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Title: Privacy-preserving federated genome-wide association studies via dynamic sampling
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.

 
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Award ID(s):
2141622
NSF-PAR ID:
10501657
Author(s) / Creator(s):
; ; ; ; ;
Editor(s):
Nikolski, Macha
Publisher / Repository:
Oxford
Date Published:
Journal Name:
Bioinformatics
Volume:
39
Issue:
10
ISSN:
1367-4811
Format(s):
Medium: X
Sponsoring Org:
National Science Foundation
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