Open adjacencies and k-breaks: Detecting simultaneous rearrangements in cancer genomes

Caleb Weinreb, Layla Oesper, Benjamin J. Raphael

Research output: Contribution to journalArticle

3 Scopus citations

Abstract

Background: The evolution of a cancer genome has traditionally been described as a sequential accumulation of mutations - including chromosomal rearrangements - over a period of time. Recent research suggests, however, that numerous rearrangements may be acquired simultaneously during a single cataclysmic event, leading to the proposal of new mechanisms of rearrangement such as chromothripsis and chromoplexy. Results: We introduce two measures, open adjacency rate (OAR) and copy-number asymmetry enrichment (CAE), that assess the prevalence of simultaneously formed breakpoints, or k-breaks with k >2, compared to the sequential accumulation of standard rearrangements, or 2-breaks. We apply the OAR and the CAE to genome sequencing data from 121 cancer genomes from two different studies. Conclusions: We find that the OAR and CAE correlate well with previous analyses of chromothripsis/chromoplexy but make differing predictions on a small subset of genomes. These results lend support to the existence of simultaneous rearrangements, but also demonstrate the difficulty of characterizing such rearrangements using different criterion.

Original languageEnglish (US)
Article numberS4
JournalBMC Genomics
Volume15
Issue number6
DOIs
StatePublished - Oct 17 2014
Externally publishedYes

All Science Journal Classification (ASJC) codes

  • Biotechnology
  • Genetics

Keywords

  • Cancer
  • Chromoplexy
  • Chromothripsis
  • DNA sequencing
  • Genome rearrangements

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