A Pleiotropy-Informed Bayesian False Discovery Rate Adapted to a Shared Control Design Finds New Disease Associations From GWAS Summary Statistics
Figure 4
Q-Q plots for T1D conditional on RA (Panel A) and PSO (Panel B).
Y axes show ; X axes show log quantile (rank) of p values in various sets of SNPs. The degree of leftward shift of a black point from the diagonal is proportional to the unconditional FDR of that p value for the principal phenotype, and the degree of leftward shift of a coloured point is proportional to the conditional FDR of the p value for the principal phenotype and the p-cutoff corresponding to the colour for the conditional phenotype. As expected, a leftward shift is seen even for the unconditional Q-Q plots (black line) owing to the use of the ImmunoChip, which focuses on potential autoimmune-associated regions. Each colour corresponds to the Q-Q plot for pT1D amongst a subset of SNPs with pRA or pPSO less than the indicated cutoff. P values for T1D are adjusted for the effect of shared controls between studies. A leftward shift with decreasing pRA or pPSO cutoff indicates that SNPs which are associated with the conditional phenotype (RA or PSO) are more likely to be associated with the principal phenotype (T1D), presumably due to pleiotropic effects on phenotypes. Good enrichment is seen for T1D conditioning on RA (Panel A), and little or no enrichment conditioning on PSO (Panel B).