genomeboy.com

• A friend emailed me yesterday, referenced this article on how Knome will offer complete personal genome sequencing for $350,000 and asked, “And you get yours for free??” (Alas no!)
• And last week, The Economist (still unencumbered by bylines) wrote, “Two firms have unveiled products that allow the ordinary punter to get his genome decoded [emphasis mine] for about $1000.” (The article also says, “All people are 99.9% identical, genetically speaking.” Come on, mates–you’re better than that!)

What we have here, I think, is a failure to communicate. According to the New York Times, for a thousand bucks deCODEme will test about a million DNA variants or SNPs, while 23andMe will test about 650,000 SNPs. That’s 0.033% and 0.022% of the haploid human genome, respectively. These “variome” analyses may prove to be incredibly useful and perhaps even a terrific bargain for punters of all stripes, but is it accurate to call them “getting one’s genome decoded?”

What PGPers will get — we think:) — are our complete exomes, that is, the entire protein-coding portion of our 20,000+ genes*. This, I’m told (anybody have a reference?) works out to about 60 million base pairs or roughly 1% of the diploid human genome. George (who, it should be noted, co-founded Knome) has told us our exomes will cost…drum roll please…about $1000. Do I sometimes tell people I’m getting my genome sequenced? As a shorthand, yes, but I shouldn’t. It’s an exome, not a genome.

For their $350k, Knome customers, I presume, will get something like 6 billion base pairs, that is, essentially complete diploid genome sequences just like Venter and presumably, Watson, received. (Read Hsien’s interview with the Knome CEO.)

Are any or all of these services worth it? I have no idea and I’m not sure anyone else does, either. This issue — a genome: what is it good for? — is at the heart of what the PGP is all about. It’s partly a matter of personal taste, of course: is an incomplete and often inscrutable translation of the Rosetta Stone at whatever resolution still worth some amount of money and the space it takes on your bookshelf? I’m inclined to say yes, but I can’t say until I’ve seen mine and lived with it for a while. I have no sense about how the rest of the world feels; however, I will say that in contrast to the enthusiasm I see in the blogosphere, a fair number of my colleagues at Duke, to say nothing of people I’ve talked to at the NIH, tend to roll their eyes when I start yammering on about personal genomics.

Can these companies make meaning out of this stuff? What are customers’ expectations and what should they be? Will new information bring clarity or confusion?

I hope to find out. Next week I will be in the Bay Area visiting some of these folks, asking questions, learning more about what they do, and eating obscene quantities of Asian food.

*Behold, the incredible shrinking genome!

UPDATE: I should add that we will also get our variomes typed via Affymetrix Genome-Wide Human SNP Arrays (don’t quote me on the version).

Thanks to Jason Bobe et al, the PGP website is now up and running. Yay! As congenial as George’s previous DIY version of the site was, I think PGP 2.0 and its easy navigation will answer almost any question one might have about the project, its mission, goals, philosophy, how and why one might participate etc.

And not only is the content put together in a clear and intuitive way, but I think it looks great, too…okay, well, with the possible exception of a certain dork’s kelly green shirt….No doubt my Y chromosome will reveal a congenital lack of fashion sense…

For better or worse, the New York Times has become a near-daily fount of genomic stories–well beyond the weekly deluge in Science Times. IMHO, so far it’s for the better (assuming they don’t bring Judith Miller back to cover science). From Sunday’s paper:

• Skip Gates, whose view of genetic ancestry seems to be, if you can’t beat ‘em, join ‘em…and then beat ‘em. I don’t know if it will work, but I think his emphasis on combining genetic data with oral history is admirable. It’s seems to me to be analogous to trying to bring phenotypes into personal genomics in a systematic way, something no one has yet succeeded in doing.
• DNA has exonerated more than 200 people…short of a cure for cancer, there may be no better endorsement for the power of genomic technology to do good. It’s after they let you out of the joint that the trouble begins. Another testament to the messiness of our species and the environments we create. These articles are absolutely heartbreaking.
• Jim Watson…boring?! A sure sign of the apocalypse.
• Eleven Romanovs, present and accounted for.

Everyday I wake up, snarf down my Honeycomb, read the newspaper and then the latest output from The DNA Network. It’s like drinking from a fire hose. As Hugh Rienhoff said so eloquently in last Sunday’s paper:

The real news is that the genetic genie is out of the bottle. The consumer’s embrace of genetic analysis is now unstoppable. And though the medical community warns how little we can actually learn from most of our genes, these caveats do not diminish our curiosity.

…here’s a real provocation*:

How is [low-cost personal genome sequencing] going to change our lives?

I think we’re going to find that in subtle ways we’re not quite as free as we think we are. When you’re 20 years old, your personality is probably determined pretty much by your genes.

*subscription only–sorry!

Over at Discovering Biology in a Digital World, Sandra Porter has a great post about the disconnect between scientists and science educators as exemplified by the frequent lack of access scientists have to pedagogy journals. Frankly, I think most scientists don’t take the education literature seriously, even when they do have access to it. There is a presumption that education research is squishy, anecdotal and not to be trusted. Is it true? Sometimes. Is it a fair generalization? Not in my (admittedly limited) experience. Social science is hard to do well, but that doesn’t mean folks in the hard sciences are justified in dismissing it wholesale.

Beyond methodological questions, I think the inferiority complex science educators feel lives on for another reason: I think the digital divide Sandra describes is emblematic of a more longstanding cultural one, namely, the divide between teaching and research. Teaching is simply not rewarded in most basic science departments the way it is in the humanities, where it is the raison d’etre as much as scholarship is (or at least it is comparable). I mean, anyone can teach, right? (insert irony emoticon here). Has anyone gotten rich doing so? How about your graduate TA and her multiple sections of Bio 101? And will your $20,000 collaborative education project with the local museum ever attract the same attention or please as many administrators as your colleague’s $5 million cancer study? Please don’t get me wrong, I’m not speaking with any bitterness whatsoever–that’s just how life is. Yes, there are funding agencies that have endeavored to reward innovative science teaching at the K-16 levels. Are they are exceptional? I don’t know.

In any case, that teaching scientists don’t have access to science education journals strikes me as shameful but hardly surprising. However much hand wringing we do over the US lag in training the next generation of scientists, if history is any guide I suspect science education will always labor in the shadow of the science itself.

Monday afternoon I spent several languid hours in the jury pool room at my local courthouse. As I sat there with my thumb up my butt watching a stirring video hosted by Charles Kuralt, it occurred to me that jury duty is really just a population database in action. Potential jurors gather and swear on Bibles just as a population under study might gather for en masse consent. Like research subjects, jurors are usually promised nothing other than very modest compensation ($12 + free coffee–woo-hoo!) plus a chance to do their civic duty and benefit society as a whole. In many cases (like mine on Monday), nothing comes of the experience–people are sent home with a parking voucher and a promise that they won’t be bothered again for at least two years. Some folks are resentful of jury duty, some bored (ahem), and some have legitimate emergencies they have to attend to that preclude them from serving. But no one I’ve met says, “Jury duty is fascist. They can put me in jail but I ain’t going.”

The analogy is hardly perfect: can we imagine compelling able-bodied people to give up their DNA/tissue/cells the way we compel them to show up at the courthouse by force of law? Um…no. Sounds like an absurd and fairly creepy scenario. But short of legislation, could at least some of the same civic spirit attached to jury service be infused into scientific research of all stripes, particularly if more scientists were willing to share results and/or let their subjects see behind the curtain?