# The Portuguese Beacon: sharing genomic variant data safely

## TL;DR

The paper introduces a privacy-protecting genomic data discovery system called the Portuguese Beacon, which prevents re-identification of individuals while allowing researchers to explore genomic datasets.

## Contribution

The first Beacon endpoint to implement a re-identification prevention algorithm for genomic data discovery.

## Key findings

- The Portuguese Beacon uses a re-identification prevention algorithm to protect data subject privacy.
- The algorithm's impact on data discovery depends on the size of the genomic dataset.
- The system supports the goals of the European Genomic Data Infrastructure project.

## Abstract

Projects such as the European 1+ Million Genomes initiative and the European Genomic Data Infrastructure project are paving the way towards the age of genomic medicine. To address the challenge of balancing genomic data privacy with biomedical research, the proposed solution is to enable discovery of private datasets through public metadata. Yet enabling data discovery based on genomic variants present in a dataset—which is the goal of Beacon—raises the risk of re-identifying data subjects. We have implemented a Portuguese Beacon endpoint within the scope of the European Genomic Data Infrastructure project, which features a re-identification prevention algorithm to ensure the privacy of data subjects—the first Beacon endpoint to do so. We assessed the impact of the algorithm on data discovery, which varies with the size of the Beacon dataset.