MHC-I and MHC-II PHBR calculations.

Perimutational amino acid sequences (21-mers for MHC-I, 29-mers for MHC-II) were derived using EnsemblDb. Based on these sequences, all 8 to 11-mers (MHC-I, top) and 15-mers (MHC-II, bottom) containing the mutation were determined as illustrated. For each peptide and MHC-I/MHC-II allele, the HLA affinities were predicted and quantified using a rank-based score. The Patient Best Rank (PBR) was then obtained from the best binding (lowest) ranks. Finally, the Patient Harmonic Best Rank (PHBR) was calculated from the PBRs. Numbers were derived from BRAF V600E (prototypical MHC genotypes, see Methods) and given for illustration purposes. Note that MHC-II DP and DQ genes form heterodimers between alpha and beta subunits.

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