Optimized homomorphic encryption solution for secure genome-wide association studies

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

Research output: Contribution to journalArticlepeer-review

2 Scopus citations

Abstract

Background: 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. Methods: 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. Results: 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". Conclusions: 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.

Original languageEnglish (US)
Article number83
JournalBMC Medical Genomics
Volume13
DOIs
StatePublished - Jul 21 2020
Externally publishedYes

All Science Journal Classification (ASJC) codes

  • Genetics
  • Genetics(clinical)

Keywords

  • Cryptography
  • Genome-wide association studies
  • Homomorphic encryption

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