期刊
CELL SYSTEMS
卷 3, 期 1, 页码 21-34出版社
CELL PRESS
DOI: 10.1016/j.cels.2016.05.007
关键词
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资金
- National Cancer Institute [CA182360]
- National Institutes of Health [HG007352, DK107965]
- National Science Foundation [1054309, 1262575]
- National Human Genome Research Institute [HG00225]
- Direct For Biological Sciences
- Div Of Biological Infrastructure [1619983] Funding Source: National Science Foundation
- Direct For Computer & Info Scie & Enginr
- Div Of Information & Intelligent Systems [1619878] Funding Source: National Science Foundation
Aneuploidy and structural variations (SVs) generate cancer genomes containing a mixture of rearranged genomic segments with extensive somatic copy number alterations. However, existing methods can identify either SVs or allele-specific copy number alterations but not both simultaneously, which provides a limited view of cancer genome structure. Here, we introduce Weaver, an algorithm for the quantification and analysis of allele-specific copy numbers of SVs. Weaver uses a Markov random field to estimate joint probabilities of allele-specific copy numbers of SVs and their inter-connectivity based on paired-end whole-genome sequencing data. Weaver also predicts the timing of SVs relative to chromosome amplifications. We demonstrate the accuracy of Weaver using simulations and findings from whole-genome optical mapping. We apply Weaver to generate allele-specific copy numbers of SVs for MCF-7 and HeLa cell lines and identify recurrent SV patterns in 44 TCGA ovarian cancer whole-genome sequencing datasets. Our approach provides a more complete assessment of the complex genomic architectures inherent to many cancer genomes.
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