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Neoantigen × AI
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№22Brief2026-06-26

pVACtools v6 Adds Splice Variant Detection to Neoantigen Prediction

The neoantigen vaccine landscape is seeing simultaneous advances in clinical strategy for head and neck cancer, computational tooling for antigen discovery, and analytical methods for TCR validation.

pVACtools v6 expands its suite with splice variant detection and improved vector design, while replicateFest addresses critical reproducibility challenges in FEST-based TCR repertoire analysis.arXivbioRxiv

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AI / MethodsyesterdayNew

pVACtools v6: A comprehensive suite for neoantigen prediction, visualization, and therapy design

pVACtools v6 introduces significant updates to its open-source neoantigen prediction suite, including pVACsplice for detecting tumor-specific cis-splicing mutations and pVACbind for noncanonical neoantigen sources. The update also features an improved pVACvector algorithm designed to increase DNA/mRNA vector vaccine design success rates with shorter runtimes. These enhancements address the growing need for robust computational prioritization as neoantigen-based vaccines advance into later-stage trials.

mRNA vaccines
arxiv · yesterday · My H. Hoang, Susanna Kiwala, Megan Richters, Luke Hendrickson, Huiming Xia, Evelyn Schmidt

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AI / Methods3 days agoNew

replicateFest: An R Package and Shiny App for Analysis of T Cell Receptor Repertoire Data from the Functional Expansion

The replicateFest R package and Shiny app provide a framework for analyzing T cell receptor repertoire data from Functional Expansion of Specific T (FEST) assays, specifically addressing variability from biological and technical replicates. By applying negative binomial modeling to replicate experiments, it identifies clonotypes significantly expanded in antigen-stimulated conditions with adjusted p-values. This tool aims to improve reproducibility in detecting neoantigen-specific T cell responses, a critical step for guiding vaccine development and assessing checkpoint blockade efficacy.

TCR & T-cell receptor
biorxiv · 3 days ago · Danilova, L.; Favorov, A.; Smith, K. N.; Cope, L.

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Relevant work from earlier we're still surfacing — not today's news.

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