Figure 4.

Cancer PheWAS ever-smoking EHR and survey comparison

(A) Manhattan plot for Cancer PheWAS using EHR ever smoking as exposure. Results are the −log10 (p value) of the corresponding logistic regression adjusted for age at last relevant EHR code, sex at birth, race and ethnicity from surveys, EHR length, and number of unique billing codes per record. Up arrows indicate non-protective associations, and down arrows indicate protective ones. Phenotype labels are given to the top ten phenotypes based on magnitude of effect size for both protective and non-protective effects.

(B) Manhattan plot for cancer PheWAS using survey ever smoking as exposure, with the same presentations as (A).

(C) Comparison of survey smoking-regression estimates (colored in blue) to EHR smoking-regression estimates (colored in red) for cancer outcomes.

(D) PheWAS EHR ever-smoking (dark blue) and survey ever-smoking (light blue) effect sizes and confidence intervals compared with published meta-analyses (orange). Estimates are presented on the natural log ratio scale (odds ratio [OR] or risk ratio [RR]). Estimates below the horizontal line represent protective effects, and estimates above the line represent non-protective effects. Each meta-analysis plot point shape represents whether the effect size from the literature was an OR, HR, or an RR, recognizing that RR and ORs are not directly comparable except in the case of rare disease.