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Genome-Wide Human SNP Array 5.0
What is the impact of the lower number of SNPs on the coverage?
The Mapping 500K has a high level of redundancy, and numerous studies have shown that dropping 10% of the SNPs will not significantly impact LD coverage. This data is show in the Barrett and Cardon Nature genetics paper. Any minor loss in LD coverage is more than compensated for by the increased power from running more samples.
For the HapMap CEPH samples, there is a 2% difference LD coverage, when measured at an R2 = 0.,8 between the 500K and the SNP 5.0