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

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...

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Bibliographic Details
Published in:BMC genomics 2014-10, Vol.15 Suppl 6 (S6), p.S4-S4, Article S4
Main Authors: Weinreb, Caleb, Oesper, Layla, Raphael, Benjamin J
Format: Article
Language:English
Subjects:
Algorithms
Animals
Asymmetry
Cancer
Chromosome Breakpoints
Genetic aspects
Genome
Genomes
Genomics
Humans
Models, Genetic
Molecular biology
Neoplasms - genetics
Scholarships & fellowships
Translocation, Genetic
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Summary: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. 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. 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.
ISSN:1471-2164
1471-2164
DOI:10.1186/1471-2164-15-S6-S4