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Identification, Replication, and Functional Fine-Mapping of Expression Quantitative Trait Loci in Primary Human Liver Tissue

Figure 4

SVA improves eQTL reproducibility.

(A) Surrogate variable regression produces more significant associations. Each point represents the BF for each UC gene expression trait and its best associated SNP. Data are plotted for associations tested after surrogate variable regression (y-axis) and unadjusted for surrogate variables (x-axis). Note that most points fall above the diagonal, indicating increased eQTL significance after surrogate variable correction. (B) Cis-eQTL replication rate (y-axis; UC vs UW or Merck) as a function of UC BF threshold. SVA adjusted associations depicted in black, unadjusted in grey.

Figure 4