. Author manuscript; available in PMC: 2016 Jan 31.

Published in final edited form as: Exp Mol Pathol. 2015 Jan 3;98(1):106–112. doi: 10.1016/j.yexmp.2014.12.009

Table 2.

Summary of validation methodologies and results

Molecular Alteration	Samples Used	Validation Parameter	QC Result

SNPs, Indels	Titration of 2 HAPMAP samples	Limit of Detection	≥ 10% AF

CNVs	2 FFPEs	Limit of Detection	≥ 6 copies at 50% neoplastic content
CNVs	HAPMAP (NA12878)	Limit of Detection	≥ 6 copies at 50% neoplastic content

SNPs, Indels	HorizonDX	Sensitivity	100% at ≥ 10% AF

≥ 10 bp Indels	HorizonDX + titration with EGFR delE746-A750	Sensitivity	100% at 5% AF

CNVs	8 FFPEs	Sensitivity	100% at ≥ 6 copies

SNPs	HAPMAP NA12878	Specificity	99.5% at ≥ 5% AF

Indels	41 FFPEs	Specificity	100% at ≥ 5% AF (confirmed by PCR)

CNVs	8 FFPEs	Specificity	99.4% at ≥ 6 copies

SNPs, Indels	12 FFPEs	Accuracy	98% concordance
SNPs, Indels	Cross-reference lab	Accuracy	98% concordance

CNVs	12 FFPEs	Accuracy	96% concordance
CNVs	Cross-reference lab	Accuracy	96% concordance