Pheno+: An Electronic Health Record-Integrated, Clinician-in-the-Loop Application for Efficient Phenotyping in Clinical Genomics
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Objective
To evaluate the efficiency and diagnostic utility of Pheno+, an electronic health record (EHR)-integrated application that streamlines the generation of structured phenotypes for genomic testing and analysis.
Materials and Methods
We developed Pheno+ as a Substitutable Medical Applications and Reusable Technologies on Fast Healthcare Interoperability Resources (SMART on FHIR) application embedded within the University of Utah Health EHR. Pheno+ applies ClinPhen to clinician-selected clinical notes to identify candidate Human Phenotype Ontology (HPO) terms, which clinicians review and curate within the EHR. We conducted an eight-case crossover evaluation comparing workflow time between Pheno+ and a standard workflow that involved physician chart review and molecular geneticist-led HPO term selection. In a separate cohort of 17 patients with confirmed monogenic diagnoses, we assessed the diagnostic utility of Pheno+-derived HPO terms by evaluating Exomiser gene prioritization performance using these terms.
Results
Pheno+ reduced mean total workflow time by 66%, from 31.1 to 10.5 minutes (p < 0.001). Incorporating Pheno+-derived HPO terms improved Exomiser’s ability to rank the causative gene first, from 11 of 17 cases (64.7%) without phenotype input to 17 of 17 cases (100%) with phenotype input (p = 0.031).
Discussion and Conclusion
Pheno+ reduced the time and personnel required to generate clinician-curated HPO term lists while producing phenotypes that improved causative gene prioritization. These findings support EHR-integrated, clinician-in-the-loop phenotyping as an efficient approach to generating diagnostically informative phenotype data for clinical genomic workflows.
