Genetic Future

The importance of confusion

i-122e0f8613209737c301d1d404f60b79-pinker_mugshot.jpgSteven Pinker’s recent article in the NY Times is a rich source of insight into the field of personal genomics and the experience of personal genomics customers – if you haven’t read it already, you really should.

This paragraph, for instance, seems to perfectly encapsulate the experience of the average intellectually curious personal genomics customer:


It became all the more confusing when I browsed for genes beyond those on the summary page. Both the P.G.P. and the genome browser turned up studies that linked various of my genes to an elevated risk of prostate cancer, deflating my initial relief at the lowered risk. Assessing risks from genomic data is not like using a pregnancy-test kit with its bright blue line. It’s more like writing a term paper on a topic with a huge and chaotic research literature. You are whipsawed by contradictory studies with different sample sizes, ages, sexes, ethnicities, selection criteria and levels of statistical significance. Geneticists working for 23andMe sift through the journals and make their best judgments of which associations are solid. But these judgments are necessarily subjective, and they can quickly become obsolete now that cheap genotyping techniques have opened the floodgates to new studies. [my emphasis]

I specify “intellectually curious” because there are probably some personal genomics customers out there who simply accept the risk predictions they get from 23andMe or deCODEme without much further introspection, but I’d guess such users are in a substantial minority. Given the type of person who is likely to fork out money for a genome scan, I suspect most customers end up doing some digging into their data – and when they do, they are inevitably faced with the same tangle of paradoxes and contradictions as Pinker was.

This confusion arises not because of poor judgement on the part of 23andMe’s geneticists, but rather because our current understanding of the genetic basis of most commonly variable human traits and complex diseases is still incredibly primitive. Despite the hundreds of associations between common variants and complex diseases like type 2 diabetes identified over the last two years, the risk predictions available for most (but not all) of these diseases are currently barely better than noise. That means that current risk predictions can vary considerably between companies, and from the same company over time, due to changes in prediction algorithms and the addition of newly-discovered risk variants.

This situation is temporary – over the next decade, as our knowledge of the molecular basis of complex diseases grows, personal genomics customers will see their risk predictions continue to fluctuate before slowly converging on some true level of genetic risk. If personal genomics can be successfully combined with high-resolution data on environmental risk factors, we will then be looking at predictions with substantial clinical and preventive utility.

OK, so personal genomics will be fantastic in ten years’ time – what about now? Does the meagre predictive value of current genomic disease risk predictions mean that people buying a genome scan right now are wasting their money? I’d argue not, for several reasons.

Firstly, there are several complex traits and diseases for which current gene-based predictions are useful: for instance, the APOE variant associated with late onset Alzheimer’s disease (which Pinker deliberately excluded from his own analysis, saying he didn’t need a boost to his “current burden of existential dread”), or the genes associated with age-related macular degeneration. If it’s ominous news you’re after, you can still luck out with current genome scans.

In addition, the variants assayed by personal genomics companies provide surprisingly powerful information about genetic ancestry, a topic of considerable interest to an extremely large audience (although it must be said that personal genomics companies are yet to exploit this information to anywhere near its full potential). While we wait for the genetic underpinnings of most complex diseases to be unravelled, ancestry can even provide rough surrogate information about genetic risk due to variation in disease risk between human populations – a particularly useful service to those who currently know little about their own deep origins (such as some adoptees).

But perhaps the most valuable contribution of personal genomic data stems, perversely, from the confusion itself: the sheer complexity and uncertainty of the data encourages customers to explore the complex interface between genetics and health for themselves. Few experiences could strike as heavy a blow against someone’s intuitive notion of genetic determinism as looking through a list of probabilities in 23andMe’s risk report. In the quote above, Pinker memorably describes the experience as akin to “writing a term paper on a topic with a huge and chaotic research literature” – a frustrating experience that few people would volunteer to perform unless, as in this case, the subject was themselves.

To use an analogy: personal genomics provides a distorted and fragmented mirror, and in the process of peering around to catch a glimpse of our own faces we instinctively learn about the flawed topology of the mirror even as we learn about ourselves. In more prosaic terms, every customer of a reputable personal genomics company is one less person who will fall for the next simplistic “gene for erectile dysfunction” story peddled by their local newspaper, or believe the absurd claims from DNA Dynasty and its ilk.

My point is that whatever the long-term health impact of the genomic revolution, the creation of a community of well-informed, genetically literate individuals will be a lasting legacy of the personal genomics industry. Hell, even if it turns out that the genetic architecture of most human traits is just too complex to ever make accurate health predictions, at least we’ll have a broader community of people who understand that this is the case.

Pinker’s own assessment of the future of the personal genomics industry is lalso optimistic:

Personal genomics is here to stay. The science will improve as efforts like the Personal Genome Project amass huge samples, the price of sequencing sinks and biologists come to a better understanding of what genes do and why they vary. People who have grown up with the democratization of information will not tolerate paternalistic regulations that keep them from their own genomes, and early adopters will explore how this new information can best be used to manage our health. There are risks of misunderstandings, but there are also risks in much of the flimflam we tolerate in alternative medicine, and in the hunches and folklore that many doctors prefer to evidence-based medicine. And besides, personal genomics is just too much fun. [emphasis in original]

The key, of course, will be ensuring that personal genomics companies continue to provide information that is accurate and sensibly portrayed. Regulators will have a role to play there, although it’s likely to be a clumsy and heavy-handed one. More importantly, I suspect, will be the policing provided by the community of personal genomics customers: by sharing information, highlighting contradictions and generally questioning everything they hear, they are likely to be a far more effective regulator than government agencies could ever be.

Such policing won’t do away with confusion – confusion is simply a fundamental feature of the world of human genetics circa 2009 – but at least it will ensure that this confusion is conveyed accurately to consumers, in all of its deep, messy, incomplete, paradoxical and tantalising glory.

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Comments

  1. #1 Steven Murphy MD
    January 12, 2009

    Daniel,
    Literacy. Truly important, but even more important is what you read and understand. I wonder if the “slack jawed” people you talk about as giving blind acceptance of DTC genomics results is less common than those “eager beavers” who read and learn about genomics……If the public is anything like high school, my guess is we will have a whole lot of DNA crib notes users out there…..To quote Caddyshack “The world needs ditch diggers Danny”

    I wouldn’t go out on a limb and say that this DTC phase will introduce a new genomically literate class. Especially when nearly half of the American public is health illiterate……Even doctors can’t get this stuff..

    Just my opinion as a genetics educator……

    -Steve
    http://www.thegenesherpa.blogspot.com

  2. #2 Mike
    January 12, 2009

    I agree with the Gene Sherpa. I’m worried that, if the DTC genetics industry gets stuffed with “bottom feeders” (as Pinker calls them), it will harm genetic literacy.

    Somebody’s got to the educating, and it’s not going to be companies whose profits depend on confused consumers buying into a non-predictive genetic test.

    If I were 23andMe, I would be pushing hard for regulation to make sure that the dubious companies are kept out of the business.

  3. #3 razib
    January 12, 2009

    great picture.

  4. #4 Daniel MacArthur
    January 13, 2009

    Steve,

    This obviously isn’t going to have a direct impact on the majority of people, who are either uninterested in such complex topics, unable to understand them, or simply lack the disposable income to afford personal genomics. Still, I don’t think there’s any question that people who do engage in personal genomics end up osmosing some level of genetic literacy as a result; and I’d argue that there will be more indirect, trickle-down effects on the rest of society.

    In terms of indirect effects, just take a look at the number of popular articles in widely-read mainstream media (NY Times etc.) that have been spawned by the personal genomics industry. How many people out there now know what a SNP is, or that complex diseases are due to more than one gene, thanks to those articles?

  5. #5 Daniel MacArthur
    January 13, 2009

    Mike,

    I’m concerned about the bottom-feeders too, which is really the purpose of my second-last paragraph. I think we as bloggers can play a major role here. For instance, try a Google search for “gene essence”, a classic personal genomics bottom-feeder, and you’ll find my post rubbishing their absurdly sub-standard service in the top 5 hits. Most potential customers are likely to try a few quick searches before they fork out hundreds of dollars for a product, and very few will click “Purchase” after reading a post like that.

    I’m sure 23andMe would love to see careful regulation that elbows out the bottom-feeders without affecting high-end services (I described this as the best-case outcome during the regulatory scuffle in California last June), but regulatory bodies do have a habit of over-reacting. I’ll be surprised if the impending regulatory crackdown is anywhere near as surgical and benign as this.

  6. #6 Dan
    January 14, 2009

    I couldn’t agree more Daniel. I think the beauty of Pinker’s article, reflected in your post, is that it drives home the point that the sequencing of one’s genome is not now – and with a near certainty will never, ever be – tantamount to predicting one’s future, or even to gaining access to a “blueprint” of oneself. Whatever issue you may take with the details or analogies that he uses, I think that Steve Pinker, the great popularizer, drives home that particular point with resounding success.

    And I also agree that, whatever DTC consumers, PGP participants or anybody else that is exposed to the “distorted and fragmented mirror” of personal genomics does or does not get out of the process, it’s impossible to leave it without a greater appreciation for the complexity of it all. There’s no way that can’t move somebody past the “Researchers discover the gene for _____” form of genetic knowledge.

    Great post. Thanks.

    - Dan

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