Methods Inf Med 2021; 60(03/04): 084-094
DOI: 10.1055/s-0041-1735619
Original Article

Optimizing Identification of People Living with HIV from Electronic Medical Records: Computable Phenotype Development and Validation

Yiyang Liu
1  Department of Epidemiology, College of Public Health and Health Professions and College of Medicine, University of Florida, Gainesville, Florida, United States
,
Khairul A. Siddiqi
2  Department of Health Outcomes and Biomedical Informatics, College of Medicine, University of Florida, Gainesville, Florida, United States
,
Robert L. Cook
1  Department of Epidemiology, College of Public Health and Health Professions and College of Medicine, University of Florida, Gainesville, Florida, United States
,
Jiang Bian
2  Department of Health Outcomes and Biomedical Informatics, College of Medicine, University of Florida, Gainesville, Florida, United States
,
Patrick J. Squires
3  Department of Pharmaceutical Outcomes and Policy, College of Pharmacy, University of Florida, Gainesville, Florida, United States
,
Elizabeth A. Shenkman
2  Department of Health Outcomes and Biomedical Informatics, College of Medicine, University of Florida, Gainesville, Florida, United States
,
Mattia Prosperi
1  Department of Epidemiology, College of Public Health and Health Professions and College of Medicine, University of Florida, Gainesville, Florida, United States
,
Dushyantha T. Jayaweera
4  Department of Medicine, Miller School of Medicine, University of Miami, Miami, Florida, United States
› Author Affiliations
Funding This work was supported by the National Institute of Allergy and Infectious Diseases (NIAID) under Award Number R01AI145552 (Co-PIs: Salemi, Prosperi) and a pilot grant from the Center for AIDS Research (CFAR) (PI: Jayaweera) from the National Institute of Allergy and Infectious Diseases (NIAID) under Award Number 5P30AI073961-13 (PI: Pahwa). The work was also, in part, funded by CDC U18DP006512 and NCI R01CA246418. Additionally, the research reported in this publication was supported by the National Center for Advancing Translational Sciences of the National Institutes of Health under University of Florida Clinical and Translational Science Awards UL1TR000064 and UL1TR001427. The OneFlorida Clinical Research Consortium was funded by the Patient-Centered Outcomes Research Institute number CDRN-1501-26692 and RI-CRN-2020-005; in part by the OneFlorida Cancer Control Alliance, funded by the Florida Department of Health's James and Esther King Biomedical Research Program #4KB16.

Abstract

Background Electronic health record (EHR)-based computable phenotype algorithms allow researchers to efficiently identify a large virtual cohort of Human Immunodeficiency Virus (HIV) patients. Built upon existing algorithms, we refined, improved, and validated an HIV phenotype algorithm using data from the OneFlorida Data Trust, a repository of linked claims data and EHRs from its clinical partners, which provide care to over 15 million patients across all 67 counties in Florida.

Methods Our computable phenotype examined information from multiple EHR domains, including clinical encounters with diagnoses, prescription medications, and laboratory tests. To identify an HIV case, the algorithm requires the patient to have at least one diagnostic code for HIV and meet one of the following criteria: have 1+ positive HIV laboratory, have been prescribed with HIV medications, or have 3+ visits with HIV diagnostic codes. The computable phenotype was validated against a subset of clinical notes.

Results Among the 15+ million patients from OneFlorida, we identified 61,313 patients with confirmed HIV diagnosis. Among them, 8.05% met all four inclusion criteria, 69.7% met the 3+ HIV encounters criteria in addition to having HIV diagnostic code, and 8.1% met all criteria except for having positive laboratories. Our algorithm achieved higher sensitivity (98.9%) and comparable specificity (97.6%) relative to existing algorithms (77–83% sensitivity, 86–100% specificity). The mean age of the sample was 42.7 years, 58% male, and about half were Black African American. Patients' average follow-up period (the time between the first and last encounter in the EHRs) was approximately 4.6 years. The median number of all encounters and HIV-related encounters were 79 and 21, respectively.

Conclusion By leveraging EHR data from multiple clinical partners and domains, with a considerably diverse population, our algorithm allows more flexible criteria for identifying patients with incomplete laboratory test results and medication prescribing history compared with prior studies.

Note

The content is solely the responsibility of the authors and does not necessarily represent the official views of the Patient-Centered Outcomes Research Institute (PCORI), its Board of Governors or Methodology, the OneFlorida Clinical Research Consortium, the University of Florida's Clinical and Translational Science Institute, the Florida Department of Health, or the National Institutes of Health.


Supplementary Material



Publication History

Received: 02 June 2021

Accepted: 20 July 2021

Publication Date:
30 September 2021 (online)

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