Cancers arise through the acquisition of oncogenic mutations and grow by clonal expansion. Here we reveal that most mutagenic DNA lesions are not resolved into a mutated DNA base pair within a single cell cycle. Instead, DNA lesions segregate, unrepaired, into daughter cells for multiple cell generations, resulting in the chromosome-scale phasing of subsequent mutations. We characterize this process in mutagen-induced mouse liver tumours and show that DNA replication across persisting lesions can produce multiple alternative alleles in successive cell divisions, thereby generating both multiallelic and combinatorial genetic diversity. The phasing of lesions enables accurate measurement of strand-biased repair processes, quantification of oncogenic selection and fine mapping of sister-chromatid-exchange events. Finally, we demonstrate that lesion segregation is a unifying property of exogenous mutagens, including UV light and chemotherapy agents in human cells and tumours, which has profound implications for the evolution and adaptation of cancer genomes. The data submitted here is analysis output based on primary data submitted to the EBI under the indicated accession PRJEB37808.

Differential binding results of ChIP-seq datasets. Results from the differential binding analyses of the CTCF ChIP-seq dataset using csaw, and of the H3K4me3 and H3K27ac datasets using DiffBind. Format: xls. File size: 20.5Â MB. (XLS 20040 kb)

Proteome quantification. Normalized protein abundances from the TMT proteomics dataset along with the results from the differential abundance analysis. Format: xls. File size: 2.9Â MB. (XLS 2840 kb)

Proteome quantification. Normalized protein abundances from the TMT proteomics dataset along with the results from the differential abundance analysis. Format: xls. File size: 2.9Â MB. (XLS 2840 kb)

Mouse and human tumor metadata and differential expression results of RNA-seq data. Sample information regarding all mouse and human tumor samples included in analyses. Results from the differential expression analysis of mouse liver tumors and human uterine and breast cancer dataset (performed using DESeq2). Gene set enrichment analysis for mouse concordant genes. Intersection results of MEF and tumor DE analyses. Format: xls. File size: 20.7Â MB. (XLS 20148 kb)

Mouse and human tumor metadata and differential expression results of RNA-seq data. Sample information regarding all mouse and human tumor samples included in analyses. Results from the differential expression analysis of mouse liver tumors and human uterine and breast cancer dataset (performed using DESeq2). Gene set enrichment analysis for mouse concordant genes. Intersection results of MEF and tumor DE analyses. Format: xls. File size: 20.7Â MB. (XLS 20148 kb)

A table of primer sequences used for targeted assay of methylation. (CSV 3 kb)

A table of primer sequences used for targeted assay of methylation. (CSV 3 kb)

Validation of Ctcf deletion. Quantification of Ctcf deletion by qRT-PCR and quantitative western blot experiments on wild-type and Ctcf +/â MEFs. Format: xls. File size: 61Â KB. (XLS 40 kb)

Validation of Ctcf deletion. Quantification of Ctcf deletion by qRT-PCR and quantitative western blot experiments on wild-type and Ctcf +/â MEFs. Format: xls. File size: 61Â KB. (XLS 40 kb)