ImmunoMap: A bioinformatics tool for T-cell repertoire analysis

John William Sidhom, Catherine A. Bessell, Jonathan J. Havel, Alyssa Kosmides, Timothy A. Chan, Jonathan P. Schneck

Research output: Contribution to journalArticlepeer-review

Abstract

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- A nd posttherapy samples.

Original languageEnglish (US)
Pages (from-to)151-162
Number of pages12
JournalCancer Immunology Research
Volume6
Issue number2
DOIs
StatePublished - Feb 2018

ASJC Scopus subject areas

  • Immunology
  • Cancer Research

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