Monday, January 14, 2008

Promethease deCodes 23andMe

Promethease annotates your genome using SNPedia.

It is possible thanks to the Personal Genome Explorer which allows 23andMe customers to export all of their 550,000 genotypes. Promethease reads this export format, and uses it to generate sample reports.

Your genotypes will probably be a bit more boring, since these random files get some pretty weird diseases. The report format isn't yet as intuitive as it should be, but you'll manage.

Your changes to SNPedia will appear in future reports. To generate a report simply drop an export file onto promethease.exe . From the DOS command line you can compare to other hapmap populations, instead of the default CEU. Runtime is about 2 hours. It doesn't eat much of your net or cpu, it just moves slowly to be courteous to others.

PGE does not yet provide information to orient snps relative to dbsnp. As a result many of the genotypes are flipped. This causes Promethease to ignore population frequencies. These SNPs will show with a 'None' along their left side.