cnvScan: a CNV screening and annotation tool to improve the clinical utility of computational CNV prediction from exome sequencing data

BMC Genomics
Pubudu Saneth SamarakoonRobert Lyle

Abstract

With 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. We 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 fami...Continue Reading

References

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Citations

Apr 19, 2018·Bioinformatics·Véronique GeoffroyJean Muller
Oct 22, 2016·Arteriosclerosis, Thrombosis, and Vascular Biology·Jian WangRobert A Hegele
Jan 27, 2017·Movement Disorders : Official Journal of the Movement Disorder Society·Nino SpataroElena Bosch
Nov 30, 2016·Molecular Genetics & Genomic Medicine·Hanne S SorteAsbjørg Stray-Pedersen
May 22, 2021·Nucleic Acids Research·Francisco RequenaAntonio Rausell

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Methods Mentioned

BETA
exome sequencing
exome collection

Software Mentioned

cnvScan
Deciphering
ClinVar
CNVAnnotator
ExomeCopy
Agilent Genomic Workbench
CONIFER
DeAnnCNV
GATK
DECIPHER

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