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 journalArticle

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 1 2018

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T-Cell Antigen Receptor
Computational Biology
T-Lymphocytes
Sequence Analysis
Tumor-Infiltrating Lymphocytes
Antigens
Autoantigens
Neoplasms
Clinical Trials
Pressure

ASJC Scopus subject areas

  • Immunology
  • Cancer Research

Cite this

ImmunoMap : A bioinformatics tool for T-cell repertoire analysis. / Sidhom, John William; Bessell, Catherine A.; Havel, Jonathan J.; Kosmides, Alyssa; Chan, Timothy A.; Schneck, Jonathan P.

In: Cancer immunology research, Vol. 6, No. 2, 01.02.2018, p. 151-162.

Research output: Contribution to journalArticle

Sidhom, John William ; Bessell, Catherine A. ; Havel, Jonathan J. ; Kosmides, Alyssa ; Chan, Timothy A. ; Schneck, Jonathan P. / ImmunoMap : A bioinformatics tool for T-cell repertoire analysis. In: Cancer immunology research. 2018 ; Vol. 6, No. 2. pp. 151-162.
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