PheValuator: Development and evaluation of a phenotype algorithm evaluator

• Published in: Journal of biomedical informatics Vol. 97; p. 103258
• Main Authors: Swerdel, Joel N., Hripcsak, George, Ryan, Patrick B.
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 01.09.2019
• Subjects: Algorithms; Atrial Fibrillation - diagnosis; Cerebral Infarction - diagnosis; Computational Biology; Current Procedural Terminology; Databases, Factual - statistics & numerical data; Diagnosis, Computer-Assisted - statistics & numerical data; Diagnostic Errors - statistics & numerical data; Diagnostic predictive modeling; Humans; Models, Statistical; Myocardial Infarction - diagnosis; Phenotype; Phenotype algorithms; Predictive Value of Tests; Probability; Renal Insufficiency, Chronic - diagnosis; Sensitivity and Specificity; Validation; Validation; eGFR; MDCR; AF; Phenotype algorithms; SNOMED; CDM; AUC; PA; ICD-9; NPV; PLP; LASSO; PPV; IRB; Diagnostic predictive modeling; CCAE; CPT-4; MDCD; AMI; CKD
• ISSN: 1532-0464; 1532-0480; 1532-0480
• DOI: 10.1016/j.jbi.2019.103258

[Display omitted] •Phenotype Algorithms (PAs) are used in research to determine presence of disease.•Evaluation of PAs for sensitivity/specificity/predictive values is rarely performed.•PheValuator uses diagnostic predictive modeling to perform PA evaluation.•The tool provides conservative sensitivity/specificity/predictive estimates for PAs.•PheValuator shows promise as a tool to assess PA performance characteristics. The primary approach for defining disease in observational healthcare databases is to construct phenotype algorithms (PAs), rule-based heuristics predicated on the presence, absence, and temporal logic of clinical observations. However, a complete evaluation of PAs, i.e., determining sensitivity, specificity, and positive predictive value (PPV), is rarely performed. In this study, we propose a tool (PheValuator) to efficiently estimate a complete PA evaluation. We used 4 administrative claims datasets: OptumInsight’s de-identified Clinformatics™ Datamart (Eden Prairie,MN); IBM MarketScan Multi-State Medicaid); IBM MarketScan Medicare Supplemental Beneficiaries; and IBM MarketScan Commercial Claims and Encounters from 2000 to 2017. Using PheValuator involves (1) creating a diagnostic predictive model for the phenotype, (2) applying the model to a large set of randomly selected subjects, and (3) comparing each subject’s predicted probability for the phenotype to inclusion/exclusion in PAs. We used the predictions as a ‘probabilistic gold standard’ measure to classify positive/negative cases. We examined 4 phenotypes: myocardial infarction, cerebral infarction, chronic kidney disease, and atrial fibrillation. We examined several PAs for each phenotype including 1-time (1X) occurrence of the diagnosis code in the subject’s record and 1-time occurrence of the diagnosis in an inpatient setting with the diagnosis code as the primary reason for admission (1X-IP-1stPos). Across phenotypes, the 1X PA showed the highest sensitivity/lowest PPV among all PAs. 1X-IP-1stPos yielded the highest PPV/lowest sensitivity. Specificity was very high across algorithms. We found similar results between algorithms across datasets. PheValuator appears to show promise as a tool to estimate PA performance characteristics.