Multi-marker methods, which use combinations of SNPs, have been suggested as an efficient way to increase both coverage and power [15]. Figures S6 and S7 show the results of simulations that implement the multi-marker tests. In these figures the dotted lines, which represent coverage, are higher for all chips in comparison to single marker approaches (Figures 2 and 3) consistent with previous observations. We find that multi-marker approaches also increase statistical power to detect disease loci, but that the increase is modest relative to coverage, and the broad conclusions above are not much affected. Interestingly, when comparing across genotyping platforms, we find for example that the Affymetrix 500 k chip gains more by combining SNPs than the Illumina 300 k chip.
