Confirmation of previously discovered mHAs. (A) Eighteen previously described HLA class I and class II mHAs were potentially identifiable in the patient genotyping data set by having the relevant cSNP contained on the NS-12 array and the appropriate HLA type contained in the patient population. For each pie chart, the total number represents the number of DRPs in the 101-patient cohort that expressed the appropriate HLA for the examined mHA. The red wedges represent the number of DRPs where the actual mHA could be presented (ie, the appropriate gMM existed in the DRP, and the actual peptide was contained in the total peptide pool). Of the 18 mHAs, 14 were successfully identified by the prediction algorithm. Two mHAs (LB-NUP133 and HA-3) were represented on rare HLAs, and no patients in the cohort had the appropriate gMMs to predict the mHA. For the other 2 mHAs not predicted, the peptide epitope from the mHA derived from HEATR has a predicted binding affinity of >500 nM, and the mHA LB-ADIR is derived from an alternative reading frame. (B) Twelve cSNPs from the SNP array data mapped to known class I mHAs that could be contained in the generated peptide data set. The HLA binding affinity for all 8- to 11-mer DRP peptide pairs to all class I HLA types contained in the patient data set for the 12 cSNPs is shown. A total of 20 926 DRP peptide pairs are shown with increasing shades of gray corresponding to the frequency of the peptide pair in the patient cohort. The 12 cSNPs have been shown to yield 17 mHA peptides that are represented by the red dots. Only 2 of the 17 mHAs fall out of our threshold Kd of 500 nM: the HEATR mHA and 1 confirmed mHA derived from LB-APOBEC3B. The UNC-GRK4-V peptide pair (see Figures 5 and 6) is also mapped (yellow dot).
