genomeboy.com

Can you spot the real scientist? (photo by Bob Cook-Deegan)

I was walking through Tower City, the teeming mall in downtown Cleveland, regretting not calling friends I used to know when I lived there, when I spied, sitting alone at the food court with a New York Times, one of the giants of genome history, Maynard Freaking Olson, in town to give a brilliant plenary address. As is my wont, I shamelessly pulled up a chair and started interviewing him. I mentioned the PGP and his eyes lit up. We talked about personal genomics, why he thinks it’s all so much “Freudian genetics,” ELSI, race, changing fields, George Church, health care, liberal politics, the disappointments of GWAS, Jim Watson, and on and on.

I was wrong: George Church is unique in many ways, but he is not the only hardcore genome sequencer who actually takes a real interest in the societal implications of his work. Thank you, Maynard!

Expression Analysis takes delivery of the first Heliscope just before the start of our state-wide month-long holiday.

I’m a few days late on this (what else is new), but ABI has sequenced a Yoruba for $60,000 at 12x coverage–that’s 36 gigabases for those of you scoring at home. As usual, it was the X chromosomes doing the heavy lifting:

The sequence files are subdivided according to the SOLiD instrument in Beverly, Mass., that initially produced the sequence. McKernan’s group names each of its instruments after a famous female scientist. The instruments contributing to this project were named Amelia, Barb, Clara, Florence, Joan and Liz.

Up Heliscope…

Helicos BioSciences announced today (5 March 2008) that it has shipped its first machine. If, as the company says, this bad boy can churn out an entire human genome at 10x coverage in eight weeks for $72,000, then the next-gen market — and personal genomics in particular — just got a whole lot more interesting.

For me (and it’s all about me, right?), one of the highlights of the Marco Island meeting beyond the amazing mango cheesecake was seeing an actual Polonator (note the human telomere sequence flowing out of it). Why should you care? Well, this is a DNA sequencing machine whose descendants will presumably yield 100,000 genomes (or at least exomes), including mine and perhaps yours. Even more interesting than the technology itself is the fact that the Polonator is open source:

The system’s operating software is fully documented and freely available for public download, as are the protocols and reagent sets. All aspects of the system are fully programmable, with parameters and sequences accessible and modifiable by its users to improve and extend the instrument. In addition, all subsystems are highly modular and easily upgraded and/or retrofitted; as a result, we fully anticipate that the instrument will evolve and improve over time. We expect a worldwide user community to develop and flourish, advancing both the design and the operational specifics of the platform, from which all users in turn will benefit.

The reactions to the open-source model from other next-gen types at the meeting ranged from unbridled enthusiasm (”a great idea”) to deep skepticism (”Who will support it?”) to bemusement/amusement (”sounds like another cute George Church concept–I have no idea if it will work”).

Jonathan Eisen has more on the Polonator as well as lots of other great stuff on Marco Island. He was also seen sporting a tee shirt that read “What Would Jesus Sequence?” An appropriate query, perhaps, in  the wake of Evolution Sunday.