Ascertainment issues might have contributed to a decreased level of tag-SNP portability seen in some non-European populations compared to what might have been predicted on the basis of their LD levels41. Although evaluations of tag-SNP portability have generally found that tag SNPs chosen from the HapMap are indeed portable to most non-European populations36,40, they have identified low-LD populations and intermediate-LD indigenous populations genetically distant from HapMap reference panels to be among those populations in which tag SNPs capture the fewest non-tag SNPs41. Tag-SNP portability can potentially be improved in populations genetically intermediate between the primary HapMap populations by using a mixture strategy to select SNPs for genotyping panels. In this approach, tag SNPs are selected to be informative for a mixture of haplotypes drawn from multiple HapMap groups, rather than from a single group64,65. However, this mixture strategy does not solve the problem of low portability in sub-Saharan African populations, whose LD levels are considerably lower than those of other populations43,49,66.
