Quantum-resilient blockchain framework for privacy-preserving genomic data sharing and analysis

Abstract

The rapid expansion of Next-Generation Sequencing (NGS) technologies has positioned genomic data at the forefront of personalized healthcare. Yet, its sensitive nature introduces significant challenges related to security, privacy, and integrity—especially in the face of emerging quantum computing threats. This paper presents a quantum-resilient blockchain framework that integrates post-quantum cryptographic primitives, privacy-preserving machine learning, and decentralized data governance to ensure secure sharing and inference of genomic data. Leveraging lattice-based encryption schemes such as CRYSTALS-Kyber and Dilithium within a Hyperledger Fabric-based permissioned blockchain, the system guarantees resistance to quantum adversaries while maintaining confidentiality and auditability of genomic transactions. The architecture employs transformer-based genomic encoders for high-fidelity mutation detection and expression profiling, alongside hybrid data structures (Cuckoo filters and B+ trees) for fast, privacy-preserving variant querying. Smart contracts enforce an incentive-driven reward-penalty model, ensuring fair access while disincentivizing dishonest behavior. Empirical evaluations demonstrate a transaction throughput of 125 transactions per second, an average block formation time of 250 ms, and a post-quantum signature verification latency of 3.8 ms. The system achieved a genomic mutation detection accuracy of 97.31% and reduced query latency by up to 55% compared to existing methods. Additionally, it exhibited 1.75$\times$ faster access response times and 40% lower on-chain resource consumption by utilizing optimized off-chain storage and computation. Beyond theoretical design, our framework highlights practical integration pathways: (i) large post-quantum key sizes are managed through hybrid key encapsulation and off-chain storage, (ii) blockchain scalability issues are mitigated via optimized consensus and cross-network channeling, achieving high throughput and low latency, and (iii) quantum protocols such as QKD and Grover-accelerated search are incorporated in a modular fashion to address state preparation and storage challenges. This end-to-end quantum-secure framework offers a scalable, high-performance solution for collaborative genomic research, enabling compliance with emerging data privacy regulations while future-proofing against quantum-era threats.