Depending on the commercial panel and population being investigated, coverage of HapMap SNPs (proportion of SNPs with r2>0.80) increased by 10–30% for low MAF alleles (MAF<5%) and by 10–20% for more common alleles (MAF>5%). In agreement with this result, the average r2 between each untyped SNP and imputed genotypes was up to 40% higher on average when using imputed genotypes than when using the best available single marker proxy. Imputation remained valuable even for panels with ~1 million directly genotyped SNPs. In practice, the results shown in Table III are likely to represent an upper bound on the performance of our method in real settings, because additional errors will result from discrepancies in genotyping protocols between individual laboratories and the HapMap and from differences in LD patterns between the HapMap and the samples being studied. Nevertheless, they suggest our method is likely to be helpful for a variety of currently available commercial SNP panels.
