title: CoNVaDING: Single Exon Variation Detection in Targeted NGS Data.
abstract: We have developed a tool for detecting single exon copy-number variations (CNVs) in targeted next-generation sequencing data: CoNVaDING (Copy Number Variation Detection In Next-generation sequencing Gene panels). CoNVaDING includes a stringent quality control (QC) metric, that excludes or flags low-quality exons. Since this QC shows exactly which exons can be reliably analyzed and which exons are in need of an alternative analysis method, CoNVaDING is not only useful for CNV detection in a research setting, but also in clinical diagnostics. During the validation phase, CoNVaDING detected all known CNVs in high-quality targets in 320 samples analyzed, giving 100% sensitivity and 99.998% specificity for 308,574 exons. CoNVaDING outperforms existing tools by exhibiting a higher sensitivity and specificity and by precisely identifying low-quality samples and regions.
authors: University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands.|University of Groningen, University Medical Center Groningen, Genomics Coordination Center, Groningen, The Netherlands.
authors: Lennart F
authors: LF
authors: Johansson
authors: University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands.|University of Groningen, University Medical Center Groningen, Genomics Coordination Center, Groningen, The Netherlands.
authors: Freerk
authors: F
authors: van Dijk
authors: University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands.
authors: Eddy N
authors: EN
authors: de Boer
authors: University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands.
authors: Krista K
authors: KK
authors: van Dijk-Bos
authors: University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands.
authors: Jan D H
authors: JD
authors: Jongbloed
authors: University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands.
authors: Annemieke H
authors: AH
authors: van der Hout
authors: University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands.
authors: Helga
authors: H
authors: Westers
authors: University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands.
authors: Richard J
authors: RJ
authors: Sinke
authors: University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands.|University of Groningen, University Medical Center Groningen, Genomics Coordination Center, Groningen, The Netherlands.
authors: Morris A
authors: MA
authors: Swertz
authors: University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands.
authors: Rolf H
authors: RH
authors: Sijmons
authors: University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands.
authors: Birgit
authors: B
authors: Sikkema-Raddatz
mesh_terms: D056915:DNA Copy Number Variations; D030541:Databases, Genetic; D005091:Exons; D020022:Genetic Predisposition to Disease / Q000235:genetics*; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software / Q000592:standards
keywords: CNV; NGS; clinical diagnostics; exon deletion/duplication; targeted next-generation sequencing