These Are a Few of My Favorite SNPs

The author tries not to laugh.

We at 23andMe are often asked, what’s the most interesting thing you’ve learned from your awesome service? I love all 78 (and counting!) of our Gene Journal (now called Health and Traits) articles equally, but there are some I love a bit more equally.

Here’s my top six, with brief explanations of what makes them so cool. Keep in mind as you read them, however, that there are other things to life besides DNA (hard to believe, but true). Compared to genetics, your chances of getting diabetes, having a heart attack or developing a venous thromboembolism may depend just as much or more on what you eat, whether you exercise regularly or how often you find yourself flying coach from New York to Auckland.

Caffeine metabolism

Although still an unproven effect, caffeine consumption has been linked to heart attack risk in several studies. Recently, a study showed that this risk may hinge on your genetics. According to my genes, I am a slow caffeine metabolizer, which means I would probably be better off with decaf. However, this study is as of yet unreplicated by other researchers. How can we help push this important research along? With 23andWe, we can ask all our users about their coffee consumption, compare these responses with their genetic data, and see if the association holds up in the 23andMe community.

Type 2 diabetes

With nine SNPs known to affect risk and more to come, we may have more information about the genetics of type 2 diabetes than any other common disease. According to my data, I have a substantially increased risk of type 2 diabetes. In fact, in comparison to my family, I have the highest risk by far. If you are lucky enough to have some of your relatives genotyped, then check out Massie’s
recent post
on how to compare your results to theirs.

Venous thromboembolism

Venous thromboembolism is a serious disease that occurs when a blood clot that forms in a vein forms an embolism (blockage). One form, deep vein thrombosis, is also called “economy-class syndrome” because it is common after long airplane trips (stretch your legs!). Depending on your genes, you could be ten times or more at risk than the average person, making this one of the strongest genetic associations known. Like most people, I am fortunate to have no increased risk. But I’ll probably still stretch my legs just in case.

Malaria resistance

A mutation in the DARC gene confers resistance to the common P. vivax species of malaria. This mutation is very common in Africa, especially, as you’d expect, in places where malaria is common. As a European, I am unlikely to carry this mutation, but genes do travel, and they can pop up in unexpected places. As it turns out, I am not a carrier, which I could have probably guessed from my ancestry painting.

HIV/AIDS resistance

The story of the CCR5 delta 32 mutation is one of the most fascinating in genetics. The deletion in the gene actually breaks the molecule it produces, a receptor that common strains of HIV use to enter your cells. If both copies of the receptor are broken, then the virus has no way to enter the cell. People with a pair of delta 32 mutations are largely resistant to infection by the most common strain of HIV. Viruses are wily though, and rarer strains of HIV enter through other channels. For reasons we do not really understand, the deletion is common only in Northern Europe, especially Scandinavia. I have two working copies, but two of my siblings have only one copy. The pattern of inheritance shows that it comes from my father’s side of the family.

Antidepressant response

This year, a group from Germany discovered that one variant of the ABCB1 gene was much more likely to respond to certain drugs than the other, including several common antidepressants. My results suggest that I will probably not respond to any of several antidepressant drugs that are carried into the brain by the transporter P-gp. This result is so new that it still part of our preliminary research section, but the effect seen was profound.

Like many of our most interesting SNPs, this SNP is only on 23andMe’s custom panel — the set of 30,000 SNPs we chose to augment the standard Illumina 550K chip. We designed the custom panel to pick up interesting SNPs like this one that are rarely found on standard chips.

That covers some of the best stuff in 23andMe’s Gene Journal (now called Health and Traits) – at least as far as I’m concerned!

The number of traits and conditions we cover is growing all the time (we have added several every month so far), so we’ll no doubt write more on this soon.

  • Andro Hsu

    Maybe now you’ll start doing yoga!

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