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

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

  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%
  1. 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