genomeboy.com

George Carlin, R.I.P.

“I think a broad-spread application of personalized genetic testing would create havoc and would likely lead to more harm than good…It will make people anxious, and it would probably push doctors to more aggressive interventions simply because of lack of information and a feeling they had to do something.”

- H. Gilbert Welch in the LA Times

If nothing else, George Church’s Personal Genome Project has spawned some blogging careers.

I loves me some Daily Scan.

This link actually points to my fellow PGPer, John Halamka, aka Participant #2, and his blog, wherein he reveals his experience in the PGP thus far. Apparently, he already has his SNP chip data…bastard. (Hello, George!) No, seriously, I love John and I love his RFID.

[Jason] Bonham’s volcanic fills on Nobody’s Fault But Mine confirmed that there are some things that can be transmitted only through DNA.

Led Zeppelin: Immutable.

(Image from The New York Times)

This morning I was on my back counting dots in the ceiling tile while a pleasant woman repeatedly asked me to turn my head toward her and Sheryl Crow quietly insisted that a change would do me good. (Ach, Honey, don’t I know it.) Alas, it’s not what you’re thinking. As the pleasant woman poked and prodded my fork-tender gums with what I swear is the same device we used to eviscerate fetal pigs back in freshman biology lab, I tried not to flinch or, at the very least, tried to ignore the tears running down my cheeks.

Our species may have undergone a spectacular makeover since its knuckle-dragging origins, and our phenotypes may change dramatically during our brief time on this mortal coil*, but I swear to Jesus Haploid Christ that I hate going to the dentist just as much as I did in 1972.

As the feeling left my lower extremities and the pleasant woman continued violating the Geneva Convention in 11 ways, stopping only to Hoover the blood and saliva from the recesses of my mouth, I tried to console myself with the idea that next month (right, George?), when George Church presents me with my genome sequence, I will somehow be vindicated. There amongst my motley collection of A’s, T’s, G’s and C’s will be evidence that the disaster that is my mouth is not my fault. The gum disease, the infections that have led to periodic root canals and implants, the chips and cracks that make my oral cavity indistinguishable from that of a Dickensian orphan–all will be revealed to have a genetic basis. I mean, it stands to reason that I must have a humoral immune defect or mutations affecting my periodontal tissues. Or some other pernicious host factor that renders me susceptible to tooth decay or worse. Must be, right? The PGP may not get much from my spartan medical records, I thought, but at the risk of immodesty, I am a dental genomicist’s dream: my paper trail of oral surgery, orthodontia and good old-fashioned fillings and crowns is a mile long. (Not that I’ll let any research-minded dentists anywhere near me…)

When the bi-annual ordeal finally ended and I extricated myself from the chair, I went across the street for what I thought was a richly deserved coffee and chocolate chip scone. It was then, bathed in warm glucose, that the voice of the genome du jour entered my head. “…you cannot define a life or any life based on DNA alone,” he writes in his forthcoming book. “An organism’s environment is ultimately as unique as its genetic code.”

Or, as my mother would say, “Don’t forget to floss.”

UPDATE: As usual, I am behind the curve. (thanks, Keith)

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*O Prostate, why hast Thou forsaken me?

So PLoS Biology is publishing a paper on Craig Venter’s genome tomorrow, Tuesday September 4. Apparently there was a press conference this morning at 10AM Eastern to discuss it. I’m very confused: this is “the first diploid human genome” and it’s unveiled with barely a heads-up on Labor Day morning?

Who are you people and what have you done with Craig Venter?

UPDATE: Um, never mind…

Genomicron offers a recipe for how to write a bad science story and pretty much nails it. I plan on sharing this with my students next semester.

A few weeks ago the Genetic Genealogist gave us a lively summary of the issues raised by this paper from Stanford’s Hank Greely. If you haven’t seen it, I think it’s probably as damning an indictment of current practice regarding human genetic research subject confidentiality and anonymity as you’ll ever read.

The current Nature Genetics features a commentary from the GAIN Collaborative Research Group (a public-private consortium of investigators carrying out genome-wide disease association studies) that offers a rather different perspective. Dig the disconnect:

GAIN:

“Investigators granted access to GAIN data should ensure confidentiality of study participants and follow any limitations specified by their informed consent.”

Greely:

“…plans for a Genome-Wide Association Studies database by the [NIH] illegally and unethically strip people of the legal status of human subjects…blanket consent, although extremely convenient for genomic biobanks, is both ethically and legally suspect.”

GAIN:

“Individual participant data will be kept secure and will not be distributed.”

Greely:

“…patient identity is not, and cannot be, effectively protected in large-scale genomic biobanks.”

GAIN:

“Data will not be used to identify or contact individual participants from any GAIN study.”

Greely:

“…the result of anonymizing data is not only nearly useless, but is itself unethical…”

“…biomedical research, including genomic biobanks, has a moral obligation, now almost always evaded, to inform research subjects of clinically significant information.”

You might say, “Yeah, well, Greely’s just one guy.” And I might say, “Yeah, well, read this article and the 15 commentaries that follow it and then talk to me about consensus.”

I don’t see a Kumbaya moment happening anytime soon.