Privacy-Preserving Federated Genome-Wide Association Studies via Dynamic Sampling

Authors

Xinyue Wang
Leonard Dervishi
Wentao Li
Erman Ayday
Xiaoqian Jiang
Jaideep Vaidya

Publication Date

10-3-2023

Journal

Bioinformatics

Abstract

MOTIVATION: Genome-wide association studies (GWAS) benefit from the increasing availability of genomic data and cross-institution collaborations. However, sharing data across institutional boundaries jeopardizes medical data confidentiality and patient privacy. While modern cryptographic techniques provide formal secure guarantees, the substantial communication and computational overheads hinder the practical application of large-scale collaborative GWAS.

RESULTS: This work introduces an efficient framework for conducting collaborative GWAS on distributed datasets, maintaining data privacy without compromising the accuracy of the results. We propose a novel two-step strategy aimed at reducing communication and computational overheads, and we employ iterative and sampling techniques to ensure accurate results. We instantiate our approach using logistic regression, a commonly used statistical method for identifying associations between genetic markers and the phenotype of interest. We evaluate our proposed methods using two real genomic datasets and demonstrate their robustness in the presence of between-study heterogeneity and skewed phenotype distributions using a variety of experimental settings. The empirical results show the efficiency and applicability of the proposed method and the promise for its application for large-scale collaborative GWAS.

AVAILABILITY AND IMPLEMENTATION: The source code and data are available at https://github.com/amioamo/TDS

Keywords

Humans, Privacy, Genome-Wide Association Study, Genomics, Confidentiality, Software

DOI

10.1093/bioinformatics/btad639

PMID

37856329

PMCID

PMC10612407

PubMedCentral® Posted Date

10-19-2023

PubMedCentral® Full Text Version

Post-print

Published Open-Access

yes