Figure 3. HLA-identical siblings present similar but not identical MIP repertoires.

(a) Venn diagram showing that 86% of MIPs from HLA-identical siblings were detected in both subjects. A total of 4,468 MIPs were identified in the siblings after analysis of eight biological samples (four biological replicates per sibling). MIPs were detected in variable number of biological replicates. For peptides exclusively detected in one subject, the number of replicates in which the peptide was found is shown. The total numbers of MIPs exclusively detected in subject 1 or 2 are shown in red and blue, respectively. (b) Scatter plot showing that 75% of identified MIPs are predicted to bind their respective HLA molecules with an IC₅₀<500 nM. The IC₅₀ for five HLA alleles was calculated with the NetMHCcons algorithm. For each peptide (represented by dots), the best binding score for a specific allele was kept. The yellow box highlights 75% of all peptides. The black lines and values indicate the average binding affinity of all peptides identified in each sibling. Red and blue lines and numbers represent the average binding affinity of 282 and 351 unshared peptides exclusively detected in subject 1 or 2, respectively. The predicted binding affinity of the two sets of unshared MIPs was statistically indistinguishable (P=8.5 × 10⁶ by two-tailed Mann–Whitney test). (c) The number of peptides associated with each HLA molecule was similar between the two subjects.