ClinSV: clinical grade structural and copy number variant detection from whole genome sequencing data.
Clinical genome
Copy number variation
Microarray
Rare disease
Structural variation
Whole genome sequencing
Journal
Genome medicine
ISSN: 1756-994X
Titre abrégé: Genome Med
Pays: England
ID NLM: 101475844
Informations de publication
Date de publication:
25 02 2021
25 02 2021
Historique:
received:
30
06
2020
accepted:
02
02
2021
entrez:
26
2
2021
pubmed:
27
2
2021
medline:
21
1
2022
Statut:
epublish
Résumé
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 .
Identifiants
pubmed: 33632298
doi: 10.1186/s13073-021-00841-x
pii: 10.1186/s13073-021-00841-x
pmc: PMC7908648
doi:
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
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