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.