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Given that thousands of HLA proteins have been discovered, each presenting thousands of different peptides, decoding the cognate HLA protein of a TCR experimentally is a challenging task. To address this problem, we combined statistical learning methods with a unique dataset of paired T cell repertoires and HLA allotypes for 6,794 individuals. This enabled us to discover 34,206\u2009T cell receptor alpha (TRA) and 891,564 beta (TRB) clonotypes that were associated with 175 unique HLA alleles. The identified clonotypes target prevalent infections,\n                    <jats:italic>e.g<\/jats:italic>\n                    . influenza, cytomegalovirus and Epstein-Barr virus. Utilizing these clonotypes, we develop statistical models that impute the carriership of common HLA alleles from the TRA- or the TRB- repertoire. In conclusion, the identified allele-associated clonotypes encode the HLA fingerprints and the antigenic exposure history of individuals and populations.\n                  <\/jats:p>","DOI":"10.1038\/s42003-025-09140-2","type":"journal-article","created":{"date-parts":[[2026,1,13]],"date-time":"2026-01-13T10:01:41Z","timestamp":1768298501000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":7,"title":["T cell receptor clonotypes predict human leukocyte antigen allele carriage and antigen exposure history"],"prefix":"10.1038","volume":"9","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-1844-8279","authenticated-orcid":false,"given":"Hesham","family":"ElAbd","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0009-6115-4429","authenticated-orcid":false,"given":"Aya K. 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