Abstract 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 which 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 PGV pipeline is modular and consists of many independently usable tools and software libraries. We draw attention to three particular tools which may be useful to other groups working on neoantigen vaccination. (1) Epidisco is a workflow which orchestrates the parallel execution of the PGV pipeline, including both common steps such as alignment as well as tools which have been developed specifically for the PGV-001 trial. (2) Vaxrank uses somatic variants and tumor RNA reads to select peptides for inclusion in a patient’s vaccine. (3) Isovar is a library used by Vaxrank to determine the mutated protein sequence associated with a genomic variant from supporting tumor RNA reads. 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.

Computational pipeline for the PGV-001 neoantigen vaccine trial