McGue et al. (2013) applied the versatile gene-based association study gene set method (VEGAS; Liu et al., 2010) in their AD/alcohol consumption GWAS in the MCTFR sample. VEGAS uses P-values for individual SNP associations to compute a per-gene association P-value and can be applied to all SNPs in a gene or restricted to SNPs associated with a phenotype at a certain threshold. After correcting for 17,567 genes tested, no genes reached statistical significance and there was no evidence that candidate genes for substance abuse or related phenotypes were enriched in their sample.
