A federated future to support genomic medicine microbiologystudy

The Federated European Genome-phenome Archive (FEGA) is transforming how sensitive human genomic data is shared and accessed. Building on the longstanding European Genome-phenome Archive (EGA)—a database for human genetic, phenotypic, and clinical data—FEGA enables researchers to securely discover and analyze human genomic data while ensuring compliance with national and international data protection regulations.

By decentralizing data storage across national nodes, FEGA ensures data remains secure within its country of origin while also being accessible to researchers worldwide.

FEGA’s paper has been published in Nature Genetics.

From centralization to federation

In the last two decades, as the volume of human genomic datasets grew larger and legal requirements to access the data were tightened, it became clear that a single repository like the EGA could no longer meet the global community’s needs. The EGA team proposed adopting a federated model, in line with local legal and ethical frameworks, while also allowing access to these data globally.

What is a federated model?

A federated model is a distributed network in which multiple entities operate under a common framework. Each node or entity retains control over its own data and processes, while agreed-upon standards and protocols allow them to collaborate and share data globally. This approach enables secure and coordinated data sharing across different countries, ensuring that local legal and ethical requirements are met.

EMBL-EBI and the Center for Genomic Regulation (CRG) in Spain have co-managed the EGA since 2008. Together, they helped shape the federated data-sharing model now used by FEGA.

Two major projects also helped make FEGA’s federated model possible. The ELIXIR-EXCELERATE initiative—a program supporting international data sharing—helped lay the early groundwork with proof-of-concept studies. ELIXIR-CONVERGE— a project to standardize data management across Europe—has accelerated the development of the first national FEGA nodes.

“In the early days of setting up FEGA, we were grappling with the limitations of a centralized system. It felt like we were facing enormous challenges,” said Mallory Freeberg, Human Genomics Team Leader at EMBL-EBI.

“Through collaboration, we overcame those obstacles to build the foundations of FEGA. I’m immensely proud to have been part of this endeavor. It’s an exciting time for this network, and there is so much more to achieve as we continue pushing the boundaries.”

By 2020, the foundation for FEGA’s federated model was set, leading to the official launch of the resource in September 2022. The first collaboration agreements were signed by nodes in Sweden, Norway, Finland, Germany, and Spain.

Impact through global collaboration

“Global health challenges like pandemics and rare diseases do not respect national borders,” said Arcadi Navarro, ICREA Research Professor at the Universitat Pompeu Fabra and Director of the EGA team at the Center for Genomic Regulation.

“By expanding beyond Europe and adding the Canadian node, we consolidate the Federated EGA as the world’s most comprehensive, secure, and diverse resource for genomic and health data to tackle these urgent questions.”

The first datasets were submitted to FEGA by late 2023, proving the federated model in practice. These data have since continued to grow, with FEGA now holding nearly 40 datasets.

The network has also expanded with nodes in Portugal and Poland joining in 2023, and Canada in December 2024. Discussions are also ongoing with many other collaborators, including a Swiss node who are currently “Observers’ of FEGA.

“This milestone partnership provides Canadian researchers with a swift, secure connection to global collaborators, fostering scientific and clinical innovation while continuing to uphold our commitment to privacy and compliance,” said Steven Jones, lead for the CGA node and Co-Director of Canada’s Michael Smith Center for Genome Sciences at BC Cancer.

FEGA aims to support global research in disease diagnosis and personalized treatment. The following are a few examples.

A federated future

Looking ahead, FEGA will also continue to refine its metadata standards, including those developed as part of the Global Alliance for Genomics and Health (GA4GH), to increase data discoverability and interoperability. This will support future integration of multi-omics datasets, as well as clinical health records for a more complete picture of disease biology.

Efforts to support more data submissions are also underway, including the development of training materials and the establishment of FEGA node-specific help desks to assist local users. Federated analytics are also in the works, which will enable secure, multi-node analyses without the need to download sensitive data.

As FEGA evolves, it sets a high standard for global human genomics data sharing. By integrating multi-omics and clinical data, FEGA will support research towards improved personalized medicine and help inform public health strategies to ultimately improve patient outcomes.