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

Evangelos Bellos; Vikrant Kumar; Clarabelle Lin; Jordi Maggi; Zai Yang Phua; Ching-Yu Cheng; Chui Ming Gemmy Cheung; Martin L Hibberd; Tien Yin Wong; Lachlan JM Coin; +1 more... Sonia Davila; (2014) cnvCapSeq: detecting copy number variation in long-range targeted resequencing data. Nucleic acids research, 42 (20). e158-. ISSN 0305-1048 DOI: 10.1093/nar/gku849
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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.


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