Table 1.

Summary of pVACview features that facilitate neoantigen prioritization

Level	Feature	Suggestion
Variant	RNA Expr: Gene expression value for the annotated gene containing the variant. RNA VAF : Tumor RNA variant allele frequency (VAF) at this position. Allele Expr: RNA Expr * RNA VAF RNA Depth : Tumor RNA depth at this position. DNA VAF : Tumor DNA variant allele frequency (VAF) at this position.	Prioritize variant(s) with high tumor variant allele fraction (VAF) and allelic expression. Interpretation of tumor VAF first requires estimation of tumor purity which may be guided by the VAF of known tumor drivers. Prioritize variants in genes known to be associated with cancer type of the investigated sample, genes listed in Cancer Gene Census.
Transcript	TSL : Transcript support level of the best peptide	Prioritize transcript(s) where the annotated splicing pattern matches the splicing observed in patient RNAseq data (transcript with TSL >= 1, cross-check in IGV recommended).
Peptide	IC50 MT : Lowest or Median ic50 binding affinity of the best-binding mutant epitope across all prediction algorithms used. %ile MT : Lowest or Median binding affinity percentile rank of the best-binding mutant epitope across all prediction algorithms used (those that provide percentile output) Elution score Immunogenicity score	Prioritize peptide(s) with favorable binding affinity to MHC (we recommend binding affinity of 500 nM or less, and percentile rank of 2 or less). Prioritize peptides with favorable anchor scenarios. (see suggestion by Xia et al., 2023 [23]) Exclude peptides with a reference match in the proteome. Prioritize peptides with favorable elution score (elution score ranges from 0 to 1, with 1 being the best elution score), with a percentile rank of 2 or less. Prioritize peptides with favorable immunogenicity score (immunogenicity score from DeepImmuno and BigMHC_IM ranges from 0 to 1, with 1 being the best elution score).