As a reference panel for imputation, we used Phase II CEU HapMap individuals; we imputed genotypes to nearly 2.5 million HapMap SNPs; further details are presented in Table S1. We used MACH v1.0.15/16 (http://www.sph.umich.edu/csg/abecasis/MACH/) in conjunction with 200 (101 Men and 99 Women) biologically independent individuals to establish parameter estimates and then used the parameter estimates to infer gene dosage for all study participants. We expressed imputed genotypes as allelic dosage (which is a decimal value ranging from 0–2).
