Computational Pipeline for the PGV-001 Neoantigen Vaccine Trial

This paper describes the sequencing protocol and computational pipeline for the PGV-001 personalized vaccine trial. PGV-001 is a therapeutic peptide vaccine targeting neoantigens identified from patient tumor samples. Peptides are selected by a computational pipeline that identifies mutations from t...

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Bibliographic Details
Published in:Frontiers in immunology 2018-01, Vol.8, p.1807-1807
Main Authors: Rubinsteyn, Alex, Kodysh, Julia, Hodes, Isaac, Mondet, Sebastien, Aksoy, Bulent Arman, Finnigan, John P, Bhardwaj, Nina, Hammerbacher, Jeffrey
Format: Article
Language:English
Subjects:
computational pipeline
genomics
immunoinformatics
Immunology
neoantigens
personalized vaccine
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Summary:This paper describes the sequencing protocol and computational pipeline for the PGV-001 personalized vaccine trial. PGV-001 is a therapeutic peptide vaccine targeting neoantigens identified from patient tumor samples. Peptides are selected by a computational pipeline that identifies mutations from tumor/normal exome sequencing and ranks mutant sequences by a combination of predicted Class I MHC affinity and abundance estimated from tumor RNA. The personalized genomic vaccine (PGV) pipeline is modular and consists of independently usable tools and software libraries. We hope that the functionality of these tools may extend beyond the specifics of the PGV-001 trial and enable other research groups in their own neoantigen investigations.
ISSN:1664-3224
1664-3224
DOI:10.3389/fimmu.2017.01807