Application of the NetMHCpan prediction algorithm to CLL cases. (A) Distribution of the number of predicted peptides with HLA binding affinity <150 (black) and 150 to 500 nM (gray) across 31 CLL patients with available HLA typing information (supplemental Table 1). (B) Peptides with predicted binding (IC50 <500 nM by NetMHCpan) from 4 patients were synthesized and tested for HLA-A and -B allele binding using a competitive MHC I allele-binding assay. The percent of predicted peptides with evidence of experimental binding (IC50 < 500 nM) are indicated. (C) The distribution of gene expression for all somatically mutated genes (n = 347) from 26 CLL patients and for the subset of gene mutations encoding neoepitopes with predicted HLA binding scores of IC50 <500 nM (n = 180). No-low, genes within the lowest quartile expression; medium, genes within the 2 middle quartiles of expression; high, genes within the highest quartile of expression.
