomenclature and typing methods have constantly evolved, which leads to difficulties in using data generated with older methodologies.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>Here, we present Easy-HLA, a web-based software suite designed to facilitate analysis and gain knowledge from HLA typing, regardless of nomenclature or typing method. Easy-HLA implements a computational and statistical method of HLA haplotypes inference based on published reference populations containing over 600\u00a0000 haplotypes to upgrade missing or partial HLA information: \u2018HLA-Upgrade\u2019 tool infers high-resolution HLA typing and \u2018HLA-2-Haplo\u2019 imputes haplotype pairs and provides additional functional annotations (e.g. amino acids and KIR ligands). We validated both tools using two independent cohorts (total n\u2009=\u20092500). For HLA-Upgrade, we reached a prediction accuracy of 92% from low- to high-resolution of European genotypes. We observed a 96% call rate and 76% accuracy with HLA-2-Haplo European haplotype pairs prediction. In conclusion, Easy-HLA tools facilitate large-scale immunogenetic analysis and promotes the multi-faceted HLA expertise beyond allelic associations by providing new functional immunogenomics parameters.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>Easy-HLA is a web application freely available (free account) at: https:\/\/hla.univ-nantes.fr.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btz875","type":"journal-article","created":{"date-parts":[[2019,11,20]],"date-time":"2019-11-20T20:11:37Z","timestamp":1574280697000},"page":"2157-2164","source":"Crossref","is-referenced-by-count":23,"title":["Easy-HLA: a validated web application suite to reveal the full details of HLA typing"],"prefix":"10.1093","volume":"36","author":[{"given":"Estelle","family":"Geffard","sequence":"first","affiliation":[{"name":"Nantes Universit\u00e9, Centrale Nantes, CHU Nantes, Inserm, Centre de Recherche en Transplantation et Immunologie , UMR 1064, ITUN, Nantes F-44000, France"}]},{"given":"Sophie","family":"Limou","sequence":"additional","affiliation":[{"name":"Nantes Universit\u00e9, Centrale Nantes, CHU Nantes, Inserm, Centre de Recherche en Transplantation et Immunologie , UMR 1064, ITUN, Nantes F-44000, France"}]},{"given":"Alexandre","family":"Walencik","sequence":"additional","affiliation":[{"name":"Nantes Universit\u00e9, Centrale Nantes, CHU Nantes, Inserm, Centre de Recherche en Transplantation et Immunologie , UMR 1064, ITUN, Nantes F-44000, France"},{"name":"Laboratoire d\u2019Histocompatibilit\u00e9 et d\u2019Immunog\u00e9n\u00e9tique, EFS Centre\u2014Pays de la Loire , Nantes F-44000, France"}]},{"given":"Michelle","family":"Daya","sequence":"additional","affiliation":[{"name":"Department of Medicine, University of Colorado Denver , Aurora, CO 80045, USA"}]},{"given":"Harold","family":"Watson","sequence":"additional","affiliation":[{"name":"Faculty of Medical Sciences Cave Hill Campus, The University of the West Indies , Bridgetown BB11000, Barbados"}]},{"given":"Dara","family":"Torgerson","sequence":"additional","affiliation":[{"name":"McGill University and Genome Quebec Innovation Centre , Montreal, QC H3A 0G1, Canada"}]},{"given":"Kathleen C","family":"Barnes","sequence":"additional","affiliation":[]},{"name":"on behalf of CAAPA","sequence":"additional","affiliation":[]},{"given":"Anne","family":"Cesbron Gautier","sequence":"additional","affiliation":[{"name":"Laboratoire d\u2019Histocompatibilit\u00e9 et d\u2019Immunog\u00e9n\u00e9tique, EFS Centre\u2014Pays de la Loire , Nantes F-44000, France"}]},{"given":"Pierre-Antoine","family":"Gourraud","sequence":"additional","affiliation":[{"name":"Nantes Universit\u00e9, Centrale Nantes, CHU Nantes, Inserm, Centre de Recherche en Transplantation et Immunologie , UMR 1064, ITUN, Nantes F-44000, France"}]},{"given":"Nicolas","family":"Vince","sequence":"additional","affiliation":[{"name":"Nantes Universit\u00e9, Centrale Nantes, CHU Nantes, Inserm, Centre de Recherche en Transplantation et Immunologie , UMR 1064, ITUN, Nantes F-44000, France"}]}],"member":"286","published-online":{"date-parts":[[2019,11,21]]},"reference":[{"key":"2023062312015105500_btz875-B1","doi-asserted-by":"crossref","first-page":"647","DOI":"10.1093\/hmg\/ddg066","article-title":"Haplotype-specific linkage disequilibrium patterns define the genetic topography of the human MHC","volume":"12","author":"Ahmad","year":"2003","journal-title":"Hum. 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