The effectiveness of this method of course depends on the available genotyping coverage of the target region. If the "true" disease susceptibility locus is not genotyped, for example if it lies on a haplotype defined by genotyped SNPs, it will not be recognized and included among the enriched set of SNPs after cross-population filtering. However, the method still can narrow down the possibilities by eliminating individual SNPs. Furthermore, as genotyping and sequencing costs continue to decline, we expect that studies will be able to thoroughly and directly assay the genetic variation and therefore apply this approach most effectively.
