PT - JOURNAL ARTICLE AU - Sidhom, John-William AU - Bessell, Catherine A. AU - Havel, Jonathan J. AU - Kosmides, Alyssa AU - Chan, Timothy A. AU - Schneck, Jonathan P. TI - ImmunoMap: A Bioinformatics Tool for T-cell Repertoire Analysis AID - 10.1158/2326-6066.CIR-17-0114 DP - 2018 Feb 01 TA - Cancer Immunology Research PG - 151--162 VI - 6 IP - 2 4099 - http://cancerimmunolres.aacrjournals.org/content/6/2/151.short 4100 - http://cancerimmunolres.aacrjournals.org/content/6/2/151.full SO - Cancer Immunol Res2018 Feb 01; 6 AB - Despite a dramatic increase in T-cell receptor (TCR) sequencing, few approaches biologically parse the data in a fashion that both helps yield new information about immune responses and may guide immunotherapeutic interventions. To address this issue, we developed a method, ImmunoMap, that utilizes a sequence analysis approach inspired by phylogenetics to examine TCR repertoire relatedness. ImmunoMap analysis of the CD8 T-cell response to self-antigen (Kb-TRP2) or to a model foreign antigen (Kb-SIY) in naïve and tumor-bearing B6 mice showed differences in the T-cell repertoire of self- versus foreign antigen-specific responses, potentially reflecting immune pressure by the tumor, and also detected lymphoid organ–specific differences in TCR repertoires. When ImmunoMap was used to analyze clinical trial data of tumor-infiltrating lymphocytes from patients being treated with anti–PD-1, ImmunoMap, but not standard TCR sequence analyses, revealed a clinically predicative signature in pre- and posttherapy samples. Cancer Immunol Res; 6(2); 151–62. ©2017 AACR.