The bottom rows in Table 2 show the results of running this experiment. To provide a point of comparison with the GWAS results in Table 2, we initially imputed only the SNPs that were used in the WTCCC2 analysis (“WTCCC2 SNPs”). The imputation accuracy at these SNPs was slightly lower in the EUR cross-validation than in the WTCCC2 analysis; e.g., pre-phasing in EUR produced mean R2 values of 0.81, 0.85, and 0.91 for SNPs in ascending MAF bins, as compared to 0.82, 0.86, and 0.91 for the WTCCC2 experiment with the same scaffold SNPs, reference panel, and phasing approach (Table 2). These differences in pre-phasing accuracy may reflect the relative amount of phase information in a sample of 381 individuals (1000 Genomes EUR) and a sample of nearly 2,500 individuals (WTCCC2). Nonetheless, the overall similarity in results suggests that our EUR cross-validation provides a good approximation to a European GWAS.
