Wednesday, August 08, 2007

Too good to be true?

A recent GenomeWeb item stated (digested from a press release) that GATC Biotech in Germany is one of the first customers for ABI SOLiD sequencing-by-ligation instrument. This machine will complement the Roche 454 FLX and Illumina/Solexa 1G which GATC already has in house, meaning that GATC has all three launched next-generation sequencing instruments.

The eyebrow-raiser in the press release is
the SOLiD™ System is expected to be installed in early autumn this year and will boost the company's current sequencing capacity from 130 gigabases to 250 gigabases a year.

Nearly doubling capacity with one SOLiD instrument in a shop that already has a 1G and an FLX? If that number is really the impact of the SOLiD, then ABI is taking a huge lead in total reads. Of course, actual performance may vary from projections. Even if that is the joint contribution of the 3 next-gen sequencers, it would underscore what an advance they are -- especially considering how much up-front sample preparation & management work can be jettisoned in comparison to feeding a conventional sequencer.

(Disclosure: my company may be in the market for such services, and I would probably be one of the decision makers in such a decision)


Anonymous said...

Yeah, but what are the read lengths? Their brochures say 'up to 35 bp', which probably means more like 25 average, putting it in the same class as Solexa. This makes it worthless for some genomics applications. There's just too much repetitive sequence in the genome.

Since these repetitve parts are some of the most interesting, from a variation standpoint, I don't see Sanger going anywhere for a while. Of course, if 454 can get up to 500 bp, as they claim, I think they'll become the sequencing platform of choice.

That said, I think there are niches for all of these technologies. So far, only Solid and Solexa are really head-to-head competitors.

Keith Robison said...

The read lengths & confidence definitely drive the applications. De novo sequencing may be extremely challenging with such read lengths, but on the other hand for sequence tag type approaches (ChIP, SAGE, etc) this is the cats pajamas

Sandra Porter said...

It's plenty long enough for genotyping. After all, many PCR methods only detect changes at a single base.