In JAMA network open
Importance : Electronic health records (EHRs) provide a low-cost means of accessing detailed longitudinal clinical data for large populations. A lung cancer cohort assembled from EHR data would be a powerful platform for clinical outcome studies.
Objective : To investigate whether a clinical cohort assembled from EHRs could be used in a lung cancer prognosis study.
Design, Setting, and Participants : In this cohort study, patients with lung cancer were identified among 76 643 patients with at least 1 lung cancer diagnostic code deposited in an EHR in Mass General Brigham health care system from July 1988 to October 2018. Patients were identified via a semisupervised machine learning algorithm, for which clinical information was extracted from structured and unstructured data via natural language processing tools. Data completeness and accuracy were assessed by comparing with the Boston Lung Cancer Study and against criterion standard EHR review results. A prognostic model for non-small cell lung cancer (NSCLC) overall survival was further developed for clinical application. Data were analyzed from March 2019 through July 2020.
Exposures : Clinical data deposited in EHRs for cohort construction and variables of interest for the prognostic model were collected.
Main Outcomes and Measures : The primary outcomes were the performance of the lung cancer classification model and the quality of the extracted variables; the secondary outcome was the performance of the prognostic model.
Results : Among 76 643 patients with at least 1 lung cancer diagnostic code, 42 069 patients were identified as having lung cancer, with a positive predictive value of 94.4%. The study cohort consisted of 35 375 patients (16 613 men [47.0%] and 18 756 women [53.0%]; 30 140 White individuals [85.2%], 1040 Black individuals [2.9%], and 857 Asian individuals [2.4%]) after excluding patients with lung cancer history and less than 14 days of follow-up after initial diagnosis. The median (interquartile range) age at diagnosis was 66.7 (58.4-74.1) years. The area under the receiver operating characteristic curves of the prognostic model for overall survival with NSCLC were 0.828 (95% CI, 0.815-0.842) for 1-year prediction, 0.825 (95% CI, 0.812-0.836) for 2-year prediction, 0.814 (95% CI, 0.800-0.826) for 3-year prediction, 0.814 (95% CI, 0.799-0.828) for 4-year prediction, and 0.812 (95% CI, 0.798-0.825) for 5-year prediction.
Conclusions and Relevance : These findings suggest the feasibility of assembling a large-scale EHR-based lung cancer cohort with detailed longitudinal clinical measurements and that EHR data may be applied in cancer progression with a set of generalizable approaches.
Yuan Qianyu, Cai Tianrun, Hong Chuan, Du Mulong, Johnson Bruce E, Lanuti Michael, Cai Tianxi, Christiani David C