Figure 4.

Impact of nature and position of amino acid substitutions on immunogenicity. Epitopes of the two affinity patterns (APs), i.e. AP1 (increased binding of mutated peptide) and AP2 (no significant increase in binding), were compared to the corresponding background control peptides. (A) The nature of amino acid substitutions does not impact immunogenicity of neoepitopes. The BLOSUM62 matrix was used to assess the degree similarity of the mutated peptide to the non-mutated counterpart in the epitope and background control datasets. The difference in similarity scores between epitopes and background control peptides was found to be significant for peptide pairs in AP2 (p = 0.003568, two-tailed Mann0Whitney test). (B) The type of specific residues found at mutated position contributes to the intrinsic immunogenicity of neoepitopes. The IEDB immunogenicity prediction tool was used to assess the immunogenicity of mutated and non-mutated peptides in the epitope and background control datasets. No significant difference between the immunogenicity scores of epitopes and background control peptides was.