Genomic Privacy Risks in GWAS Summary Statistics

This repository contains the scripts used in the research:
Lan Ao, Pawitan Yudi, Shen Xia (2025) Genomic privacy risks in GWAS summary statistics eLife 14:RP108844

Repository Overview

This repository is organized to facilitate the reproduction and understanding of the analyses conducted in the study. Below is the structure and description of the included scripts:

scripts  
├── 01-theoretical-simulation.ipynb
├── 02-simulation-in-1kg-eur
├── 03-GTEx
└── 04-sample-identification

• 01-theoretical-simulation.ipynb This notebook contains scripts for theoretical simulations exploring genomic privacy risks. It provides a mathematical and conceptual foundation for the study.

• 02-simulation-in-1kg-eur Scripts in this folder use genotype data from the 1000 Genomes Project (European population) to conduct empirical simulations, evaluating privacy risks in real-world genomic datasets.

• 03-GTEx This directory includes scripts for applying privacy risk assessments to GTEx data.

• 04-sample-identification Scripts in this folder focus on sample identification tests, demonstrating potential vulnerabilities in GWAS summary statistics.

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