He has received travel reimbursement from 10X Genomics and Illumina. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.Ĭompeting interests: I have read the journal’s policy and the authors of this manuscript have the following competing interests: Paul G Thomas consults for Johnson and Johnson, Immunoscape, Cytoagents, and PACT Pharma. FAM received funding from the National Institutes of Health ( ) R01 AI146028, U19 AI117891, a Faculty Scholar grant from the Howard Hughes Medical Institute ( ) and the Simons Foundation ( ). PB received funding from the National Institutes of Health ( ) R35 GM141457, R01 AI146028. SAS and PGT received funding from the National Institutes of Health ( ) R01 AI121832, R01 AI136514, U01 AI150747, and the American Lebanese Syrian Associated Charities at St. įunding: BJO received funding from the National Institutes of Health ( ) R01 AI146028, U19 AI117891. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.ĭata Availability: All relevant data are within the manuscript and corresponding GitHub repository. Received: MaAccepted: OctoPublished: December 7, 2022Ĭopyright: © 2022 Olson et al. PLoS Comput Biol 18(12):Ĭolumbia University Medical Center: Columbia University Irving Medical Center, UNITED STATES We demonstrate that our method can identify biologically meaningful repertoire differences using several case studies.Ĭitation: Olson BJ, Schattgen SA, Thomas PG, Bradley P, Matsen IV FA (2022) Comparing T cell receptor repertoires using optimal transport. We present a complementary method of comparing TCR repertoires that detects significantly different TCRs between two given repertoires using a distance rather than a model, summary statistics, or dimension reduction. Current methods of comparing TCR repertoires either rely on statistical models which may not adequately describe the data, use summary statistics that may lose information, or are difficult to interpret. Because of this, immunologists are often interested in comparing different sets (or repertoires) of these TCRs in hopes of identifying groups of particular interest, such as TCRs that are responding to a particular vaccination using pre- and post-vaccination samples. These T cell receptors (TCRs) recognize peptides that may be foreign invaders such as viruses or bacteria. T cells are critical for a successful adaptive immune response, largely due to the expression of highly diverse receptor proteins on their surfaces.
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