Figure 5. Validation of neoantigens identified in silico from the novel workflow through enzyme-linked immunospot (ELISpot) assays conducted on four colorectal cancer (CRC) patients.

(A) A schematic diagram illustrates the procedural steps of neoantigen prioritization and the ELISpot assay. (B) The count of neoantigens identified from each pipeline. (C) The fold change in IFN-γ spots, relative to the wild-type peptides, is shown for 21 long peptides. Note: Only the mutants that result in a positive value in ELISpot are depicted, along with their corresponding amino acid changes and their associated rankings. (D) ELISpot assays on six long peptides resulting in at least a twofold change in IFN-γ spots. (E) The bar graphs display the ranking of validated long peptides identified from the NetMHCpan tool (blue bar) or the combined method (red bar) for individual patients and all patients.

Figure 5—figure supplement 1. The rank coverage score of the combined model compared to NetMHCpan.

The bar graphs display rank coverage scores of validated long peptides identified by the NetMHCpan tool (blue bars) and the combined method (red bars) for individual patients and all patients collectively.