Efficient privacy-preserving whole-genome variant queries

Abstract

Motivation Diagnosis and treatment decisions on genomic data have become widespread as the cost of genome sequencing decreases gradually. In this context, disease-gene association studies are of great importance. However, genomic data is very sensitive when compared to other data types and contains information about individuals and their relatives. Many studies have shown that this information can be obtained from the query-response pairs on genomic databases. In this work, we propose a method that uses secure multi-party computation (MPC) to query genomic databases in a privacy-protected manner. The proposed solution privately outsources genomic data from arbitrarily many sources to the two non-colluding proxies and allows genomic databases to be safely stored in semi-honest cloud environments. It provides data privacy, query privacy, and output privacy by using XOR-based sharing and unlike previous solutions, it allows queries to run efficiently on hundreds of thousands of genomic data. Results We measure the performance of our solution with parameters similar to real-world applications. It is possible to query a genomic database with 3, 000, 000 variants with five genomic query predicates under 400 ms. Querying 1, 048, 576 genomes, each containing 1, 000, 000 variants, for the presence of five different query variants can be achieved approximately in 6 minutes with a small amount of dedicated hardware and connectivity. These execution times are in the right range to enable real-world applications in medical research and healthcare. Unlike previous studies, it is possible to query multiple databases with response times fast enough for practical application. To the best of our knowledge, this is the first solution that provides this performance for querying large-scale genomic data. Availability https://gitlab.com/DIFUTURE/privacy-preserving-variant-queries Supplementary information Supplementary data are available at Bioinformatics online.

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