For the initial GWA analysis, HelixTree Software (http://www.goldenhelix.com/SNP_Variation/HelixTree/index.html) was used to assess control genotype data for conformity with Hardy-Weinberg equilibrium (HWE). To test for association with MaxDrinks as a quantitative trait, linear regression, adjusted for age and sex, was performed by PLINK 1.07 (Purcell et al., 2007) to obtain the regression coefficient and standard error as well as Wald test asymptotic p-value. For statistical significance, we used a significance level of α = 5×10−7 (Wellcome Trust Case Control Consortium, 2007). At the same time, we also used a less stringent criterion of “suggestive association” with a cut-off of α = 10−4. In addition to obtaining nominal p-values, empirical p-values were generated by 100,000 permutation tests using the Max (T) permutation procedure implemented in PLINK. In this procedure, two sets of empirical significance values were calculated: pointwise estimates of an individual SNP’s significance (empirical pointwise p-values) and corrected values for multiple testing (corrected empirical p-values).
