Toward owner governance in genomic data privacy with Governome

Advancements in sequencing technologies grant individuals unprecedented access to their genomic data. However, existing data management systems or protocols are inadequate in privacy protection, limiting individuals' control over their genomic information, hindering data sharing, and posing challenges for biomedical research. Therefore, demand exists for an owner-governed system fulfilling owner authority, life cycle data encryption, and verifiability simultaneously. Here, we realized Governome, an owner-governed data management system empowering individuals with real-time control over their genomic data. Governome leverages a blockchain to manage transactions and permissions, granting data owners dynamic permission management with full transparency on data usage. It uses homomorphic encryption and zero-knowledge proofs to enable genomic data storage and computation in an encrypted and verifiable form throughout its life cycle. Governome can support versatile genomic applications. We implemented and tested individual variant query, cohort study, genome-wide association study (GWAS) analysis, and forensics on 2,504 1000 Genomes Project (1kGP) genomes, demonstrating its robustness and scalability. Governome is open-source at https://github.com/HKU-BAL/Governome.