Development and evaluation of an EHR-based computable phenotype for identification of pediatric Crohn's disease patients in a National Pediatric Learning Health System

Objectives: To develop and evaluate the classification accuracy of a computable phenotype for pediatric Crohn's disease using electronic health record data from PEDSnet, a large, multi-institutional research network and Learning Health System. Study Design: Using clinician and informatician input, algorithms were developed using combinations of diagnostic and medication data drawn from the PEDSnet clinical dataset which is comprised of 5.6 million children from eight U.S. academic children's health systems. Six test algorithms (four cases, two non-cases) that combined use of specific medications for Crohn's disease plus the presence of Crohn's diagnosis were initially tested against the entire PEDSnet dataset. From these, three were selected for performance assessment using manual chart review (primary case algorithm, n = 360, primary non-case algorithm, n = 360, and alternative case algorithm, n = 80). Non-cases were patients having gastrointestinal diagnoses other than inflammatory bowel disease. Sensitivity, specificity, and positive predictive value (PPV) were assessed for the primary case and primary non-case algorithms. Results: Of the six algorithms tested, the least restrictive algorithm requiring just ≥1 Crohn's diagnosis code yielded 11 950 cases across PEDSnet (prevalence 21/10 000). The most restrictive algorithm requiring ≥3 Crohn's disease diagnoses plus at least one medication yielded 7868 patients (prevalence 14/10 000). The most restrictive algorithm had the highest PPV (95%) and high sensitivity (91%) and specificity (94%). False positives were due primarily to a diagnosis reversal (from Crohn's disease to ulcerative colitis) or having a diagnosis of “indeterminate colitis.” False negatives were rare. Conclusions: Using diagnosis codes and medications available from PEDSnet, we developed a computable phenotype for pediatric Crohn's disease that had high specificity, sensitivity and predictive value. This process will be of use for developing computable phenotypes for other pediatric diseases, to facilitate cohort identification for retrospective and prospective studies, and to optimize clinical care through the PEDSnet Learning Health System.