Massively parallel sequencing fails to detect minor resistant subclones in tissue samples prior to tyrosine kinase inhibitor therapy

Table 4 Summary of allele frequencies at each secondary KIT mutation position in primary GISTs

Mutation	Assay	With emerging secondary mutation [%]	Without emerging secondary mutation [%]	Limit of detection [%]
p.V654A	GS Junior	0.000 - 0.850	0.000 - 0.790	1.00
	Qiagen panel	0.146 - 0.248	0.107 - 0.233	0.25
	AmpliSeq panel	0.216 - 0.415	0.254 - 0.363	0.45
p.N680K	GS Junior	0.000	0.000	1.00
	Qiagen panel	0.039	0.006 - 0.092	0.10
	AmpliSeq panel	0.013 - 0.026	0.008 - 0.055 (0.385)	0.07
p.D820E	GS Junior	0.000	0.000	1.00
	Qiagen panel	0.019 - 0.035	0.010 - 0.094	0.10
	AmpliSeq panel	0.010 - 0.021	0.012 - 0.028	0.03
p.N822Y	GS Junior	0.000	0.000	1.00
	Qiagen panel	0.017 - 0.047	0.011 - 0.074	0.08
	AmpliSeq panel	0.008 - 0.012	0.008 - 0.019	0.02

Shown are the allele frequencies in primary GISTs (FFPE) with and without emerging secondary mutation in the recurrent tumours in comparison to the limit of detection. The positions of the mutations p.V654A, p.N680K, p.D820E, p.N822Y were analysed with each assay.
[%]: Allele frequency in percent.
(): Falsely higher allele frequency due to read bias in one run.

ISSN: 1471-2407