ArticleGenetics in medicine : official journal of the American College of Medical Genetics2019
Atlas-CNV: a validated approach to call single-exon CNVs in the eMERGESeq gene panel.
Article in Genetics in medicine : official journal of the American College of Medical Genetics, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- Computational strategies for copy number variation detection, disease association, and beyond.Genome biology · 2026Review
- A 33-year diagnostic odyssey in an Ashkenazi Jewish patient with Aicardi-Goutières syndrome.The journal of allergy and clinical immunology. Global · 2025Article
- Detection of germline CNVs from gene panel data: benchmarking the state of the art.Briefings in bioinformatics · 2024Article
- Prevalence of germline variants in Brazilian pancreatic carcinoma patients.Scientific reports · 2024Article
- Closing the gap: Solving complex medically relevant genes at scale.medRxiv : the preprint server for health sciences · 2024Article
- Next-generation sequencing and bioinformatics in rare movement disorders.Nature reviews. Neurology · 2024Review
- What Has the Undiagnosed Diseases Network Taught Us About the Clinical Applications of Genomic Testing?Annual review of medicine · 2022Review
- Article
- Genetic testing in ambulatory cardiology clinics reveals high rate of findings with clinical management implications.Genetics in medicine : official journal of the American College of Medical Genetics · 2021Article
- Neptune: an environment for the delivery of genomic medicine.Genetics in medicine : official journal of the American College of Medical Genetics · 2021Article
- Detecting copy number variation in next generation sequencing data from diagnostic gene panels.BMC medical genomics · 2021Article
- Targeted Next-Generation Sequencing Identifies Pathogenic Variants in Diabetic Kidney Disease.American journal of nephrology · 2021Article
- Genetic profiling of primary and secondary tumors from patients with lung adenocarcinoma and bone metastases reveals targeted therapy options.Molecular medicine (Cambridge, Mass.) · 2020Article
- Deficiency of Adenosine Deaminase 2 (DADA2): Hidden Variants, Reduced Penetrance, and Unusual Inheritance.Journal of clinical immunology · 2020Article
- Harmonizing Clinical Sequencing and Interpretation for the eMERGE III Network.American journal of human genetics · 2019Article
Corrections and comments
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Authors and funding
30 authors.
Funding
Abstract
purposeTo provide a validated method to confidently identify exon-containing copy-number variants (CNVs), with a low false discovery rate (FDR), in targeted sequencing data from a clinical laboratory with particular focus on single-exon CNVs.
methodsDNA sequence coverage data are normalized within each sample and subsequently exonic CNVs are identified in a batch of samples, when the target log
resultsThirteen CNVs were used as a truth set to validate Atlas-CNV and compared with VisCap. We demonstrated FDR reduction in validation, simulation, and 10,926 eMERGESeq samples without sensitivity loss. Sixty-four multiexon and 29 single-exon CNVs with high C-scores were assessed by Multiplex Ligation-dependent Probe Amplification (MLPA).
conclusionAtlas-CNV is validated as a method to identify exonic CNVs in targeted sequencing data generated in the clinical laboratory. The ExonQC and C-score assignment can reduce FDR (identification of targets with high variance) and improve calling accuracy of single-exon CNVs respectively. We propose guidelines and criteria to identify high confidence single-exon CNVs.
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