🧬🔒 PP-GWAS: Privacy Preserving Multi-Site Genome-wide Association Studies

This repository is associated with the paper titled "PP-GWAS: Privacy Preserving Multi-Site Genome-wide Association Studies". It provides all the necessary code to reproduce the experiments described in the paper, including synthetic dataset generation, dataset loading, distributed computations, and experiment results.

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📂 Repository Structure

• Code/
  PP-GWAS implementation for HPC clusters (SLURM-ready).
  Default outputs are written to test_site/.

• Data_Generation/
  Scripts for simulating synthetic genotype/phenotype data with pysnptools.
  Generated datasets are saved to test_site/ by default.

• REGENIE/
  Instructions to restructure synthetic data into REGENIE-supported formats and run REGENIE.

• Results/
  .txt outputs from the experiments reported in the paper.

• local_run/
  Self-contained setup (Jupyter notebook + simple GUI) for running PP-GWAS locally on small datasets.

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🧭 Pick a Workflow

• Prepare data and run PP-GWAS locally (small data): use local_run/.

• Prepare data and run PP-GWAS on a cluster: use Code/. Outputs go to test_site/.

• Run REGENIE: go to REGENIE/ and follow the steps there.

• Prepare data: use Data_Generation/; outputs appear in test_site/.

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📝 Citation

Please consider citing our work if it is beneficial to your research.

• Paper

@article{swaminathan2024pp,
  title={PP-GWAS: Privacy Preserving Multi-Site Genome-wide Association Studies},
  author={Swaminathan, Arjhun and Hannemann, Anika and {\"U}nal, Ali Burak and Pfeifer, Nico and Akg{\"u}n, Mete},
  journal={arXiv preprint arXiv:2410.08122},
  year={2024}
}

• Code

@software{swaminathan2025code,
  author   = {Swaminathan, Arjhun and Hannemann, Anika and {\"U}nal, Ali Burak and Pfeifer, Nico and Akg{\"u}n, Mete},
  title    = {PP-GWAS: Privacy Preserving Multi-Site Genome-wide Association Studies — code},
  version  = {v1.0},
  publisher= {Zenodo},
  year     = {2025},
  doi      = {10.5281/zenodo.17580283},
  url      = {https://doi.org/10.5281/zenodo.17580283}
}

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📜 License

This project is released under the MIT License. See LICENSE for details.

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📧 Contact for Questions

[email protected], [email protected]