News from around the web.
Go to Source
Daniel MacArthur tweeted this morning about “Interpretome,” which is browser-based software that can be used to examine autosomal testing results from 23andMe and Lumigenix. There is also an interesting blog post about the software at the blog of Konrad J. Karczewski, one of the co-creators of the software, and one by Daniel at Genomes Unzipped.
Users load their raw data files, and then can use that information to explore their genome. There are a number of different exercises that a user can run through with their data, including health issues (diabetes, warfarin sensitivity, many other diseases, etc.), ancestry analyses, and determination of “Neanderthal SNPs,” which are SNPs that have been suggested to derive from Neanderthal ancestry (note that this science is still VERY early stage and subject to change OFTEN!).
There are two very features that I find very interesting. First, there is an “Advanced Settings” tab where users can make several important adjustments to their analysis. Second, the site allows for “imputation” when looking up a SNP, which means that “If the SNP is not found in your file, the utility attempts to impute the SNP using Hapmap data.“ I haven’t tried this yet, but it will be interesting to see how well it works.
Interpretome allows users to create, among other things, an “Ancestry Painting” using either HapMap2 or HapMap3 data. For example, using the HapMap2 data, my Interpretome ancestry painting is very similar to my 23andMe ancestry painting. For those who aren’t familiar, here are the HapMap2 populations (HapMap3 can be found here):
YRI (Ibadan, Nigeria)
CEU (Northern/western Europe)
CHB+JPT (Beijing, China and Tokyo, Japan)
Medically-Relevant Information and Privacy Issues
The creators of Interpretome do address several issues, including the medical information controversy:
No information should be considered diagnostic and as with any genetic testing service, the interpretation is not regulated by the FDA.
And the important privacy issue:
Your genome will not be sent to any server, it remains on your computer. This website will make requests to a database that only contain “rsid” (without genotypes) and “population” (self-reported in the top-right) information. At no point will any genotypes be sent across the wires (all computation will be done in the browser).
However, the creators do go on to note that some exercises have the option of submitting personal information, which “will be anonymously stored on a secure server.” So be cautious if you’re worried about privacy, as with any testing or analysis service. As my genome is public domain, I’m not concerned.
Family Tree DNA Results?
For fun, I also tried my Family Tree DNA results. Since FTDNA raw data results do not contain most, if any, medically-relevant SNPs, most of the “exercises” were fruitless. I did have some luck with the ancestry sections, although I have yet to compare my 23andMe analysis with my FTNDA analysis to determine if there is consistency.