TCGA real patient analysis.

PHBR scores were calculated considering TCGA MHC-I genotypes (as in Fig 1). (A) Scatter plot showing the correlation between mutation frequency and median PHBR values. Thirteen weak HLA affinity mutations, as identified in Fig 3, are highlighted in red and labelled. Loess regression line shown in red. Median PHBR value from all 688 analyzed driver genes indicated by dashed line. (B) Box plot comparing PHBR values for the 10/30/100 most frequent mutations as indicated. (C) Bar plot showing the effect size (%) of the 20 driver mutations in the dataset with the largest effect. See Fig 3 for details on effect size calculations. Bars corresponding to the 13 weak HLA affinity mutations from the main analysis are colored in black. (D) Comparison of PHBR scores between patients with observed and unobserved mutations. Box plots show scores for the 13 weak HLA affinity mutations identified in the main analysis (left) and the 3 additional mutations with minimal effect size of 1% as identified in panel C (right). 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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