A proposed de-identification framework for a cohort of children presenting at a health facility in Uganda

Data sharing has enormous potential to accelerate and improve the accuracy of research, strengthen collaborations, and restore trust in the clinical research enterprise. Nevertheless, there remains reluctancy to openly share raw data sets, in part due to concerns regarding research participant confidentiality and privacy. Statistical data de-identification is an approach that can be used to preserve privacy and facilitate open data sharing. We have proposed a standardized framework for the de-identification of data generated from cohort studies in children in a low-and-middle income country. We applied a standardized de-identification framework to a data sets comprised of 241 health related variables collected from a cohort of 1750 children with acute infections from Jinja Regional Referral Hospital in Eastern Uganda. Variables were labeled as direct and quasi-identifiers based on conditions of replicability, distinguishability, and knowability with consensus from two independent evaluators. Direct identifiers were removed from the data sets, while a statistical risk-based de-identification approach using the k-anonymity model was applied to quasi-identifiers. Qualitative assessment of the level of privacy invasion associated with data set disclosure was used to determine an acceptable re-identification risk threshold, and corresponding k-anonymity requirement. A de-identification model using generalization, followed by suppression was applied using a logical stepwise approach to achieve k-anonymity. The utility of the de-identified data was demonstrated using a typical clinical regression example. The de-identified data sets was published on the Pediatric Sepsis Data CoLaboratory Dataverse which provides moderated data access. Researchers are faced with many challenges when providing access to clinical data. We provide a standardized de-identification framework that can be adapted and refined based on specific context and risks. This process will be combined with moderated access to foster coordination and collaboration in the clinical research community. Author summary Open Data is data that anyone can access, use, and share. Open Data has the potential to facilitate collaboration, enrich research, and advance the analytic capacity to inform decisions. Importantly, Open Data plays a role in fulfilling obligations to research participants and honoring the nature of medical research as a public good. Leaders in industry, academia, and regulatory agencies recognize the value in increased transparency and are focusing on how to openly share data while minimizing the safety risks to research participants. For example, making data open can pose a privacy risk to research participants who have shared personal health information. This risk can be mitigated using data de-identification, a process of removing personal information from a data sets so that an individual’s identity is no longer apparent or cannot be reasonably ascertained from the data. We introduce a simple, statistical risk-based framework for de-identification of clinical data that can be followed by any researcher. This framework will guide open data sharing while improving the protection of research participants.