Homogeneity across populations can also be evaluated using a stratified Cochran-Mantel-Haenszel analysis and testing for homogeneity of the odds ratio with the Breslow-Day test. In general, we expect the results to be similar to those obtained by our logistic regression analysis. In our dataset, the Breslow-Day test appeared slightly less sensitive and filtered out only two SNPs at an α of 0.05; the Breslow-Day p-value was 0.0092 for rs9788721, 0.0596 for rs8034191, and 0.0305 for rs10519203. We favor using the heterogeneity test within the logistic regression framework because it is a natural extension of the logistic regression analysis, without the population-by-genotype term, that is already popular for the analysis of GWAS data and has been used by our group [6,7] and others.
