Fig. 1.

Personalized neoantigen prioritization and therapy development pipeline. The process of developing personalized neoantigen therapy includes six main steps as depicted in this figure. The first step involves patient enrollment and collection of a tumor biopsy and matched normal sample. Next the samples undergo whole genome/exome and RNA sequencing, followed by variant calling to identify somatic variants unique to the cancer, as well as HLA typing. Information regarding the patients’ variants and HLA type are fed to an ensemble of algorithms that predict neoantigen candidates. The candidates are then prioritized based on a multitude of criteria such as binding affinity, presentation, immunogenicity, variant clonality, and variant expression. Finally, the selected candidates are sent to therapy manufacturers (e.g., peptide or nucleic acid cancer vaccines), subjected to safety testing, and ultimately delivered to the patient. pVACview is developed to aid the candidate prioritization and selection step