Optimized homomorphic encryption solution for secure genome-wide association studies.

BMC Medical Genomics
Marcelo BlattVinod Vaikuntanathan

Abstract

Genome-Wide Association Studies (GWAS) refer to observational studies of a genome-wide set of genetic variants across many individuals to see if any genetic variants are associated with a certain trait. A typical GWAS analysis of a disease phenotype involves iterative logistic regression of a case/control phenotype on a single-neuclotide polymorphism (SNP) with quantitative covariates. GWAS have been a highly successful approach for identifying genetic-variant associations with many poorly-understood diseases. However, a major limitation of GWAS is the dependence on individual-level genotype/phenotype data and the corresponding privacy concerns. We present a solution for secure GWAS using homomorphic encryption (HE) that keeps all individual data encrypted throughout the association study. Our solution is based on an optimized semi-parallel GWAS compute model, a new Residue-Number-System (RNS) variant of the Cheon-Kim-Kim-Song (CKKS) HE scheme, novel techniques to switch between data encodings, and more than a dozen crypto-engineering optimizations. Our prototype can perform the full GWAS computation for 1,000 individuals, 131,071 SNPs, and 3 covariates in about 10 minutes on a modern server computing node (with 28 cores). Our ...Continue Reading

References

Apr 19, 2018·JMIR Medical Informatics·Miran KimXiaoqian Jiang

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Citations

May 14, 2020·Proceedings of the National Academy of Sciences of the United States of America·Marcelo BlattShafi Goldwasser

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Software Mentioned

iDASH
mathcal
SEAL
CKKS
PALISADE
UTHealth

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