Friday, November 18, 2011

Using Promethease

Last year 23andMe introduced a pricing model with a one year minimum subscription. I think it's a great service and will continue to pay my monthly fee to continue participating in the online discussions and get their updated analysis, but I'm sure a few people will decide updated genetic information is not in their budget this year. This post will show you how to keep getting new information about your genome for many years to come, with zero further expense.

To do this, you will need to download your raw data while your account is still in good standing. To begin, visit

After logging in, you will be presented with security questions such as these

23andMe security questions.

After a few moments your download will begin and you will receive a file named similar to Remember where you save it, once your subscription runs out you won't be able to get it again!

Now visit and download the latest version from the bottom of the page.

Run Promethease.

Here you can see the Windows and Mac versions side by side.

Screen shot 2011-11-19 at 6.46.14 PM

Click Next to move to the Genotype Files page.

Screen shot 2011-11-19 at 6.40.35 PM

Click on the Load button and then find your file from the beginning of this walk-through.

Screen shot 2011-11-19 at 6.42.40 PM

Then click Open to select your file. The filename will appear in the box.

Screen shot 2011-11-19 at 6.42.57 PM

Press Next to validate your file and move to the next screen. Along the way it will show how many genotypes are in your file. The number is probably just a bit below 1 million.

Screen shot 2011-11-19 at 6.43.09 PM

The next screen asks you to choose your Ethnicity. For many of us there is no perfect match, and that's fine. It has only a minor effect on the report that will be produced. This just shows some reference values for comparison to highlight how rare or common your genotypes are. Pick whatever seems closest and don't worry if it is rather distant from your true origins.

Screen shot 2011-11-19 at 6.43.26 PM

There are several more screens to go. You can just click Next on all of them until you get to the last one.

Screen shot 2011-11-19 at 4.42.39 PM Output Folder -- On this screen you choose where to store your completed analysis. You are specifying both the directory for all of the supporting files as well as the name for the top level report. The default values are based on your usual 'My Documents' folder and the name of your genotype file from the earlier step.

Screen shot 2011-11-19 at 7.23.14 PM Optional -- This screen allows registered commercial users of Promethease to identify themselves after their initial email to . But if you're just running Promethease for youself or familiy members and not charging you should just leave it blank and click Next.

Screen shot 2011-11-19 at 4.42.59 PM Payment -- Click this button to pay $2 and unlock extra features such as running much faster or predicting the genetics of your children based on your partner's genotype file. That also introduces extra screens which are fairly self explanatory, but not further discussed in this blog post.

Screen shot 2011-11-19 at 4.43.11 PM Promethease Wizard -- The last screen before the system begins your analysis. Just click Next to begin.

Screen shot 2011-11-19 at 4.43.21 PM Status -- Promethease has begun your analysis and will contact the central server to figure out what SNPedia knows about your genotypes. This will need approximately 4 hours to run.

Screen shot 2011-11-19 at 6.26.09 PM

After approximately 4 hours you will see text similar to the above. It should have launched your web browser and showed you the report which looks similar to this one. In the report click on ' more...' to drill deep into everything SNPedia knows about your data. Click on hyperlinks to be taken into SNPedia to see the full text, and find links to primary sources. As you learn more about your genome we hope you'll make edits to SNPedia and help teach all of us more. It's a big genome and we can't understand it without your help. We hope what we've learned so far is helpful to you. Rerun your report every few months to watch our growth and improved understanding.