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

Bellos, Evangelos, Kumar, Vikrant, Lin, Clarabelle, Maggi, Jordi, Yang Phua, Zai Yang, Cheng, Ching-Yu, Cheung, Chui Ming Gemmy, Hibberd, Martin L., Wong, Tien Yin, Coin, Lachlan J. M. and Davila, Sonia (2014) cnvCapSeq: detecting copy number variation in long-range targeted resequencing date. Nucleic Acids Research, 42 20: . doi:10.1093/nar/gku849

Author Bellos, Evangelos
Kumar, Vikrant
Lin, Clarabelle
Maggi, Jordi
Yang Phua, Zai Yang
Cheng, Ching-Yu
Cheung, Chui Ming Gemmy
Hibberd, Martin L.
Wong, Tien Yin
Coin, Lachlan J. M.
Davila, Sonia
Title cnvCapSeq: detecting copy number variation in long-range targeted resequencing date
Journal name Nucleic Acids Research   Check publisher's open access policy
ISSN 1362-4962
Publication date 2014-11-10
Year available 2014
Sub-type Article (original research)
DOI 10.1093/nar/gku849
Open Access Status DOI
Volume 42
Issue 20
Total pages 9
Place of publication Oxford, United Kingdom
Publisher Oxford University Press
Collection year 2015
Language eng
Abstract 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.
Keyword Targeted resequencing technologies
Genomic variants
Q-Index Code C1
Q-Index Status Confirmed Code
Institutional Status UQ
Additional Notes Article no. e158

Document type: Journal Article
Sub-type: Article (original research)
Collections: Official 2015 Collection
Institute for Molecular Bioscience - Publications
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Created: Mon, 05 Jan 2015, 14:55:13 EST by Susan Allen on behalf of Institute for Molecular Bioscience