Disease associations depend on visit type: results from a visit-wide association study

INTRODUCTION: Widespread adoption of Electronic Health Records (EHR) increased the number of reported disease association studies, or Phenome-Wide Association Studies (PheWAS). Traditional PheWAS studies ignore visit type (i.e., department/service conducting the visit). In this study, we investigate the role of visit type on disease association results in the first Visit-Wide Association Study or ‘VisitWAS’. RESULTS: We studied this visit type effect on association results using EHR data from the University of Pennsylvania. Penn EHR data comes from 1,048 different departments and clinics. We analyzed differences between cancer and obstetrics/gynecologist (Ob/Gyn) visits. Some findings were expected (i.e., increase of neoplasm diagnoses among cancer visits), but others were surprising, including an increase in infectious disease conditions among those visiting the Ob/Gyn. CONCLUSION: We conclude that assessing visit type is important for EHR studies because different medical centers have different visit type distributions. To increase reproducibility among EHR data mining algorithms, we recommend that researchers report visit type in studies. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s13040-019-0203-2) contains supplementary material, which is available to authorized users.