{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,2]],"date-time":"2026-10-02T05:55:22Z","timestamp":1790920522246,"version":"4.1.0"},"reference-count":15,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2026,10,2]],"date-time":"2026-10-02T00:00:00Z","timestamp":1790899200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Immunol."],"abstract":"<jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>The Functional Expansion of Specific T cell (FEST)-based assays combine short-term peptide stimulation with TCR sequencing to identify clonotypes that expand in response to specific antigens. These approaches have proven invaluable for detecting antigen-specific T cell responses, guiding vaccine development, and assessing checkpoint blockade efficacy. However, variability introduced by biological and technical replicates poses challenges for reproducibility and interpretation, and existing computational tools do not address replicate-level analysis in these assays.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>\n                      We developed replicateFest, a computational framework implemented as an R package and Shiny web application, to analyze FEST-based TCR-seq data with and without replicates. replicateFest applies Fisher\u2019s exact test for non-replicate datasets and negative binomial modeling for replicate experiments, returning adjusted p-values and odds ratios to identify clonotypes significantly expanded in antigen-stimulated conditions. The framework distinguishes FEST-expanded clonotypes (relative to a no-antigen control) and FEST-positive clonotypes (expanded compared to all other conditions). Validation using\n                      <jats:italic>in silico<\/jats:italic>\n                      datasets confirmed accurate detection of antigen-specific clonotypes. Application to published HIV-1 epitope stimulation data reproduced original findings and demonstrated replicateFest\u2019s utility for reproducibility assessment and quality control.\n                    <\/jats:p>\n                  <\/jats:sec>","DOI":"10.3389\/fimmu.2026.1937788","type":"journal-article","created":{"date-parts":[[2026,10,2]],"date-time":"2026-10-02T05:35:30Z","timestamp":1790919330000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":0,"title":["replicateFest: an R package and shiny app for analysis of T cell receptor repertoire data from the functional expansion"],"prefix":"10.3389","volume":"17","author":[{"given":"Ludmila","family":"Danilova","sequence":"first","affiliation":[{"name":"Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine","place":["Baltimore, MD, United States"]},{"name":"Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins School of Medicine","place":["Baltimore, MD, United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alexander V.","family":"Favorov","sequence":"additional","affiliation":[{"name":"Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine","place":["Baltimore, MD, United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kellie N.","family":"Smith","sequence":"additional","affiliation":[{"name":"Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine","place":["Baltimore, MD, United States"]},{"name":"Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins School of Medicine","place":["Baltimore, MD, United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Leslie","family":"Cope","sequence":"additional","affiliation":[{"name":"Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine","place":["Baltimore, MD, United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2026,10,2]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","DOI":"10.1158\/2326-6066.CIR-18-0129","article-title":"The mutation-associated neoantigen functional expansion of specific T cells (MANAFEST) assay: A sensitive platform for monitoring antitumor immunity","volume":"6","author":"Danilova","year":"2018","journal-title":"Cancer Immunol Res"},{"key":"B2","doi-asserted-by":"publisher","DOI":"10.1056\/NEJMoa1716078","article-title":"Neoadjuvant PD-1 blockade in resectable lung cancer","volume":"378","author":"Forde","year":"2018","journal-title":"N Engl J Med"},{"key":"B3","doi-asserted-by":"publisher","DOI":"10.3389\/fimmu.2020.00591","article-title":"A T cell receptor sequencing-based assay identifies cross-reactive recall CD8+ T cell clonotypes against autologous HIV-1 epitope variants","volume":"11","author":"Chan","year":"2020","journal-title":"Front Immunol"},{"key":"B4","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pbio.3000314","article-title":"Detecting T cell receptors involved in immune responses from single repertoire snapshots","volume":"17","author":"Pogorelyy","year":"2019","journal-title":"PloS Biol"},{"key":"B5","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1808594115","article-title":"High-resolution repertoire analysis reveals a major bystander activation of Tfh and Tfr cells","volume":"115","author":"Ritvo","year":"2018","journal-title":"Proc Natl Acad Sci"},{"key":"B6","doi-asserted-by":"publisher","first-page":"291","DOI":"10.1007\/978-1-0716-2712-9_15","article-title":"Grouping T-cell antigen receptors by specificity","volume":"2574","author":"Wang","year":"2022","journal-title":"Methods Mol Biol"},{"key":"B7","doi-asserted-by":"publisher","first-page":"89","DOI":"10.1038\/nature22383","article-title":"Quantifiable predictive features define epitope specific T cell receptor repertoires","volume":"547","author":"Dash","year":"2017","journal-title":"Nature"},{"key":"B8","doi-asserted-by":"publisher","DOI":"10.3389\/fbinf.2025.1641491","article-title":"TCRscape: A single-cell multi-omic TCR profiling toolkit","volume":"5","author":"Perik-Zavodskii","year":"2025","journal-title":"Front Bioinform"},{"key":"B9","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1812800116","article-title":"Regulation of T cell expansion by antigen presentation dynamics","volume":"116","author":"Mayer","year":"2019","journal-title":"Proc Natl Acad Sci"},{"key":"B10","unstructured":"Population dynamics of immune repertoires\n          \n          \n            \n              Desponds\n              J\n            \n            \n              Mayer\n              A\n            \n            \n              Mora\n              T\n            \n            \n              Walczak\n              AM\n            \n          \n        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Immunol"},{"key":"B14","doi-asserted-by":"publisher","DOI":"10.1016\/j.cels.2025.101345","article-title":"T cell receptor cross-reactivity prediction improved by a comprehensive mutational scan database","volume":"16","author":"Banerjee","year":"2025","journal-title":"cels"},{"key":"B15","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-021-03752-4","article-title":"Transcriptional programs of neoantigen-specific TIL in anti-PD-1-treated lung cancers","volume":"596","author":"Caushi","year":"2021","journal-title":"Nature"}],"container-title":["Frontiers in Immunology"],"original-title":[],"link":[{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fimmu.2026.1937788\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,10,2]],"date-time":"2026-10-02T05:35:32Z","timestamp":1790919332000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fimmu.2026.1937788\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,10,2]]},"references-count":15,"alternative-id":["10.3389\/fimmu.2026.1937788"],"URL":"https:\/\/doi.org\/10.3389\/fimmu.2026.1937788","relation":{},"ISSN":["1664-3224"],"issn-type":[{"value":"1664-3224","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,10,2]]},"article-number":"1937788"}}