23andMe, Alzheimer’s disease, and ApoE
January 12, 2008
Like other early 23andme customers, I’ve been struggling to find something interesting to do with my genetic results. After quickly learning [what kind of earwax](http://www.nytimes.com/2006/01/29/science/29cnd-ear.html) I’m predisposed to have, the path fades out amidst a tangle of SNPs.
Here’s an example of a typical quest, and its results.
It is well known that particular variants of the ApoE gene, which is found on chromosome 19, are associated with an [elevated risk of Alzheimer’s ](http://www.nia.nih.gov/Alzheimers/Publications/geneticsfs.htm)disease. Other variants are associated with reduced sensitivity to statins, which are commonly used to lower cholesterol in patients at risk for heart disease. [Lab Tests Online](http://www.labtestsonline.org/index.html) provides a good, brief description of how [genetic testing of the ApoE gene](http://www.labtestsonline.org/understanding/analytes/apoe/test.html) can be used in mainstream medical practice.
Reporting an upcoming Wired story on a different topic, I recently visited an M.D. outside Denver who takes an aggressive approach to longevity treatment, and found that he routinely orders ApoE tests for his patients, as part of a panel of 11 genetic markers that costs about $500. He told me that if I wanted just the ApoE results, I could get them for about $90.
But who needs to pay by the gene when you’ve got 23andme? More than 600,000 SNPs for $1000 bucks is awfully cheap compared to $90 for a single genetic test, or so it seems.
I began hunting around the Web. I quickly discovered that I was following in the footsteps of Mark Fletcher, also an [early 23andme adopter](http://www.wingedpig.com/archives/2007/12/23andme_results_266.html). When I read Fletcher’s entry, I knew I had found a fellow traveler. Like me, Fletcher immediately wrote to 23andme upon getting his results, asking if he could download them in a more convenient format for analysis. He got the same email back that I did:
> At this time 23andMe does not have a way to give customers their genetic data on a CD, flash drive or other downloadable or stored format. But we are working to make that possible, and hope to be able to distribute raw data to our customers in the near future.
> The 23andMe Team
There is of course something unconvincing about this answer. Having launched a company premised on giving consumers access to their genetic data, it is hard to believe that 23andme can’t manage to make this data available in a standard, easily downloadable format. But they are just beginning, so let’s cut them some slack. Besides, we are curious about ApoE.
Like Mark, I first consulted the great [SNPedia](http://www.snpedia.com/). Here, I learned that ApoE variants, known as alleles, are indicated by the following SNPs:
> ApoE2 allele = rs429358(T) + rs7412(T)
> ApoE3 allele = rs429358(T) + rs7412(C)
> ApoE4 allele = rs429358(C) + rs7412(C)
That’s just what I needed to know. I went to 23andme and entered rs429358 into the Genome Explorer. My results:
Then I entered the rs7412 into the Genome Explorer. My results:
According to SNPedia, another SNP, [Rs4420638,](http://www.snpedia.com/index.php?title=Rs4420638) is relevant to my quest. Says SNPedia:
> One form of this SNP is very commonly inherited together with the APOE variant ApoE4 and thus predicts its presence.
So I searched on Rs4420638. My results:
Mark went on a largely parallel journey, ending in similar [non-satisfaction](http://www.wingedpig.com/archives/2007/12/23andme_and_snpedia_267.html).
Mark Fletcher says he spoke to another 23andme user who had a no call at the Rs7412 location. Today I received an email from yet a fourth user who had a no call at this location, too. So far, 23andme is zero for four at this SNP.
Like many early adopters, my interest in sequencing my genome is driven more by intellectual curiosity than by pressing health reasons. So I’m hoping that George Church gets his [Personal Genome Project](http://www.technologyreview.com/BioTech/wtr_16169,259,p1.html) geared up quickly. I’ve registered to participate.
But for now, I’m looking for ways to make my 23andme results more relevant. I welcome suggestions.