{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,8]],"date-time":"2026-10-08T23:21:52Z","timestamp":1791501712627,"version":"4.3.4"},"reference-count":33,"publisher":"National Academy of Sciences","issue":"50","license":[{"start":{"date-parts":[[2018,11,20]],"date-time":"2018-11-20T00:00:00Z","timestamp":1542672000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0\/"}],"content-domain":{"domain":["www.pnas.org"],"crossmark-restriction":true},"short-container-title":["Proc. Natl. Acad. Sci. U.S.A."],"published-print":{"date-parts":[[2018,12,11]]},"abstract":"<jats:p>T cell receptor (TCR) repertoire data contain information about infections that could be used in disease diagnostics and vaccine development, but extracting that information remains a major challenge. Here we developed a statistical framework to detect TCR clone proliferation and contraction from longitudinal repertoire data. We applied this framework to data from three pairs of identical twins immunized with the yellow fever vaccine. We identified 600 to 1,700 responding TCRs in each donor and validated them using three independent assays. While the responding TCRs were mostly private, albeit with higher overlap between twins, they could be well-predicted using a classifier based on sequence similarity. Our method can also be applied to samples obtained postinfection, making it suitable for systematic discovery of new infection-specific TCRs in the clinic.<\/jats:p>","DOI":"10.1073\/pnas.1809642115","type":"journal-article","created":{"date-parts":[[2018,11,20]],"date-time":"2018-11-20T11:24:27Z","timestamp":1542713067000},"page":"12704-12709","update-policy":"https:\/\/doi.org\/10.1073\/pnas.cm10313","source":"Crossref","is-referenced-by-count":138,"title":["Precise tracking of vaccine-responding T cell clones reveals convergent and personalized response in identical twins"],"prefix":"10.1073","volume":"115","author":[{"given":"Mikhail V.","family":"Pogorelyy","sequence":"first","affiliation":[{"name":"Department of Genomics of Adaptive Immunity, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia;"},{"name":"Department of Molecular Technologies, Pirogov Russian National Research Medical University, 117997 Moscow, Russia;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anastasia A.","family":"Minervina","sequence":"additional","affiliation":[{"name":"Department of Genomics of Adaptive Immunity, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Maximilian Puelma","family":"Touzel","sequence":"additional","affiliation":[{"name":"Laboratoire de Physique Th\u00e9orique, CNRS, Sorbonne Universit\u00e9, \u00c9cole Normale Sup\u00e9rieure (PSL), 75005 Paris, France;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anastasiia L.","family":"Sycheva","sequence":"additional","affiliation":[{"name":"Department of Genomics of Adaptive Immunity, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ekaterina A.","family":"Komech","sequence":"additional","affiliation":[{"name":"Department of Genomics of Adaptive Immunity, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia;"},{"name":"Department of Molecular Technologies, Pirogov Russian National Research Medical University, 117997 Moscow, Russia;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Elena I.","family":"Kovalenko","sequence":"additional","affiliation":[{"name":"Department of Immunology, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Galina G.","family":"Karganova","sequence":"additional","affiliation":[{"name":"Laboratory of Biology of Arboviruses, Chumakov Institute of Poliomyelitis and Viral Encephalitides, 142782 Moscow, Russia;"},{"name":"Department of Virology, Sechenov First Moscow State Medical University, 119146 Moscow, Russia;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Evgeniy S.","family":"Egorov","sequence":"additional","affiliation":[{"name":"Department of Genomics of Adaptive Immunity, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia;"},{"name":"Department of Molecular Technologies, Pirogov Russian National Research Medical University, 117997 Moscow, Russia;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alexander Yu.","family":"Komkov","sequence":"additional","affiliation":[{"name":"Department of Genomics of Adaptive Immunity, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia;"},{"name":"Laboratory of Cytogenetics and Molecular Genetics, Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, 117198 Moscow, Russia;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dmitriy M.","family":"Chudakov","sequence":"additional","affiliation":[{"name":"Department of Genomics of Adaptive Immunity, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia;"},{"name":"Department of Molecular Technologies, Pirogov Russian National Research Medical University, 117997 Moscow, Russia;"},{"name":"Center for Data-Intensive Biomedicine and Biotechnology, Skoltech, 121205 Moscow, Russia;"},{"name":"Central European Institute of Technology, Masaryk University, 62500 Brno, Czech Republic;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ilgar Z.","family":"Mamedov","sequence":"additional","affiliation":[{"name":"Department of Genomics of Adaptive Immunity, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia;"},{"name":"Department of Molecular Technologies, Pirogov Russian National Research Medical University, 117997 Moscow, Russia;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Thierry","family":"Mora","sequence":"additional","affiliation":[{"name":"Laboratoire de Physique Statistique, CNRS, Sorbonne Universit\u00e9, Universit\u00e9 Paris-Diderot, \u00c9cole Normale Sup\u00e9rieure (PSL), 75005 Paris, France;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Aleksandra M.","family":"Walczak","sequence":"additional","affiliation":[{"name":"Laboratoire de Physique Th\u00e9orique, CNRS, Sorbonne Universit\u00e9, \u00c9cole Normale Sup\u00e9rieure (PSL), 75005 Paris, France;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yuri B.","family":"Lebedev","sequence":"additional","affiliation":[{"name":"Department of Genomics of Adaptive Immunity, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia;"},{"name":"Biological Faculty, Moscow State University, 119991 Moscow, Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"341","published-online":{"date-parts":[[2018,11,20]]},"reference":[{"key":"e_1_3_4_1_2","doi-asserted-by":"crossref","first-page":"183","DOI":"10.1111\/j.1365-2567.2011.03527.x","article-title":"Rep-seq: Uncovering the 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Immunology 135, 183\u2013191 (2012).","journal-title":"Immunology"},{"key":"e_1_3_4_2_2","doi-asserted-by":"crossref","first-page":"89","DOI":"10.1038\/nature22383","article-title":"Quantifiable predictive features define epitope-specific T cell receptor repertoires","volume":"547","author":"Dash P","year":"2017","unstructured":"P Dash, , Quantifiable predictive features define epitope-specific T cell receptor repertoires. Nature 547, 89\u201393 (2017).","journal-title":"Nature"},{"key":"e_1_3_4_3_2","doi-asserted-by":"crossref","first-page":"94","DOI":"10.1038\/nature22976","article-title":"Identifying specificity groups in the T cell receptor repertoire","volume":"547","author":"Glanville J","year":"2017","unstructured":"J Glanville, , Identifying specificity groups in the T cell receptor repertoire. 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J Virol 87, 12794\u201312804 (2013).","journal-title":"J Virol"},{"key":"e_1_3_4_28_2","doi-asserted-by":"crossref","first-page":"16161","DOI":"10.1073\/pnas.1212755109","article-title":"Statistical inference of the generation probability of T-cell receptors from sequence repertoires","volume":"109","author":"Murugan A","year":"2012","unstructured":"A Murugan, T Mora, AM Walczak, CG Callan, Statistical inference of the generation probability of T-cell receptors from sequence repertoires. 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