Maliciously Secure and Efficient Large-Scale Genome-Wide Association Study With Multi-Party Computation

Abstract

Genome-Wide Association Study (GWAS) aims at detecting the association between diseases and Single-Nucleotide Polymorphisms (SNPs) with statistical techniques and has great potential for disease diagnosis. To obtain high-quality results, GWAS requires large-scale genomic data containing individuals’ privacy information. Thus, how to improve the efficiency of GWAS while protecting the privacy of genomic data becomes a critical challenge. In this paper, we propose a secure and efficient GWAS scheme. By using secure three-party computation, we present a series of protocols, i.e., Secure Quality Control, Secure Principle Component Analysis, Secure Cochran-Armitage trend test, and Secure Logistic Regression, to cover the most significant procedures of secure GWAS. In these protocols, a new comparison protocol is designed to reduce communication and improve efficiency. Furthermore, by extending the above comparison protocol to be maliciously secure and utilizing other technologies, e.g., consistency check, we extend the whole GWAS scheme to malicious security with rationally additional overhead. Experimental results demonstrate that our protocols achieve about 33% performance improvement than the state-of-art secure GWAS scheme using two-party computation in terms of runtime and communication in the semi-honest setting. The cost of our scheme in the malicious setting is around 1.5X than that in the semi-honest setting.