Cancer cell line analysis.

PHBR scores were calculated for all hot spot driver mutations in cancer cells from the Cancer Cell Line Encyclopedia (CCLE), for which HLA allele calls were available. Analysis in (A-E) are based on sample-specific HLA alleles, while (F-G) are based on the prototypical MHC-I genotype. (A) Pie chart showing the different primary tumors where the cell lines were derived from. (B) Box plots compare PHBR values between observed (+) and unobserved (-) mutations. (C) Logistic regression analysis between log PHBR (observed variable) and mutation status (response variable). Analysis was performed using both the within-patient and within-mutation regression model as indicated (see main analysis for details). (D) Scatter plot showing 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. (E) Box plot comparing PHBR values for 10/30/100 most frequent mutations as indicated. (F-G) Similar as panels (B) and (C) but with PHBR values calculated based on the prototypical MHC-I genotypes. 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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