Title |
A novel independence test for somatic alterations in cancer shows that biology drives mutual exclusivity but chance explains most co-occurrence
|
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Published in |
Genome Biology, December 2016
|
DOI | 10.1186/s13059-016-1114-x |
Pubmed ID | |
Authors |
Sander Canisius, John W. M. Martens, Lodewyk F. A. Wessels |
Abstract |
In cancer, mutually exclusive or co-occurring somatic alterations across genes can suggest functional interactions. Existing tests for such patterns make the unrealistic assumption of identical gene alteration probabilities across tumors. We present Discrete Independence Statistic Controlling for Observations with Varying Event Rates (DISCOVER), a novel test that is more sensitive than other methods and controls its false positive rate. A pan-cancer analysis using DISCOVER finds no evidence for widespread co-occurrence, and most co-occurrences previously detected do not exceed expectation by chance. Many mutual exclusivities are identified involving well-known genes related to cell cycle and growth factor signaling, as well as lesser known regulators of Hedgehog signaling. |
X Demographics
Geographical breakdown
Country | Count | As % |
---|---|---|
United States | 5 | 33% |
India | 1 | 7% |
France | 1 | 7% |
United Kingdom | 1 | 7% |
Unknown | 7 | 47% |
Demographic breakdown
Type | Count | As % |
---|---|---|
Scientists | 9 | 60% |
Members of the public | 5 | 33% |
Science communicators (journalists, bloggers, editors) | 1 | 7% |
Mendeley readers
Geographical breakdown
Country | Count | As % |
---|---|---|
United Kingdom | 3 | 2% |
Netherlands | 1 | <1% |
Unknown | 163 | 98% |
Demographic breakdown
Readers by professional status | Count | As % |
---|---|---|
Student > Ph. D. Student | 38 | 23% |
Researcher | 36 | 22% |
Student > Master | 15 | 9% |
Student > Bachelor | 13 | 8% |
Student > Doctoral Student | 8 | 5% |
Other | 22 | 13% |
Unknown | 35 | 21% |
Readers by discipline | Count | As % |
---|---|---|
Biochemistry, Genetics and Molecular Biology | 47 | 28% |
Agricultural and Biological Sciences | 22 | 13% |
Computer Science | 18 | 11% |
Medicine and Dentistry | 17 | 10% |
Engineering | 7 | 4% |
Other | 11 | 7% |
Unknown | 45 | 27% |