Fig. 3

Landscape of filtered neoantigen candidates. This figure illustrates the landscape of neoantigen vaccine candidates in patient MEL21 after being prioritized using the pVAC-Seq pipeline. The points represent the overall sequencing information: exome and RNA VAFs, gene expression in terms of log2 FPKM value, as well log2 fold change, calculated as the ratio of WT binding affinity over mutant binding affinity. Recommended exome and RNA VAF cutoffs are also indicated. Candidates that were incorporated in the vaccine are labeled based on the genes containing these somatic mutations. Red boxes depict naturally occurring (that is, pre-existing T cell response) and blue boxes denote vaccine-induced neoantigens that were recognized by T cells. Since BRAF was used as a guide for assessing clonality of other mutations, it is also shown in each of three metachronous tumors (from the same patient)