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Toward GDPR compliance with the Helmholtz Munich genotype imputation server

Nature Genetics volume 56, pages 2580–2581 (2024)Cite this article

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Genomics has the potential to revolutionize healthcare, empowering personalized disease management, including precision prevention. Genome-wide association studies (GWAS) have been instrumental in generating new biological insights into complex human diseases1. The power of GWAS can be increased by increasing sample size through meta-analysis, which requires the imputation and analysis of genotypes that may be untyped across some studies. Imputation relies on the availability of phased haplotype reference panels of whole-genome-sequenced individuals2. These are not amenable to sharing with researchers who need to impute their GWAS data, primarily for reasons of data access and security, dataset size, and scale of computing resources required to enable imputation. Imputation servers have, therefore, been developed to provide a solution: researchers upload their genotyped dataset to the imputation server that hosts the reference panels and imputation machinery, where the data are imputed, and then downloaded back to the researchers’ individual local computing environment. There are a number of imputation servers that serve the global community of researchers, including two based in the USA (University of Michigan, https://imputationserver.sph.umich.edu/index.html and TOPMed, https://imputation.biodatacatalyst.nhlbi.nih.gov/), one based in the UK (Wellcome Sanger Institute, https://imputation.sanger.ac.uk/?about=1) and one based at Kiel University in Germany (https://hybridcomputing.ikmb.uni-kiel.de). Here, we have developed a European Union (EU)-based imputation server serving the community at large, based in Munich, Germany (https://imputationserver.helmholtz-munich.de/), to assist users in complying with their General Data Protection Regulation (GDPR) requirements.

The need for EU-based imputation servers arises from restrictions imposed by GDPR law3, a comprehensive data privacy law in the EU. Genetic data are considered a special category of personal data under GDPR, and hence they are subject to strict data sharing rules and safeguards4. Uploading of genotype data to imputation servers not residing within the EU or covered by an adequacy agreement constitutes a breach of GDPR, unless explicitly covered in informed consent forms for the respective study. Here, we introduce the Helmholtz Munich Imputation Server, designed to provide a cost-free genotype imputation service in a GDPR-compliant manner for EU-based researchers, as well as for researchers globally.

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Fig. 1: Overview of the Helmholtz Munich Imputation Server, highlighting the major processing steps.

Code availability

All code is available at https://github.com/hmgu-itg/cloudgene (https://doi.org/10.5281/zenodo.13897820) and https://github.com/hmgu-itg/imputationserver (https://doi.org/10.5281/zenodo.13898518).

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Acknowledgements

The authors are grateful to A. Chowdhary, S. Horn, L. Forer and S. Schoenherr for their input.

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Authors and Affiliations

  1. Institute of Translational Genomics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany

    N. William Rayner, Young-Chan Park, Andrei Barysenka & Eleftheria Zeggini

  2. Institute for Biomedicine, Eurac Research, Bolzano, Italy

    Christian Fuchsberger

  3. Institute of Genetic Epidemiology, Medical University of Innsbruck, Innsbruck, Austria

    Christian Fuchsberger

  4. TUM School of Medicine and Health, Technical University of Munich and Klinikum Rechts der Isar, Munich, Germany

    Eleftheria Zeggini

Authors
  1. N. William Rayner
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  2. Young-Chan Park
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  3. Christian Fuchsberger
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  4. Andrei Barysenka
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  5. Eleftheria Zeggini
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Corresponding authors

Correspondence to N. William Rayner or Eleftheria Zeggini.

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The authors declare no competing interests.

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Nature Genetics thanks Magdalena Kogout and the other, anonymous reviewer(s) for their contribution to the peer review of this work.

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Rayner, N.W., Park, YC., Fuchsberger, C. et al. Toward GDPR compliance with the Helmholtz Munich genotype imputation server. Nat Genet 56, 2580–2581 (2024). https://doi.org/10.1038/s41588-024-02012-1

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