ArticleGenetics in medicine : official journal of the American College of Medical Genetics2016
VisCap: inference and visualization of germ-line copy-number variants from targeted clinical sequencing data.
Article in Genetics in medicine : official journal of the American College of Medical Genetics, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 40 papers.
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Who cites it
40 citing papers in PubMed.
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- Detection of germline CNVs from gene panel data: benchmarking the state of the art.Briefings in bioinformatics · 2024Article
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- Review
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- Case report: Compound heterozygosity inFrontiers in pediatrics · 2022Article
- Development and Validation of Targeted Gene Sequencing Panel Based Companion Diagnostic for Korean Patients with Solid Tumors.Cancers · 2021Article
- Review
- Compound heterozygous variants including a novel copy number variation in a child with atypical ataxia-telangiectasia: a case report.BMC medical genomics · 2021Article
- Clinical cancer research : an official journal of the American Association for Cancer Research · 2021Article
- Review
- CIRCNV: Detection of CNVs Based on a Circular Profile of Read Depth from Sequencing Data.Biology · 2021Article
- Bioinformatics Accelerates the Major Tetrad: A Real Boost for the Pharmaceutical Industry.International journal of molecular sciences · 2021Review
- New Tmc1 Deafness Mutations Impact Mechanotransduction in Auditory Hair Cells.The Journal of neuroscience : the official journal of the Society for Neuroscience · 2021Article
- TMPRSS3 Gene Variants With Implications for Auditory Treatment and Counseling.Frontiers in genetics · 2021Article
- Focus on Biochemical and Clinical Predictors of Response to Immune Checkpoint Inhibitors in Metastatic Urothelial Carcinoma: Where Do We Stand?International journal of molecular sciences · 2020Review
- Mammalian SWI/SNF Complex Genomic Alterations and Immune Checkpoint Blockade in Solid Tumors.Cancer immunology research · 2020Article
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Authors and funding
9 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
purposeTo develop and validate VisCap, a software program targeted to clinical laboratories for inference and visualization of germ-line copy-number variants (CNVs) from targeted next-generation sequencing data.
methodsVisCap calculates the fraction of overall sequence coverage assigned to genomic intervals and computes log2 ratios of these values to the median of reference samples profiled using the same test configuration. Candidate CNVs are called when log2 ratios exceed user-defined thresholds.
resultsWe optimized VisCap using 14 cases with known CNVs, followed by prospective analysis of 1,104 cases referred for diagnostic DNA sequencing. To verify calls in the prospective cohort, we used droplet digital polymerase chain reaction (PCR) to confirm 10/27 candidate CNVs and 72/72 copy-neutral genomic regions scored by VisCap. We also used a genome-wide bead array to confirm the absence of CNV calls across panels applied to 10 cases. To improve specificity, we instituted a visual scoring system that enabled experienced reviewers to differentiate true-positive from false-positive calls with minimal impact on laboratory workflow.
conclusionsVisCap is a sensitive method for inferring CNVs from targeted sequence data from targeted gene panels. Visual scoring of data underlying CNV calls is a critical step to reduce false-positive calls for follow-up testing.Genet Med 18 7, 712-719.Genetics in Medicine (2016); 18 7, 712-719. doi:10.1038/gim.2015.156.
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