TCRMatch: Predicting T-Cell Receptor Specificity Based on Sequence Similarity to Previously Characterized Receptors

• DOI: 10.3389/fimmu.2021.640725
• Publication Date: 2021-03-11T05:18:26Z
• Authors: William D. Chroni...; Austin Crinklaw; Swapnil Mahajan; Randi Vita; Zeynep Koşaloğlu-...; Zhen Yan; Jason A. Greenbaum; Leon E. Jessen; Morten Nielsen; Scott Christley; Lindsay G. Cowell; Alessandro Sette; Bjoern Peters
• Keywords: immune repertoire analysis; 0301 basic medicine; epitope; Internet; epitope prediction tool; Immunology; Receptors, Antigen, T-Cell; T cell; Datasets as Topic; Epitopes, T-Lymphocyte; T-Cell Antigen Receptor Specificity; RC581-607; 3. Good health; sequence similarity; 03 medical and health sciences; IEDB; Humans; /dk/atira/pure/sustainabledevelopmentgoals/good_health_and_well_being; name=SDG 3 - Good Health and Well-being; Immunologic diseases. Allergy; Algorithms

The adaptive immune system in vertebrates has evolved to recognize non-self antigens, such as proteins expressed by infectious agents and mutated cancer cells. T cells play an important role antigen recognition expressing a diverse repertoire of antigen-specific receptors, which bind epitopes mount targeted responses. Recent advances high-throughput sequencing have enabled the routine generation T-cell receptor (TCR) data. Identifying specific different TCRs these data would be valuable. To accomplish that, we took advantage ever-increasing number with known epitope specificity curated Immune Epitope Database (IEDB) since 2004. We compared seven metrics sequence similarity determine their power predict if two same specificity. found that comprehensive k -mer matching approach produced best results, implemented into TCRMatch, openly accessible tool ( http://tools.iedb.org/tcrmatch/ ) takes TCR β-chain CDR3 sequences input, identifies match IEDB, reports each match. anticipate this will provide new insights cell responses captured single experiments facilitate development strategies for monitoring treatment infectious, allergic, autoimmune diseases, well cancer.