In this study we used both the Affymetrix and Illumina genotyping platforms, providing for increased power to detect cis and trans eQTL in the HLC compared to the detections achieved using the Affymetrix and Illumina sets independently [49]. Conditional on the sample size and FDR, the Illumina SNP set provided for roughly 15% more eQTLs than the Affymetrix SNP set, corresponding to a 15% increase in the relative power. This increase in power is primarily due to the higher genetic coverage of the Illumina SNP set compared to the Affymetrix SNP set. Further, given the ∼40,000 expression traits profiled in the HLC, we were able to estimate the genetic coverage of the Illumina and Affymetrix SNP sets on a cohort that is independent of the HapMap CEU (Utah residents with ancestry from Northern and Western Europe) subjects. Interestingly, we observed significantly lower genetic coverage (78%) than previously reported (90%) (electronic database: http://www.cidr.jhmi.edu/download/HumanHap650Y_info.pdf). Finally, in comparing whether more samples or more SNPs enhanced power most dramatically, we found that a modest increase in sample size (19%) had a more profound impact
