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Got a note from Harvard/MIT's George Church re: my story on personal genomics and 23andMe (he's on the 23andMe scientific advisory board and is quoted in the story).

Nice job on the article. Many of my colleagues agree. However some (including me) are concerned that the message about "œlimitations" of linkage-based chips is not coming through (despite the basic forthrightness of the first three Personal Genomics companies). The limitations are significant for research -- and even more so for diagnostics. Common diseases are not necessarily caused by common DNA variants – but also by DNA variants individually rare but collectively common. Associations can be statistically significant in a research population but have unacceptably high false positives and negatives in the individuals of that population. A good example is one of the oldest success stories in personal genomics -- BRCA1 & 2 which Myriad Genetics offers. Could those gene tests be done with any of the 3 new personal genomics chip assays? Probably not, since the causative alleles are “new” (i.e. less than 100,000 years old) and numerous. The causative alleles are not in linkage disequilibrium with the common alleles on the chips and hence require actual sequencing at Myriad. Despite the various limitations, early adopters may be richly rewarded by their insider-view if/when personal genomics takes off like personal computers. Thanks, --George

 

The December issue of Wired, on newsstands next week, has a story I've written on the debut of genomic medicine, via 23andMe, the much-anticipated startup. The story is now up here on Wired.com. I was fortunate enough to get an up close look at the inner workings of 23andMe, shadowing company founders Linda Avey and Anne Wojcicki (shown here) off and on over the course of the past few months. The story, though, isn't just about the company as another Silicon Valley startup. I was especially interested in the challenge they face in turning the very raw science of genetic discovery into a consumer friendly, retail service. Given that research into genetic associations is still quite early, and given that the medical establishment is just barely on the case, it's an especially compelling story about how individuals will be responsible for learning a huge amount in order to make sense of - and take advantage of - the genetic information 23andMe offers.

More on pharmacogenomics from the Personalized Medicine Meeting at UCSF

In the opening panel this am, David Parkinson from Nodality offered a choice: Put yourself in a pharmaceutical company's shoes: Would you rather have a drug that’s 10% effective for 100,000 or 100% effective for 10,000?

I dropped in today on the Personalized Medicine Meeting, an annual conference put together by Burrill & Co, a health care/technology consultancy. Amid all the hype over personalized medicine, I was glad to hear lots of attention paid to early stage interventions - meaning predictive and preventative strategies, rather than pharmacogenomics, which is the traditional face of personalized medicine. Indeed, there was a fairly manifest distinction drawn throughout the day between the pharmaceutical industry's approach to medicine and biotech's - and Steve Burrill set the tone when he called pharma's business model all but dead.

More proof that dark data can be unexpectedly illuminating: researchers at Stanford re-analyzed 49 experiments and found statistical evidence of an association between two genes and obesity. This story is a little vague on details - which genes? what's the strength of the association? But it's fascinating to me that the studies used a variety of animals, from humans to rats to worms.

A nice analysis in the Guardian dissects what, if any, basis in fact might lay behind James Watson's recent remarks about race. (Note: the juice is in a podcast, link here).

Apologies for the, uh, toilet humor, but couldn't resist this little news item on the first World Toilet Summit, bought to you by the World Toilet Organization.

Forget Peoria. Sioux Falls is the new arbiter of American values. Especially when it comes to the portent of genetics on public health. A very telling story in the Sioux Falls, SD, Argus Leader about the implications of genetic medicine. It is a 500 word story (ie, short), and it's a great indication of where the perception of genetic medicine is in the greater US (I say this as a Minnesotan; I have no prejudice against South Dakotans, on the contrary. Wisconsinites, on the other hand...). The story hinges on the visit of a speech by Eugene Hoyme, a geneticist and "Dell Rapids native who recently became chief pediatric medical officer for Sanford USD Medical Center," according to the Argus Leader. (USD is University of South Dakota).

I have to say, of all public-health/food-safety issues out there, whether or not to eat fish is one of the most confusing. Seems like every week someone's asking me about fish - usually a woman friend of child-bearing inclination - and seems like every week, there's a study that either says, in Column A: Eat Fish: It's Good For You! or in Column B: Beware of Fish: It's Bad For You!

I've written about electronic health records here and elsewhere, so it's been fascinating to me watching the health industry lurch its way towards an EHR future. While I've endorsed WorldVista - an open-source EHR based on the VA's EHR system - I'm really platform agnostic, so long as a) there's a premise of openness, so that the records are portable for the patient and the data useful (albeit anonymized as neccesary) for researchers and b) the industry stop talking about it and start loading it. So the arrival of Microsoft HealthVault is, to my mind, a welcome kick in the pants for every hospital administrator and HMO CTO - the realization that this is not an optional future; if the health care industry just keeps sitting around, the market will create its own solutions and innovation will happen. The notion that Google, too, is out there with a looming Health product (whatever form it may take), is probably even greater catalyst for change.