title: SCNVSim: somatic copy number variation and structure variation simulator.
abstract: BACKGROUND
  Somatically 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.
  
  
  RESULTS
  SCNVSim 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.
  
  
  CONCLUSIONS
  SCNVSim 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.
authors.affiliation: Department of Biostatistics and Bioinformatics, Roswell Park Cancer Institute, Buffalo, NY, 14263, USA. Maochun.Qin@RoswellPark.org.
authors.forename: Maochun
authors.initials: M
authors.lastname: Qin
authors.affiliation: Center for Personalized Medicine, Roswell Park Cancer Institute, Buffalo, NY, 14263, USA. Biao.Liu@RoswellPark.org.
authors.forename: Biao
authors.initials: B
authors.lastname: Liu
authors.affiliation: Center for Personalized Medicine, Roswell Park Cancer Institute, Buffalo, NY, 14263, USA. Jeffrey.Conroy@RoswellPark.org.
authors.forename: Jeffrey M
authors.initials: JM
authors.lastname: Conroy
authors.affiliation: Center for Personalized Medicine, Roswell Park Cancer Institute, Buffalo, NY, 14263, USA. Carl.Morrison@RoswellPark.org.
authors.forename: Carl D
authors.initials: CD
authors.lastname: Morrison
authors.affiliation: Department of Biostatistics and Bioinformatics, Roswell Park Cancer Institute, Buffalo, NY, 14263, USA. Qiang.Hu@RoswellPark.org.
authors.forename: Qiang
authors.initials: Q
authors.lastname: Hu
authors.affiliation: Department of Biostatistics and Bioinformatics, Roswell Park Cancer Institute, Buffalo, NY, 14263, USA. Yubo.Cheng@RoswellPark.org.
authors.forename: Yubo
authors.initials: Y
authors.lastname: Cheng
authors.affiliation: Center for Personalized Medicine, Roswell Park Cancer Institute, Buffalo, NY, 14263, USA. Mitsuko.Korobkin@RoswellPark.org.
authors.forename: Mitsuko
authors.initials: M
authors.lastname: Murakami
authors.affiliation: Department of Gynecologic Oncology, Roswell Park Cancer Institute, Buffalo, NY, 14263, USA. Kunle.Odunsi@RoswellPark.org.
authors.forename: Adekunle O
authors.initials: AO
authors.lastname: Odunsi
authors.affiliation: Department of Pharmacology and Therapeutics, Roswell Park Cancer Institute, Buffalo, NY, 14263, USA. Candace.Johnson@RoswellPark.org.
authors.forename: Candace S
authors.initials: CS
authors.lastname: Johnson
authors.affiliation: Department of Biostatistics and Bioinformatics, Roswell Park Cancer Institute, Buffalo, NY, 14263, USA. Lei.Wei@RoswellPark.org.
authors.forename: Lei
authors.initials: L
authors.lastname: Wei
authors.affiliation: Department of Biostatistics and Bioinformatics, Roswell Park Cancer Institute, Buffalo, NY, 14263, USA. Song.Liu@RoswellPark.org.
authors.forename: Song
authors.initials: S
authors.lastname: Liu
authors.affiliation: Department of Biostatistics and Bioinformatics, Roswell Park Cancer Institute, Buffalo, NY, 14263, USA. Jianmin.Wang@RoswellPark.org.
authors.forename: Jianmin
authors.initials: J
authors.lastname: Wang
mesh_terms: D000782:Aneuploidy; D003198:Computer Simulation; D056915:DNA Copy Number Variations / Q000235:genetics*; D015894:Genome, Human; D023281:Genomics / Q000379:methods; D005854:Germ Cells; D006579:Heterozygote; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D019656:Loss of Heterozygosity; D009369:Neoplasms / Q000235:genetics*; D017422:Sequence Analysis, DNA / Q000379:methods*