CoNVaDING: single exon variation detection in targeted NGS data: Single Exon Variation Detection in Targeted NGS Data

Lennart F Johansson, Freerk van Dijk, Eddy N de Boer, Krista K van Dijk-Bos, Jan DH Jongbloed, Annemieke H van der Hout, Helga Westers, Richard J Sinke, Morris A Swertz, Rolf H Sijmons

Research output: Contribution to journalArticlepeer-review

73 Citations (Scopus)

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. 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 metric, that excludes or flags low quality exons. Since this quality control shows exactly which exons can be reliably analysed and which exons are in need of an alternative analysis method, CoNVaDING is also useful for CNV detection in clinical diagnostics.

Original languageUndefined/Unknown
Pages (from-to)457-464
Number of pages8
JournalHuman mutation
Volume37
Issue number5
DOIs
Publication statusPublished - 2016
Externally publishedYes

Keywords

  • CNV
  • Clinical diagnostics
  • Exon deletion/duplication
  • NGS
  • Targeted next-generation sequencing

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