Patterns of somatic structural variation in human cancer genomes
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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 chromosomes1,2,3,4,5,6,7. 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.
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 , PCAWG Structural Variation Working Group , Weischenfeldt , J , Beroukhim , R , Campbell , P J & PCAWG Consortium 2020 , ' Patterns of somatic structural variation in human cancer genomes ' , Nature , vol. 578 , no. 7793 , pp. 112-121 . https://doi.org/10.1038/s41586-019-1913-9
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DescriptionThis work was supported by the Wellcome Trust, Pediatric Low-Grade Astrocytoma Fund and the Fund for Innovation in Cancer Informatics. P.J.C. is a Wellcome Trust Senior Clinical Fellow (WT088340MA). We acknowledge the contributions of the many clinical networks across ICGC and TCGA, which provided samples and data to the PCAWG Consortium, and the contributions of the Technical Working Group and the Germline Working Group of the PCAWG Consortium for the collation, realignment and harmonized variant-calling of the cancer genomes used in this study. We thank the patients and their families for their participation in the individual ICGC and TCGA projects.
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