Personal genomics: more than fun & games

By Razib Khan | November 10, 2011 11:48 am

My main current interest in personal genomics right now is pure recreation. I don’t expect much utility out of it, because a lot of correlations between genes (SNPs, etc. ) and traits/diseases are rather weak. But there are some exceptions. Recently I was temporarily put on a prescription medication and I wanted to check if I was a fast or slow metabolizer. The material you see in the medical literature is that Europeans tend to be slow metabolizers, while Asians tend to be fast metabolizers. Since I’m Asian, I’m probably a fast metabolizer, right? Not so fast! Though I’m geographically Asian (my family hails from Asia), in terms of ancestry South Asians tend to be closer to Europeans, though with some affinity to East Eurasian populations as well. But another issue for me is that I clearly have 10-15% more recent East Asian ancestry, which is not typical in South Asians. In other words, I can’t infer with any confidence from generalizations about Asians and Europeans in the American medical literature to my personal status.

 

But that’s OK. It turns out that one locus determines most of the effect of this trait, and that locus has been genotyped in 23andMe. Using Promethease I ran my genotype, and it concluded I was a slow metabolizer. This has some utility in terms of when I take my medication. And it’s the first time that I can think of 23andMe giving me “actionable” information.

More broadly I realized that this sort of genotyping service is particularly useful for those of us who fall between the European/East Asian/African categories used in much of the American medical literature. The main concern is that genetic background might matter. That is, a SNP or set of makers correlated with a disease or trait in one population may not be correlated in another population. But this concern is less of an issue for me now after the past few years. Though some different risk alleles are being found across populations, by and large they’re pretty portable. Though the utility of this service for South Asians is obvious, in the American context it will probably be most useful to mixed-race Latinos, who are going to segregate out in traits at large effect loci between their parental populations (if those traits do differ).

CATEGORIZED UNDER: Genomics, Health, Personal Genomics
MORE ABOUT: Personal genomics
  • Justin Loe

    Incidentally, there’s another company, Genelex, that specifically tests for genes related to drug metabolism. Their advantage is that they provide a detailed report on each gene and its drug-related pathways that is more comprehensive than 23andme or snpedia. (I don’t have stock in Genelex).

  • Roger Bigod

    Is it a gene for a cytochrome P450? I suspect some of them reflect long residence in environments with different toxins. The genetics are complicated enough that it may take a long time to work out the details.

    There’s a theory that Parkinson’s is due to chronic exposure to low-level toxins like house fungus.

  • Cindy

    Roger: There are dozens of cytochrome P450 genes (Such as CYP2C19, CYP2D6, CYP1B1, etc.)

    In response to this article, I disagree about there being a lack of correlation between genetic variants and phenotypes – I would say we have over 3 decades of clear cause of mutations associated with monogenic diseases and over 15 years of associations studies for polygenic and multifactorial diseases.

    Check this out – Existence Genetics is now providing a Rare Disease Screen of over 1,000 rare monogenic phenotypes at a single time for $299, all based upon very established studies. And this is in-addition to the multifactorial disease assessments they offer. http://www.existencegenetics.com/rarediseasescreen.php

    For me, the value in genetic testing has always been disease prevention, not recreation, although I do understand that for some people the recreational part is fun. But the true value I see in personal genomics is in disease prevention.

  • http://www.wired.com/wiredscience/neuronculture David Dobbs

    I just ordered my 23andme. I think one of the beauties of this is that people do this for recreation — but it’s creating this huge genomic database.

  • Sandgroper

    Just offhand, does anyone know why 23andme don’t ship to anywhere in E, S or SE Asia except Singapore?

    I have been trying to find a way to ask them directly but so far can’t find a convenient way. Plus if I get a ‘corporate’ reply I might miss the nuances due to cultural factors. I’m not looking to make a federal case out of it, I just want to know.

    It seems kind of odd, for example, that they ship to Azerbaijan, but not say Thailand or Malaysia.

    And nowhere in Africa either that I can see.

    It’s likely to mean they are creating a huge genomic database with big gaping holes in it.

  • Sandgroper
  • Douglas Knight

    Is there any example of pharmacogenetics that is not about rate of metabolizing the drug?

    Why not directly measure serum levels? This would catch unknown genetic variation in metabolism rates, interaction with other drugs, etc.

  • Onur

    23andMe has an idiotic shipping policy. They lack the mentality and sense of responsibility that have to be found in a company of international personal genomics. They are too profit-oriented rather than scientific-oriented.

    This is my observation of them after my long correspondence with them to learn the reasons behind their exclusion of most countries and most world regions from their services. They have no reason for that exclusion other than short-term profit.

  • Sandgroper

    Doesn’t add up.

    From what I have seen of them, they don’t strike me as a stupid or irresponsible company, or lacking in vision for what they could achieve.

    I don’t get the short term profit motive either – all they are doing is shipping off a sampler and getting some spit back. It doesn’t make a blind bit of difference where they ship to, as long as they get paid. Maybe that’s the concern.

    Hmmm, I wonder if they need a local agent…

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This blog is about evolution, genetics, genomics and their interstices. Please beware that comments are aggressively moderated. Uncivil or churlish comments will likely get you banned immediately, so make any contribution count!

About Razib Khan

I have degrees in biology and biochemistry, a passion for genetics, history, and philosophy, and shrimp is my favorite food. In relation to nationality I'm a American Northwesterner, in politics I'm a reactionary, and as for religion I have none (I'm an atheist). If you want to know more, see the links at http://www.razib.com

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