The PedCheck program (O’Connell and Weeks 1998) was used to detect any genotyping inconsistencies. To avoid potential bias, the 41 inconsistencies in the AA sample and 24 in the EA sample, detected in approximately 46,200 assays (i.e., 0.14% genotyping error) for 22 SNPs across all DNA samples, were excluded from statistical analysis. Pair-wise linkage LD between all possible SNP pairs was assessed using the Haploview (v. 4.0) program (Barrett and others 2005) with the option of determining haplotype blocks according to the definitions proposed by Gabriel et al. (2002). Associations between individual SNPs and the three ND measures were determined with the PBAT (v. 3.5) program using generalized estimating equations (Lange and others 2003). Associations between each ND measure and haplotypes from various SNP combinations were calculated using the FBAT (v. 1.7.3) program with the option of computing the P value of the Z statistic using Monte Carlo sampling under the null distribution of no linkage and no association (Horvath and others 2004). Three genetic models (additive, dominant, and recessive) were tested for both individual and multi-locus SNPs (i.e., haplotypes).
