{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,16]],"date-time":"2026-07-16T20:27:40Z","timestamp":1784233660458,"version":"3.55.0"},"reference-count":12,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2020,7,8]],"date-time":"2020-07-08T00:00:00Z","timestamp":1594166400000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2020,7,8]],"date-time":"2020-07-08T00:00:00Z","timestamp":1594166400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"funder":[{"name":"Collaborative Innovation Center of High Performance Computing"},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["61433009"],"award-info":[{"award-number":["61433009"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003453","name":"Guangdong Natural Science Foundation","doi-asserted-by":"crossref","award":["2015A030308017"],"award-info":[{"award-number":["2015A030308017"]}],"id":[{"id":"10.13039\/501100003453","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2020,12]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Background<\/jats:title>\n                    <jats:p>The human leukocyte antigen (HLA) gene family plays a key role in the immune response and thus is crucial in many biomedical and clinical settings. Utilizing Sanger sequencing, the golden standard technology for HLA typing enables accurate identification of HLA alleles in high-resolution. However, only the commercial software, such as uTYPE, SBT-Assign, and SBTEngine, and very few open-source tools could be applied to perform HLA typing based on Sanger sequencing.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>We developed a user-friendly, cross-platform and open-source desktop application, known as SOAPTyping, for Sanger-based typing in HLA class I and II alleles. SOAPTyping can produce accurate results with a comprehensible protocol and featured functions. Moreover, SOAPTyping supports a more advanced group-specific sequencing primers (GSSP) module to solve the ambiguous typing results. We used SOAPTyping to analyze 36 samples with known HLA typing from the University of California Los Angeles (UCLA) International HLA DNA Exchange platform and 100 anonymous clinical samples, and the HLA typing results from SOAPTyping are identical to the golden results and 5.5 times faster than commercial software uTYPE, which shows the usability of SOAPTyping.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusions<\/jats:title>\n                    <jats:p>We introduce the SOAPTyping as the first open-source and cross-platform HLA typing software with the capability of producing high-resolution HLA typing predictions from Sanger sequence data.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1186\/s12859-020-03624-0","type":"journal-article","created":{"date-parts":[[2020,7,8]],"date-time":"2020-07-08T09:03:51Z","timestamp":1594199031000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":13,"title":["SOAPTyping: an open-source and cross-platform tool for sequence-based typing for HLA class I and II alleles"],"prefix":"10.1186","volume":"21","author":[{"given":"Yong","family":"Zhang","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yongsheng","family":"Chen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Huixin","family":"Xu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Junbin","family":"Fang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zijian","family":"Zhao","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Weipeng","family":"Hu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiaoqin","family":"Yang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jia","family":"Ye","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yun","family":"Cheng","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jiayin","family":"Wang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Weiqiang","family":"Sun","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jian","family":"Wang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Huanming","family":"Yang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jing","family":"Yan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5954-3435","authenticated-orcid":false,"given":"Lin","family":"Fang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2020,7,8]]},"reference":[{"issue":"5","key":"3624_CR1","doi-asserted-by":"publisher","first-page":"325","DOI":"10.1038\/nri.2017.143","volume":"18","author":"C Dendrou","year":"2018","unstructured":"Dendrou C, Petersen J, Rossjohn J, Fugger L. HLA variation and disease. Nat Rev Immunol. 2018;18(5):325\u201339.","journal-title":"Nat Rev Immunol"},{"issue":"1","key":"3624_CR2","doi-asserted-by":"publisher","first-page":"6","DOI":"10.1186\/2001-1326-2-6","volume":"2","author":"B Mahdi","year":"2013","unstructured":"Mahdi B. A glow of HLA typing in organ transplantation. Clin Transl Med. 2013;2(1):6.","journal-title":"Clin Transl Med"},{"key":"3624_CR3","doi-asserted-by":"publisher","first-page":"D1234","DOI":"10.1093\/nar\/gks1140","volume":"41","author":"J Robinson","year":"2013","unstructured":"Robinson J, Halliwell JA, McWilliam H, Lopez R, Marsh SGE. IPD - the Immuno polymorphism database. Nucleic Acids Res. 2013;41:D1234\u201340.","journal-title":"Nucleic Acids Res"},{"key":"3624_CR4","first-page":"D948","volume":"48","author":"J Robinson","year":"2020","unstructured":"Robinson J, Barker DJ, Georgiou X, Cooper MA, Marsh SGE. The IPD-IMGT\/HLA database. 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Hum Immunol. 2016;77:1016\u201323.","journal-title":"Hum Immunol"},{"issue":"3","key":"3624_CR10","doi-asserted-by":"publisher","first-page":"141","DOI":"10.1111\/tan.12736","volume":"87","author":"J Duke","year":"2016","unstructured":"Duke J, Lind C, Mackiewicz K, Ferriola D, Papazoglou A, Gasiewski A, Heron S, et al. Determining performance characteristics of an NGS-based HLA typing method for clinical applications. HLA. 2016;87(3):141\u201352.","journal-title":"HLA"},{"issue":"3","key":"3624_CR11","doi-asserted-by":"publisher","first-page":"247","DOI":"10.1111\/j.1399-0039.2010.01616.x","volume":"77","author":"T Lebedeva","year":"2011","unstructured":"Lebedeva T, Mastromarino S, Lee E, Ohashi M, Alosco S, Yu N. Resolution of HLA class I sequence-based typing ambiguities by group-specific sequencing primers. 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Accessed 14 May 2020."}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-020-03624-0.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1186\/s12859-020-03624-0\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-020-03624-0.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,7,7]],"date-time":"2021-07-07T19:05:34Z","timestamp":1625684734000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/s12859-020-03624-0"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2020,7,8]]},"references-count":12,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2020,12]]}},"alternative-id":["3624"],"URL":"https:\/\/doi.org\/10.1186\/s12859-020-03624-0","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/674648","asserted-by":"object"}]},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2020,7,8]]},"assertion":[{"value":"30 December 2019","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"22 June 2020","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"8 July 2020","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"Informed consent was obtained from all 100 participators who agreed to take HLA testing. Ethic approvals were obtained by the institutional review board of BGI-Shenzhen.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethics approval and consent to participate"}},{"value":"Not applicable.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Consent for publication"}},{"value":"The authors declare that they have no competing interests.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"295"}}