ICAT: diagnostic assessment tool of immunological history using high-throughput T-cell receptor sequencing.

ABSTRACT: The pathogen exposure history of an individual is recorded in their T-cell repertoire and can be accessed through the study of T-cell receptors (TCRs) if the tools to identify them were available. For each T-cell, the TCR loci undergoes genetic rearrangement that creates a unique DNA sequence. In theory these unique sequences can be used as biomarkers for tracking T-cell responses and cataloging immunological history. We developed the immune Cell Analysis Tool (iCAT), an R software package that analyzes TCR sequencing data from exposed (positive) and unexposed (negative) samples to identify TCR sequences statistically associated with positive samples. The presence and absence of associated sequences in samples trains a classifier to diagnose pathogen-specific exposure. We demonstrate the h

SUBMITTER: Rajeh A 

PROVIDER: S-EPMC8276190 | biostudies-literature | 2021

REPOSITORIES: biostudies-literature