Figure 2.

HLA class I binding affinity of neoepitopes is an excellent predictor of immunogenicity. (A) Predicted affinities for mutant and non-mutant peptide pairs of a benchmark set of epitopes and background control peptides. HLA binding predictions were performed using NetMHCpan and predicted percentile ranks of mutated peptides were plotted against those of non-mutated peptides. A threshold of 10 percentile ranks was determined to discriminate epitopes (blue squares) from background control peptides (grey dots). (B) ROC curves of different NetMHCpan binding prediction methods. Performance of the different NetMHCpan prediction methods IC50 (blue), percentile rank (red), and length-rescaled ranks (green) was assessed and prediction based on length-rescaled ranks was found to outperform the other methods.