title: SeqCNV: a novel method for identification of copy number variations in targeted next-generation sequencing data.
abstract: BACKGROUND
  Targeted next-generation sequencing (NGS) has been widely used as a cost-effective way to identify the genetic basis of human disorders. Copy number variations (CNVs) contribute significantly to human genomic variability, some of which can lead to disease. However, effective detection of CNVs from targeted capture sequencing data remains challenging.
  
  
  RESULTS
  Here we present SeqCNV, a novel CNV calling method designed to use capture NGS data. SeqCNV extracts the read depth information and utilizes the maximum penalized likelihood estimation (MPLE) model to identify the copy number ratio and CNV boundary. We applied SeqCNV to both bacterial artificial clone (BAC) and human patient NGS data to identify CNVs. These CNVs were validated by array comparative genomic hybridization (aCGH).
  
  
  CONCLUSIONS
  SeqCNV is able to robustly identify CNVs of different size using capture NGS data. Compared with other CNV-calling methods, SeqCNV shows a significant improvement in both sensitivity and specificity.
authors.affiliation: Shanghai Key Lab of Intelligent Information Processing, Shanghai, China.|School of Computer Science and Technology, Fudan University, Shanghai, China.
authors.forename: Yong
authors.initials: Y
authors.lastname: Chen
authors.affiliation: Structural and Computational Biology & Molecular Biophysics Graduate Program, Baylor College of Medicine, Houston, TX, USA.|Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA.
authors.forename: Li
authors.initials: L
authors.lastname: Zhao
authors.affiliation: School of Life Sciences, Fudan University, Shanghai, China.
authors.forename: Yi
authors.initials: Y
authors.lastname: Wang
authors.affiliation: University of Texas Health Science Center, Houston, TX, USA.
authors.forename: Ming
authors.initials: M
authors.lastname: Cao
authors.affiliation: Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA.|Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
authors.forename: Violet
authors.initials: V
authors.lastname: Gelowani
authors.affiliation: Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA.|Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
authors.forename: Mingchu
authors.initials: M
authors.lastname: Xu
authors.affiliation: Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA.|Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
authors.forename: Smriti A
authors.initials: SA
authors.lastname: Agrawal
authors.affiliation: Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA.|Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
authors.forename: Yumei
authors.initials: Y
authors.lastname: Li
authors.affiliation: Department of Ophthalmology and Visual Sciences, University of Texas Health Science Center, Houston, TX, USA.
authors.forename: Stephen P
authors.initials: SP
authors.lastname: Daiger
authors.affiliation: Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA.
authors.forename: Richard
authors.initials: R
authors.lastname: Gibbs
authors.affiliation: Shanghai Key Lab of Intelligent Information Processing, Shanghai, China. wangfei@fudan.edu.cn.|School of Computer Science and Technology, Fudan University, Shanghai, China. wangfei@fudan.edu.cn.
authors.forename: Fei
authors.identifier: http://orcid.org/0000-0001-5890-0448
authors.initials: F
authors.lastname: Wang
authors.affiliation: Structural and Computational Biology & Molecular Biophysics Graduate Program, Baylor College of Medicine, Houston, TX, USA. ruichen@bcm.edu.|Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA. ruichen@bcm.edu.|Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA. ruichen@bcm.edu.
authors.forename: Rui
authors.initials: R
authors.lastname: Chen
mesh_terms: D056915:DNA Copy Number Variations; D015894:Genome, Human; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D016013:Likelihood Functions; D012680:Sensitivity and Specificity; D017422:Sequence Analysis, DNA / Q000379:methods; D012984:Software
keywords: Copy number variation; Maximum penalized likelihood estimation; Next-generation sequencing