Because we’re total suckers for punishment
…we’ve also installed one of these:
Yes, that’s a Roche GS-FLX, which will be fully loaded with their latest “Titanium” upgrade. Actually, it might already have it – I confess I’d have to ask someone in the lab, or maybe the office next door. Joining the other instruments from Illumina and Applied Biosystems, and promising greater than 400-base paired-end reads, this should solve a lot of (biological) problems. We hope.
But – are we behind the curve, again? Pacific Biosciences has announced that they are gearing up for an early-access program in the first half of 2009 (and I apologize if you can’t see that article, which might be subscription-only), meaning that they might actually have functional instruments on the market in 2010 as they’ve been saying since February. If this thing actually works as advertised, it will be game-changing in the extreme, and will make the other three competing instruments look stodgy, expensive, and slow.
PacBio has thoughtfully provided a nice little video on their website for you, if you’re interested in this technology. Warning – the term “zero-mode waveguide” is used, although the rest of the description is very basic. The claim is made that entire genomes (or, presumably, genome-sized complex template mixtures, like transcriptomes) will be sequenced in under an hour, at a cost of hundreds of dollars. If true, this will just about spell the end of the microarray for most applications.
We’ll see, I guess. Applied Biosystems certainly has other, competing technologies in the pipeline, but I doubt very much that Illumina has the resources, or Roche has the vision, to stay competitive in the long run. As for Helicos, well, I’ve changed my previous optimistic tone and have switched to predicting their demise for a while now, although they recently bravely reported that they will sell five to ten instruments by the end of the year. I’m not convinced, but I guess we’ll see. In the meantime, the Illumina, Roche and AB instruments appear to be working now, and our three-pronged, high-throughput attack on biology is continuing unabated.
Interesting times.
Posted on Wednesday, December 3rd, 2008 at 7:21 pm Categorized as:Suppliers You can skip to the end and leave a response. Pinging is currently not allowed.
December 4th, 2008 at 5:11 pm
NOOOOO! I don’t want to know about any more of these!
Actually, today I was just discussing ChIP-sequencing with another colleague on site here, and how we sent our sample to be sequenced with lots of short reads on an Illumina/Solexa platform, instead of trying to do it here on the brand new Roche which may or may not have been set up by now, and she has done the same independently.
It all depends what you want to use them for, of course. But three seems already a bit much, unless you’ll be churning out personal genomes in the near future?
December 6th, 2008 at 10:58 am
The idea here is that these are all going to be useful for different things. ChIP-seq is well suited to the AB or Illumina instruments, where you can get away with short reads as long as the error rate is low enough. The 454 is much better suited to de novo genome sequencing (e.g. bacterial metagenomics and suchlike, or sequencing plant genomes that haven’t got a good reference sequence). The longer reads coupled with paired end capability will make de novo assembly much, much easier, the trade-off being run cost.
The Illumina instrument was our first purchase, but was such a pain in the tail that once it came time to add a second, the AB was the logical choice.
Personal genomes, no – but we do a lot of work on structural variation of human genomes (and other species, potentially), so we do envision running lots of samples. Remember, we’re a big genome centre (~80 staff), so keeping three of these running won’t be a problem with the number of projects we support.