23andMe and SNPedia

In my last post about 23andMe, I mentioned that there didn’t seem to be a central place where one could look up diseases and the SNPs associated with them. In the comments, I was pointed to SNPedia.com, a wiki that aims to do exactly that. It’s fairly basic at this point, but it does have a decent amount of information on 69 different diseases and traits.
I’m interested in Alzheimer’s Disease (AD), and SNPedia has a lot of information on the SNPs that have been associated with that disease. For example, Rs4420638 (SNPs are referred to by these RS numbers), has been associated with an increased risk of late-onset AD. Looking at the SNPedia page for this SNP, you can see that specifically it’s when this SNP is GG does one have the increased risk for AD. This is exactly the information I should be able to use with the data that 23andMe has on my genotype. So I took the Rs4420638 number and plugged it into the Genome Explorer of 23andMe. But here is one of the two problems I’ve run into with 23andMe. There’s no data on this SNP because this is not one of the 600,000 SNPs that 23andMe has sequenced. The technology doesn’t yet exist to sequence an entire genome cheaply, so 23andMe has chosen to do a subset, as represented by 600,000 SNPs. To be fair to 23andMe, they have always been up front about this.
In addition to an incomplete list of SNPs, some of the SNPs that 23andMe does try to sequence don’t result in valid data. This manifests as a No Call indicator when looking up an affected SNP. According to the web site, the chip that 23andMe uses results in a 99% call rate, meaning that 99% of the SNPs sequenced should yield valid results. I haven’t been able to verify this with my data, as there doesn’t appear to be a way to export my entire data set yet. But I did run into the No Call indicator when looking up another SNP related to AD, Rs7412. Interestingly, I talked with another person who also went through the 23andMe process, and their Rs7412 SNP was also marked as No Call.
These two issues do limit the value of the results. I look forward to the day when full genome sequencing is cheap and reliable. Im going to continue to play with my results and I’ll post more if I find out more.

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