ArticleBMC genomics2016
cnvScan: a CNV screening and annotation tool to improve the clinical utility of computational CNV prediction from exome sequencing data.
Article in BMC genomics, 2016. 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.
- Genomic Variations Explorer (GenVarX): a toolset for annotating promoter and CNV regions using genotypic and phenotypic differences.Frontiers in genetics · 2023Article
- Annotation of structural variants with reported allele frequencies and related metrics from multiple datasets using SVAFotate.BMC bioinformatics · 2022Article
- Biallelic KIF24 Variants Are Responsible for a Spectrum of Skeletal Disorders Ranging From Lethal Skeletal Ciliopathy to Severe Acromesomelic Dysplasia.Journal of bone and mineral research : the official journal of the American Society for Bone and Mineral Research · 2022Article
- Automated prediction of the clinical impact of structural copy number variations.Scientific reports · 2022Article
- Article
- Dominant Distal Myopathy 3 (MPD3) Caused by a Deletion in theNeurology. Genetics · 2021Article
- Uncovering potential single nucleotide polymorphisms, copy number variations and related signaling pathways in primary Sjogren's syndrome.Bioengineered · 2021Article
- CNVxplorer: a web tool to assist clinical interpretation of CNVs in rare disease patients.Nucleic acids research · 2021Article
- Clinical analysis of germline copy number variation in DMD using a non-conjugate hierarchical Bayesian model.BMC medical genomics · 2018Article
- Ximmer: a system for improving accuracy and consistency of CNV calling from exome data.GigaScience · 2018Article
- Article
- iCopyDAV: Integrated platform for copy number variations-Detection, annotation and visualization.PloS one · 2018Article
- Detection of genomic rearrangements from targeted resequencing data in Parkinson's disease patients.Movement disorders : official journal of the Movement Disorder Society · 2017Article
- A potential founder variant inMolecular genetics & genomic medicine · 2016Article
- Integrating Epigenomic Elements and GWASs Identifies BDNF Gene Affecting Bone Mineral Density and Osteoporotic Fracture Risk.Scientific reports · 2016Article
Corrections and comments
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundWith advances in next generation sequencing technology and analysis methods, single nucleotide variants (SNVs) and indels can be detected with high sensitivity and specificity in exome sequencing data. Recent studies have demonstrated the ability to detect disease-causing copy number variants (CNVs) in exome sequencing data. However, exonic CNV prediction programs have shown high false positive CNV counts, which is the major limiting factor for the applicability of these programs in clinical studies.
resultsWe have developed a tool (cnvScan) to improve the clinical utility of computational CNV prediction in exome data. cnvScan can accept input from any CNV prediction program. cnvScan consists of two steps: CNV screening and CNV annotation. CNV screening evaluates CNV prediction using quality scores and refines this using an in-house CNV database, which greatly reduces the false positive rate. The annotation step provides functionally and clinically relevant information using multiple source datasets. We assessed the performance of cnvScan on CNV predictions from five different prediction programs using 64 exomes from Primary Immunodeficiency (PIDD) patients, and identified PIDD-causing CNVs in three individuals from two different families.
conclusionsIn summary, cnvScan reduces the time and effort required to detect disease-causing CNVs by reducing the false positive count and providing annotation. This improves the clinical utility of CNV detection in exome data.
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