A comprehensive DNA panel next generation sequencing approach supporting diagnostics and therapy prediction in neurooncology

Table 2 Validations performed for quality control according to the ILAC (DAkkS) standards for inspection bodies (ISO/IEC 17020)

	Abberation	# Cases	# Validations	Validation method	Sensitivity	Specificity
Single assay validation	IDH1/2	34	68	Sanger seq.	100%	100%
	1p/19q LOH	15	35	Microsatellite PCR	100%	100%
	BRAF V600	2	3	Sanger seq.	100%	100%
	H3F3A	2	3	Sanger seq.	100%	100%
	TERTp	47	50	Sanger seq.	100%	100%
	CDKN2A HomDel	8	11	quantitative PCR	100%	100%
	EGFR Highcopy	12	14	quantitative PCR	100%	100%
QC cohort	other SNPs / InDels	17	28	Sanger seq.	100%	n.d.
	other LOH	8	28	Oncoscan Array	90%	97%
	all CNVs	8	47	Oncoscan Array	94%	97%
Overall performance					97%	98%

DNA panel results were compared to quality-controlled single assays in our routine diagnostic lab for the established molecular biomarkers IDH1/2, BRAF and H3F3A mutation as well as 1p/19q codeletion. TERTp mutations, CDKN2A homozygous deletions and EGFR highcopy amplifications were validated by direct sanger sequencing or quantitative PCR. Intensified quality assurance approval was performed in a cohort of 17 tumors. In these cases, the majority of detected SNPs and small InDels were reanalyzed using direct Sanger sequencing. Other LOH results and CNV results were reanalyzed using an OncoScan CNV analysis. Comparison of DNA panel and validation results yielded excellent sensitivity and specificity. n.d.: negative results were not validated, QC: quality control cohort

ISSN: 2051-5960