Title |
ReMixT: clone-specific genomic structure estimation in cancer
|
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Published in |
Genome Biology, July 2017
|
DOI | 10.1186/s13059-017-1267-2 |
Pubmed ID | |
Authors |
Andrew W. McPherson, Andrew Roth, Gavin Ha, Cedric Chauve, Adi Steif, Camila P. E. de Souza, Peter Eirew, Alexandre Bouchard-Côté, Sam Aparicio, S. Cenk Sahinalp, Sohrab P. Shah |
Abstract |
Somatic evolution of malignant cells produces tumors composed of multiple clonal populations, distinguished in part by rearrangements and copy number changes affecting chromosomal segments. Whole genome sequencing mixes the signals of sampled populations, diluting the signals of clone-specific aberrations, and complicating estimation of clone-specific genotypes. We introduce ReMixT, a method to unmix tumor and contaminating normal signals and jointly predict mixture proportions, clone-specific segment copy number, and clone specificity of breakpoints. ReMixT is free, open-source software and is available at http://bitbucket.org/dranew/remixt . |
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Geographical breakdown
Country | Count | As % |
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United States | 5 | 33% |
United Kingdom | 2 | 13% |
Spain | 1 | 7% |
Montenegro | 1 | 7% |
Sweden | 1 | 7% |
Belgium | 1 | 7% |
Unknown | 4 | 27% |
Demographic breakdown
Type | Count | As % |
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Scientists | 9 | 60% |
Members of the public | 5 | 33% |
Science communicators (journalists, bloggers, editors) | 1 | 7% |
Mendeley readers
Geographical breakdown
Country | Count | As % |
---|---|---|
Unknown | 67 | 100% |
Demographic breakdown
Readers by professional status | Count | As % |
---|---|---|
Researcher | 15 | 22% |
Student > Ph. D. Student | 12 | 18% |
Student > Master | 9 | 13% |
Student > Bachelor | 8 | 12% |
Student > Doctoral Student | 4 | 6% |
Other | 1 | 1% |
Unknown | 18 | 27% |
Readers by discipline | Count | As % |
---|---|---|
Biochemistry, Genetics and Molecular Biology | 17 | 25% |
Agricultural and Biological Sciences | 14 | 21% |
Computer Science | 7 | 10% |
Medicine and Dentistry | 6 | 9% |
Immunology and Microbiology | 1 | 1% |
Other | 4 | 6% |
Unknown | 18 | 27% |