MY SNPedia REPORT

Services like 23andMe and deCODEme test for hundreds of thousands of SNPs (genetic datapoints). Yet, these services only attempt to interpret less than 100 traits in their web reports. [1]

Fortunately, these services allow you to download the raw data from your test to be interpreted elsewhere.

For example, recently Mike Cariaso “creatively profiled” Lilly Mendel (23andMe’s female demo user) using the public SNPedia database and Promethease software to win the 23andMe Win Your Genome Contest.

• Lilly Mendel’s Promethease Report
• SNPedia (wikipedia-like public database for the human genome)
  
• Promethease Home

These tools are not yet user friendly, and they certainly exist beyond the general consumer. However, I purchased a 23andMe test a couple months ago, and as a power user, I wanted ALL the data. Yes, I know that the research is new, the interpretations can be highly speculative, and 23andMe is making a laudable effort to make the best research accessible. But hey, I spent $1000; I want to know everything. Further, while these services do not report many high-penetrance genes like BRCA (breast cancer) for legal reasons [2], some of that information is in the raw test data “for your own interpretation.”

If 23andMe is the Apple I of genomics, this is the box of parts for garage assembly. Enjoy!

How To Use SNPedia for 23andMe and deCODEme

1) Get Data

Download your test results. If you do not have a 23andMe or deCODEme account, you may download a sample dataset from 23andMe’s trial users. (deCODEme’s trial user does not yet support data download)

Download Lilly Mendel’s raw data from ThinkGene

23andMe:

1. Login (either as your account or as a Mendel trial user)
2. Go to “Browse Raw Data” in the left menu
3. Click “download raw data” link at the top right of the “browse raw data” page
4. Enter password, secret question, select profile, and click “Download Data”
5. The download will be about a 2MB zipped text file.

Here is what raw 23andMe data looks like from my genome:

# rsid       chromosome    position    genotype
rs3094315    1             742429      AA
rs12562034   1             758311      GG
rs3934834    1             995669      CC
rs9442372    1             1008567     AA
rs3737728    1             1011278     AG
rs11260588   1             1011521     GG
rs6687776    1             1020428     CC
rs9651273    1             1021403     AG
rs4970405    1             1038818     AA
rs12726255   1             1039813     AA
rs11807848   1             1051029     CT
rs9442373    1             1052501     CC
...

and so on for over 570,000 lines.

Raw deCODEme data looks like this:

Name,Variation,Chromosome,Position,Strand,YourCode
rs2278544,A/G,2,136262580,+,AG
rs4954633,C/T,2,136263105,+,CC
rs3213890,A/G,2,136268658,+,AG
rs1807356,A/G,2,136271954,-,AA
rs2015532,A/C,2,136271995,-,AC
rs2322659,C/T,2,136272129,+,CT
rs3769013,A/G,2,136272652,-,AG
rs2304371,C/T,2,136278027,-,CT
rs2304370,C/T,2,136278205,-,CT
rs3739022,C/T,2,136278942,-,CC
rs12988076,A/C,2,136286318,+,AC
rs6719488,G/T,2,136291669,+,GT
...

and so on for over 1,000,000 lines.

2) Get Software

Download Promethease (windows only, version 0.1.14) from SNPepida. Also, see Promethease’s homepage.

3) Run Software

Launch Promethease and select your data file. Select your race. Begin Analysis. Note that Promethease automatically detects which service generated your SNP data.

WARNING: generating a report with Promethease may take hours. If there is demand (and time), I’ll write / help write better Open SNP software. Please contact me if this interests you.

4) View Report

MY REPORT: Andrew Yates’s SNPedia report via Promethease [3]

Promethease outputs a final report of about SNP 1300 entries as an HTML file to your desktop. It’s not pretty or easy to read —let alone understand as actionable medical information. But this is the best that Open SNP software has to offer today.

See Interpreting Promethease / SNPedia Results for help understanding your Promethease report.

5) Report Reflection

While my SNPedia report contained more information about my SNPs, I didn’t learn anything worth knowing that 23andMe (or deCODEme) didn’t already tell me. Further, running and understanding my “open SNP” report, while interesting, took hours. While much potential exists for community efforts to understand our genome, SNPedia is not yet ready for the majority of genetics enthusiasts, let alone the general public.

Notes

[1] 23andMe and deCODEme officially report less than one hundred traits, plus ancestry. 23andMe tests for about 500,000 SNPs; deCODE tests for about 1,000,000. However, the useful information in both tests is about the same (for now).

[2] The industry line is that users shouldn’t know about some high-penetrance genes for reasons including “it’s for your own good” and “high penetrance genes are not common enough,” but the real reason is that these genes are defended by walls of patents, expensive licenses, and litigious companies. See “Low penetrance genes v high penetrance genes”

[3] At first, I was leery about posting my genome online, but then I realized: hey, if I’m ever discriminated against (and I can easily check my server logs to see who has viewed my genome report), maybe I’ll get to participate in a landmark judicial case!