Imputation was performed using the MACH program26 (http://www.sph.umich.edu/csg/abecasis/MACH/download/). In all analyses, the set of samples whose genotypes were imputed did not overlap the set of samples used to construct reference panels. For the 1958 British birth cohort analysis, we imputed all available SNPs on chromosome 20. The 1958 British birth cohort samples had been previously genotyped on the Affymetrix 500K and Illumina 550K chips, so we used the 1958 British birth cohort Illumina 550K genotypes in tandem with either reference panel (HMII-CEU or CEU+TSI) to impute the known (but masked) Affymetrix 500K SNPs (Supplementary Information).
