Journal Article

DKFZ-2020-02053

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Patterns of somatic structural variation in human cancer genomes.

Li, Y. ; Roberts, N. D. ; Wala, J. A. ; Shapira, O. ; Schumacher, S. E. ; Kumar, K. ; Khurana, E. ; Waszak, S. ; Korbel, J. O. ; Haber, J. E. ; Imielinski, M. ; PCAWGStructuralVariationWorkingGroup ; Weischenfeldt, J. ; Beroukhim, R. ; Campbell, P. J. ; PCAWGConsortium

2020
Nature Publ. Group52462 London [u.a.]

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Please use a persistent id in citations: doi:10.1038/s41586-019-1913-9

Abstract: A key mutational process in cancer is structural variation, in which rearrangements delete, amplify or reorder genomic segments that range in size from kilobases to whole chromosomes1-7. Here we develop methods to group, classify and describe somatic structural variants, using data from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA), which aggregated whole-genome sequencing data from 2,658 cancers across 38 tumour types8. Sixteen signatures of structural variation emerged. Deletions have a multimodal size distribution, assort unevenly across tumour types and patients, are enriched in late-replicating regions and correlate with inversions. Tandem duplications also have a multimodal size distribution, but are enriched in early-replicating regions-as are unbalanced translocations. Replication-based mechanisms of rearrangement generate varied chromosomal structures with low-level copy-number gains and frequent inverted rearrangements. One prominent structure consists of 2-7 templates copied from distinct regions of the genome strung together within one locus. Such cycles of templated insertions correlate with tandem duplications, and-in liver cancer-frequently activate the telomerase gene TERT. A wide variety of rearrangement processes are active in cancer, which generate complex configurations of the genome upon which selection can act.

Keyword(s): Gene Rearrangement: genetics (MeSH) ; Genetic Variation (MeSH) ; Genome, Human: genetics (MeSH) ; Genomics (MeSH) ; Humans (MeSH) ; Mutagenesis, Insertional (MeSH) ; Neoplasms: genetics (MeSH) ; Telomerase: genetics (MeSH) ; TERT protein, human ; Telomerase

Note: siehe Correction: DKFZ Autoren affiliiert im PCAWG Consortium: https://inrepo02.dkfz.de/record/265691 / https://doi.org/10.1038/s41586-022-05597-x

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Contributing Institute(s):

1. Epigenomik (B370)
2. Angewandte Bioinformatik (B330)
3. Bioinformatik und Omics Data Analytics (B240)
4. DKTK HD zentral (HD01)
5. Theoretische Bioinformatik (B080)
6. B060 Molekulare Genetik (B060)
7. B062 Pädiatrische Neuroonkologie (B062)
8. Pädiatrische Gliomforschung (B360)
9. B260 Bioinformatik der Genomik und Systemgenetik (B260)
10. DKTK Koordinierungsstelle Berlin (BE01)
11. B063 Krebsgenomforschung (B063)
12. B087 Neuroblastom Genomik (B087)
13. Core Facility Omics IT (W610)
14. Hochdurchsatz-Sequenzierung (W190)
15. B066 Chromatin-Netzwerke (B066)

Research Program(s):

1. 312 - Functional and structural genomics (POF3-312) (POF3-312)

Appears in the scientific report 2020

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