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Table 1 Overview of the samples distributed during the EQA schemes between 2013 and 2018

From: Sensitive detection methods are key to identify secondary EGFR c.2369C>T p.(Thr790Met) in non-small cell lung cancer tissue samples

ProviderScheme yearSample type1stEGFR VariantVAF variant 1 (in %)2nd (and 3rd) EGFR variantVAF variant 2 (in %)# participants# correct (%)# false-negative (%)# wrong mutation (%)# technical failure (%)
ESP2013Cell linec.2369C>T p.(Thr790Met)25bc.2573T>G p.(Leu858Arg)25b10765 (70.7)27 (29.3)0 (0.0)15 (14.0)
2014Cell linec.2369C>T p.(Thr790Met)45bc.2573T>G p.(Leu858Arg)45b144133 (92.4)10 (6.9)1 (0.7)0 (0.0)
Cell line25bc.2573T>G p.(Leu858Arg)25b144135 (93.8)8 (5.6)1 (0.7)0 (0.0)
Resection27c.2155G>A p.(Gly719Ser) + c.2327G>A p.(Arg776His)79
76
14477 (53.5)66 (45.8)1 (0.7)0 (0.0)
2015Resectionc.2369C>T p.(Thr790Met)15c.2573T>G p.(Leu858Arg)8911492 (84.4)16 (14.7)1 (0.9)5 (4.4)
2016Resectionc.2369C>T p.(Thr790Met)19c.2235_2249del p.(Glu746_Ala750del)304342 (97.7)1 (2.3)0 (0.0)0 (0.0)
2017 (Jun.)aResectionc.2369C>T p.(Thr790Met)18c.2573T>G p.(Leu858Arg) + c.2389T>A p.(Cys797Ser)35
18
10787 (81.3)20 (18.7)0 (0.0)0 (0.0)
2017 (Oct.)aCell linec.2369C>T p.(Thr790Met)20//10297 (99.0)1 (1.0)0 (0.0)4 (3.9)
2018Resectionc.2369C>T p.(Thr790Met)22c.2573T>G p.(Leu858Arg)22101101 (100.0)0 (0.0)0 (0.0)0 (0.0)
Resection43c.2236_2248delinsCAAC p.(E746_A750delinsQP)80101101 (100.0)0 (0.0)0 (0.0)0 (0.0)
Gen&Tiss2014Cell linec.2369C>T p.(Thr790Met)17//4339 (92.8)2 (4.8)1 (2.4)1 (2.3)
2016Cell linec.2369C>T p.(Thr790Met)22c.2573T>G p.(Leu858Arg)184039 (100.0)0 (0.0)0 (0.0)1 (2.5)
  1. ESP schemes: all samples were provided on glass slides, Gen&Tiss schemes: cell lines were provided as curls from a cytoblock. For each sample, the percentage of correct, false-negative results, wrong mutations and technical failures is based on c.2369C>T p.(Thr790Met) detection irrespective of the performance to detect the additional variants. Technical failures are represented with respect to the total number of tests. Correct results, false-negatives and wrong mutations are calculated in relation to the total number of analyzable tests (total tests minus technical failures). Refseq EGFR: LRG_304t1 (NM_005228.5). aThe 2017 ESP scheme was organized in 2 distribution rounds (one in June and one in October). bVariant allele frequency based on the percentage of tumor cells. E.g. cell line of 50% tumor cells in a wild-type background was considered as a VAF of 25%. Abbreviations: EGFR Epidermal growth factor receptor; ESP European Society of Pathology; LRG Locus Reference Genomic; VAF variant allele frequency; #, number; /, No second variant and VAF given as sample only contains c.2369C>T p.(Thr790Met)