Any SNVs showing significant association were checked (e.g., by visual inspection of the intensity cluster plots and investigation of consistency of LD with surrounding markers) and those SNVs deemed unreliable were removed. The final data sets of high-quality SNVs were prephased with SHAPEIT31 and subsequently used to perform imputation with IMPUTE2,32 the 1000 Genomes reference panel (integrated variant set, release March 2012).33 In the Irish AD collection (Table S1), case and control subjects were genotyped on different platforms, and therefore only the 131,692 SNVs in common between the platforms were used to inform imputation.