The family-based association test (FBAT)(Horvath et al., 2001; Horvath et al., 2004) was used to test the association of the single SNPs and haplotypes of various SNPs to AD+DD. The FBAT model and parameters used included an additive genetic model under the null hypothesis of no linkage and no association, biallelic mode, minimum number of informative families of 20 for each analysis, and offset of zero. The “hbat” command in FBAT was issued to analyze haplotypic association with an assumption of a biallelic mode of inheritance for haplotype-specific association and a multi-allelic mode for testing all haplotypes as a whole for the global association test. Permutation tests (with 100,000 iterations) were used to calculate all p-values of global associations. The significance level of haplotype-specific tests was set up the same as that in the case-control design.
