Fig. 5

Cancer driver genes evolve under strong positive selection, and cancer mutations are enriched in healthy tissues. a Percentage of COSMIC cancer mutations observed per sample and grouped by tissue; p values for enrichment were calculated using a hypergeometric test accounting for sequencing coverage, total number of mutations per sample, total number of COSMIC mutations, and the three possible alternate alleles that any given reference allele can have (see the “Methods” section). p values are Bonferroni-corrected across all samples. b Relative mutation rates of a selected group of 53 genes known to carry cancer driver mutations [2] (only 31 of them had at least 1 mutation in this study); the tissue-wide average is indicated with the dotted line. Significant deviation from the tissue-wide average was calculated using the binomial distribution and the tissue-wide average mutation rate. Benjamini-Hochberg FDR: ***FDR < 0.001, **FDR < 0.01, *FDR < 0.05. c Individual mutation rates for each cancer driver gene across all tissues. d Percentage of mutations for each cancer driver gene stratified by impact to amino acid sequence; n is the total number of mutations observed in a gene. e dN/dS values for missense (blue) and nonsense mutations (orange) in cancer driver genes calculated using dndsloc [9, 36] (see the “Methods” section); averages per group are shown as rhomboids, and their respective genome-wide averages are shown as dashed lines along with their 95% confidence intervals after bootstrapping 10,000 times. p values indicate the probability of observing a higher average dN/dS from 10,000 equally sized randomly sampled groups of genes (see the “Methods” section). f Median variant allele frequency (VAF) for each mutation type based on their impact to the amino acid sequence and colored by their cancer status. Mutations “in cancer” (purple bars) are those that overlap with the COSMIC database in both base change and position, and mutations “not in cancer” (yellow bars) are those that overlap with COSMIC only in position but not in base change. Error bars represent the 95% confidence interval after bootstrapping 1000 times; p values are from two-sided Mann-Whitney tests. g Mutation maps of five cancer driver genes; oncogenic state was obtained from oncoKB [37], and clustered mutation annotations were obtained from the databases Cancer Hotspots [38] and 3D Hotspots of mutations occurring in close proximity at the protein level [39]