MACH (version 1.00.15)65 was used for imputation based on 378,163 autosomal SNPs remaining after exclusions for HWE P<10−6, call rate<97%, differential missingness related to genotype (mishap procedure in PLINK69) with P<10−9, Mendelian errors>100, MAF<1%, or those not present in HapMap. Two hundred unrelated individuals with high call rate were used to infer model parameters, which were subsequently applied to all 8,481 individuals. Imputation, using HapMap CEU (release 22, build 36),70 produced genotype dosages on 2,543,887 genotyped or imputed SNPs.
