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Table 1 Performance summary ClinSV. Summary of ClinSV’s performance by metric, variant type, and size. Input variants were pass and high confidence. Determining the false positive rate and false negatives, input variants were further visually reviewed prior the performance analysis

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

Metric Reference data or technology Preceding visual review Value Results table
Sensitivity Simulated ClinVar    Table 2
Deletions No 99.7% > 10 kb
88.2% < 10 kb
 
Duplications No 100.0% > 10 kb
63.4% < 10 kb
 
GIAB1    
Deletions No 97.1% > 10 kb
87.8% < 10 kb
Additional file 1: Table S7
GIAB2    
Deletions No 97.0% > 10 kb
71.4% < 10 kb
Additional file 1: Table S8
Duplications No 100.0% > 10 kb
2.3% < 10 kb
Additional file 1: Table S9
Microarray No 100% pathogenic CNVs
> 99% any CNVs
 
False positive rate PacBio data Yes 1.5%
4.5% incl. inconclusive
Additional file 1: Table S10
MLPA Yes 0%
10% incl. Inconclusive
Additional file 1: Table S11
False negatives MLPA Yes 30% Additional file 1: Table S13
Reproducibility WGS No 99.1% high CNVs
83.9% high and pass SVs
Table 3