Paper 2019/223

Optimized Homomorphic Encryption Solution for Secure Genome-Wide Association Studies

Marcelo Blatt, Alexander Gusev, Yuriy Polyakov, Kurt Rohloff, and Vinod Vaikuntanathan


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 solution for a smaller dataset was awarded co-first place in iDASH'18 Track 2: ``Secure Parallel Genome Wide Association Studies using HE''. Many of the HE optimizations presented in our paper are general-purpose, and can be used in solving challenging problems with large datasets in other application domains.

Note: Fixed a typo

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Publication info
Published elsewhere. Minor revision. BMC Medical Genomics 13, 83 (2020)
implementationpublic-key cryptographygenome-wide associate studies
Contact author(s)
ypolyakov @ duality cloud
2020-07-24: last of 3 revisions
2019-02-27: received
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      author = {Marcelo Blatt and Alexander Gusev and Yuriy Polyakov and Kurt Rohloff and Vinod Vaikuntanathan},
      title = {Optimized Homomorphic Encryption Solution for Secure Genome-Wide Association Studies},
      howpublished = {Cryptology ePrint Archive, Paper 2019/223},
      year = {2019},
      doi = {10.1186/s12920-020-0719-9},
      note = {\url{}},
      url = {}
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