Detection of low prevalence somatic mutations in solid tumors with ultra-deep targeted sequencing

Table 1 Prevalence of all somatic mutations identified by UDT-Seq using a 5% prevalence detection threshold

Cancer		Validation	Prevalence estimated by UDT-Seq
type	Mutation	assay	Primary	Xenograft	Xenograft + WGA
Colon	FGFR3-R327C	Sanger	0.47	0.59
	CSF1R-R710H	SNaPshot	0.43	0.56
	APC-R405X	SNaPshot	0.42	0.51
	APC-R230C	Not assayed	0.4	0.49
	KRAS-G12D	SNaPshot	0.35	0.51
	TP53-intron	SNaPshot	0.35	0.47
	NF1-P1553H	SNaPshot	0.32	0.51
	APC-R283X	SNaPshot	0.23	0.49
	BRAF-intron	Not assayed	0.1	< 0.05
	KIT-R49C	Sanger	0.1	< 0.05
	STK11-R304W	SNaPshot	< 0.05*	0.66
	HRAS-R73C	SNaPshot	< 0.05	0.55
	FGFR1-L457V	SNaPshot	< 0.05	0.44
Breast	HRAS-G12V	Not assayed	0.51	0.48	0.48
Ovarian	TP53-R248Q	Not assayed		1

*Inspection showed it to be a false negative (present by visual inspection). Independently validated mutations (or absence thereof) are indicated in bold. WGA, whole genome amplification.

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