James Watson's Genome, Annotated

One of the coolest things from SciFoo was a presentation by Lincoln Stein of Colds Springs Harbor Lab. Lincoln is an intriguing guy, a computational biologist who is extremely handy with code.

Stein's presentation was titled something like: "Genomic Voyeurism". He had spent the previous week (just one week!) whipping up a little website called the James Watson Genome Browser. Stein matched Watson's genome, which was made public on May 31, to the reference genome from the Human Genome Project. He also input data from the Human HapMap Project, which indicates the position of common polymorphisms in the human genome, and OMIM associations that list so common genomic variants associated with disease risk.

The result is a Genotype Viewer that lets you scan Watson's sequence to see where his genome differs from the "reference" sequence, as well as to view some genes and potential disease associations. As Stein introduced the Browser, he made the point that this is almost entirely an academic scan, not a clinical one - at nearly 80, Watson has pretty much had happen whatever's gonna happen to him. That is, whatever risks he might have, he's clearly beat the odds.

The browser is not an easy thing to navigate - most of the information in it is over my head, and scanning page by page or mousing over the popups, it's a bit difficult to make sense of what exactly the genome is telling you. But there's a nifty search function that lets you, say, enter a gene with a known association (Stein suggests trying "HTR2A") and seeing whether Watson has said gene.

What's amazing about this is that 1) Stein did this in a week and that 2) it's the first time I've seen a hint at what information lies inside a genome on a practical level. As I say, it's a mite impenetrable for the non-geneticist, but it does open the window onto all of our genetic futures.

[Duncan Hull has a thorough play by play of Stein's talk here.]