Privacy preserving-probabilistic record linkage to assess cancer outcomes in people living with HIV in South Africa

Background: Privacy-preserving probabilistic record linkage (PPPRL) methods were developed and applied in high-income countries to link records within and between organizations under strict privacy protections. PPPRL has not yet been used in African settings. Methods: We used HIV-related laboratory records from National Health Laboratory Services (NHLS) in South Africa to construct a cohort of HIV-positive patients and link them to the National Cancer Registry (NCR) with PPPRL. The study was restricted to Gauteng province from 2004 to 2014. We used records with national IDs (gold standard) to determine precision, recall, and f-measure of the linkages. We included all patients with ≥ 2 HIV-related lab records measured in the cohort and assessed the number of cancers diagnosed in people living with HIV (PLWH). Results: We included 11,480,118 HIV-related laboratory records and 664,869 cancer records in the linkage. We included 1,173,908 persons in the HIV cohort; 66.6% were female and median age at first HIV-related lab test was 33.9 years (IQR 27.4-41.3). Of the patients in the cohort, 26,348 were diagnosed with at least one cancer and 8,329 of these cancers were diagnosed before or on the date of the patient’s first HIV-related record; 18,019 were diagnosed after their first HIV-related record. For all linkages, precision, recall, and f-measures were high. Conclusion: Our study showed it is feasible to use PPPRL in an African setting to link routinely collected health records from different data sources and create a longitudinal HIV cohort with cancer outcomes while strictly protecting patient privacy. This work served as the foundation to create a nationwide population-based cohort including all South African provinces which will be used to inform cancer control programs.