A modular, Galaxy-based immunopeptidogenomic (iPepGen) analysis pipeline for discovery, verification, and prioritization of candidate cancer neoantigen peptides
Mehta, S.; Wagner, R.; Do, K. T.; Johnson, J. E.; Yu, F.; Jubenville, T.; Richards, K.; Coleman, S.; Popescu, F. E.; Nesvizhskii, A. I.; Largaespada, D. A.; Jagtap, P. D.; Griffin, T. J.
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Characterizing tumor-specific neoantigen peptides, derived from genomic or transcriptomic aberrations and presented to the immune system, is critical for immuno-oncology studies. To this end, the modular iPepGen immunopeptidogenomics pipeline provides these functions: (1) Neoantigen prediction and protein database generation from genomic or transcriptomic sequencing data; (2) Peptide identification (3) Verification from immunopeptidomic mass spectral data; (4) Neoantigen classification and visualization; (5) Candidate prioritization for further study. Easy access via a publicly available, scalable cloud-based gateway coupled with online, interactive training materials streamlines the adoption by cancer researchers who require immunopeptidogenomic analysis tools but lack advanced computational expertise and resources.
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