All polymorphisms were first assessed to determine if the observed genotype frequencies were consistent with Hardy-Weinberg proportions using Pearson chi-square tests within Stata (version 8.1; Stata Corporation, College Station, TX, USA). Pair-wise marker-marker linkage disequilibrium (LD) was assessed in Haploview (version 4.0) [19]. To test for association between each SNP and the continuously distributed 'AUDIT score', we performed analysis of variance models (ANOVA) using PROC GLM within the SAS software system (version 8.0; SAS Institute, Cary, NC, USA). Genotype was first tested for general association (no mode of inheritance assumption) using a two-degrees of freedom F-test. Further testing of the SNP effects assuming genetic modes of inheritance for that SNP were then performed. For dominant or recessive genetic transmission models, a single indicator variable (eg Idom is an indicator variable taking the value 1 ifan individual has genotype 1/2 or 2/2, and 0 otherwise) was used. A variable taking the values -1 for genotype 1/1; 0 for genotype 1/2; and 1 for genotype 2/2 was used to test for additive genetic effects.
