Somatic mutations in cancer genomes are caused by multiple mutational processes, each of which generates a characteristic mutational signature 1. Here, as part of the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium 2 of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA), we characterized mutational signatures using 84,729,690 somatic mutations from 4,645 whole-genome and 19,184 exome sequences that encompass most types of cancer. We identified 49 single-base-substitution, 11 doublet-base-substitution, 4 clustered-base-substitution and 17 small insertion-and-deletion signatures. The substantial size of our dataset, compared with previous analyses 3-15 , enabled the discovery of new signatures, the separation of overlapping signatures and the decomposition of signatures into components that may represent associated-but distinct-DNA damage, repair and/or replication mechanisms. By estimating the contribution of each signature to the mutational catalogues of individual cancer genomes, we revealed associations of signatures to exogenous or endogenous exposures, as well as to defective DNA-maintenance processes. However, many signatures are of unknown cause. This analysis provides a systematic perspective on the repertoire of mutational processes that contribute to the development of human cancer. Somatic mutations in cancer genomes are caused by mutational processes of both exogenous and endogenous origin that operate during the cell lineage between the fertilized egg and the cancer cell 16. Each mutational process may involve components of DNA damage or modification, DNA repair and DNA replication (which may be normal or abnormal), and generates a characteristic mutational signature that potentially includes base substitutions, small insertions and deletions (indels), genome rearrangements and chromosome copy-number changes 1. The mutations in an individual cancer genome may have been generated by multiple mutational processes, and thus incorporate multiple superimposed mutational signatures. Therefore, to systematically characterize the mutational processes that contribute to cancer, mathematical methods have previously been used to decipher mutational signatures from somatic mutation catalogues, estimate the number of mutations that are attributable to each signature in individual samples and annotate each mutation class in each tumour with the probability that it arose from each signature 6,9,17-27. Previous studies of multiple types of cancer have identified more than 30 single-base substitution (SBS) signatures, some of knownbut many of unknown-aetiologies, some ubiquitous and others rare, some part of normal cell biology and others associated with abnormal exposures or neoplastic progression 3-5,7-15. Genome rearrangement signatures have also previously been described 11,25,28-30. However, the analysis of other classes of mutation has been relatively limited 3,11,31-33 .

We analysed whole genome sequences of 560 breast cancers to advance understanding of the driver mutations conferring clonal advantage and the mutational processes generating somatic mutations. 93 protein-coding cancer genes carried likely driver mutations. Some non-coding regions exhibited high mutation frequencies but most have distinctive structural features probably causing elevated mutation rates and do not harbour driver mutations. Mutational signature analysis was extended to genome rearrangements and revealed 12 base substitution and six rearrangement signatures. Three rearrangement signatures, characterised by tandem duplications or deletions, appear associated with defective homologous recombination based DNA repair: one with deficient BRCA1 function; another with deficient BRCA1 or BRCA2 function; the cause of the third is unknown. This analysis of all classes of somatic mutation across exons, introns and intergenic regions highlights the repertoire of cancer genes and mutational processes operative, and progresses towards a comprehensive account of the somatic genetic basis of breast cancer.

The pan-cancer analysis of whole genomes The expansion of whole-genome sequencing studies from individual ICGC and TCGA working groups presented the opportunity to undertake a meta-analysis of genomic features across tumour types. To achieve this, the PCAWG Consortium was established. A Technical Working Group implemented the informatics analyses by aggregating the raw sequencing data from different working groups that studied individual tumour types, aligning the sequences to the human genome and delivering a set of high-quality somatic mutation calls for downstream analysis (Extended Data Fig. 1). Given the recent meta-analysis

40 Somatic mutations in cancer genomes are caused by multiple mutational processes each of 41 which generates a characteristic mutational signature. Using 84,729,690 somatic mutations 42 from 4,645 whole cancer genome and 19,184 exome sequences encompassing most cancer 43 types we characterised 49 single base substitution, 11 doublet base substitution, four 44 clustered base substitution, and 17 small insertion and deletion mutational signatures. The 45 substantial dataset size compared to previous analyses enabled discovery of new signatures, 46 separation of overlapping signatures and decomposition of signatures into components that 47 may represent associated, but distinct, DNA damage, repair and/or replication mechanisms. 48 Estimation of the contribution of each signature to the mutational catalogues of individual 49 cancer genomes revealed associations with exogenous and endogenous exposures and 50 defective DNA maintenance processes. However, many signatures are of unknown cause. 51 This analysis provides a systematic perspective on the repertoire of mutational processes 52 contributing to the development of human cancer including a comprehensive reference set 53 of mutational signatures in human cancer. 54 55 56