ArticleNucleic acids research2014
cnvCapSeq: detecting copy number variation in long-range targeted resequencing data.
Article in Nucleic acids research, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed, 17 citations in OpenAlex.
- Review
- varAmpliCNV: analyzing variance of amplicons to detect CNVs in targeted NGS data.Bioinformatics (Oxford, England) · 2023Article
- Variation in CFHR3 determines susceptibility to meningococcal disease by controlling factor H concentrations.American journal of human genetics · 2022Article
- Atlas-CNV: a validated approach to call single-exon CNVs in the eMERGESeq gene panel.Genetics in medicine : official journal of the American College of Medical Genetics · 2019Article
- Detection of structural variation using target captured next-generation sequencing data for genetic diagnostic testing.Genetics in medicine : official journal of the American College of Medical Genetics · 2019Article
- Detection of de novo copy number deletions from targeted sequencing of trios.Bioinformatics (Oxford, England) · 2019Article
- Simulating the dynamics of targeted capture sequencing with CapSim.Bioinformatics (Oxford, England) · 2018Article
- Systematic evaluation of a targeted gene capture sequencing panel for molecular diagnosis of retinitis pigmentosa.PloS one · 2018Article
- An evaluation of copy number variation detection tools for cancer using whole exome sequencing data.BMC bioinformatics · 2017Article
Corrections and comments
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Authors and funding
11 authors at 6 institutions in 4 countries.
Funding
No grant is acknowledged in the PubMed record.
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.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.