SPA

Spatial Ancestry analysis (SPA) is a method for predicting ancestry or where an individual is from using the individual's DNA. Accurately modeling ancestry is an important step in identifying genetic variation involved in disease.

SPA was created by Wen-Yun Yang, John Novembre, Eleazar Eskin and Eran Halperin

For general questions, comments or suggestions about SPA, please email Eleazar Eskin (eeskin (AT) cs.ucla.edu).

How to analyze your origin using SPA?

SPA can predict the ancestral origins for 23andMe users with genotype file. Let's assume that you have an account with 23andMe. Then you can follow the below steps to get your prediction.

Download your genotype file from 23andme

1. In the Account tab in the top right corner, select Browse Raw Data

2. Click on download raw data

3. Type in your password and secret answer and then click on Download Data

4. A download should then start. When it is finished, click on the downloaded file to unzip the file.

5. The uncompressed file (ending with a .txt) contains the DNA information which is ready to be analyzed.

Analyze your origin using SPA

1. Download SPA software.

2. Download the models for world and europe and decompress them.

3. Put your 23andMe genotype file into the same directory as the above two.

4. Open a terminal if you are using Mac OS X, or a command window if you are using Windows.

5. Go to the directory where you put SPA software, models and 23andMe genotype file.

6. Run the following command in your terminal or command window. Make sure to replace 23andMe.txt with your 23andMe genotype file name.

7. Double click the resulting world.loc.html or europe.loc.html to check where your ancestral origin is. Note that if you are European population, you only need to check europe.loc.html for a better resolution and if you are non-European population, you only need to check world.loc.html

8. SPA can also predict two origins in the case that your mother and father are from different locations. In order to do that, use the versions of the command lines that include -n 2 below.

./spa --mfile 23andMe.txt --model-input world.model --location-output world.loc
./spa --mfile 23andMe.txt --model-input europe.model --location-output europe.loc
./spa --mfile 23andMe.txt --model-input world.model --location-output world.loc -n 2
./spa --mfile 23andMe.txt --model-input europe.model --location-output europe.loc -n 2
(use spa.exe instead of ./spa if you are using Microsoft Windows)

Enjoy SPA prediction of your ancestral origins. An example output is as follows