Table 3. Performance of Counsyl Inherited Cancer Screen for SNPs and indels.

Counsyl ICS	1000 Genomes reference data		Results (95% confidence interval)
	Variant present	Variant not present
Variant detected	536 true positives	0 false positives	100% accuracy (0.999–1.0) 100% sensitivity (0.993–1.0) 100% specificity (0.999–1.0) 0% FDR (0–0.7%)
Variant not detected	0 false negatives	12,920 true negatives

Notes.

Only samples with reference data for the entire region of interest were used to calculate the analytic concordance. Validation metrics were defined as: Accuracy = (TP + TN)/(TP + FP + TN + FN); Sensitivity = TP/(TP + FN); Specificity = TN/(TN + FP); FDR = FP/(TP + FP). For true negative and true positive calculations, all polymorphic positions (positions at which we observed non-reference bases in any sample) across all samples were considered.