Pan-cancer analysis of whole genomes

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Pan-cancer analysis of whole genomes. / The ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium.

I: Nature, Bind 578, Nr. 7793, 02.2020, s. 82-93.

Publikation: Bidrag til tidsskrift/Konferencebidrag i tidsskrift /Bidrag til avisTidsskriftartikelForskningpeer review

Harvard

The ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium 2020, 'Pan-cancer analysis of whole genomes', Nature, bind 578, nr. 7793, s. 82-93. https://doi.org/10.1038/s41586-020-1969-6

APA

The ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium (2020). Pan-cancer analysis of whole genomes. Nature, 578(7793), 82-93. https://doi.org/10.1038/s41586-020-1969-6

CBE

The ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium. 2020. Pan-cancer analysis of whole genomes. Nature. 578(7793):82-93. https://doi.org/10.1038/s41586-020-1969-6

MLA

The ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium. "Pan-cancer analysis of whole genomes". Nature. 2020, 578(7793). 82-93. https://doi.org/10.1038/s41586-020-1969-6

Vancouver

The ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium. Pan-cancer analysis of whole genomes. Nature. 2020 feb.;578(7793):82-93. doi: 10.1038/s41586-020-1969-6

Author

The ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium. / Pan-cancer analysis of whole genomes. I: Nature. 2020 ; Bind 578, Nr. 7793. s. 82-93.

Bibtex

@article{0f58cf53186643dba6d3d935174ec9a3,
title = "Pan-cancer analysis of whole genomes",
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.",
keywords = "COMPREHENSIVE CHARACTERIZATION, DNA-DAMAGE, EVOLUTION, LANDSCAPE, PATTERNS, REARRANGEMENTS, SIGNATURES, SOMATIC MUTATIONS, SYSTEMATIC ANALYSIS, TERT PROMOTER MUTATIONS",
author = "Nielsen, {Morten Muhlig} and Pedersen, {Jakob Skou} and Henrik Hornsh{\o}j and Johanna Bertl and Qianyun Guo and Shengjie Gao and Asger Hobolth and Juul, {Randi Istrup} and Tobias Madsen and Miller, {Jessica K.} and {The ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium}",
year = "2020",
month = feb,
doi = "10.1038/s41586-020-1969-6",
language = "English",
volume = "578",
pages = "82--93",
journal = "Nature",
issn = "0028-0836",
publisher = "Nature Publishing Group",
number = "7793",

}

RIS

TY - JOUR

T1 - Pan-cancer analysis of whole genomes

AU - Nielsen, Morten Muhlig

AU - Pedersen, Jakob Skou

AU - Hornshøj, Henrik

AU - Bertl, Johanna

AU - Guo, Qianyun

AU - Gao, Shengjie

AU - Hobolth, Asger

AU - Juul, Randi Istrup

AU - Madsen, Tobias

AU - Miller, Jessica K.

AU - The ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium

PY - 2020/2

Y1 - 2020/2

N2 - 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.

AB - 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.

KW - COMPREHENSIVE CHARACTERIZATION

KW - DNA-DAMAGE

KW - EVOLUTION

KW - LANDSCAPE

KW - PATTERNS

KW - REARRANGEMENTS

KW - SIGNATURES

KW - SOMATIC MUTATIONS

KW - SYSTEMATIC ANALYSIS

KW - TERT PROMOTER MUTATIONS

UR - http://www.scopus.com/inward/record.url?scp=85079038817&partnerID=8YFLogxK

U2 - 10.1038/s41586-020-1969-6

DO - 10.1038/s41586-020-1969-6

M3 - Journal article

C2 - 32025007

AN - SCOPUS:85079038817

VL - 578

SP - 82

EP - 93

JO - Nature

JF - Nature

SN - 0028-0836

IS - 7793

ER -