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arXiv · 2506.02942

An Algorithmic Pipeline for GDPR-Compliant Healthcare Data Anonymisation: Moving Toward Standardisation

Hamza Khan·Lore Menten·Liesbet M. Peeters
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Abstract

High-quality real-world data (RWD) is essential for healthcare but must be transformed to comply with the General Data Protection Regulation (GDPR). GDPRs broad definitions of quasi-identifiers (QIDs) and sensitive attributes (SAs) complicate implementation. We aim to standardise RWD anonymisation for GDPR compliance while preserving data utility by introducing an algorithmic method to identify QIDs and SAs and evaluate utility in anonymised datasets. We conducted a systematic literature review via ProQuest and PubMed to inform a three-stage anonymisation pipeline: identification, de-identification, and quasi-identifier dimension evaluation. The pipeline was implemented, validated, and tested on two mock RWD datasets (500 and 1000 rows). Privacy was assessed using k-anonymity, l-diversity, and t-closeness; utility was measured by non-uniform entropy (NUE). The review yielded two studies on QID/SA identification and five on utility metrics. Applying the pipeline, attributes were classified by re-identification risk using alpha and beta thresholds (25 percent/1 percent for 500 rows; 10 percent/1 percent for 1000 rows). Privacy metrics improved k-anonymity from 1 to 4 (500 rows) and 1 to 110 (1000 rows). NUE scores were 69.26 percent and 69.05 percent, respectively, indicating consistent utility despite varying privacy gains. We present a GDPR-compliant anonymisation pipeline for healthcare RWD that provides a reproducible approach to QID/SA identification and utility evaluation; publicly available code promotes standardisation, data privacy, and open science.

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Hamza Khan, Lore Menten, Liesbet M. Peeters. 2025-06-03. An Algorithmic Pipeline for GDPR-Compliant Healthcare Data Anonymisation: Moving Toward Standardisation. https://arxiv.org/abs/2506.02942

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