ArticleGenes2021
CNV Detection from Exome Sequencing Data in Routine Diagnostics of Rare Genetic Disorders: Opportunities and Limitations.
Article in Genes, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 38 papers.
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Who cites it
38 citing papers in PubMed.
- Pangenomes aid accurate detection of large insertions and deletions from targeted sequencing: the case of cardiomyopathies.Genome medicine · 2026Article
- Computational strategies for copy number variation detection, disease association, and beyond.Genome biology · 2026Review
- Phenocopies of 22q11.2DS: revealing genetic diversity in clinically suspected 22q11.2 deletion syndrome.Molecular and cellular pediatrics · 2026Article
- High Concordance of Copy Number Variants Detected by Chromosomal Microarray and Exome Sequencing in Clinical Diagnostics.Clinical genetics · 2026Article
- Whole exome sequencing: a new era in prenatal diagnostics.Journal of translational medicine · 2026Article
- A Novel Technique for Validating Copy Number Variants and Its Application in Familial Exudative Vitreoretinopathy.Human mutation · 2026Article
- Targeted long-read nanopore sequencing as a complementary approach for detecting STRC variants and distinguishing the STRCP1 pseudogene.Scientific reports · 2025Article
- Diagnostic Utility of Next-Generation Sequencing-based CNV Analysis in Eleven Patients with Peters-Plus Syndrome: A Single-Center ExperienceJournal of clinical research in pediatric endocrinology · 2025Article
- Linking Genotype to Clinical Features inGenes · 2025Review
- Analytical Validation of a Genomic Newborn Screening Workflow.International journal of neonatal screening · 2025Article
- A systematic analysis of contemporary whole exome sequencing capture kits to optimise high-coverage capture of CCDS regions.NAR genomics and bioinformatics · 2025Article
- Integrated genomic analysis of NF1-associated peripheral nerve sheath tumors: an updated biorepository dataset.Scientific data · 2025Article
- Heterozygous deletion of 10q24.31-q24.33- a new syndrome associated with multiple congenital anomalies: case report and literature review.Neurological research and practice · 2025Article
- Clinical Exome Sequencing in Pediatric Patients.Cureus · 2025Article
- The known structural variations in hearing loss and their diagnostic approaches: a comprehensive review.Molecular biology reports · 2025Review
- Genetic Findings in Short Turkish Children Born to Consanguineous Parents.Hormone research in paediatrics · 2025Observational
- Two-Compound Heterozygous Deletions AffectingMolecular syndromology · 2024Article
- Comprehensive reanalysis for CNVs in ES data from unsolved rare disease cases results in new diagnoses.NPJ genomic medicine · 2024Article
- Biallelic Deletion ofMolecular syndromology · 2024Article
- Identification of Pathogenic Copy Number Variants in Mexican Patients With Inherited Retinal Dystrophies Applying an Exome Sequencing Data-Based Read-Depth Approach.Molecular genetics & genomic medicine · 2024Article
Corrections and comments
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
To assess the potential of detecting copy number variations (CNVs) directly from exome sequencing (ES) data in diagnostic settings, we developed a CNV-detection pipeline based on ExomeDepth software and applied it to ES data of 450 individuals. Initially, only CNVs affecting genes in the requested diagnostic gene panels were scored and tested against arrayCGH results. Pathogenic CNVs were detected in 18 individuals. Most detected CNVs were larger than 400 kb (11/18), but three individuals had small CNVs impacting one or a few exons only and were thus not detectable by arrayCGH. Conversely, two pathogenic CNVs were initially missed, as they impacted genes not included in the original gene panel analysed, and a third one was missed as it was in a poorly covered region. The overall combined diagnostic rate (SNVs + CNVs) in our cohort was 36%, with wide differences between clinical domains. We conclude that (1) the ES-based CNV pipeline detects efficiently large and small pathogenic CNVs, (2) the detection of CNV relies on uniformity of sequencing and good coverage, and (3) in patients who remain unsolved by the gene panel analysis, CNV analysis should be extended to all captured genes, as diagnostically relevant CNVs may occur everywhere in the genome.
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