ArticleEuropean journal of human genetics : EJHG2021
Detection of copy-number variations from NGS data using read depth information: a diagnostic performance evaluation.
Article in European journal of human genetics : EJHG, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed, 42 citations in OpenAlex.
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- High Concordance of Copy Number Variants Detected by Chromosomal Microarray and Exome Sequencing in Clinical Diagnostics.Clinical genetics · 2026Article
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- Revealing the impact of partial gene duplications in ASH1L: integration of optical genome mapping and RNA sequencing.Molecular cytogenetics · 2025Article
- Should Scotland provide genome-wide sequencing for the diagnosis of rare developmental disorders? A cost-effectiveness analysis.The European journal of health economics : HEPAC : health economics in prevention and care · 2025Article
- Diagnostic Utility of Trio-Exome Sequencing for Children With Neurodevelopmental Disorders.JAMA network open · 2025Article
- Uncovering genetic contributors to developmental delay and intellectual disability: a focus on CNVs in pediatric patients.Frontiers in genetics · 2025Article
- A Novel Pathogenic Large Duplication in EXT1 Identified in a Family with Multiple Osteochondromas.Genes · 2024Article
- On the core segmentation algorithms of copy number variation detection tools.Briefings in bioinformatics · 2024Article
- Novel JAG1 variants leading to Alagille syndrome in two Chinese cases.Scientific reports · 2024Article
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- ifCNV: A novel isolation-forest-based package to detect copy-number variations from various targeted NGS datasets.Molecular therapy. Nucleic acids · 2022Article
- Clustered Regularly Interspaced short palindromic repeats-Based Microfluidic System in Infectious Diseases Diagnosis: Current Status, Challenges, and Perspectives.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2022Review
- Genetic abnormalities in biopsy-proven, adult-onset hemolytic uremic syndrome and C3 glomerulopathy.Journal of molecular medicine (Berlin, Germany) · 2022Article
- Exome first approach to reduce diagnostic costs and time - retrospective analysis of 111 individuals with rare neurodevelopmental disorders.European journal of human genetics : EJHG · 2022Article
- Diagnostic genetic testing for neurodevelopmental psychiatric disorders: closing the gap between recommendation and clinical implementation.Current opinion in genetics & development · 2021Review
- NGLY1 Deficiency: A Rare Newly Described Condition with a Typical Presentation.Life (Basel, Switzerland) · 2021Article
- Next-Generation Molecular Investigations in Lysosomal Diseases: Clinical Integration of a Comprehensive Targeted Panel.Diagnostics (Basel, Switzerland) · 2021Article
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Authors and funding
33 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The detection of copy-number variations (CNVs) from NGS data is underexploited as chip-based or targeted techniques are still commonly used. We assessed the performances of a workflow centered on CANOES, a bioinformatics tool based on read depth information. We applied our workflow to gene panel (GP) and whole-exome sequencing (WES) data, and compared CNV calls to quantitative multiplex PCR of short fluorescent fragments (QMSPF) or array comparative genomic hybridization (aCGH) results. From GP data of 3776 samples, we reached an overall positive predictive value (PPV) of 87.8%. This dataset included a complete comprehensive QMPSF comparison of four genes (60 exons) on which we obtained 100% sensitivity and specificity. From WES data, we first compared 137 samples with aCGH and filtered comparable events (exonic CNVs encompassing enough aCGH probes) and obtained an 87.25% sensitivity. The overall PPV was 86.4% following the targeted confirmation of candidate CNVs from 1056 additional WES. In addition, our CANOES-centered workflow on WES data allowed the detection of CNVs with a resolution of single exons, allowing the detection of CNVs that were missed by aCGH. Overall, switching to an NGS-only approach should be cost-effective as it allows a reduction in overall costs together with likely stable diagnostic yields. Our bioinformatics pipeline is available at: https://gitlab.bioinfo-diag.fr/nc4gpm/canoes-centered-workflow .
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