cnvCapSeq: detecting copy number variation in long-range targeted resequencing data.

Journal Article (Journal Article)

Targeted resequencing technologies have allowed for efficient and cost-effective detection of genomic variants in specific regions of interest. Although capture sequencing has been primarily used for investigating single nucleotide variants and indels, it has the potential to elucidate a broader spectrum of genetic variation, including copy number variants (CNVs). Various methods exist for detecting CNV in whole-genome and exome sequencing datasets. However, no algorithms have been specifically designed for contiguous target sequencing, despite its increasing importance in clinical and research applications. We have developed cnvCapSeq, a novel method for accurate and sensitive CNV discovery and genotyping in long-range targeted resequencing. cnvCapSeq was benchmarked using a simulated contiguous capture sequencing dataset comprising 21 genomic loci of various lengths. cnvCapSeq was shown to outperform the best existing exome CNV method by a wide margin both in terms of sensitivity (92.0 versus 48.3%) and specificity (99.8 versus 70.5%). We also applied cnvCapSeq to a real capture sequencing cohort comprising a contiguous 358 kb region that contains the Complement Factor H gene cluster. In this dataset, cnvCapSeq identified 41 samples with CNV, including two with duplications, with a genotyping accuracy of 99%, as ascertained by quantitative real-time PCR.

Full Text

Duke Authors

Cited Authors

  • Bellos, E; Kumar, V; Lin, C; Maggi, J; Phua, ZY; Cheng, C-Y; Cheung, CMG; Hibberd, ML; Wong, TY; Coin, LJM; Davila, S

Published Date

  • November 10, 2014

Published In

Volume / Issue

  • 42 / 20

Start / End Page

  • e158 -

PubMed ID

  • 25228465

Pubmed Central ID

  • PMC4227763

Electronic International Standard Serial Number (EISSN)

  • 1362-4962

Digital Object Identifier (DOI)

  • 10.1093/nar/gku849


  • eng

Conference Location

  • England