ArticleBMC bioinformatics2013
CNV-TV: a robust method to discover copy number variation from short sequencing reads.
Article in BMC bioinformatics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed.
- Genome-Wide Detection of Copy Number Variation and Association Studies With Physiological and Anatomical Indicators of Heat Stress Response in Lactating Sows.Journal of animal breeding and genetics = Zeitschrift fur Tierzuchtung und Zuchtungsbiologie · 2026Article
- A copy number variation detection method based on OCSVM algorithm using multi strategies integration.Scientific reports · 2025Article
- LoRA-TV: read depth profile-based clustering of tumor cells in single-cell sequencing.Briefings in bioinformatics · 2024Article
- Genome-wide association study between copy number variation and feeding behavior, feed efficiency, and growth traits in Nellore cattle.BMC genomics · 2024Article
- Detection of copy number variations based on a local distance using next-generation sequencing data.Frontiers in genetics · 2023Article
- A shortest path-based approach for copy number variation detection from next-generation sequencing data.Frontiers in genetics · 2022Article
- Comparative study of whole exome sequencing-based copy number variation detection tools.BMC bioinformatics · 2020Article
- DINTD: Detection and Inference of Tandem Duplications From Short Sequencing Reads.Frontiers in genetics · 2020Article
- RKDOSCNV: A Local Kernel Density-Based Approach to the Detection of Copy Number Variations by Using Next-Generation Sequencing Data.Frontiers in genetics · 2020Article
- Copy Number Variation Detection Using Total Variation.ACM-BCB ... ... : the ... ACM Conference on Bioinformatics, Computational Biology and Biomedicine. ACM Conference on Bioinformatics, Computational Biology and Biomedicine · 2019Article
- SM-RCNV: a statistical method to detect recurrent copy number variations in sequenced samples.Genes & genomics · 2019Article
- iCopyDAV: Integrated platform for copy number variations-Detection, annotation and visualization.PloS one · 2018Article
- A Total-variation Constrained Permutation Model for Revealing Common Copy Number Patterns.Scientific reports · 2017Article
- nbCNV: a multi-constrained optimization model for discovering copy number variants in single-cell sequencing data.BMC bioinformatics · 2016Article
- A Sparse Model Based Detection of Copy Number Variations From Exome Sequencing Data.IEEE transactions on bio-medical engineering · 2016Article
- VEGAWES: variational segmentation on whole exome sequencing for copy number detection.BMC bioinformatics · 2015Article
- Changepoint detection in base-resolution methylome data reveals a robust signature of methylated domain landscape.BMC genomics · 2015Article
- CNV-CH: A Convex Hull Based Segmentation Approach to Detect Copy Number Variations (CNV) Using Next-Generation Sequencing Data.PloS one · 2015Article
- Population clustering based on copy number variations detected from next generation sequencing data.Journal of bioinformatics and computational biology · 2014Article
- Common copy number variation detection from multiple sequenced samples.IEEE transactions on bio-medical engineering · 2014Article
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
backgroundCopy number variation (CNV) is an important structural variation (SV) in human genome. Various studies have shown that CNVs are associated with complex diseases. Traditional CNV detection methods such as fluorescence in situ hybridization (FISH) and array comparative genomic hybridization (aCGH) suffer from low resolution. The next generation sequencing (NGS) technique promises a higher resolution detection of CNVs and several methods were recently proposed for realizing such a promise. However, the performances of these methods are not robust under some conditions, e.g., some of them may fail to detect CNVs of short sizes. There has been a strong demand for reliable detection of CNVs from high resolution NGS data.
resultsA novel and robust method to detect CNV from short sequencing reads is proposed in this study. The detection of CNV is modeled as a change-point detection from the read depth (RD) signal derived from the NGS, which is fitted with a total variation (TV) penalized least squares model. The performance (e.g., sensitivity and specificity) of the proposed approach are evaluated by comparison with several recently published methods on both simulated and real data from the 1000 Genomes Project.
conclusionThe experimental results showed that both the true positive rate and false positive rate of the proposed detection method do not change significantly for CNVs with different copy numbers and lengthes, when compared with several existing methods. Therefore, our proposed approach results in a more reliable detection of CNVs than the existing methods.
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