Genotyping was performed with the Human670-QuadCustom Illumina BeadChip at the Welcome Trust Sanger Institute, and with the Illumina Human Core Exome BeadChip at the Welcome Trust Sanger Institute and at the Broad Institute of MIT and Harvard. Standard post-genotyping quality control thresholds were applied for SNPs (minor allele frequency (MAF) <0.01, SNP call rate <0.95, and Hardy Weinberg Equilibrium (HWE) p<1E-06). Further, subjects with a call rate <0.95 were excluded, and a sample heterozygosity test, as well as sex and Multidimensional Scaling (MDS) outlier checks were done. Pre-phasing of the data was done with SHAPEIT2 [36] and imputation with IMPUTE2 [37] using the 1000 Genomes Phase I integrated haplotypes (produced using SHAPEIT2) reference panel [38]. For data generated with the Human670-QuadCustom Illumina BeadChip the following post-imputation exclusion criteria were applied for SNPs: MAF<0.01, SNP call rate <0.95 (<0.99 for SNPs with MAF<0.05), HWE p<1E-06, and imputation info <0.4. For data generated with the Illumina Human Core Exome BeadChip the SNP exclusion criteria were otherwise identical, except that a threshold of minor allele count <2 was applied instead of a MAF
