Figure 4

Stratified Q-Q plot for SNPs Associated with QIDS-SR. For SNP association with QIDS-SR, the ranked observed meta-analysis probabilities (P values) are plotted versus the expected probabilities. The scale is –log₁₀(P), so that points above and to the right represent more significant (i.e. smaller) P values. Unlike Figure 3, only the 614 SNPs are plotted for which meta-analysis P values were available both for the QIDS-SR (Additional file 1, worksheet 1) and for DSPS classification in a dominant logistic genetic model. The P values for QIDS-SR association are stratified by whether the association of that SNP with DSPS was nominally significant (P<0.05). The expectation for 614 SNPs with random association is plotted in the black dashed line. Since the distance of the most deviant p values for P_DSPS<0.05 (red line) is approximately 1 log unit from the random expectation (black dotted line) and from the line for P_DSPS>0.05 (blue line), one may estimate that the probability of false discovery of pleiotropy for the most significant SNPs was ~0.10. FMR1 SNPs were not included in Figure 4 because the dominant model could not be computed for this part of the X chromosome, but no FMR1 SNP was significantly associated with DSPS in an additive model.