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Cell Syst DOI:10.1016/j.cels.2021.08.001

Privacy-preserving genotype imputation in a trusted execution environment.

Publication TypeJournal Article
Year of Publication2021
AuthorsDokmai, N, Kockan, C, Zhu, K, Wang, X, S Sahinalp, C, Cho, H
JournalCell Syst
Date Published2021 Aug 20

Genotype imputation is an essential tool in genomics research, whereby missing genotypes are inferred using reference genomes to enhance downstream analyses. Recently, public imputation servers have allowed researchers to leverage large-scale genomic data resources for imputation. However, privacy concerns about uploading one's genetic data to a server limit the utility of these services. We introduce a secure hardware-based solution for privacy-preserving genotype imputation, which keeps the input genomes private by processing them within Intel SGX's trusted execution environment. Our solution features SMac, an efficient and secure imputation algorithm designed for Intel SGX, which employs a state-of-the-art imputation strategy also utilized by existing imputation servers. SMac achieves imputation accuracy equivalent to existing tools and provides protection against known side-channel attacks on SGX while maintaining scalability. We also show the necessity of our enhanced security by identifying vulnerabilities in existing imputation software. Our work represents a step toward privacy-preserving genomic analysis services.


Alternate JournalCell Syst
PubMed ID34450045