DNA was extracted from blood samples. Genotyping was performed on Illumina platforms (Illumina, San Diego, CA, USA) in all studies, except in SardiNIA in which an Affymetrix platform (Affymetrix, Santa Clara, CA, USA) was used. Genotype data were checked in each study independently, using slightly different inclusion criteria. Among the basic checks that were performed are checks for European ancestry, Mendelian errors, gender inconsistencies and high genome-wide homozygosity. Genotype data were further cleaned based on Hardy–Weinberg equilibrium, minor allele frequencies, SNP call rate (% of subjects with missing genotypes per SNP) and sample call rate (% of missing SNPs per subject). Imputation to ∼2.5 common SNPs included in HapMap was performed using the HapMap phase II CEU data as the reference sample (NCBI build 36/UCSC hg18, Bethesda, MD, USA). Imputation was carried out using IMPUTE for SAGE and EGPUT samples.41 For the other samples, genotype data were imputed using MACH software.42
