Computational phenotyping with the All of Us Research Program: identifying underrepresented people with HIV or at risk of HIV

Objective: This study aims to identify the people living with HIV (PWH) and pre-exposure prophylaxis (PrEP) users in the All of Us (AoU) database by integrating information from both electronic health record (EHR)- and self-reported survey data. Methods: We identified PWH and PrEP users if they met the inclusion criterion by conditions, lab measurements, or medications related to HIV in EHR data or confirmed questions in the Survey data. Results: We evaluated the latest data release through July 1, 2022 in AoU. Through computational phenotyping, we identified 4575 confirmed and 3092 probable adult PWH and 564 PrEP users. PWH was most identified by a combination of medications and conditions (3324, 43.4%) and drug exposure alone (2191, 28.6%), then less commonly by survey data alone (608, 7.9%) and lab alone (81, 1.1%). Discussion and conclusion: Our methods serve as an overall framework for other researchers using AoU data for conducting HIV-related research. LAY SUMMARY The electronic health record (EHR) data refers to administrative and billing data, electronic medical records, or other digital records of information pertinent to individual or population health. In this study, we fully leveraged the information in EHR data and survey data from All of Us (AoU) platform to identify potential people with HIV (PWH) and individuals who are taking pre-exposure prophylaxis (PrEP) for HIV prevention. The AoU Research Program aims to recruit participants from groups that have been historically underrepresented in biomedical research. Using information from different domains of EHR data (ie, diagnostic code, drug prescription record, and lab results) and questions in the Survey, we conducted computational phenotyping (ie, the process of transforming the noisy, massive EHR data into meaningful medical concepts that can be used for case detection or predict the risk of disease for an individual) and identified 4575 confirmed and 3092 probable adult PWH and 564 PrEP users. PWH was most identified by a combination of medications and conditions and drug exposure alone, then less commonly by survey data alone and lab alone. Our methods for the HIV and PrEP case detection could help other researchers using AoU data for conducting HIV-related research.