Genotype and allele frequencies for each SNP were determined in the case and control groups. The chi-square test, with significance defined as p<0.05 for any single SNP comparison, was employed to determine goodness of fit between observed and expected genotype or allele frequencies comparing AD subjects with controls. Single marker association analysis was also carried out in a logistic regression with additive genetic model, and ancestry proportion and subject recruitment site as covariates. Analysis of haplotypic association was performed using the chi-square test to compare frequencies of haplotypes composed of all 6 tagging SNPs, spanning both loci. Bonferroni correction was employed to control for multiple testing. Frequencies for the commonly observed haplotypes were estimated using the computer program PHASE (Stephens and Donnelly, 2003) (version 2.1.1 available at fttp://www.stat.washington.edu/stephens/phase.html). We also computed global tests of significance for single SNP and the 6-SNP haplotypic associations between AD and controls subjects.
