Table 2.

SNP array/next-generation sequencer cost and feasibility comparison

Genome-wide interrogation goal	Estimated cost per sample
	SNP arraya	Next-generation sequencerb	References
SNP genotypingc	$700	$36 000d	(12,13)
SNP/point mutation discoveryc	NA	$180 000	(84,85)
LOH detectione	$1400	$72 000d	(12,13)
Copy number assessment	$700	$2000	(31,60,82,83)
Inversion detection	NA	$2000–$180 000f	(82,83)
Translocation detection	NA	$2000–$180 000f	(82,83)

^aAt flat cost of $700 per array.

^bAt $2000 per experiment, each producing 1 Gb of sequence.

^cAt 30X coverage for reliable SNP/mutation calling.

^dAfter first performing a complexity-reduction step (similar to SNP array protocols) yielding ∼1 M fragments of average size 600 bp.

^eUsing both tumor and matched normal DNA samples.

^fDepending upon level of resolution desired.

N.B. All costs are very approximate, and will vary with different platforms, economies of scale and other factors.