Pan-cancer analysis of whole genomes identifies driver rearrangements promoted by LINE-1 retrotransposition

PCAWG Structural Variation Working Group, PCAWG Consortium

Research output: Contribution to journalArticle

Abstract

About half of all cancers have somatic integrations of retrotransposons. Here, to characterize their role in oncogenesis, we analyzed the patterns and mechanisms of somatic retrotransposition in 2,954 cancer genomes from 38 histological cancer subtypes within the framework of the Pan-Cancer Analysis of Whole Genomes (PCAWG) project. We identified 19,166 somatically acquired retrotransposition events, which affected 35% of samples and spanned a range of event types. Long interspersed nuclear element (LINE-1; L1 hereafter) insertions emerged as the first most frequent type of somatic structural variation in esophageal adenocarcinoma, and the second most frequent in head-and-neck and colorectal cancers. Aberrant L1 integrations can delete megabase-scale regions of a chromosome, which sometimes leads to the removal of tumor-suppressor genes, and can induce complex translocations and large-scale duplications. Somatic retrotranspositions can also initiate breakage–fusion–bridge cycles, leading to high-level amplification of oncogenes. These observations illuminate a relevant role of L1 retrotransposition in remodeling the cancer genome, with potential implications for the development of human tumors.

Original languageEnglish (US)
Pages (from-to)306-319
Number of pages14
JournalNature genetics
Volume52
Issue number3
DOIs
StatePublished - Mar 1 2020

ASJC Scopus subject areas

  • Genetics

Fingerprint Dive into the research topics of 'Pan-cancer analysis of whole genomes identifies driver rearrangements promoted by LINE-1 retrotransposition'. Together they form a unique fingerprint.

  • Cite this