Using 500k Affymetrix arrays, we have evaluated pooling using equal and varying amounts of DNA from CEPH individuals. Overall data for 150,000 SNPs from these comparisons produces correlations between pooled and individually-determined genotypes of r2 = 0.95 (Figure 3). These overall results derive from studies of 5475 and 6230 informative Nsp I and Sty I SNPs in experiments in which equal amounts of DNA from homozygotes were mixed (correlation ca 0.9); 10,032 informative Nsp I and 10,249 informative Sty I SNPs in experiments in which these same DNAs were mixed in 1:1, 1:5, and 1:15 ratios (correlations 0.96 and 0.98, respectively) and 31,201 informative Nsp I and 39,827 Sty I SNPs for studies of one homozygote and one heterozygote (correlations 0.89 and 0.92, respectively). When we compare these results with those reported using long range PCR products, using the reported procedure of eliminating the 9% of SNPs that yielded the more problematic correlations [127], the overall correlations for the remaining SNPs is 0.98. Correlations using 1M Affymetrix SNP arrays are at least as strong, with r2 > 0.98.
