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.
Therapeutic vaccines targeting mutant tumor antigens ("neoantigens") are an increasingly popular form of personalized cancer immunotherapy. Vaxrank is a computational tool for selecting neoantigen vaccine peptides from tumor mutations, tumor RNA data, and patient HLA type. Vaxrank is freely available at www.github.com/hammerlab/vaxrank under the Apache 2.0 open source license and can also be installed from the Python Package Index.
: 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.
pileup.js is a new browser-based genome viewer. It is designed to facilitate the investigation of evidence for genomic variants within larger web applications. It takes advantage of recent developments in the JavaScript ecosystem to provide a modular, reliable and easily embedded library.Availability and implementation: The code and documentation for pileup.js is publicly available at https://github.com/hammerlab/pileup.js under the Apache 2.0 license.Contact: correspondence@hammerlab.org
Abstractpileup.js is a new browser-based genome viewer. It is designed to facilitate the investigation of evidence for genomic variants within larger web applications. It takes advantage of recent developments in the JavaScript ecosystem to provide a modular, reliable and easily embedded library.
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