SCNVSim: somatic copy number variation and structure variation simulator |
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Authors: | Maochun Qin Biao Liu Jeffrey M Conroy Carl D Morrison Qiang Hu Yubo Cheng Mitsuko Murakami Adekunle O Odunsi Candace S Johnson Lei Wei Song Liu Jianmin Wang |
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Affiliation: | .Department of Biostatistics and Bioinformatics, Roswell Park Cancer Institute, Buffalo, NY 14263 USA ;.Center for Personalized Medicine, Roswell Park Cancer Institute, Buffalo, NY 14263 USA ;.Department of Gynecologic Oncology, Roswell Park Cancer Institute, Buffalo, NY 14263 USA ;.Department of Pharmacology and Therapeutics, Roswell Park Cancer Institute, Buffalo, NY 14263 USA |
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Abstract: | BackgroundSomatically acquired structure variations (SVs) and copy number variations (CNVs) can induce genetic changes that are directly related to tumor genesis. Somatic SV/CNV detection using next-generation sequencing (NGS) data still faces major challenges introduced by tumor sample characteristics, such as ploidy, heterogeneity, and purity. A simulated cancer genome with known SVs and CNVs can serve as a benchmark for evaluating the performance of existing somatic SV/CNV detection tools and developing new methods.ResultsSCNVSim is a tool for simulating somatic CNVs and structure variations SVs. Other than multiple types of SV and CNV events, the tool is capable of simulating important features related to tumor samples including aneuploidy, heterogeneity and purity.ConclusionsSCNVSim generates the genomes of a cancer cell population with detailed information of copy number status, loss of heterozygosity (LOH), and event break points, which is essential for developing and evaluating somatic CNV and SV detection methods in cancer genomics studies. |
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