Privacy-preserving record linkage across disparate institutions and datasets to enable a learning health system: The national COVID cohort collaborative (N3C) experience

Umberto Tachinardi, Shaun J. Grannis*, Sam G. Michael, Leonie Misquitta, Jayme Dahlin, Usman Sheikh, Abel Kho, Jasmin Phua, Sara S. Rogovin, Benjamin Amor, Maya Choudhury, Philip Sparks, Amin Mannaa, Saad Ljazouli, Joel Saltz, Fred Prior, Ahmen Baghal, Kenneth Gersing, Peter J. Embi

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review


Introduction: Research driven by real-world clinical data is increasingly vital to enabling learning health systems, but integrating such data from across disparate health systems is challenging. As part of the NCATS National COVID Cohort Collaborative (N3C), the N3C Data Enclave was established as a centralized repository of deidentified and harmonized COVID-19 patient data from institutions across the US. However, making this data most useful for research requires linking it with information such as mortality data, images, and viral variants. The objective of this project was to establish privacy-preserving record linkage (PPRL) methods to ensure that patient-level EHR data remains secure and private when governance-approved linkages with other datasets occur. Methods: Separate agreements and approval processes govern N3C data contribution and data access. The Linkage Honest Broker (LHB), an independent neutral party (the Regenstrief Institute), ensures data linkages are robust and secure by adding an extra layer of separation between protected health information and clinical data. The LHB's PPRL methods (including algorithms, processes, and governance) match patient records using “deidentified tokens,” which are hashed combinations of identifier fields that define a match across data repositories without using patients' clear-text identifiers. Results: These methods enable three linkage functions: Deduplication, Linking Multiple Datasets, and Cohort Discovery. To date, two external repositories have been cross-linked. As of March 1, 2023, 43 sites have signed the LHB Agreement; 35 sites have sent tokens generated for 9 528 998 patients. In this initial cohort, the LHB identified 135 037 matches and 68 596 duplicates. Conclusion: This large-scale linkage study using deidentified datasets of varying characteristics established secure methods for protecting the privacy of N3C patient data when linked for research purposes. This technology has potential for use with registries for other diseases and conditions.

Original languageEnglish (US)
JournalLearning Health Systems
StateAccepted/In press - 2024


  • clinical research
  • data privacy
  • learning health systems
  • record linkage
  • translational research

ASJC Scopus subject areas

  • Health Informatics
  • Public Health, Environmental and Occupational Health
  • Health Information Management


Dive into the research topics of 'Privacy-preserving record linkage across disparate institutions and datasets to enable a learning health system: The national COVID cohort collaborative (N3C) experience'. Together they form a unique fingerprint.

Cite this