Genomewide association genotyping for 600,000 SNPs was conducted by Perlegen Sciences (Mountain View, CA, USA). After a series of quality control processes (Sullivan et al., 2009), individual genotype data for 427,037 autosomal SNPs were available. This set of SNPs was used as the basis for an imputation procedure whereby ~2.5M HapMap (The International HapMap Consortium., 2003) SNPs were imputed. Imputation was carried out in IMPUTE (Marchini et al., 2007) using the HAPMAP Phase II CEU data (Build 35) available on the IMPUTE website (http://www.stats.ox.ac.uk/~marchini/software/gwas/impute.html#). The threshold (for genotype uncertainty) to include SNPs in the analyses was 0.70. Genome wide association analyses were carried out in PLINK (Purcell et al., 2007) (option --assoc and --model, no covariates were included).
