Aside from the technology, another important consideration is the SNPs that each platform has selected for assay. This can be important depending on the specific human population being studied. For example, it is important to use a chip that has more SNPs with better overall genomic coverage for a study of Africans than Europeans. This is because African genomes have had more time to recombine and therefore have less LD between alleles at different SNPs. More SNPs are needed to capture the variation across the African genome.
