Marco Island sequencing frenzy - are we getting lost in all the data?

So - the Marco Island meeting could be summed up as a sequencing frenzy. Everyone and their mother presented something about how the next generation sequencers are revolutionizing their work. People are using these systems (well, people are using mostly Illumina and Roche sequencers and some are using ABI Solid) to do all sorts of new things - RNAi, gene expression, methylation, mutations, population genetics, comparative genomics, metagenomics, infectious disease, etc etc etc.

Certainly, much of this new work is truly revolutionary. Sequencing has gotten so cheap, and so easy, relative to even 3-4 years ago, that it can be used in all sorts of new ways. And new developments in sequencing seem poised to happen too, to make sequencing even cheaper and even better. Sequencing will get even better for a few reasons.

First, the current players in the market (Roche, Illumina, and possibly soon ABI Solid) are improving both their systems and their informatics such that they are getting more and more robust and easy to use and producing more data (Roche for example presented details on how they can extend their sequence reads to ~350 base pairs mostly by software and reagent changes). Lots of companies can say "We have some sequencing system about ready to be introduced" And lots of them are doing this at this meeting. But there is nothing like having sequencers in the hands of scientists to really test how well they work and to really help push the development of the technology.

Second, it does seem like some competitors for Illumina and Roche are coming. ABI presented multiple results from ABI Solid technology that makes it seem like these systems are ready for prime time. Whether other systems are ready for prime time is unclear. Helicos presented what could be seen as data. It was disappointingly minimal on detail but though I am rooting for them, it was far from convincing. But the discussions in the hallway seemed to suggest that Helicos is getting close. And there are 5+ other players itching to get into the market (some of which are apparently presenting later today). Some will fail. Some will succeed. And as long as their are a couple of good systems, the competition will push further development and reductions in costs. Thus everyone at the meeting I talked to said basically the same thing --- this is an exciting time in sequencing.

So - sequencing is getting better and cheaper. That certainly will be good in many ways. But there are some negative aspects to this frenzy. I see two in particular. The first, which was discussed extensively at the meeting, is that nobody is really prepared to deal with the sheer volume of data coming out of these new systems. Data storage, transfer and analysis will unquestionably be the rate limiting steps in turining the new sequence data into knowledge.

And this is the other negative aspect of the new frenzy. Right now there seems to be a mad rush to apply the new sequencing methods to everything under the sun. And the data piles up. And piles up. And the biology seems to have taken a back seat in some cases. Perhaps the bext example of this is exemplified by something Neil Hall pointed out yesterday to me. There has been almost no mention at this whole meeting of things related to function of genes. For example, I have not heard "gene ontology" once. I do not think I have even heard "annotation" once. Function and process have been replaced by terms like "systems biology" and "SNPs" and "networks" and "massively parallel." We have in a way regressed in terms of treating organisms (or communities) as a black box. Fine scale detail has been lost in a sea of data. In a way, we have all become born again geneticists. And I do not mean to disparage genetics. But I mean the part of genetics that treats organisms as a bit of a black box and focuses just on transmission of traits. We need to find a way to not get lost in all the data. I am not sure how to do that, but when we do, then the full potential of the new sequencing methods will be realized.