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Pan-cancer analysis of whole genomes

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Lynch_2020_nature_pan_cancer_82_CC.pdf (22.58Mb)
Date
06/02/2020
Author
The ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium
Keywords
QH426 Genetics
RC0254 Neoplasms. Tumors. Oncology (including Cancer)
3rd-DAS
SDG 3 - Good Health and Well-being
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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 scale1–3. 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 promoter4; identifies new signatures of mutational processes that cause base substitutions, small insertions and deletions and structural variation5,6; analyses timings and patterns of tumour evolution7; describes the diverse transcriptional consequences of somatic mutation on splicing, expression levels, fusion genes and promoter activity8,9; and evaluates a range of more-specialized features of cancer genomes8,10–18.
Citation
The ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium 2020 , ' Pan-cancer analysis of whole genomes ' , Nature , vol. 578 , no. 7793 , pp. 82-93 . https://doi.org/10.1038/s41586-020-1969-6
Publication
Nature
Status
Peer reviewed
DOI
https://doi.org/10.1038/s41586-020-1969-6
ISSN
0028-0836
Type
Journal article
Rights
© Copyright The Author(s) 2020. Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the articleʼs Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the articleʼs Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.
Collections
  • University of St Andrews Research
URI
http://hdl.handle.net/10023/19568

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