genomeboy.com

The book-trailer equivalent of The Player:

In an effort to stop DNA testing on state campuses, a bill was introduced in the California legislature last week that would prevent the University of California system from:

“making an unsolicited request to an enrolled or prospective student of that segment for a DNA sample for the purpose of genetic testing.” It would also require that the universities report how much they are spending on such tests; the schools would then have their funding reduced by that amount.

Keep moving those goalposts, boys and girls. We may not be able to legislate morality, but ignorance is clearly within our grasp.

(hat tip: Dan Vorhaus)

This month, PLoS Genetics is publishing an article from the company 23andMe reporting the first genome-wide association studies (GWAS) on multiple traits ascertained by self-reported information provided through the Internet from over 10,000 participants who pay the company for providing whole genome genotypes [1]. The paper passed through scientific review by a panel of three experts relatively quickly and is sure to attract the attention of anyone with freckles, curly hair, or an aversion to asparagus. Novel associations are described for four intrinsically interesting traits (out of 22 considered), while known associations with hair and eye color are replicated in a dynamic data-gathering context. Additionally, intriguing observations on the interaction between genetic self-knowledge and self-report of phenotypes are described. The implications of the successful application of this Internet-enabled approach to GWAS research were considered to be more than sufficient to warrant publication in the journal.

 

***

The editors of PLoS Genetics recognize that the decision to publish this study, without IRB review as human subjects research and with some concerns over the consent document, and the fact that there is limited access to the raw data, will not sit well with some, perhaps many, readers. As outlined above, though, a prima facie valid IRB exemption was obtained, and, while there are ambiguities in the consent form, there was no evidence that these amount to an inadequate document. After considering all of the evidence, we decided that publication, accompanied by an editorial providing transparent documentation of the process of consideration, was the most appropriate course.

Seems like this Interwebs thing might be starting to catch on.

(Hat tip: the indefatigable Bora Z) 

I have a piece in the June 23, 2010 edition of Slate (is it fair to call it an edition?) on the recent kerfuffle surrounding personal genomic testing on Bay Area college campuses:

A new kind of testing is coming to university campuses across the country. In the last month or so, Berkeley and Stanford each announced that their students would be offered the opportunity to have their DNA analyzed from saliva samples. The range of reactions to this news—from horror at the thought of young people misinterpreting their results to unbridled enthusiasm at the chance for large-scale genetics education—confirms that the field of personal genomics continues to mystify. Genetic testing for disease has been around for 50 years now, yet we have no consensus on how and even whether it should be used in healthy people.

ALBUQUERQUE, NM—The process of evolution, through which single-celled organisms slowly developed over billions of years into exponentially more sophisticated forms of life, has inexplicably culminated in local Albuquerque resident Mitch Szabo, leading evolutionary biologists reported Monday.

***

“I know this is controversial, but we have to consider the possibility that Darwin was wrong, ” said Victor Siles, a geneticist at the University of California–Berkeley. “Nothing we currently know about DNA, no fully mapped genome, can account for the presence of someone whose apartment smells that much like Chef Boyardee.”

If you’re like me and you go to way too many scientific and professional meetings, it’s easy to get jaded. I am trying to limit my travel to stuff that 1) I can afford; and 2) actually interests me. One meeting I am totally geeked up for is the Open Science Summit in Berkeley, California from July 29-31, and organized by Joseph Jackson and his merry band of paradigm-shifting partners in crime:

The well known “10/90” gap references the fact that only 10% of biomedical spending goes toward conditions that affect 90% of the world’s population.  Under this regime, “diseases of the poor,” such as malaria, are neglected, while companies focus on “blockbuster” drugs for conditions that affect citizens of the wealthiest nations.  This situation, appalling though it is, actually grossly understates the systemic flaws of the prevailing biomedical innovation paradigm.  Framing this as a tradeoff between Market vs Social Values or the need for balancing commercial interests with public health, implies that the bio-pharma industrial complex works for what it purports to do.  If only we could find some way to engage or tweak existing mechanisms, we’ll make it through.  Wrong! 

There will be sessions on synthetic biology, gene patents, open data/open access, biodefense, microfinance, entrepreneurship, drug discovery, tech transfer, and more. There will be smart, talented and good-looking presenters (and, uh, me). And it’s cheap!

Why am I pimping this so hard? I am supportive of the cause. These are ideas and approaches that are less likely to be embraced by funding agencies and academia (as you will learn in my forthcoming book). I like and respect the organizers and want to see them succeed.

See you in Berzerkeley!

This is 17 kinds of awesome:

Scientists are to map Ozzy Osbourne’s genetic code in a bid to find out how he is still alive after decades of drug and alcohol abuse.

(hat tip)

UPDATE: “Throw some fag ash on his cornflakes.”

(hat tip #2)

Dr. Alberto Gutierrez—the FDA’s director of the Office of In Vitro Diagnostics in the Center for Devices and Radiological Health—talks to NEWSWEEK about the personal genomics crackdown:

So the problem is that the companies are testing for genetic variants that might affect the way consumers make medical decisions?
That’s correct … If you’re making a claim about [a genetic variant that affects the metabolism of the anticoagulant drug] warfarin, and somebody decides based on the result they get that they want to change their dosing, that is a fairly risky decision. That could affect their health. If they’re not feeling well on their current dose and the drug is expensive, we don’t know what they would do.

Last time I checked, one could not buy warfarin over-the-counter. Oh well, I guess there’s still no way we could ever know what they would do. Fortunately the NIH would never support a website where anyone could input her own genotype data to evaluate her own warfarin dosing.

***

What Knome sells is more of a service than a device. It’s basically a software program that explains genetic data that consumers can have generated elsewhere. Can you explain to me why it requires pre-market clearance?
Software is a medical device, and they’re making medical claims. They’re taking results and making medical claims that come out of those results.

Gosh, I sure hope WebMD, mayoclinic.com, yourdiagnosis.com, medhelp.org, medicinenet.com, healthcaremagic.com, emedicine, MedicineNet, and healthline.com have pre-market clearance.  And fortunately the NIH would never support software blah blah blah…

UPDATE: In contrast to my screed, the Genomics Law Report offers a more balanced, detailed and sober analysis. 

We are going to start hearing stories about people getting their entire genome sequenced. What might these stories miss?

One thing that they might do, is try to interpret the data the same way they did for companies like 23andMe and focus on common variants.

The real story is in the rare alleles. One in ten of us are very affected by these, and the sequencing tests reveal them as long as we are looking for them. Almost all common diseases have a rare allele component to [them]. What happened before is that we went through a fad. Scientists were looking where the light was in the common variants and they mostly ignored rare alleles.

(Hat tip: @DivaBiotech)

But Dovekie’s test results were utterly baffling. The “Canine Heritage” swab test from MMI Genomics showed four breeds in the mix — in order of prevalence, golden retriever, wirehaired pointing griffon, bearded collie and miniature schnauzer. This means that Dovekie’s mom, Charlie, whom we met and felt confident was a purebred golden retriever, was anything but. It also meant that Romeo was no Chocolate Lab.

Typical. When you’re in heat, they always tell you what you want to hear. “Hey, Baby, I’m totally Chocolate Lab.”