{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,9]],"date-time":"2026-04-09T01:40:29Z","timestamp":1775698829475,"version":"3.50.1"},"reference-count":41,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2019,6,7]],"date-time":"2019-06-07T00:00:00Z","timestamp":1559865600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000185","name":"DARPA","doi-asserted-by":"publisher","award":["W911NF-16-2-0035"],"award-info":[{"award-number":["W911NF-16-2-0035"]}],"id":[{"id":"10.13039\/100000185","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["U54CA193313"],"award-info":[{"award-number":["U54CA193313"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["R01-GM117591"],"award-info":[{"award-number":["R01-GM117591"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,1,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>The human leukocyte antigen (HLA) locus plays a critical role in tissue compatibility and regulates the host response to many diseases, including cancers and autoimmune di3orders. Recent improvements in the quality and accessibility of next-generation sequencing have made HLA typing from standard short-read data practical. However, this task remains challenging given the high level of polymorphism and homology between HLA genes. HLA typing from RNA sequencing is further complicated by post-transcriptional modifications and bias due to amplification.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>Here, we present arcasHLA: a fast and accurate in silico tool that infers HLA genotypes from RNA-sequencing data. Our tool outperforms established tools on the gold-standard benchmark dataset for HLA typing in terms of both accuracy and speed, with an accuracy rate of 100% at two-field resolution for Class I genes, and over 99.7% for Class II. Furthermore, we evaluate the performance of our tool on a new biological dataset of 447 single-end total RNA samples from nasopharyngeal swabs, and establish the applicability of arcasHLA in metatranscriptome studies.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>arcasHLA is available at https:\/\/github.com\/RabadanLab\/arcasHLA.<\/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\/btz474","type":"journal-article","created":{"date-parts":[[2019,6,3]],"date-time":"2019-06-03T19:11:27Z","timestamp":1559589087000},"page":"33-40","source":"Crossref","is-referenced-by-count":185,"title":["arcasHLA: high-resolution HLA typing from RNAseq"],"prefix":"10.1093","volume":"36","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-4678-0837","authenticated-orcid":false,"given":"Rose","family":"Orenbuch","sequence":"first","affiliation":[{"name":"Department of Systems Biology, Columbia University , New York, NY 10032, USA"},{"name":"Department of Computer Science, Columbia University , New York, NY 10027, USA"}]},{"given":"Ioan","family":"Filip","sequence":"additional","affiliation":[{"name":"Department of Systems Biology, Columbia University , New York, NY 10032, USA"}]},{"given":"Devon","family":"Comito","sequence":"additional","affiliation":[{"name":"Department of Environmental Health Sciences, Mailman School of Public Health , Columbia University, New York, NY 10032, USA"}]},{"given":"Jeffrey","family":"Shaman","sequence":"additional","affiliation":[{"name":"Department of Environmental Health Sciences, Mailman School of Public Health , Columbia University, New York, NY 10032, USA"}]},{"given":"Itsik","family":"Pe\u2019er","sequence":"additional","affiliation":[{"name":"Department of Computer Science, Columbia University , New York, NY 10027, USA"}]},{"given":"Raul","family":"Rabadan","sequence":"additional","affiliation":[{"name":"Department of Systems Biology, Columbia University , New York, NY 10032, USA"}]}],"member":"286","published-online":{"date-parts":[[2019,6,7]]},"reference":[{"key":"2023013109510864600_btz474-B1","doi-asserted-by":"crossref","DOI":"10.1093\/database\/baw093","article-title":"The Ensembl gene annotation system","author":"Aken","year":"2016","journal-title":"Database"},{"key":"2023013109510864600_btz474-B2","doi-asserted-by":"crossref","first-page":"403","DOI":"10.1016\/S0022-2836(05)80360-2","article-title":"Basic local alignment search tool","volume":"215","author":"Altschul","year":"1990","journal-title":"J. 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