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Early in 2007, GS FLX sequencer (a higher throughput iteration of GS20) from 454/Roche became available; in October 2007, Baylor college of medicine purchased 10 FLX instruments; also in 2007, Project Jim resulted in the first whole human genome to be sequenced using second-generation sequencing technology.

Early in 2007, GS FLX sequencer (a higher throughput iteration of GS20) from 454/Roche became available; in October 2007, Baylor college of medicine purchased 10 FLX instruments; also in 2007, Project Jim resulted in the first whole human genome to be sequenced using second-generation sequencing technology.

Gene sequencing speed/cost is moving faster than Moore's law

This system does 400-600 million base pairs per 10 hour run.

149,000,000,000bp/400,000,000bp/run ~ 373 runs

3,730 hours ~ 155 days

I don't how long setup times between runs might be or what other factors are involved, though. On the other hand, a big lab would have more than one sequencer.

It may not be as expensive as you think, especially if it uses a bioanalyser useful for other research. This reminds me of some of the new techniques for DNA sequencing http://www.454.com/, but is probably just beads with anywhere from 20 to 100 nucleotide pieces of DNA attached, each bead specific to one virus. If a PCR product http://en.wikipedia.org/wiki/Polymerase_chain_reaction/ attaches to the single stranded DNA on the bead then a stain like ethidium bromide will light up the bead (under UV light in the bioanalyzer). Anyway my point on the expense is that machines with UV lamps and cameras are not that pricey, just marked up that way. :P

I think, since as you point out few viruses are specifically treatable, this might be more useful for use at selected hospitals across a country or the world to track the dispersion and spread of viruses. Especcially since scaling up the kit to include many hundreds of viruses and/or bacteria should be easy, look at how many beads the 454 DNA sequencing chips fit, it's amazing.

IAAB (I am a biochemist), but I don't work on medical diagnostics, cheers!

hmm..correct and incorrect, imho. Sure, there has been significant advances in the way sequencing works; the lastest being 454 sequencing http://www.454.com/, or Solexa http://www.illumina.com/pages.ilmn?ID=203 or SOLID http://www.illumina.com/pages.ilmn?ID=203, which has significantly reduced cost to sequencing. However, with each of these new techniques come new challenges in statistics and data analysis that are not just technological problems - they require significant, real breakthroughs in algorithms and statistical methods - how do you identify genes? what statistical methods would you use to identify distant repeats separated by millions of years? How accurate and reliable are these identification methods? We've come to a point where getting the data is now almost trivial and cheap - making sense of it, even being able to order it in the right way - we're just beginning to make headway there. So its not all tech - there is a lot of science there - only, it is difficult to argue it is biology any more - more chemistry and math and a bit of CS :)

We recently had a speaker here to introduced us to the new methods of DNA sequencing that are so brilliant you might think we stole the tech from aliens. If you're interested, check out the 454 Life Sciences Corporation or THIS ARTICLE for a scoop on one such new method that'll knock your socks off if you're an old-school biologist. Their process (click through and read the slides) is light-years beyond where we were only 5 years ago. The speaker we had reported that their lab was able to sequence massive pools of DNA from bacteria that lives in our intestines (well, monkey intestines, but close enough) and were able to determine that we have upwards of 1000 different species of bacteria living in us, mostly likely helping our system.

To summarize the sequencing method very briefly and un-technically (if you want the tech, read the site above): it manages to sequence thousands of little pieces of DNA at once... something we had to do one at a time or with the best machines, 96 at a time with a good bit of manual labor. Now we're talking thousands at once, on one machine, in one reaction, on one array. Holy smokes. A single lab worker could potentially sequence more in a day than 10 people working for a month.

With new technology such as this, the thought of sequencing a person's entire Genome in an hour is far closer than we could have ever dreamed. We're talking a couple years here. A decade ago that thought was unimaginable and downright crazy talk. And as the article said, it can also give us glimpses into genetic interactions between organisms in populations from a perspective we could never see before. See "Lateral DNA Transfer: Mechanisms and Consequences".

We recently had a speaker here to introduced us to the new methods of DNA sequencing that are so brilliant you might think we stole the tech from aliens. If you're interested, check out the 454 Life Sciences Corporation or THIS ARTICLE for a scoop on one such new method that'll knock your socks off if you're an old-school biologist. Their process (click through and read the slides) is light-years beyond where we were only 5 years ago. The speaker we had reported that their lab was able to sequence massive pools of DNA from bacteria that lives in our intestines (well, monkey intestines, but close enough) and were able to determine that we have upwards of 1000 different species of bacteria living in us, mostly likely helping our system.

To summarize the sequencing method very briefly and un-technically (if you want the tech, read the site above): it manages to sequence thousands of little pieces of DNA at once... something we had to do one at a time or with the best machines, 96 at a time with a good bit of manual labor. Now we're talking thousands at once, on one machine, in one reaction, on one array. Holy smokes. A single lab worker could potentially sequence more in a day than 10 people working for a month.

With new technology such as this, the thought of sequencing a person's entire Genome in an hour is far closer than we could have ever dreamed. We're talking a couple years here. A decade ago that thought was unimaginable and downright crazy talk. And as the article said, it can also give us glimpses into genetic interactions between organisms in populations from a perspective we could never see before. See "Lateral DNA Transfer: Mechanisms and Consequences".

Not really - NimbleGen's technology - while powerful - would not allow for sequencing of the Entire Genome. Affymetrix for example makes a set of 100 arrays that would sort of allow you to obtain sequence information (still not quite - not enough detail) from only 1/3 of the genome. With the NimbleGen technology it would take 1000s of arrays to reach this level - and still you do not have detailed sequence of the whole genome for even one person.

If I had to take a guess I would say a technology like 454 http://www.454.com/ will provide the next breakthrough.

Is the prize for sequencing or for sequencing and assembling?

Some companies like 454 have got the technology to quickly sequence large genomes but assembling them is a completely different problem. And anyway we understand (roughly) about (roughly) 30% of the genes of any species that has been completely sequenced (mostly bacteria). I wish there was a prize for technics to annotate genomes accurately.