We used the program BEAGLE version 3.3.1 (Browning and Browning 2007) to impute SNPs on autosomes and X chromosome that were not genotyped on the Illumina Omni Express array. Since our sample was European American, we used as a reference set the genotypic data from the EUR in the August 2010 release of the 1000 Genomes Project, provided with the Beagle 3.3.1 release. SNPs with a correlation between the best-guess genotype and allele dosage greater than 0.3 (r2>0.3) were used in the analyses. For individual-level genotype data, we retained genotypes having a probability ≥80% (from the gprob metric in Beagle); all other genotypes were set to missing. We converted genotypic probability data into most-likely genotypes. This helped us in detecting genotypic errors in families. We used these most-likely genotypes in further cleaning and analysis. The imputed SNPs were cleaned using the same methods as genotyped SNPs. Mendelian errors in the imputed data were removed. After a careful quality review, a total of 4,058,415 SNPs were used for association analysis. To account for uncertainty, we used the mean of the distribution of imputed genotypes, which corresponds to an expected allelic or genotypic count (dosage) for each individual.
