Pan-cancer analysis of whole genomes
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Abstract
Abstract Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale 1–3 . Here we report the integrative analysis of 2,658 whole-cancer genomes and their matching normal tissues across 38 tumour types from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). We describe the generation of the PCAWG resource, facilitated by international data sharing using compute clouds. On average, cancer genomes contained 4–5 driver mutations when combining coding and non-coding genomic elements; however, in around 5% of cases no drivers were identified, suggesting that cancer driver discovery is not yet complete. Chromothripsis, in which many clustered structural variants arise in a single catastrophic event, is frequently an early event in tumour evolution; in acral melanoma, for example, these events precede most somatic point mutations and affect several cancer-associated genes simultaneously. Cancers with abnormal telomere maintenance often originate from tissues with low replicative activity and show several mechanisms of preventing telomere attrition to critical levels. Common and rare germline variants affect patterns of somatic mutation, including point mutations, structural variants and somatic retrotransposition. A collection of papers from the PCAWG Consortium describes non-coding mutations that drive cancer beyond those in the TERT promoter 4 ; identifies new signatures of mutational processes that cause base substitutions, small insertions and deletions and structural variation 5,6 ; analyses timings and patterns of tumour evolution 7 ; describes the diverse transcriptional consequences of somatic mutation on splicing, expression levels, fusion genes and promoter activity 8,9 ; and evaluates a range of more-specialized features of cancer genomes 8,10–18 .
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The record
- Venue
- Nature
- Topic
- Cancer Genomics and Diagnostics
- Field
- Biochemistry, Genetics and Molecular Biology
- Canadian institutions
- SickKids FoundationBC Cancer AgencyUniversity of British ColumbiaProstate Cancer CanadaUniversité de MontréalHospital for Sick ChildrenLunenfeld-Tanenbaum Research InstituteMount Sinai HospitalUniversity of CalgaryPrincess Margaret Cancer CentreSimon Fraser UniversityUniversity of OttawaMcGill UniversityVector InstituteUniversity of TorontoMcGill University and Génome Québec Innovation CentreToronto General HospitalUniversity Health NetworkGenome CanadaCanada's Michael Smith Genome Sciences CentreInstitute of Cancer ResearchOntario Institute for Cancer Research
- Funders
- National Human Genome Research InstituteNational Institute of General Medical SciencesMedical Research CouncilNational Institute of Environmental Health SciencesNational Institute for Health and Care ResearchPancreatic Cancer UKWellcome TrustFrancis Crick InstituteNational Cancer InstituteCancer Research UK
- Keywords
- GenomeCancerComputational biologyBiologyGeneticsEvolutionary biologyGene
- Has abstract in OpenAlex
- yes