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- Title
ClinSV: clinical grade structural and copy number variant detection from whole genome sequencing data.
- Authors
Minoche, Andre E.; Lundie, Ben; Peters, Greg B.; Ohnesorg, Thomas; Pinese, Mark; Thomas, David M.; Zankl, Andreas; Roscioli, Tony; Schonrock, Nicole; Kummerfeld, Sarah; Burnett, Leslie; Dinger, Marcel E.; Cowley, Mark J.
- 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.
- Subjects
EXOMES; DNA copy number variations; VISUALIZATION; RARE diseases
- Publication
Genome Medicine, 2021, Vol 13, Issue 1, p1
- ISSN
1756-994X
- Publication type
Article
- DOI
10.1186/s13073-021-00841-x