Secure and federated genome-wide association studies for biobank-scale datasets

Sharing data across institutions for genome-wide association studies (GWAS) would enhance the discovery of genetic variation linked to health and disease^1,2. However, existing data-sharing regulations limit the scope of such collaborations³. Although cryptographic tools for secure computation promise to enable collaborative analysis with formal privacy guarantees, existing approaches either are computationally impractical or do not implement current state-of-the-art methods^4-6. We introduce secure federated genome-wide association studies (SF-GWAS), a combination of secure computation frameworks and distributed algorithms that empowers efficient and accurate GWAS on private data held by multiple entities while ensuring data confidentiality. SF-GWAS supports widely used GWAS pipelines based on principal-component analysis or linear mixed models. We demonstrate the accuracy and practical runtimes of SF-GWAS on five datasets, including a UK Biobank cohort of 410,000 individuals, showcasing an order-of-magnitude improvement in runtime compared to previous methods. Our work enables secure collaborative genomic studies at unprecedented scale.