literature) were forced in during the selection process. The performance of the initially selected SNP set was validated by the manufacturer and replacements made where necessary. In total, there were 1536 SNPs on this Illumina array, including 1350 SNPs from the 130 candidate genes, and 186 ancestry informative markers (AIMs). Our Irish population showed more linkage disequilibrium than the African population for which the chip was designed: the median r2 between neighboring variants was 0.21; 145 pairs of neighbors had r2 > 0.8. By construction of the algorithm SNPs in high LD could not both count toward the significance of a gene set.
