| PubMed ID |
|
25572114 |
Publish Date |
|
2014 Oct |
| Journal |
|
BMC Genomics |
Species |
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| Disease Type |
|
|
Technology |
|
|
| Title |
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Open adjacencies and k-breaks: detecting simultaneous rearrangements in cancer genomes. |
| Authors |
|
Weinreb C, Oesper L, Raphael BJ |
| Affiliation |
|
Center for Computational Molecular Biology, Brown University, Providence, RI, USA |
| Chromothripsis Definition |
|
Close-by breakpoints: NA
Copy number states: NA
Fragments random joining: NA |
| 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. |
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