Gene Expression

Genetic Future (and again), John Hawks and FuturePundit have all touched upon a new Steven Pinker piece in The New York Times Magazine, My Genome, My Self. If you read all the weblogs which talk about personal genomics, I suspect we’ll look back at this era like those who read PC Magazine in the early 1980s must feel right now. The future is often bigger and stranger than we perceive from the present, and the near future is often more banal than the more exaggerated propagandist might assert. Pinker’s strength as a scientific intellectual is the ability to distill these sorts of truths into engaging prose, and the added angle of using his own genome as a window into the possibilities of personalized genomics is a definite value-add.

It seems that he used several different tests from different companies for varied purposes:

Last fall I submitted to the latest high-tech way to bare your soul. I had my genome sequenced and am allowing it to be posted on the Internet, along with my medical history. The opportunity arose when the biologist George Church sought 10 volunteers to kick off his audacious Personal Genome Project. The P.G.P. has created a public database that will contain the genomes and traits of 100,000 people. Tapping the magic of crowd sourcing that gave us Wikipedia and Google rankings, the project seeks to engage geneticists in a worldwide effort to sift through the genetic and environmental predictors of medical, physical and behavioral traits.

The Personal Genome Project is an initiative in basic research, not personal discovery. Yet the technological advance making it possible — the plunging cost of genome sequencing — will soon give people an unprecedented opportunity to contemplate their own biological and even psychological makeups. We have entered the era of consumer genetics. At one end of the price range you can get a complete sequence and analysis of your genome from Knome (often pronounced “know me”) for $99,500. At the other you can get a sample of traits, disease risks and ancestry data from 23andMe for $399. The science journal Nature listed “Personal Genomics Goes Mainstream” as a top news story of 2008.

The genes analyzed by a new company called Counsyl are more actionable, as they say in the trade. Their “universal carrier screen” is meant to tell prospective parents whether they carry genes that put their potential children at risk for more than a hundred serious diseases like cystic fibrosis and alpha thalassemia. If both parents have a copy of a recessive disease gene, there is a one-in-four chance that any child they conceive will develop the disease. With this knowledge they can choose to adopt a child instead or to undergo in-vitro fertilization and screen the embryos for the dangerous genes. It’s a scaled-up version of the Tay-Sachs test that Ashkenazi Jews have undergone for decades.

As they used to say, let a thousand flowers bloom. Infant industries are often characterized by diversity and niche specialization, and much of the value-add is not going to be in the pure sequence itself, but the analytic tools to extract useful information from the data, and a stylistic presentation which is amenable to consumer preferences. Even clicking through the websites of the some of the sequencing projects and companies one gets a sense of their strengths and inclinations, 23andMe with its bright colors & play, Counsyl which seems more sober and aimed at families, and the Personal Genome Project‘s more straightforward academic formatting, though I’m not sure that the conceit of Knome‘s hook is reflected in its spare and harsh website. With the coming cheapness of genomic sequencing I doubt you’ll see a Microsoft or Intel of this industry attempting to be all things to all people; rather many boutiques will cater to the diverse clientele. After all, it is personalized genomics.

In any case, here’s an interesting bit:

Direct-to-consumer companies are sometimes accused of peddling “recreational genetics,” and there’s no denying the horoscopelike fascination of learning about genes that predict your traits. Who wouldn’t be flattered to learn that he has two genes associated with higher I.Q. and one linked to a taste for novelty? It is also strangely validating to learn that I have genes for traits that I already know I have, like light skin and blue eyes. Then there are the genes for traits that seem plausible enough but make the wrong prediction about how I live my life, like my genes for tasting the bitterness in broccoli, beer and brussels sprouts (I consume them all), for lactose-intolerance (I seem to tolerate ice cream just fine) and for fast-twitch muscle fibers (I prefer hiking and cycling to basketball and squash). I also have genes that are nothing to brag about (like average memory performance and lower efficiency at learning from errors), ones whose meanings are a bit baffling (like a gene that gives me “typical odds” for having red hair, which I don’t have), and ones whose predictions are flat-out wrong (like a high risk of baldness).

Like “portable phones” in the 1980s we live in the age of novelty and play. In the future we’ll live in the age of ubiquitous utility. Between now and then should be interesting.

Comments

  1. #1 hibob
    January 12, 2009

    The other comparison to the 1980s that comes to my mind is Betamax, specifically the 1984 supreme court case that ended up ruling that VCR manufacturers aren’t liable for copyright infringement so long as the VCRS are also being used for non-infringing purposes. That to me spells a possible end to high prices for patented genetic tests. I don’t think KNOWME is allowed to tell you which BRCA1, etc, alleles you have and your corresponding risk for breast cancer: Myriad wouldn’t license them to do so. Ditto for other patented genetic tests. But there’s nothing Myriad can do to keep a company from handing you your own raw DNA sequence, and nothing they can do to keep you from finding out the answer your own. Granted, that would be a daunting task for 99% of people right now, but if genomic sequencing becomes at all common, people will be writing and releasing software on the web that score the tests for free in short order.
    It’s also an end run around labs being certified to perform medical tests.

  2. #2 SNPperson
    January 13, 2009

    One effort that Stephen Pinker refers to – but not by name – is the one (SNPedia) that complements the commercial companies you mention, in being a wiki that solicits information from researchers, patients, counselors, and other interested parties, and keeps evolving as interests (and data) evolve.

    Today it may lack the ‘bright colors’ of the 23etAl companies, but like hibob predicts, SNPedia already has free companion software, Promethease, that takes a customer’s data, as provided by any of these companies, and creates a comprehensive e-report linking all reported risks back to the references within SNPedia.

    As Stephen Pinker realizes, this gives anyone the ability to get a second opinion (or just lots of new information and, admittedly, complexity) compared to the more simplistic story they are typically told (sold?) by any given company generating some DNA data and then being highly selective, for better or for worse, in choosing what to report back to their paying customer.

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