ArticleMolecular cytogenetics2017
Evaluation of three read-depth based CNV detection tools using whole-exome sequencing data.
Article in Molecular cytogenetics, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 66 papers.
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66 citing papers in PubMed.
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- Computational strategies for copy number variation detection, disease association, and beyond.Genome biology · 2026Review
- Consensus-based detection of aetiologic copy number variants for syndromic orofacial clefts utilising whole exome sequencing of case parent trios.BMC genomic data · 2026Article
- Consensus-based Detection of Aetiologic Copy Number Variants For Syndromic Orofacial Clefts Utilising Whole Exome Sequencing of Case Parent Trios.Research square · 2026Article
- Decoding structural birth defects through genomic landscapes: Innovative frameworks for diagnosis (Review).International journal of molecular medicine · 2026Review
- Ending diagnostic odyssey by reanalysis of whole exome sequencing data: reclassification of suspected Fanconi anemia cases to dyskeratosis congenita and Diamond-Blackfan anemia.Orphanet journal of rare diseases · 2025Article
- Comparative study of tools for copy number variation detection using next-generation sequencing data.Scientific reports · 2025Article
- Validation of the NovaSeq6000 platform and automated library preparation for CE-IVD equivalence.Computational and structural biotechnology journal · 2025Article
- Comprehensive reanalysis for CNVs in ES data from unsolved rare disease cases results in new diagnoses.NPJ genomic medicine · 2024Article
- Genetic aspects of ataxias in a cohort of Turkish patients.Neurological sciences : official journal of the Italian Neurological Society and of the Italian Society of Clinical Neurophysiology · 2024Article
- Biallelic structural variants in three patients with ERCC8-related Cockayne syndrome and a potential pitfall of copy number variation analysis.Scientific reports · 2024Article
- HMZDupFinder: a robust computational approach for detecting intragenic homozygous duplications from exome sequencing data.Nucleic acids research · 2024Article
- Bioinformatics of germline variant discovery for rare disease diagnostics: current approaches and remaining challenges.Briefings in bioinformatics · 2024Review
- Case Report: Whole exome sequencing identifies compound heterozygous variants in theFrontiers in genetics · 2024Article
- Next-generation variant exon screening: Moving forward in routine genetic disease investigations.Genetics in medicine open · 2024Article
- Long-read sequencing revealing intragenic deletions in exome-negative spastic paraplegias.Journal of human genetics · 2023Article
- Validation of clinical exome sequencing in the diagnostic procedure of patients with intellectual disability in clinical practice.Orphanet journal of rare diseases · 2023Review
- Compound heterozygosity of a de novo submicroscopic deletion and an inherited frameshift pathogenic variant in theClinical case reports · 2023Article
- Review of genetic testing in kidney disease patients: Diagnostic yield of single nucleotide variants and copy number variations evaluated across and within kidney phenotype groups.American journal of medical genetics. Part C, Seminars in medical genetics · 2022Review
- Algorithmic improvements for discovery of germline copy number variants in next-generation sequencing data.BMC bioinformatics · 2022Article
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Abstract
backgroundWhole exome sequencing (WES) has been widely accepted as a robust and cost-effective approach for clinical genetic testing of small sequence variants. Detection of copy number variants (CNV) within WES data have become possible through the development of various algorithms and software programs that utilize read-depth as the main information. The aim of this study was to evaluate three commonly used, WES read-depth based CNV detection programs using high-resolution chromosomal microarray analysis (CMA) as a standard.
methodsPaired CMA and WES data were acquired for 45 samples. A total of 219 CNVs (size ranged from 2.3 kb - 35 mb) identified on three CMA platforms (Affymetrix, Agilent and Illumina) were used as standards. CNVs were called from WES data using XHMM, CoNIFER, and CNVnator with modified settings.
resultsAll three software packages detected an elevated proportion of small variants (< 20 kb) compared to CMA. XHMM and CoNIFER had poor detection sensitivity (22.2 and 14.6%), which correlated with the number of capturing probes involved. CNVnator detected most variants and had better sensitivity (87.7%); however, suffered from an overwhelming detection of small CNVs below 20 kb, which required further confirmation. Size estimation of variants was exaggerated by CNVnator and understated by XHMM and CoNIFER.
conclusionLow concordances of CNV, detected by three different read-depth based programs, indicate the immature status of WES-based CNV detection. Low sensitivity and uncertain specificity of WES-based CNV detection in comparison with CMA based CNV detection suggests that CMA will continue to play an important role in detecting clinical grade CNV in the NGS era, which is largely based on WES.
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