Expression reflects population structure
Fig 5
Consequences for eQTL analysis.
A comparison of a standard eQTL pipeline when using either the first PCs of genotype or the first gene and genotype PCCA coordinates as covariates in the regression. (A) When using PEER to correct for batch effects, the separation of the YRI population is removed while the structure within the EUR populations remains. (B) The number of genes with an eQTL as a function of the significance cutoff for both methods, showing that the PCCA approach discovers slightly fewer genes at all levels. (C) A Q-Q plot of–log10(p) for the eQTL results using either method against a uniform distribution, showing reduced inflation at the high end. (D) Overlap of the genes discovered by the two methods at a nominal significance level of α = 1e-6. Though the overlap is large, the genes discovered using PCCA co-ordinates as covariates are not a strict subset of the genes discovered using PCs of genotype as covariates.