AUTHOR=Rubinsteyn Alex , Kodysh Julia , Hodes Isaac , Mondet Sebastien , Aksoy Bulent Arman , Finnigan John P. , Bhardwaj Nina , Hammerbacher Jeffrey 

TITLE=Computational Pipeline for the PGV-001 Neoantigen Vaccine Trial

JOURNAL=Frontiers in Immunology

VOLUME=8

YEAR=2018

URL=https://www.frontiersin.org/journals/immunology/articles/10.3389/fimmu.2017.01807

DOI=10.3389/fimmu.2017.01807

ISSN=1664-3224

ABSTRACT=<p>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.</p>