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Tuesday, June 14, 2011

Interpretome: online genome analysis

This is an awesome idea. Basically, you analyze your 23andMe raw data with a variety of tools, without actually having to send it anywhere. Unfortunately, it's still a bit buggy in places, but I'm sure all of that will be sorted out eventually. Included is an ancestry chromosome "painting", with some very cool advanced options. I'm told that this is the most experimental feature on the site at the moment. But I checked it, and it does appear accurate at the most basic settings, using the HapMap 2 references.


For me, the really interesting tool is the Principal Component Analysis (PCA) plot featuring the European POPRES dataset. Initially, I got some funny results using PC1 v. PC2. However, here's the advice I got from Interpretome team member Konrad Karczewski: "For the POPRES PCA with (23andMe) v2, please use the 43,000 SNPs option, plotting PC1 vs. PC4. The map is then rotated 90 degrees and mirrored, but if you use your imagination, you'll get the map of Europe back." Fair enough, although based on my ancestry and PCA-MDS plots elsewhere, I would've expected to be closer to the center of the Polish cluster.

In any case, this is a fantastic initiative. Obviously it's a work in progress, so one needs to keep that in mind and not take all the results too literally at this stage. However, I'll be checking back regularly to see how things are looking.