reference panel, but that controlling for an equal number of founders in both reference panels eliminated most of this difference (Table VI). The results imply that, on average, the levels of linkage disequilibrium (and consequently, the average lengths of haplotype blocks) are similar in the phase III ASW and YRI reference panels, whereas linkage disequilibrium is more pronounced in the phase III CEU reference panel. In summary, given equivalent sampling with respect to the numbers of founders and SNP density, we anticipate that YRI and ASW may perform similarly well as reference panels for our African American study sample.
