A generalized linear model (GLM implemented in the R Project for Statistical Computing) was used to test single marker genotypic additive effects for the relevant traits (AD+DD or AD-only), adjusting for the covariates sex and age. Haplotype-based association analysis was also completed in a GLM framework using the Haplo.stats Package in R (Schaid et al., 2002). The permutation test on global haplotypic effect was implemented by randomly permuting the case vs. control status (null hypothesis of no association), computing and comparing the test statistic with the observed one, replicating the simulation an appropriate number of times, and summarizing with the p-value, which is the probability of the permutated test statistic being greater than the observed one. Only haplotypes with frequency greater than 5.0% were examined for the haplotype-specific tests. The critical level of significance for the haplotype-specific tests within each haplotype set was adjusted by Bonferroni correction, i.e., the conventional α = 0.05 was divided by the number of major haplotypes observed in each case. The LD contrast test (Zaykin et al., 2006) was employed to investigate differences in LD
