Rare and Common Regulatory Variation in Population-Scale Sequenced Human Genomes
Figure 1
Comparison of eQTL discovery in HapMap 3 and 1000 genomes project data.
We compared the discovery of eQTLs from HapMap 3 (black) and 1000 genomes (red) project variants by expression platform (LCL expression interrogated on arrays from 56 Africans and 57 Europeans, and by RNA sequencing of 60 Europeans) across log-mean permutation threshold. At all levels of FDR across the permutation threshold range, we observe similar levels of detection of eQTL genes between HapMap 3 SNPs and 1000 genomes project SNPs. This indicates that given our sample sizes, similar levels of regulatory haplotypes are recovered despite the 5–7× increase in the number of common variants from DNA-sequencing. Comparison relative to observed p-value instead of FDR (Figure S1) accentuates the effect of increased number of tests in the 1000 genomes project data. Furthermore, the comparison between array and RNA sequencing data shows a reduction in the FDR relative to the total number of genes for relaxed permutation thresholds, indicating improved performance of the platform to uncover eQTLs in this FDR range.