In order to determine the coverage of regions inferred to be undergoing recent adaptive selection [12], [13], all SNPs detected by the LD decay (LDD) test in the Perlegen and HapMap datasets were compared to the Illumina 1M and Affymetrix 6.0 SNPs. Uncovering evidence for recent selection is an additional approach to defining functional human genomic variation. The LDD test identifies alleles undergoing selection by searching for an expected increase with distance in the fraction of inferred recombinant chromosomes surrounding a selected variant. This method is insensitive to local recombination rate because it relies on LD differences between the two alleles at a site, while the local rate influences the extent of LD surrounding both alleles. While over 99.9% of the selected regions defined by the LDD test fall within +/−10 kb of a SNP present on these microarrays, there are some important exceptions. For example, the extensive LD surrounding the selected DRD4 7R allele [14] is not captured by these arrays, which contain very few SNPs in the region (only 1 in 100 kb). In general, however, the extensive
