Not all phenotypes are created equal: covariates of success in e-phenotype specification. (7th September 2022)

• Record Type: Journal Article
• Authors: Hamidi, Bashir; Flume, Patrick A; Simpson, Kit N; Alekseyenko, Alexander V
• Is Part Of: Journal of the American Medical Informatics Association. Volume 30:Number 2(2023)
• Page Start: 213
• Page End: 221
• Publication Date: 2022-09-07
• Subjects: electronic phenotyping -- phenotyped data -- validation -- translational research services -- electronic health record; Medical informatics -- Periodicals; Information Services -- Periodicals; Medical Informatics -- Periodicals; Médecine -- Informatique -- Périodiques; Informatica; Geneeskunde; Informatique médicale; Computer network resources; Electronic journals; 610.285
• DOI: 10.1093/jamia/ocac157
• Languages: English
• ISSNs: 1067-5027

Abstract

Abstract: Background: Electronic (e)-phenotype specification by noninformaticist investigators remains a challenge. Although validation of each patient returned by e-phenotype could ensure accuracy of cohort representation, this approach is not practical. Understanding the factors leading to successful e-phenotype specification may reveal generalizable strategies leading to better results. Materials and Methods: Noninformaticist experts ( n = 21) were recruited to produce expert-mediated e-phenotypes using i2b2 assisted by a honest data-broker and a project coordinator. Patient- and visit-sets were reidentified and a random sample of 20 charts matching each e-phenotype was returned to experts for chart-validation. Attributes of the queries and expert characteristics were captured and related to chart-validation rates using generalized linear regression models. Results: E-phenotype validation rates varied according to experts' domains and query characteristics (mean = 61%, range 20–100%). Clinical domains that performed better included infectious, rheumatic, neonatal, and cancers, whereas other domains performed worse (psychiatric, GI, skin, and pulmonary). Match-rate was negatively impacted when specification of temporal constraints was required. In general, the increase in e-phenotype specificity contributed positively to match-rate. Discussions and Conclusions: Clinical experts and informaticists experience a variety of challenges when building e-phenotypes, including the inability to differentiate clinical events from patient characteristics or appropriately configure temporal constraints; a lack of access to available and quality data; and difficulty in specifying routes of medication administration. Biomedical query mediation by informaticists and honest data-brokers in designing e-phenotypes cannot be overstated. Although tools such as i2b2 may be widely available to noninformaticists, successful utilization depends not on users' confidence, but rather on creating highly specific e-phenotypes.