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Tuesday, June 14, 2011

Interpretome -personal genome analysis webservice

David of Eurogenes blog and Zack of Harappa DNA project have posted a link to a  very promising  personal genome analysis webservice Interpretome.  The webservice has an extended set of online utilities useful for different types of analysis (imputation of missing SNPS in 23andme raw data file; clinical assesment of genetic risks; different types of the ancestry analysis, such as IBS, PCA and chromosome painting). However,  the coolest feature of this webservice is that webservice leverages data from various genetic diversity panels, such as HGDP, POPRES, and other data sources (below), which have generated genotype data from individuals around the world. For the individuals of European origin, the most informative genetic diversity  panel is The Population Reference Sample POPRES, whose controlled-access data can otherwise only be obtained if a user has been authorized by the appropriate Data Access Committee (DAC).
I, therefore, encourage all participants of the MDL project to analyze their ancestry using Intrepretome's ancestry online utilities. To get started, choose a reference panel onto which to project yourself and the number of SNPs to use for the projection. First, start with "HGDP: World" or "Hapmap: World" to explore your ancestry on a global population scale. For more detail in a specific region, choose the reference panel from the relevant population. If applicable, choose a level of detail for the results to be plotted.

For the POPRES dataset use 43,000 SNPs (23andme Raw data v2) or 74,000 SNPs (23andme Raw data v3). If you want to recapitulate the results of  paper Novembre J. Genes mirror geography within Europe. Nat 456:98 (2008), plot PC1 vs. PC4.


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