CHI Next-Gen Conference, Day 1

Interesting set of talks today. I never did explicitly check on the blogging policy, but given that the session chair kidded a speaker that I would be blogging her live, it wouldn't seem to be a problem. I would honor a ban (particularly since blogging is a bit hard to hide after the fact!), but quite a few folks were photographing slides despite an admonition not to (one person was clearly worried neither about being caught nor being courteous nor being clever; he had his flash on, which is clearly useless for projected images!).

The morning talks ended up as just a trio. The best of the three was Robert Cook-Deegan's talk "So my genome costs less than my bike, what's the big deal?". He obviously has more expensive tastes in bicycles than I do -- or knows a really cheap genome shop! He covered a lot of the ground around what sort of regulatory model will encompass personal genome sequencing. The U.S. weakly and Germany strongly have gone with the model that genome sequencing should be treated like a diagnostic with M.D.s as the absolute gatekeeper (a position which is rather vocally promoted by certain bloggers). Cook-Deegan pointed out something that increasingly worries me, which is that this locks genome sequencing into a very expensive cost model which doesn't improve with scale; you are locking in some very pricey labor that will only increase in price. Cook-Deegan also felt that M.D.s were being picked as the gatekeeper primarily because they are who the regulators are comfortable with historically, not because they are particularly well-trained for the job.

Jonathan Rothberg gave an entertaining talk on his various ventures, which built up to Ion Torrents but where the crescendo was expected by the audience there was instead the request for audience questions. Ion Torrents seems to be a company (Joule is another) which is still trying to be in the public eye without releasing any key information. Understandable, but frustrating.

Henry Erlich gave a nice presentation on using PCR amplification and 454 sequencing to do HLA typing for transplantation. All sorts of advantages to 454 over Sanger here, but cost will probably remain an issue and definitely corral this in very large centers (one 454 run, with multiplexing, can type ~20 samples).

Lunch was given over to IT stuff. CycleComputing presented their bioinformatics-friendly gateway to Amazon's cloud computing stuff (plus some benchmarking). I'll confess to checking email during the presentation on compressing data on servers; far too IT for me.

The afternoon was devoted to a series of presentations by the 6 next gen sequencing platforms with some flavor of being here-and-now: 454, SOLiD, GA2, Helicos, Dover (Polonator) & Complete Genomics. Actually, that was an interesting theme running through some talks, with Illumina saying "we're now gen, not next gen" whereas Complete Genomics calls themselves "third gen". The talks were all genteel but contained pokes at each other.

For example, 454 trumpeted a comparison of two unpublished cucumber genome sequences, one by Illumina+Sanger and one by 454. The 454 16X assembly had a contig N50 of 87Kb vs. 9Kb for a 50X Illumina assembly (no mention made of the amount of paired end data in either, I think -- though now I'm not sure). 454 also declared they've had one perfect read 997 long, though they were open that commercial runs near this are long in the future.

The SOLiD speaker emphasized all the different applications of their technology, using a published graphic that later turned out to have been commissioned by Helicos. Illumina's speaker emphasized the simpler sample prep over emulsion PCR systems (i.e. 454, SOLiD & Polonator).

Helicos promised even simpler sample prep and offered tantalizing hints of good stuff to come -- such as my nemesis of sequencing from FFPE slides. Helicos did detail their paired-end protocol, which is very clever (after reading a bunch of sequence, a set of timed extensions with all 4 nucleotides gives jumps of various distributions which are then followed by more reads. Clearly this will only work with single molecule sequencing, at least in that form (must ponder thought of how to either improve this or get it to work on Illumina-style platform). Helicos also tantalized with a bunch of data from different applications, suggesting that some more publications from this platform are imminent.

Danaher's talk was mostly on details of the instrument, which is the only one actually at the conference & is running. Always fascinated by moving machines, I watched it for a while -- and it demos very nicely, with the stage moving & illuminator flashing & filter wheel spinning. Polonator has very short reads compared to the other platforms, but is promising very low cost which could make it a contender.

Finally, Complete showed off their sequencing center approach. One striking fact is that their read lengths are actually extremely short -- but they extract a quartet of paired short reads. Clearly their recent announced delivery of genomes has improved their credibility & they also detailed some very neat medical genetics results which are presumably going to hit the journals very soon -- in which case they will have complete lab cred. It was pointed out in the discussion panel & in several talks that human sequencing is not the whole world, but even their competitors did not violently object (and therefore seemed to grudgingly acquiesce) that Complete may grab the lion's share of the human genome sequencing market, with the other players going after non-human sequencing or human areas like FFPE or transcriptome sequence where Complete isn't positioning themselves.