Evolutionary conservation analysis.

Box plots compare MHC-I PHBR scores (A) and 2 evolutionary conservation scores (B, pastCons; C, phyloP) between different somatic mutation datasets. From left to right and as indicated: 500 random missense mutations that were never observed in the TCGA dataset; 500 random missense mutations that were not recurrent (occurred once in the TCGA dataset) and are not known as a Cancer Gene Census (CGC) gene; 500 recurrent missense mutations that are not known as CGC genes; 500 non-recurrent missense mutations in CGC genes; 688 recurrent missense mutations in CGC genes (the dataset used for the main analysis) that are further divided depending on the presence of the gene in the 13-gene weak HLA affinity mutation dataset identified in the main analysis. phastCons (B) and phyloP (C) were derived from multiple alignments between 100 vertebrate species and calculated for the genomic region extending +/- 10 base pairs from the mutation (21 base pairs in total). Box plots indicate median values and lower/upper quartiles with whiskers extending to 1.5 times the interquartile range. P values calculated using Wilcoxon rank-sum test.

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