{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,21]],"date-time":"2025-11-21T18:15:27Z","timestamp":1763748927496,"version":"3.41.2"},"reference-count":23,"publisher":"Oxford University Press (OUP)","issue":"4","license":[{"start":{"date-parts":[[2023,6,19]],"date-time":"2023-06-19T00:00:00Z","timestamp":1687132800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/pages\/standard-publication-reuse-rights"}],"funder":[{"DOI":"10.13039\/501100021671","name":"National Cancer Institute","doi-asserted-by":"publisher","award":["R01CA234629"],"award-info":[{"award-number":["R01CA234629"]}],"id":[{"id":"10.13039\/501100021671","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["R03CA270725"],"award-info":[{"award-number":["R03CA270725"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"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 T-cell receptor (TCR) repertoire is highly diverse among the population and plays an essential role in initiating multiple immune processes. TCR sequencing (TCR-seq) has been developed to profile the T cell repertoire. Similar to other high-throughput experiments, contamination can happen during several steps of TCR-seq, including sample collection, preparation and sequencing. Such contamination creates artifacts in the data, leading to inaccurate or even biased results. Most existing methods assume \u2018clean\u2019 TCR-seq data as the starting point with no ability to handle data contamination. Here, we develop a novel statistical model to systematically detect and remove contamination in TCR-seq data. We summarize the observed contamination into two sources, pairwise and cross-cohort. For both sources, we provide visualizations and summary statistics to help users assess the severity of the contamination. Incorporating prior information from 14 existing TCR-seq datasets with minimum contamination, we develop a straightforward Bayesian model to statistically identify contaminated samples. We further provide strategies for removing the impacted sequences to allow for downstream analysis, thus avoiding any need to repeat experiments. Our proposed model shows robustness in contamination detection compared with a few off-the-shelf detection methods in simulation studies. We illustrate the use of our proposed method on two TCR-seq datasets generated locally.<\/jats:p>","DOI":"10.1093\/bib\/bbad230","type":"journal-article","created":{"date-parts":[[2023,6,20]],"date-time":"2023-06-20T07:35:26Z","timestamp":1687246526000},"source":"Crossref","is-referenced-by-count":3,"title":["A novel statistical method for decontaminating T-cell receptor sequencing data"],"prefix":"10.1093","volume":"24","author":[{"given":"Ruoxing","family":"Li","sequence":"first","affiliation":[{"name":"Department of Biostatistics and Data Science, The University of Texas Health Science Center at Houston , 77030, Texas, Houston , USA"},{"name":"Department of Biostatistics, The University of Texas MD Anderson Cancer Center , 77030, Texas, Houston , USA"}]},{"given":"Mehmet","family":"Altan","sequence":"additional","affiliation":[{"name":"Department of Thoracic-Head & Neck Medical Oncology, The University of Texas MD Anderson Cancer Center , 77030, Texas, Houston , USA"}]},{"given":"Alexandre","family":"Reuben","sequence":"additional","affiliation":[{"name":"Department of Thoracic-Head & Neck Medical Oncology, The University of Texas MD Anderson Cancer Center , 77030, Texas, Houston , USA"}]},{"given":"Ruitao","family":"Lin","sequence":"additional","affiliation":[{"name":"Department of Biostatistics, The University of Texas MD Anderson Cancer Center , 77030, Texas, Houston , USA"}]},{"given":"John V","family":"Heymach","sequence":"additional","affiliation":[{"name":"Department of Thoracic-Head & Neck Medical Oncology, The University of Texas MD Anderson Cancer Center , 77030, Texas, Houston , USA"}]},{"given":"Hai","family":"Tran","sequence":"additional","affiliation":[{"name":"Department of Thoracic-Head & Neck Medical Oncology, The University of Texas MD Anderson Cancer Center , 77030, Texas, Houston , USA"}]},{"given":"Runzhe","family":"Chen","sequence":"additional","affiliation":[{"name":"Department of Thoracic-Head & Neck Medical Oncology, The University of Texas MD Anderson Cancer Center , 77030, Texas, Houston , USA"}]},{"given":"Latasha","family":"Little","sequence":"additional","affiliation":[{"name":"Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center , 77030, Texas, Houston , USA"}]},{"given":"Shawna","family":"Hubert","sequence":"additional","affiliation":[{"name":"Department of Thoracic-Head & Neck Medical Oncology, The University of Texas MD Anderson Cancer Center , 77030, Texas, Houston , USA"}]},{"given":"Jianjun","family":"Zhang","sequence":"additional","affiliation":[{"name":"Department of Thoracic-Head & Neck Medical Oncology, The University of Texas MD Anderson Cancer Center , 77030, Texas, Houston , USA"}]},{"given":"Ziyi","family":"Li","sequence":"additional","affiliation":[{"name":"Department of Biostatistics, The University of Texas MD Anderson Cancer Center , 77030, Texas, Houston , USA"}]}],"member":"286","published-online":{"date-parts":[[2023,6,19]]},"reference":[{"issue":"1","key":"2023072020145184100_ref1","doi-asserted-by":"crossref","first-page":"175","DOI":"10.1146\/annurev.iy.07.040189.001135","article-title":"The structure, function, and molecular genetics of the gamma\/delta t cell receptor","volume":"7","author":"Raulet","year":"1989","journal-title":"Annu Rev Immunol"},{"issue":"5441","key":"2023072020145184100_ref2","doi-asserted-by":"crossref","first-page":"958","DOI":"10.1126\/science.286.5441.958","article-title":"A direct estimate of the human $\\alpha \\beta $ t cell receptor diversity","volume":"286","author":"Petteri Arstila","year":"1999","journal-title":"Science"},{"issue":"10","key":"2023072020145184100_ref3","first-page":"1088","article-title":"Tcr repertoire intratumor heterogeneity in localized lung adenocarcinomas: an association with predicted neoantigen heterogeneity and postsurgical recurrence. Cancer","volume":"7","author":"Reuben","year":"2017","journal-title":"Discovery"},{"key":"2023072020145184100_ref4","article-title":"Single-cell tcr sequencing reveals phenotypically diverse clonally expanded cells harboring inducible hiv proviruses during art. Nature","volume":"11","author":"Gantner","year":"2020","journal-title":"Communications"},{"issue":"2","key":"2023072020145184100_ref5","doi-asserted-by":"crossref","first-page":"456","DOI":"10.1016\/j.ygeno.2020.12.036","article-title":"Comprehensive analysis of tcr repertoire in covid-19 using single cell sequencing","volume":"113","author":"Wang","year":"2021","journal-title":"Genomics"},{"key":"2023072020145184100_ref6"},{"key":"2023072020145184100_ref7","article-title":"Overview of methodologies for t-cell receptor repertoire analysis","volume":"17","author":"Elisa Rosati","year":"2017","journal-title":"BMC Biotechnol"},{"key":"2023072020145184100_ref8","first-page":"1","article-title":"A peripheral immune signature of responsiveness to pd-1 blockade in patients with classical hodgkin lymphoma","author":"Cader","year":"2020","journal-title":"Nat Med"},{"key":"2023072020145184100_ref9","doi-asserted-by":"crossref","first-page":"126","DOI":"10.1038\/s41586-021-03752-4","article-title":"Transcriptional programs of neoantigen-specific til in anti-pd-1-treated lung cancers","volume":"596","author":"Caushi","year":"2021","journal-title":"Nature"},{"key":"2023072020145184100_ref10","doi-asserted-by":"crossref","DOI":"10.1002\/path.4260","article-title":"High-throughput sequencing of t-cell receptors reveals a homogeneous repertoire of tumour-infiltrating lymphocytes in ovarian cancer","volume":"231","author":"Emerson","year":"2013","journal-title":"J Pathol"},{"issue":"12","key":"2023072020145184100_ref11","doi-asserted-by":"crossref","DOI":"10.1038\/s41591-018-0232-2","article-title":"Radiotherapy induces responses of lung cancer to CTLA-4 blockade","volume":"24","author":"Formenti","year":"2018","journal-title":"Nat Med"},{"issue":"8","key":"2023072020145184100_ref12","first-page":"4","article-title":"Lymphohematopoietic graft-versus-host responses promote mixed chimerism in patients receiving intestinal transplantation","volume":"131","author":"Jianing","year":"2021","journal-title":"J Clin Invest"},{"issue":"5","key":"2023072020145184100_ref13","doi-asserted-by":"crossref","first-page":"412","DOI":"10.1158\/2326-6066.CIR-15-0240","article-title":"Tcr sequencing can identify and track glioma-infiltrating t cells after dc vaccination","volume":"4","author":"Hsu","year":"2016","journal-title":"Cancer Immunol Res"},{"issue":"10","key":"2023072020145184100_ref14","doi-asserted-by":"crossref","first-page":"1663","DOI":"10.1084\/jem.20150585","article-title":"Altered bcr and tlr signals promote enhanced positive selection of autoreactive transitional b cells in wiskott-Aldrich syndrome","volume":"212","author":"Kolhatkar","year":"2015","journal-title":"J Exp Med"},{"key":"2023072020145184100_ref15","first-page":"1","article-title":"T cell receptor repertoire among women who cleared and failed to clear cervical human papillomavirus infection: an exploratory proof-of-principle study","volume":"13","author":"Lang","year":"2018","journal-title":"PloS One"},{"key":"2023072020145184100_ref16","article-title":"Response and recurrence correlates in individuals treated with neoadjuvant anti-PD-1 therapy for resectable oral cavity squamous cell carcinoma","volume":"2","author":"Liu","year":"2021","journal-title":"Cell Rep Med"},{"issue":"2","key":"2023072020145184100_ref17","doi-asserted-by":"crossref","first-page":"137","DOI":"10.1158\/2326-6066.CIR-16-0210","article-title":"Tumor-infiltrating merkel cell polyomavirus-specific t cells are diverse and associated with improved patient survival","volume":"5","author":"Miller","year":"2017","journal-title":"Cancer Immunol Res"},{"key":"2023072020145184100_ref18","doi-asserted-by":"crossref","DOI":"10.1038\/s41591-019-0522-3","article-title":"Clonal replacement of tumor-specific t cells following pd-1 blockade","author":"Yost","year":"2019","journal-title":"Nat Med"},{"issue":"12","key":"2023072020145184100_ref19","doi-asserted-by":"crossref","first-page":"1496","DOI":"10.1158\/2326-6066.CIR-20-0252","article-title":"Long-term sculpting of the b-cell repertoire following cancer immunotherapy in patients treated with sipuleucel-t","volume":"8","author":"Zhang","year":"2020","journal-title":"Cancer Immunol Res"},{"issue":"1","key":"2023072020145184100_ref20","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1038\/s41467-021-22890-x","article-title":"Immune evolution from preneoplasia to invasive lung adenocarcinomas and underlying molecular features","volume":"12","author":"Dejima","year":"2021","journal-title":"Nat Commun"},{"issue":"2","key":"2023072020145184100_ref21","doi-asserted-by":"crossref","first-page":"451","DOI":"10.1016\/S0031-3203(02)00060-2","article-title":"The global k-means clustering algorithm","volume":"36","author":"Likas","year":"2003","journal-title":"Pattern Recognit"},{"issue":"3","key":"2023072020145184100_ref22","doi-asserted-by":"crossref","first-page":"241","DOI":"10.1007\/BF02289588","article-title":"Hierarchical clustering schemes","volume":"32","author":"Johnson","year":"1967","journal-title":"Psychometrika"},{"issue":"1","key":"2023072020145184100_ref23","doi-asserted-by":"crossref","first-page":"86","DOI":"10.1002\/widm.53","article-title":"Algorithms for hierarchical clustering: an overview","volume":"2","author":"Murtagh","year":"2012","journal-title":"Wiley Interdiscip Rev Data Min Knowl Discov"}],"container-title":["Briefings in Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bib\/article-pdf\/24\/4\/bbad230\/50916837\/bbad230.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bib\/article-pdf\/24\/4\/bbad230\/50916837\/bbad230.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,7,20]],"date-time":"2023-07-20T20:16:41Z","timestamp":1689884201000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bib\/article\/doi\/10.1093\/bib\/bbad230\/7202085"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,6,19]]},"references-count":23,"journal-issue":{"issue":"4","published-print":{"date-parts":[[2023,7,20]]}},"URL":"https:\/\/doi.org\/10.1093\/bib\/bbad230","relation":{},"ISSN":["1467-5463","1477-4054"],"issn-type":[{"type":"print","value":"1467-5463"},{"type":"electronic","value":"1477-4054"}],"subject":[],"published-other":{"date-parts":[[2023,7]]},"published":{"date-parts":[[2023,6,19]]},"article-number":"bbad230"}}