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ClinSV: clinical grade structural and copy number variant detection from whole genome sequencing data


Whole genome sequencing (WGS) has the potential to outperform clinical microarrays for the detection of structural variants (SV) including copy number variants (CNVs), but has been challenged by high false positive rates. Here we present ClinSV, a WGS based SV integration, annotation, prioritization, and visualization framework, which identified 99.8% of simulated pathogenic ClinVar CNVs > 10 kb and 11/11 pathogenic variants from matched microarrays. The false positive rate was low (1.5-4.5%) and reproducibility high (95-99%). In clinical practice, ClinSV identified reportable variants in 22 of 485 patients (4.7%) of which 35-63% were not detectable by current clinical microarray designs. ClinSV is available at .

Type Journal
ISBN 1756-994X (Electronic) 1756-994X (Linking)
Authors Minoche, A. E.; Lundie, B.; Peters, G. B.; Ohnesorg, T.; Pinese, M.; Thomas, D. M.; Zankl, A.; Roscioli, T.; Schonrock, N.; Kummerfeld, S.; Burnett, L.; Dinger, M. E.; Cowley, M. J.
Publisher Name Genome Medicine
Published Date 2021-02-28
Published Volume 13
Published Issue 1
Published Pages 32
Status Published in-print
DOI 10.1186/s13073-021-00841-x
URL link to publisher's version