Fig. 3

Comparing Cox regression and logistic regression for the ability to detect known genotype-phenotype associations for the 50 phenotypes analyzed. Known significant associations (P ≤ 5·10^− 8) were curated from the NHGRI-EBI GWAS Catalog and aggregated by LD for each phenotype. a Sensitivity of each method, i.e., fraction of known and tested associations that gave a p-value less than or equal to the specified cutoff. The sequential strategy used the p-value from Cox regression, if the unadjusted p-value from logistic regression was ≤10^− 4. The sequential line overlaps the Cox line. b Relative change in sensitivity between logistic and Cox regression, i.e., difference between the sensitivities for Cox and logistic, divided by the sensitivity for logistic. The gray line corresponds to the raw value at each cutoff, while the black line corresponds to the smoothed value according to a penalized cubic regression spline in a generalized additive model