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It is well known that conventional association tests can lead to excessive false positives when there is population stratification. We propose a new test for detecting genetic association with a case-control study design. Unlike some other methods for handling population stratification, we treat the cases as a population and the controls as another one even though each of them may be a mixture of several sub-populations. A likelihood-ratio test is used to test whether the allele frequency of a testing single-nucleotide polymorphism in the case population is the same as that in the control population. This new test is applied to the Genetic Analysis Workshop 16 Problem 1 data on rheumatoid arthritis. Compared with the Pearson chi-square genotype test, the association strength of many single-nucleotide polymorphisms is decreased while the signal at the HLA region on 6p21 is maintained.

bmc proceedings

Accommodating population stratification in case-control association analysis: a new test and its application to genome-wide study on rheumatoid arthritis