{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,18]],"date-time":"2026-06-18T22:34:04Z","timestamp":1781822044995,"version":"3.54.5"},"reference-count":38,"publisher":"Oxford University Press (OUP)","issue":"4","funder":[{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["2041984"],"award-info":[{"award-number":["2041984"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["2135954"],"award-info":[{"award-number":["2135954"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["R01AI173172"],"award-info":[{"award-number":["R01AI173172"]}],"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":["K08 CA241088"],"award-info":[{"award-number":["K08 CA241088"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Hyundai Hope on Wheels Hope Scholar Award"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,7,20]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>The ability to identify and track T-cell receptor (TCR) sequences from patient samples is becoming central to the field of cancer research and immunotherapy. Tracking genetically engineered T cells expressing TCRs that target specific tumor antigens is important to determine the persistence of these cells and quantify tumor responses. The available high-throughput method to profile TCR repertoires is generally referred to as TCR sequencing (TCR-Seq). However, the available TCR-Seq data are limited compared with RNA sequencing (RNA-Seq). In this paper, we have benchmarked the ability of RNA-Seq-based methods to profile TCR repertoires by examining 19 bulk RNA-Seq samples across 4 cancer cohorts including both T-cell-rich and T-cell-poor tissue types. We have performed a comprehensive evaluation of the existing RNA-Seq-based repertoire profiling methods using targeted TCR-Seq as the gold standard. We also highlighted scenarios under which the RNA-Seq approach is suitable and can provide comparable accuracy to the TCR-Seq approach. Our results show that RNA-Seq-based methods are able to effectively capture the clonotypes and estimate the diversity of TCR repertoires, as well as provide relative frequencies of clonotypes in T-cell-rich tissues and low-diversity repertoires. However, RNA-Seq-based TCR profiling methods have limited power in T-cell-poor tissues, especially in highly diverse repertoires of T-cell-poor tissues. The results of our benchmarking provide an additional appealing argument to incorporate RNA-Seq into the immune repertoire screening of cancer patients as it offers broader knowledge into the transcriptomic changes that exceed the limited information provided by TCR-Seq.<\/jats:p>","DOI":"10.1093\/bib\/bbad220","type":"journal-article","created":{"date-parts":[[2023,5,24]],"date-time":"2023-05-24T21:16:49Z","timestamp":1684963009000},"source":"Crossref","is-referenced-by-count":14,"title":["Rigorous benchmarking of T-cell receptor repertoire profiling methods for cancer RNA sequencing"],"prefix":"10.1093","volume":"24","author":[{"given":"Kerui","family":"Peng","sequence":"first","affiliation":[{"name":"Department of Clinical Pharmacy , USC Alfred E. Mann School of Pharmacy and Pharmaceutical Sciences, , Los Angeles, CA , USA"},{"name":"University of Southern California , USC Alfred E. Mann School of Pharmacy and Pharmaceutical Sciences, , Los Angeles, CA , USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Theodore S","family":"Nowicki","sequence":"additional","affiliation":[{"name":"Department of Pediatrics , Division of Pediatric Hematology\/Oncology, , Los Angeles, CA , USA"},{"name":"University of California , Division of Pediatric Hematology\/Oncology, , Los Angeles, CA , USA"},{"name":"Department of Microbiology , Immunology, & Molecular Genetics, , Los Angeles, CA , USA"},{"name":"University of California , Immunology, & Molecular Genetics, , Los Angeles, CA , USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Katie","family":"Campbell","sequence":"additional","affiliation":[{"name":"Department of Medicine , Division of Hematology-Oncology, , Los Angeles, CA , USA"},{"name":"University of California , Division of Hematology-Oncology, , Los Angeles, CA , USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mohammad","family":"Vahed","sequence":"additional","affiliation":[{"name":"Department of Clinical Pharmacy , USC Alfred E. Mann School of Pharmacy and Pharmaceutical Sciences, , Los Angeles, CA , USA"},{"name":"University of Southern California , USC Alfred E. Mann School of Pharmacy and Pharmaceutical Sciences, , Los Angeles, CA , USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dandan","family":"Peng","sequence":"additional","affiliation":[{"name":"Department of Quantitative and Computational Biology , USC Dornsife College of Letters, Arts and Sciences, , Los Angeles, CA , USA"},{"name":"University of Southern California , USC Dornsife College of Letters, Arts and Sciences, , Los Angeles, CA , USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yiting","family":"Meng","sequence":"additional","affiliation":[{"name":"Department of Clinical Pharmacy , USC Alfred E. Mann School of Pharmacy and Pharmaceutical Sciences, , Los Angeles, CA , USA"},{"name":"University of Southern California , USC Alfred E. Mann School of Pharmacy and Pharmaceutical Sciences, , Los Angeles, CA , USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anish","family":"Nagareddy","sequence":"additional","affiliation":[{"name":"Viterbi School of Engineering, University of Southern California , Los Angeles, CA , USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yu-Ning","family":"Huang","sequence":"additional","affiliation":[{"name":"Department of Clinical Pharmacy , USC Alfred E. Mann School of Pharmacy and Pharmaceutical Sciences, , Los Angeles, CA , USA"},{"name":"University of Southern California , USC Alfred E. Mann School of Pharmacy and Pharmaceutical Sciences, , Los Angeles, CA , USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Aaron","family":"Karlsberg","sequence":"additional","affiliation":[{"name":"Department of Clinical Pharmacy , USC Alfred E. Mann School of Pharmacy and Pharmaceutical Sciences, , Los Angeles, CA , USA"},{"name":"University of Southern California , USC Alfred E. Mann School of Pharmacy and Pharmaceutical Sciences, , Los Angeles, CA , USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zachary","family":"Miller","sequence":"additional","affiliation":[{"name":"Department of Pharmaceutical Sciences , USC Alfred E. Mann School of Pharmacy and Pharmaceutical Sciences, , Los Angeles, CA , USA"},{"name":"University of Southern California , USC Alfred E. Mann School of Pharmacy and Pharmaceutical Sciences, , Los Angeles, CA , USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jaqueline","family":"Brito","sequence":"additional","affiliation":[{"name":"Department of Clinical Pharmacy , USC Alfred E. Mann School of Pharmacy and Pharmaceutical Sciences, , Los Angeles, CA , USA"},{"name":"University of Southern California , USC Alfred E. Mann School of Pharmacy and Pharmaceutical Sciences, , Los Angeles, CA , USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Brian","family":"Nadel","sequence":"additional","affiliation":[{"name":"Department of Clinical Pharmacy , USC Alfred E. Mann School of Pharmacy and Pharmaceutical Sciences, , Los Angeles, CA , USA"},{"name":"University of Southern California , USC Alfred E. Mann School of Pharmacy and Pharmaceutical Sciences, , Los Angeles, CA , USA"},{"name":"Department of Molecular , Cell and Developmental Biology, , CA , USA"},{"name":"University of California, Los Angeles , Cell and Developmental Biology, , CA , USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Victoria M","family":"Pak","sequence":"additional","affiliation":[{"name":"Emory Nell Hodgson School of Nursing, Emory University , Atlanta, GA , USA"},{"name":"Department of Epidemiology , Rollins School of Public Health, , Atlanta, GA , USA"},{"name":"Emory University , Rollins School of Public Health, , Atlanta, GA , USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1786-3366","authenticated-orcid":false,"given":"Malak S","family":"Abedalthagafi","sequence":"additional","affiliation":[{"name":"Department of Pathology & Laboratory Medicine, Emory University Hospital , Atlanta, GA , USA"},{"name":"King Salman Center for Disability Research , Riyadh , Saudi Arabia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Amanda M","family":"Burkhardt","sequence":"additional","affiliation":[{"name":"Department of Clinical Pharmacy , USC Alfred E. 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