Propensity of of POLE-exo* Group A mutations to cluster on DNA strands. (A) POLE-exo* context mutations (TCT→TAT and AGA→ATA) were counted in 50-kb windows across POLE-exo* tumors F5-6814, AA-A00N, EI-6917, CA-6718, AA-3555, and A6-6141 from TCGA. Normalized density of TCT→TAT mutations divided by total POLE-exo* context is shown in red, and randomized contexts are shown in blue. POLE-exo* tumors with high mutation rates show enrichment for extreme ratios of TCT→TAT mutations indicating clusters of same-strand mutation within the 50-kb windows. Four of six significantly deviate from random expectation by Kolmogorov-Smirnov (KS) P-value < 0.05. Two with KS P-value > 0.05 had low mutation frequencies and too few windows available (N) for a valid test (see Methods). (B) POLE-exo* context mutations were paired such that for each mutation, the partner was the next mutation at the indicated minimum genomic distance upstream. The POLE-exo* (CA-6718) tumor showed an enrichment for the same context (TCT→TAT, TCT→TAT or AGA→ATA, AGA→ATA) versus different context (TCT→TAT, AGA→ATA or AGA→ATA, TCT→TAT). This enrichment was not observed in the POLE-exowt (AA-3666) tumor. The blue bar in the 1-bp to 5-kb range of the POLE-wt only had 10 observations across the entire genome and may be a statistical outlier due to the limited number of observations. (See also Supplemental Fig. S5 for analysis of other patients.)
