iCAT: diagnostic assessment tool of immunological history using high-throughput T-cell receptor sequencing.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.  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.  We demonstrate the high accuracy of iCAT by testing on three TCR sequencing datasets.  First, iCAT successfully diagnosed smallpox vaccinated versus naïve samples in an independent cohort of mice with 95% accuracy.  Second, iCAT displayed 100% accuracy classifying naïve and monkeypox vaccinated mice.   Finally, we demonstrate the use of iCAT on human samples before and after exposure to SARS-CoV-2, the virus behind the COVID-19 global pandemic.  These experimental results show that iCAT capitalizes on the power of TCR sequencing to simplify infection diagnostics.  iCAT provides the option of a graphical, user-friendly interface on top of usual R interface allowing it to reach a wider audience.
iCAT