BamQuery a proteogenomic tool to explore the immunopeptidome and prioritize actionable tumor antigens
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Maria Virginia Ruiz Cuevas’s article, “BamQuery: a proteogenomic tool to explore the immunopeptidome and prioritize actionable tumor antigens”, has been published in BMC Genome Biology and is now publicly available online. Congratulations, Maria!
Abstract: MHC-I-associated peptides deriving from non-coding genomic regions and mutations can generate tumor-specific antigens, including neoantigens. Quantifying tumor-specific antigens’ RNA expression in malignant and benign tissues is critical for discriminating actionable targets. We present BamQuery, a tool attributing an exhaustive RNA expression to MHC-I-associated peptides of any origin from bulk and single-cell RNA-sequencing data. We show that many cryptic and mutated tumor-specific antigens can derive from multiple discrete genomic regions, abundantly expressed in normal tissues. BamQuery can also be used to predict MHC-I-associated peptides immunogenicity and identify actionable tumor-specific antigens de novo.