{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,30]],"date-time":"2026-09-30T00:39:42Z","timestamp":1790728782076,"version":"4.1.0"},"reference-count":9,"publisher":"Wiley","issue":"1","license":[{"start":{"date-parts":[[2021,11,25]],"date-time":"2021-11-25T00:00:00Z","timestamp":1637798400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/onlinelibrary.wiley.com\/termsAndConditions#vor"}],"content-domain":{"domain":["onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["HLA"],"published-print":{"date-parts":[[2022,1]]},"abstract":"<jats:p>HLA molecules are expressed in almost all nucleated cells of the body. These molecules are extremely variable and responsible for tissue specificity recognition. Precise HLA typing is crucial for tissue and organ transplantation. Usually, HLA\u2010typing NGS methods are based on the assignment of reads to a certain previously reported HLA allele presented in the IPD\u2010IMGT\/HLA Database. But there is a limited number of tools able to identify novel alleles that have not yet been reported and thus absent in the database. Such alleles carry mismatches distinguishing them from all known alleles in the database. Therefore, manual evaluation of the identified HLA alleles in the genome browser is a compulsory step in the analysis, and one that is labor intensive and time consuming. We present the development and validation of a freely available web\u2010application for the identification of novel HLA alleles in the most relevant HLA class I and II genes from NGS data. The tool can also be used for automated data quality assessment. The software was validated by analyzing 330 alleles. The results are concordant with orthogonal methods.<\/jats:p>","DOI":"10.1111\/tan.14491","type":"journal-article","created":{"date-parts":[[2021,11,18]],"date-time":"2021-11-18T04:03:20Z","timestamp":1637208200000},"page":"3-11","update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":123,"title":["<scp>NovAT<\/scp>\n                    tool\u2014Reliable novel\n                    <scp>HLA<\/scp>\n                    alleles identification from next\u2010generation sequencing data"],"prefix":"10.1111","volume":"99","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-9023-4852","authenticated-orcid":false,"given":"Tamara","family":"Simakova","sequence":"first","affiliation":[{"name":"R&amp;D Department Parseq Lab Co. Ltd.  St. Petersburg Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9137-7943","authenticated-orcid":false,"given":"Arina","family":"Suvorova","sequence":"additional","affiliation":[{"name":"R&amp;D Department Parseq Lab Co. Ltd.  St. Petersburg Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0363-460X","authenticated-orcid":false,"given":"Kristina","family":"Krivonosova","sequence":"additional","affiliation":[{"name":"R&amp;D Department Parseq Lab Co. Ltd.  St. Petersburg Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1236-1757","authenticated-orcid":false,"given":"Anna","family":"Abramova","sequence":"additional","affiliation":[{"name":"R&amp;D Department Parseq Lab Co. Ltd.  St. Petersburg Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7088-3986","authenticated-orcid":false,"given":"Maria","family":"Loginova","sequence":"additional","affiliation":[{"name":"Federal State Budget Research Institution Kirov Hematology and Blood Transfusion Research Institute under the Federal Medicine and Biology Agency  Kirov Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7205-912X","authenticated-orcid":false,"given":"Igor","family":"Paramonov","sequence":"additional","affiliation":[{"name":"Federal State Budget Research Institution Kirov Hematology and Blood Transfusion Research Institute under the Federal Medicine and Biology Agency  Kirov Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2021,11,25]]},"reference":[{"key":"e_1_2_8_2_1","first-page":"D948","article-title":"IPD\u2010IMGT\/HLA Database","volume":"48","author":"Robinson J","year":"2020","journal-title":"Nucleic Acids Res"},{"key":"e_1_2_8_3_1","doi-asserted-by":"publisher","DOI":"10.1155\/2012\/842141"},{"key":"e_1_2_8_4_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.cll.2018.07.006"},{"issue":"2","key":"e_1_2_8_5_1","first-page":"179","article-title":"Melbourne genomics health Alliance, Natalie P Thorne, evaluation of computational programs to predict HLA genotypes from genomic sequencing data","volume":"19","author":"Bauer DC","year":"2018","journal-title":"Brief Bioinform"},{"key":"e_1_2_8_6_1","doi-asserted-by":"publisher","DOI":"10.1159\/000502487"},{"key":"e_1_2_8_7_1","unstructured":"Standards for Histocompatibility & Immunogenetics testing.Version 8.0 [Electronic resource].https:\/\/efi-web.org\/committees\/standards-committee."},{"key":"e_1_2_8_8_1","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-018-1388-2"},{"key":"e_1_2_8_9_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41587-019-0201-4"},{"key":"e_1_2_8_10_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btu548"}],"container-title":["HLA"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/pdf\/10.1111\/tan.14491","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/full-xml\/10.1111\/tan.14491","content-type":"application\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/pdf\/10.1111\/tan.14491","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,8,28]],"date-time":"2023-08-28T06:16:59Z","timestamp":1693203419000},"score":1,"resource":{"primary":{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/10.1111\/tan.14491"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2021,11,25]]},"references-count":9,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2022,1]]}},"alternative-id":["10.1111\/tan.14491"],"URL":"https:\/\/doi.org\/10.1111\/tan.14491","archive":["Portico"],"relation":{},"ISSN":["2059-2302","2059-2310"],"issn-type":[{"value":"2059-2302","type":"print"},{"value":"2059-2310","type":"electronic"}],"subject":[],"published":{"date-parts":[[2021,11,25]]},"assertion":[{"value":"2021-06-23","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2021-11-09","order":1,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2021-11-25","order":2,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}]}}