Classification of changes in predicted peptide HLA binding affinity due to amino acid changes.

The impact on binding affinity associated with amino acid changes arising in cluster transition was determined. Based on impact of the mutations on predicted binding affinity a classification code was assigned to each peptide for each of the affected MHC molecules. The threshold of −1σ was selected based on the outcome of recursive partitioning (Figure S1). The peptides were then assigned to different one of five different classifications according to whether high affinity binding was gained, lost or retained above the threshold. Only high binders were considered, so some peptides that did not surpass the threshold were not included in the analysis of the particular transition.