Sample and SNP-level QC in all Finnish cohorts proceeded using the same protocols. Individuals were excluded if they were missing >5% of data, if there was a discrepancy between reported sex and sex determined from the X chromosome, if they were sibs or half-sibs of other subjects or if they withdrew consent. YFS and NFBC subjects were excluded if they had low IQ (<70). Fewer than 5% of subjects were excluded during QC. Genotyped SNPs were excluded with call rate <95%, P-value from an exact test of Hardy–Weinberg Equilibrium (HWE) <10−4 and minor allele frequency <1%. Imputation to HapMap2 (HM2) was done at the Wellcome Trust Sanger Institute, separately by cohort, using all samples that passed QC and all genotyped SNPs that passed QC in an individual cohort. Imputation was done using Markov Chain Haplotyper (MaCH),27 and all data were imputed to the forward/positive strand. The following numbers of SNPs were successfully imputed with r2>0.30: NFBC: 2 454 909, YFS: 2 489 350, HBCS: 2 492 667.
