Extended Data Fig. 2: Mutational alterations in TA-UC.

(a) Mutational matrix of TA-UC (discovery cohort) decomposed into four signatures; colors represent the six base substitution types (top y-axis), further stratified by 5’ and 3’ flanking bases (bottom y-axis). Patterns were matched to COSMIC reference signatures; known etiologies are shown on the right. (b) Mutational signature activity per sample, shown as count (left) and fraction (right) of mutations attributed to each signature (color-coded; identified as in a). (c) Rank order of UC driver genes powered to detect differences (higher or lower) in mutation frequencies (mut freq) between TCGA de novo UC and TA-UC (discovery cohort); lines connect gene ranks between cohorts. (d) UC driver genes powered to detect lower mutation frequencies in TA-UC compared to de novo UC (P-value threshold for statistical power analysis at <0.05, genes mutated in at least 76 de novo UC samples can potentially be considered significantly less mutated in TA-UC). Genes are colored by pathway. Gray line indicates equal frequencies; data points represent number (no) of mutated tumors; error bars reflect Poisson-based standard deviation estimate. Significance analysis by one-sided Fisher’s exact test with Benjamini-Hochberg procedure (Q-values added for all Q < 0.1 and/or PI3K pathway genes; * and sign denote significance). (e) Bar plot of mean gene coverage across samples, ordered high to low; gray line indicates the low-coverage threshold; white crosses indicate presence of a mutation. (f) Integrated plot of PIK3CA mutations in TA-UC samples detected by whole-exome sequencing (WES; blue; cancer cell fraction [CCF] shown) and droplet digital PCR (ddPCR; red; variant allele frequency [VAF; %] shown), ordered top to bottom by protein change (NA, not available). (g) Density histogram showing fraction of tumors grouped by number (no.) of mutations in key PI3K pathway genes per sample; error bars reflect standard deviation from the β-distribution; significance analysis by two-sided Wilcoxon test; numbers in bars indicate mutated tumor counts per group. (h) Violin plots showing timing differences of early clonal driver mutations between TA-UC and TCGA de novo UC; significance values from permutation tests with Benjamini-Hochberg procedure.