provides a large but less determinate collection of SNPs designed to give good coverage of the entire genome. There is not necessarily much overlap between the SNPs genotyped on two different platforms. For example, there were 140,325 SNPs in the overlap between the 508,123 markers on the Illumina HumanHap550 chip and the 606,625 markers on the Affymetrix Genome-Wide Human 6.0 array we use in this study. Thus, if we restricted to SNPs in the overlap, we would drop about three-quarters of the SNPs we have available on each of these chips.
