These results suggest that a significant amount of common genetic variation in these addiction related genes is unaccounted for by these commercial SNP microarrays. The deficiency is particularly high in the African sample. This is likely due to the lower LD in this older population, which means more SNPs are required for tagging. While the Illumina 1M clearly provides the best coverage, we would still need to add 23,441 SNPs to tag all common SNPs in the HapMap African sample for these 910 genes. The best-case scenario is when the Illumina 1M is used for European-Americans. But even in this case, there are still 5,117 SNPs that are not well represented.
