Testing for homogeneity of gametic disequilibrium across strata

Background: Assessing the non-random associations of alleles at different loci, or gametic disequilibrium, can provide clues about aspects of population histories and mating behavior and can be useful in locating disease genes. For gametic data which are available from several strata with different allele probabilities, it is necessary to verify that the strata are homogeneous in terms of gametic disequilibrium. Results: Using the likelihood score theory generalized to nuisance parameters we derive a score test for homogeneity of gametic disequilibrium across several independent populations. Simulation results demonstrate that the empirical type I error rates of our score homogeneity test perform satisfactorily in the sense that they are close to the pre-chosen 0.05 nominal level. The associated power and sample size formulae are derived. We illustrate our test with a data set from a study of the cystic fibrosis transmembrane conductance regulator gene. Conclusion: We propose a large-sample homogeneity test on gametic disequilibrium across several independent populations based on the likelihood score theory generalized to nuisance parameters. Our simulation results show that our test is more reliable than the traditional test based on the Fisher's test of homogeneity among correlation coefficients.