Optimized Homomorphic Encryption Solution for Secure Genome-Wide Association Studies

Marcelo Blatt; Alexander Gusev; Yuriy Polyakov; Kurt Rohloff; Vinod Vaikuntanathan

Paper 2019/223

Optimized Homomorphic Encryption Solution for Secure Genome-Wide Association Studies

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

Metadata

Available format(s): PDF
Category: Implementation
Publication info: Published elsewhere. Minor revision. BMC Medical Genomics 13, 83 (2020)
DOI: 10.1186/s12920-020-0719-9
Keywords: implementation public-key cryptography genome-wide associate studies
Contact author(s): ypolyakov @ duality cloud
History: 2020-07-24: last of 3 revisions; 2019-02-27: received; See all versions
Short URL: https://ia.cr/2019/223
License: CC BY

BibTeX

@misc{cryptoeprint:2019/223,
      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{https://eprint.iacr.org/2019/223}},
      url = {https://eprint.iacr.org/2019/223}
}