PSAT - Population Stratification Association Test 

Gad Kimmel (UC Berkeley and ICSI)
Michael Jordan (UC Berkeley)
Eran Halperin (ICSI)
Ron Shamir (Tel Aviv University)
Richard Karp (UC Berkeley and ICSI)

Population stratification can be a serious obstacle in the analysis of genome-wide association studies. We have developed a method for evaluating the significance of association scores in whole-genome cohorts with stratification. Our approach is a randomization test akin to a standard permutation test. It conditions on the genotype matrix and thus takes account not only of the population structure but also of the complex linkage disequilibrium structure of the genome. As we show in simulation experiments, our method achieves higher power and significantly better control over false positive rates than existing methods. In addition, it can be easily applied to whole genome association studies.

The method is implemented as a software called PSAT. To download PSAT see
A randomization test for controlling population stratification in whole-genome association studies
G. Kimmel, M.I. Jordan, E. Halperin, R. Shamir and R.M. Karp RM
American Journal of Human Genetics (2007) , Vol. 81 No. 5, 895-905 (2007)