Illumina announced their new HiSeq 2000 instrument today. There are some great summaries at Genetic Future and PolitGenomics; read both for the whole scoop. Perhaps just as jaw dropping as some of the operating statistics on the new beast is the fact that Beijing Genome Institute has already ordered 128 of them. Yow! That's (back-of-envelope) around $100M in instruments which will consume >$30M/year in reagents. I wish I had that budget!
Illumina's own website touts not only the cost (reagents only) of $10K per human genome, but also that this works out to 200 gene expression profiles per run at $200/profile. That implies multiplexing, as there are 32 lanes on the machine (16 lanes x 2 flow cells -- or is it 32 lanes per flowcell? I'm still trying to figure this out based on the note that it images the flowcell both from the top and bottom). That also implies being able to generate high resolution copy number profiles -- which need about 0.1X coverage given published reports for similar cost.
But it's not just Illumina. If a Helicos run is $10K and it has >50 channels, then that would also suggest around $200/sample to do copy number analysis. I've heard some wild rumors about what some goosed Polonators can do now.
The one devil in trying to do lots of profiles is that means making that many libraries, which is the step that everyone still groans about (particularly my vendors!). Beckman Coulter just announced an automated instrument, but it sounds like it's not a huge step forward. Of course, on the Helicos there really isn't much to do -- it's the amplification based systems that need size selection, which is one major bottleneck.
But, once the library throughput question is solved it would seem that arrays are going to be in big trouble. Of course, all of the numbers above ignore the instrument acquisition costs, which are substantial. Array costs may still be under these numbers, which for really big studies will add up. On the other hand, from what I've seen in the literature the sequencer-based info is always superior to array based -- better dynamic range, higher resolution for copy number breakpoints. Will 2010 be the year that the high density array market goes into a tailspin?
Illumina, of course, has both bases covered. Agilent has a big toe in the sequencing field, though by supplying tools around the space. But there's one obvious big array player so far MIA from the next generation sequencing space. That would seem to be a risky trajectory to continue, by anyone's metrix...