ArticleBioMed research international2013
Comparative study of exome copy number variation estimation tools using array comparative genomic hybridization as control.
Article in BioMed research international, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 29 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
29 citing papers in PubMed, 60 citations in OpenAlex.
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- Consensus-based Detection of Aetiologic Copy Number Variants For Syndromic Orofacial Clefts Utilising Whole Exome Sequencing of Case Parent Trios.Research square · 2026Article
- Copy Number Variant Architecture of Child Psychopathology and Cognitive Development in the ABCD Study.The American journal of psychiatry · 2025Article
- Enhancing Lung Cancer Classification through Integration of Liquid Biopsy Multi-Omics Data with Machine Learning Techniques.Cancers · 2023Article
- Incorporating CNV analysis improves the yield of exome sequencing for rare monogenic disorders-an important consideration for resource-constrained settings.Frontiers in genetics · 2023Review
- Article
- Next Generation Sequencing Based Multiplex Long-Range PCR for Routine Genotyping of Autoinflammatory Disorders.Frontiers in immunology · 2021Article
- Comparative study of whole exome sequencing-based copy number variation detection tools.BMC bioinformatics · 2020Article
- SECNVs: A Simulator of Copy Number Variants and Whole-Exome Sequences From Reference Genomes.Frontiers in genetics · 2020Article
- Development and interlaboratory evaluation of a NIST Reference Material RM 8366 for EGFR and MET gene copy number measurements.Clinical chemistry and laboratory medicine · 2019Article
- Comprehensively benchmarking applications for detecting copy number variation.PLoS computational biology · 2019Article
- Ximmer: a system for improving accuracy and consistency of CNV calling from exome data.GigaScience · 2018Article
- Reliability of algorithmic somatic copy number alteration detection from targeted capture data.Bioinformatics (Oxford, England) · 2017Article
- panelcn.MOPS: Copy-number detection in targeted NGS panel data for clinical diagnostics.Human mutation · 2017Article
- Gene-based comparative analysis of tools for estimating copy number alterations using whole-exome sequencing data.Oncotarget · 2017Article
- arrEYE: a customized platform for high-resolution copy number analysis of coding and noncoding regions of known and candidate retinal dystrophy genes and retinal noncoding RNAs.Genetics in medicine : official journal of the American College of Medical Genetics · 2017Article
- Evaluation of three read-depth based CNV detection tools using whole-exome sequencing data.Molecular cytogenetics · 2017Article
- Certified DNA Reference Materials to Compare HER2 Gene Amplification Measurements Using Next-Generation Sequencing Methods.The Journal of molecular diagnostics : JMD · 2016Article
- Assessing the reproducibility of exome copy number variations predictions.Genome medicine · 2016Article
- Evaluation of somatic copy number estimation tools for whole-exome sequencing data.Briefings in bioinformatics · 2016Article
Corrections and comments
- Erratum issued
Authors and funding
7 authors at 1 institution in 1 country.
Funding
Abstract
Exome sequencing using next-generation sequencing technologies is a cost-efficient approach to selectively sequencing coding regions of the human genome for detection of disease variants. One of the lesser known yet important applications of exome sequencing data is to identify copy number variation (CNV). There have been many exome CNV tools developed over the last few years, but the performance and accuracy of these programs have not been thoroughly evaluated. In this study, we systematically compared four popular exome CNV tools (CoNIFER, cn.MOPS, exomeCopy, and ExomeDepth) and evaluated their effectiveness against array comparative genome hybridization (array CGH) platforms. We found that exome CNV tools are capable of identifying CNVs, but they can have problems such as high false positives, low sensitivity, and duplication bias when compared to array CGH platforms. While exome CNV tools do serve their purpose for data mining, careful evaluation and additional validation is highly recommended. Based on all these results, we recommend CoNIFER and cn.MOPs for nonpaired exome CNV detection over the other two tools due to a low false-positive rate, although none of the four exome CNV tools performed at an outstanding level when compared to array CGH.
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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.