Genomics Blog

August 7, 2008 7:00 AM
Mike's Genotyping Update
Filed Under: Mikenomics

I've used Promethease to update my 23andMe and deCODE analyses.
For those who haven't really been following the blog (or forgot where we were in the gap since my earlier posts! ) Promethease is a piece of software created by Greg Lennon and Mike Carioso. You can use it to take the raw data file that 23andMe or deCODE make available to and analyse it to produce results that go beyond the summary report the companies offer. A data file of a million lines or so is not something you want to go through manually and you still need the information for each SNP to figure out what it means. As Mike Carioso put it "I knew 500,000 facts about myself, but had no idea about their implications".
Apart from the software to look at all the information you also need a reliable and consistent database of information so he was also instrumental in developing SNPedia.

Like a wiki, SNPedia relies on the science and research community at large to add information and make the database more useful. The database currently has more that 3200 SNPs in it. The folks running the site apply some rigour in choosing the SNPs to add and use peer-reviewed journals as one of the criteria so the data should be reliable.
Promethease is currently at version 0.1.24 and SNPedia is constantly being updated so if you have had a personal genotyping done it isn't a matter of using the database and software once and letting it go at that.

Mike sees the software and the database as having something for researchers and for the 'recreational' user who wants to find out more. I'd probably add that it is an important step in the broad public understanding of genomics. SNPedia has enough general information on it to give yourself a bit of an education and anyone who has, or is thinking of having a direct-to-consumer test done should check it out. It offers enough of the basics to let you draw your own conclusions, enter into some discussions with other users and more importantly help build a bridge between the publics and the medical research community. 

You can also download my latest deCODE genotyping summary as the company provides it. Far less information than what you glean from the Promethease data but a more consumer friendly run down in plain English and based on what deCODE sees as the most reliable information.


Tammy Grady -

That's fascinating Mike! Thanks for sharing it with us.

Wanderer -

Well at least you will not have to worry about prostate cancer =)

Mike Spear -

Well I'll assume that part is right. One of the 2 tests said I should be well into Male Pattern Baldness but I still have my hippie era head of hair.

It is a roll of the dice on some of the probabilities so I'll hope on the problematic markers that it rolls in my direction.


John -

Hey Mike, are there any alternatives to promethease that does similar job? More info than it does? I am looking for databases that I can use to compare my genotyping info to get risk information for diseases.

URL (remove the http://)
Do you have human DNA?*