Electronic Health Record Coding of Self-Reported Diagnoses in the All of Us Research Program

Abstract Importance: Conditions that are hard to diagnose, several more common in women, may be missing from electronic health records (EHRs), hiding patients from research cohorts and case finding. Objective: To measure how often the EHR contains a diagnosis code for chronic conditions that participants report, and to compare this with national survey benchmarks. Design, Setting, and Participants: This cross-sectional study used the All of Us Research Program Registered Tier Dataset v9. Participants were adults with EHR visits in both 12-month periods from July 2021 to June 2023 who completed a health history survey. We analyzed the data in October 2026. Exposures: Self-reported clinician diagnosis of 10 conditions with ongoing visits or treatment, as well as sex at birth, race and ethnicity, age, and years of EHR records. Main Outcomes and Measures: Share of participants reporting current care who had a qualifying diagnosis code, alone and relative to hypertension and type 2 diabetes, and the ratio of age-standardized coded shares to national survey prevalence. Results: Of 161,480 respondents, 114,610 (73,870 female [64.5%], median [IQR] age 63 [50-72] years) had at least 5 years of EHR records before the survey. Among those reporting current care, 84.6% (95% CI, 84.2%-85.0%) with hypertension and 87.0% (95% CI, 86.5%-87.6%) with type 2 diabetes had a code, compared with 41.3% (95% CI, 38.9%-43.8%) for endometriosis, 39.4% (95% CI, 34.3%-44.8%) for Lyme disease, and 24.4% (95% CI, 23.2%-25.6%) for chronic fatigue. Counting ICD-9-CM and other mapped codes, 55.3%, 51.5%, and 28.3%, respectively, had any qualifying record. Women had lower coded shares than men for hypertension, type 2 diabetes, obesity, depression, and anxiety (crude ratios 0.93-0.96, within-health-system ratios 0.98-1.02) and higher shares for migraine and fibromyalgia (within health systems, 1.11 [95% CI, 1.07-1.15] and 1.41 [95% CI, 1.29-1.57]). Age-standardized coded shares among active patients were 1.1 to 2.4 times national prevalence of the same self-reported diagnoses. Conclusions and Relevance: In this cross-sectional study, fewer than half of participants reporting ongoing care for chronic fatigue, Lyme disease, or endometriosis had a qualifying ICD-10-CM code. Linking each participant's report to their own record measured this gap directly. Competing Interest Statement The authors have declared no competing interest. Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: All of Us Research Program, National Institutes of Health: participants provide informed consent under the program protocol approved by the All of Us Institutional Review Board. We analyzed de-identified data from the All of Us Registered Tier Dataset v9 as authorized researchers on the All of Us Researcher Workbench (https://www.researchallofus.org). I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines, such as any relevant EQUATOR Network research reporting checklist(s) and other pertinent material, if applicable. Yes Data Availability The All of Us Registered Tier Dataset v9 is available to authorized researchers through the All of Us Researcher Workbench. The NHANES 2021-2023 and NHIS 2023 public-use files are available from the National Center for Health Statistics. The aggregate statistics behind every table and figure, and the code and a notebook that regenerate them, are available at https://github.com/AsiaeeLab/unom-self-report-coding.