{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,3]],"date-time":"2026-04-03T20:53:29Z","timestamp":1775249609509,"version":"3.50.1"},"update-to":[{"DOI":"10.12688\/f1000research.27214.1","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2021,6,29]],"date-time":"2021-06-29T00:00:00Z","timestamp":1624924800000}}],"reference-count":16,"publisher":"F1000 Research Ltd","license":[{"start":{"date-parts":[[2021,6,29]],"date-time":"2021-06-29T00:00:00Z","timestamp":1624924800000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Federal Bureau of Investigations"}],"content-domain":{"domain":["f1000research.com"],"crossmark-restriction":false},"short-container-title":["F1000Res"],"abstract":"<ns3:p>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.\u00a0For 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.\u00a0We demonstrate the high accuracy of iCAT by testing on three TCR sequencing datasets.\u00a0First, iCAT successfully diagnosed smallpox vaccinated versus na\u00efve samples in an independent cohort of mice with 95% accuracy.\u00a0Second, iCAT displayed 100% accuracy classifying na\u00efve 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.\u00a0We were able to correctly classify the exposed samples with perfect accuracy.\u00a0These experimental results show that iCAT capitalizes on the power of TCR sequencing to simplify infection diagnostics.\u00a0iCAT provides the option of a graphical, user-friendly interface on top of usual R interface allowing it to reach a wider audience.<\/ns3:p>","DOI":"10.12688\/f1000research.27214.2","type":"journal-article","created":{"date-parts":[[2021,6,29]],"date-time":"2021-06-29T05:15:21Z","timestamp":1624943721000},"page":"65","update-policy":"https:\/\/doi.org\/10.12688\/f1000research.crossmark-policy","source":"Crossref","is-referenced-by-count":3,"title":["iCAT: diagnostic assessment tool of immunological history using high-throughput T-cell receptor 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R.D. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.","order":2,"name":"grant-information","label":"Grant Information"},{"value":"This is an open access article distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.","order":0,"name":"copyright-info","label":"Copyright"}]}}