Table 3

Comparison of “universal cost equivalents” of “prescreening” BRCA1 for mutations (exclusive of sequence confirmation)

	SSCP	CSGE	TDGS	DHPLC
PCR amplicons		40 amplicons		30 amplicons	7 primary	35 amplicons
PCR amplicons		40 amplicons		30 amplicons	37 secondary	35 amplicons
Primers		Standard		M13 tailed	Primary standard	Standard
Primers		Standard		M13 tailed	Secondary GC clamps	Standard
PCR reactions		40, ³²P labelled		20	1 primary reaction	35
PCR reactions		40, ³²P labelled		20	4 secondary reactions	35
Additional pooling pre-analysis	40 to 20	20 to 6	4 to 1	None
Instrument	Owl Scientific sequencing gel box	ABI 377 pipetting robot	CBS Scientific auto 2-D gel system	Transgenomic dHPLC system
Lanes/sample	20	6	1^3-150	54^3-151
Run time	8–20 h/gel	4 h/gel	19 h/gel^3-152	8 min/sample
% PCR reactions requiring repeat analysis	5%	9%	13.5%^3-153	<10%

↵3-150 Products of the four multiplex groups were pooled and analysed on a single gel. Thus, the analysis requires one gel per subject.
↵3-151 For DHPLC, 19 of the 35 amplicons are analysed at two different temperatures. Thus, analysis of 35 PCR amplicons requires 54 DHPLC runs.
↵3-152 The gel run can now be performed in three hours (see Results).
↵3-153 Because only individual component PCR reactions fail (rather than the whole multiplex PCR), repeats are performed with one dimensional DGGE.