Friday, May 8, 2009


Today, for the first time in more than two weeks, I have some time to spend on this page. These last few days, I’ve dedicated myself full-time to writing and publishing news stories in PÚBLICO about other genes – namely, those the new flu virus.

It’s amazing how such a tiny genome as that, made of just a few genes, can be so hard to dissect and comprehend. But in fact, it’s fairly easy to understand why: the virus changes from one person to another – and to find out, for instance, where it came from, you have to construct its genetic evolution tree taking into account an ever-growing number of infected people. It’s is a different kind of “personal genomics” - but one which becomes extremely important in pre-pandemic circumstances such as those we are experiencing right now.

Let’s go back to my genes. The Spittoon, 23andme’s blog, which I have already mentioned, includes in its SNPWatch section very up-to-date reports on studies involving (reduced or increased) genetic risks links to disease as they are published in the major scientific journals around the world. Here is some of the more momentous “spittle” of the last weeks – which I have of course been comparing to the raw data from my own DNA.

These potential relationships between a given point mutation (or SNP) and a given disease haven’t been confirmed – and for the most part, they only represent slight deviations from the normal risk level for the general population. Nevertheless, they can give you an idea of the feeling you get when it’s not just some anonymous person’s SNPs you’re looking at – but your very own. Some excerpts from SNPWatch:

1 – New England Journal of Medicine (April 15)
Combined analysis of data from Caucasian study participants from the United States and the Netherlands revealed that the A version of [the SNP bearing the code name] rs12425791 is associated with a 1.29 times increased risk of ischemic stroke.

At the end of the article there’s a direct link to the pair of DNA “letters”, or bases (one inherited from my mother and the other from my father) that make up my own rs12425791 SNP. I click on the link, and go directly to my data at that position. They turn out to be: AG.

2– Nature (SNPWatch, April 28)
[The team] found several SNPs associated with autism. All were located in a region of DNA between two genes, CDH9 and CDH10, which encode proteins called cadherins. “These molecules are expressed on the cell surfaces of neurons, and they are involved with shaping both the physical structure of the developing brain and the functional connections among different brain regions. Although a particular gene variant may contribute a small risk for an ASD [Autism Spectrum Disorders] in a particular individual, we estimate that the variants we discovered may contribute to as many as 15 percent of ASD cases in a population,” said [one of the team members] in a statement. The strongest signal came from rs4307059 — compared to two copies of a C, each copy of the more common T version increased the odds of autism by 1.19 times.

My own rs4307059: CT. (For those who are wondering what I might conclude from this: I decided that any “autistic spectrum” personality traits I might have in real life I will only share with my image in the mirror.)

3 – Archives of Ophthalmology (April 14)
The researchers found that one SNP in the TGF-β1 gene in particular was associated with high myopia [-8.00 diopters or worse]. Each A at rs4803455 decreased the odds of developing the condition by 0.67 times.

My own rs4803455: AA (Doubly reduced risk? You don’t say! It seems that I don’t qualify for what they consider “high myopia” in the study, since I don’t quite make it to minus 8 diopters, but I’m pretty close to it. So I don’t give much credence to this result.)

4 – Journal of the American Society of Nephrology (May 1)Researchers studied 260 people who had had bypass surgery and found that those who carried an A at both copies of rs4680 went into shock more often compared to those with other genotypes (69% vs. 57% in AG people and 46.6% in GG people). (...) Prolonged shock, lasting more than 48 hours, was also more frequent in people with two As (25% vs. 13% for AG and 6.8% for GG). (...) people with two As at rs4680 also had greater frequency of acute kidney injury. The median hospital stay after bypass surgery was longer for people with two As at rs4680: nine days vs. eight days for AG and seven days for GG.

My own rs4680: AG (Right in the mid-range; could spell trouble, I suppose.)

(Main image credit: net_efekt/Flickr)

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