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

Year: 2021
Type: article
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 > 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 https://github.com/KCCG/ClinSV .
DOI: 10.1186/s13073-021-00841-x
Authors: Andre E Minoche, Ben Lundie, Greg B Peters, Thomas Ohnesorg, Mark Pinese, David M Thomas, Andreas Zankl, Tony Roscioli, Nicole Schonrock, Sarah Kummerfeld, Leslie Burnett, Marcel E Dinger, Mark J Cowley
Institutions: Garvan Institute of Medical Research, UNSW Sydney, Children's Hospital at Westmead, The Kinghorn Cancer Centre, The University of Sydney, Sydney Children's Hospital, Sydney Children’s Hospitals Network, NSW Health Pathology, Neuroscience Research Australia
Language: English
Subfield: Genetics
Open Access status: gold
Estimated APC paid: $4,480
Funders: National Computational Infrastructure, Australian Government, NSW Health Pathology, Cancer Institute NSW, NSW Health, Kinghorn Foundation
OpenAlex ID: W3132356904
FWCI: 8.481
Cites: 69
Cited by: 70
Related to: 10