Fig. 5: Nucleotide excision repair is mutagenic when lesions on opposing strands are in close proximity.

a, Mechanism of NER translesion resynthesis-induced mutagenesis (NER-TRIM). Lesion-containing single-stranded DNA is excised and consequently a residual lesion in close proximity on the opposite strand would be used as a low-fidelity template for repair synthesis. This creates isolated mutations with opposite strand asymmetry to the genomic locality (for example, A→N within a T→N segment). Most lesion-induced mutations are not shared between daughter lineages, whereas those from NER-TRIM can be shared (black arrow). b, The rate of A→N mutations on the genic template strand increases with gene expression, mirroring the decrease in mutations from other bases due to TCR. The relative difference (y axis) in mutation rate for each nucleotide is (obs − exp)/(obs + exp); exp is the mutation rate for that nucleotide in non-expressed genes, and obs is the rate observed in the body of genes with the indicated expression level (x axis). Rates shown for lesions on the transcription template strand, with 95% confidence interval (shaded areas) from 100 bootstrap samples of genes. c, Schematic illustrating the generation of a mutationally symmetric tumour through the survival of both post-mutagenesis daughter genomes. NER-TRIM mutations in symmetric tumours will be characterized by abnormally high VAF as they will be shared by both contributing genomes (Extended Data Fig. 10b). d, Contingency table illustrating the enrichment of mutations with high VAF (0.995–1.0 quantile) in highly expressed genes of mutationally symmetric tumours (n = 8) compared with asymmetric tumours (n = 237). Statistical significance by two-tailed Fisher’s exact test. e, Symmetric tumours are highly enriched for high VAF mutations in highly expressed genes. Odds ratios (y axis) are as in d, for VAF quantile bins of 0.005 (x axis). The black arrow shows the odds ratio calculated in d.