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

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

Provider	Scheme year	Sample type	1^stEGFR Variant	VAF variant 1 (in %)	2^nd (and 3^rd) *EGFR* variant	VAF variant 2 (in %)	# participants	# correct (%)	# false-negative (%)	# wrong mutation (%)	# technical failure (%)
ESP	2013	Cell line	c.2369C>T p.(Thr790Met)	25^b	c.2573T>G p.(Leu858Arg)	25^b	107	65 (70.7)	27 (29.3)	0 (0.0)	15 (14.0)
	2014	Cell line	c.2369C>T p.(Thr790Met)	45^b	c.2573T>G p.(Leu858Arg)	45^b	144	133 (92.4)	10 (6.9)	1 (0.7)	0 (0.0)
		Cell line		25^b	c.2573T>G p.(Leu858Arg)	25^b	144	135 (93.8)	8 (5.6)	1 (0.7)	0 (0.0)
		Resection		27	c.2155G>A p.(Gly719Ser) + c.2327G>A p.(Arg776His)	79 76	144	77 (53.5)	66 (45.8)	1 (0.7)	0 (0.0)
	2015	Resection	c.2369C>T p.(Thr790Met)	15	c.2573T>G p.(Leu858Arg)	89	114	92 (84.4)	16 (14.7)	1 (0.9)	5 (4.4)
	2016	Resection	c.2369C>T p.(Thr790Met)	19	c.2235_2249del p.(Glu746_Ala750del)	30	43	42 (97.7)	1 (2.3)	0 (0.0)	0 (0.0)
	2017 (Jun.)^a	Resection	c.2369C>T p.(Thr790Met)	18	c.2573T>G p.(Leu858Arg) + c.2389T>A p.(Cys797Ser)	35 18	107	87 (81.3)	20 (18.7)	0 (0.0)	0 (0.0)
	2017 (Oct.)^a	Cell line	c.2369C>T p.(Thr790Met)	20	/	/	102	97 (99.0)	1 (1.0)	0 (0.0)	4 (3.9)
	2018	Resection	c.2369C>T p.(Thr790Met)	22	c.2573T>G p.(Leu858Arg)	22	101	101 (100.0)	0 (0.0)	0 (0.0)	0 (0.0)
	2018	Resection	c.2369C>T p.(Thr790Met)	43	c.2236_2248delinsCAAC p.(E746_A750delinsQP)	80	101	101 (100.0)	0 (0.0)	0 (0.0)	0 (0.0)
Gen&Tiss	2014	Cell line	c.2369C>T p.(Thr790Met)	17	/	/	43	39 (92.8)	2 (4.8)	1 (2.4)	1 (2.3)
Gen&Tiss	2016	Cell line	c.2369C>T p.(Thr790Met)	22	c.2573T>G p.(Leu858Arg)	18	40	39 (100.0)	0 (0.0)	0 (0.0)	1 (2.5)

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)

ISSN: 1471-2407