Electronic Health Record Coding of Self-Reported Diagnoses in the All of Us Research Program
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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.
Key Points
Question
Among adults who report a clinician-diagnosed chronic condition, how often does their electronic health record contain a corresponding diagnosis code?
Findings
In this cross-sectional study of 114,610 All of Us participants with at least 5 years of preceding electronic health records, 83% to 90% of those reporting ongoing care for hypertension or type 2 diabetes had a corresponding code, compared with 41% for endometriosis, 39% for Lyme disease, and 24% for chronic fatigue.
Meaning
These findings suggest that cohorts defined by diagnosis codes may omit many patients who report care for chronic fatigue, Lyme disease, or endometriosis.
