ClinSV: clinical grade structural and copy number variant detection from whole genome sequencing data
Open Access
- 24 February 2021
- journal article
- research article
- Published by Springer Science and Business Media LLC in Genome Medicine
- Vol. 13 (1), 1-19
- https://doi.org/10.1186/s13073-021-00841-x
Abstract
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 >10kb 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 https://github.com/KCCG/ClinSV.Funding Information
- Kinghorn Foundation
- Cancer Institute NSW
- NSW Health
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