Implementing a hash-based privacy-preserving record linkage tool in the OneFlorida clinical research network

JAMIA Open. 2019 Sep 27;2(4):562-569. doi: 10.1093/jamiaopen/ooz050. eCollection 2019 Dec.


Objective: To implement an open-source tool that performs deterministic privacy-preserving record linkage (RL) in a real-world setting within a large research network.

Materials and methods: We learned 2 efficient deterministic linkage rules using publicly available voter registration data. We then validated the 2 rules' performance with 2 manually curated gold-standard datasets linking electronic health records and claims data from 2 sources. We developed an open-source Python-based tool-OneFL Deduper-that (1) creates seeded hash codes of combinations of patients' quasi-identifiers using a cryptographic one-way hash function to achieve privacy protection and (2) links and deduplicates patient records using a central broker through matching of hash codes with a high precision and reasonable recall.

Results: We deployed the OneFl Deduper ( in the OneFlorida, a state-based clinical research network as part of the national Patient-Centered Clinical Research Network (PCORnet). Using the gold-standard datasets, we achieved a precision of 97.25∼99.7% and a recall of 75.5%. With the tool, we deduplicated ∼3.5 million (out of ∼15 million) records down to 1.7 million unique patients across 6 health care partners and the Florida Medicaid program. We demonstrated the benefits of RL through examining different disease profiles of the linked cohorts.

Conclusions: Many factors including privacy risk considerations, policies and regulations, data availability and quality, and computing resources, can impact how a RL solution is constructed in a real-world setting. Nevertheless, RL is a significant task in improving the data quality in a network so that we can draw reliable scientific discoveries from these massive data resources.

Keywords: PCORnet; clinical research network; privacy-preserving record linkage.