Human Data Use Case

DNA and RNA sequencing have become increasingly important in medical and translational research. The data generated from these techniques has led to a huge demand for secure means to store, transfer and analyse the human biomedical data that has been consented for research.

The Use Case takes the European Genome-phenome Archive (EGA) as its primary data source, access to which is controlled. The EGA allows an authorised user to search sequenced material, patient samples stored in biobanks, and the metadata around patients (their illnesses, treatments, outcomes). It also queries national search engines on behalf of the users. Datasets can then be downloaded into an EGA compatible cloud or cluster local to the researcher.

The Human Data Use Case extends and generalises the system of access authorisation and secure data transfer developed in the EGA. It aims to provide a framework for the secure submission, archiving, dissemination and analysis of human biomedical data across Europe.

What the Use Case does

  • Provides life scientists with a sustainable infrastructure for the storage, coordination and distribution of human data. It will provide standardised tools that researchers can use to discover and access this data.
  • Brings together experts from ELIXIR Nodes and external partners to develop a long-term management policy for human data.
  • Ensures that human data in ELIXIR services is handled in accordance with the appropriate legal framework.

Current activities

TraIT (Translational research IT)

TraIT is a project by the Dutch Center for Translational Molecular Medicine (CTMM) to implement an IT infrastructure for translational biomedical research. In 2015 ELIXIR initiated a collaborative project with TraIT with two main goals:

  1. To connect TraIT’s data analyses platform and the data portal TranSMART with the European Genome-phenome Archive (EGA), a joint project between EMBL-EBI and the CRG in Barcelona.
  2. To enable the Dutch researchers to use the EGA as long-term storage for raw data from all TraIT projects. Once this project is completed, the TraIT data stored in EGA will be available on demand to the TraIT researchers for further analysis in a cloud service, using the Galaxy workflow.


OncoTrack is an Innovative Medicine Initiative (IMI) project pioneering the use of large-scale genomics to improve the early diagnosis of colon cancer. It began working with ELIXIR on a joint feasibility project to explore options for the provision of long-term storage and data-discovery services for data generated within the project.

Global Alliance for Genomics and Health: Beacons Project

In 2015, ELIXIR initiated the ELIXIR Beacon project with the Global Alliance for Genomics and Health (GA4GH) to provide data-discovery services for genomics that balance efficient data sharing and data protection.

The goal of the project is to provide consent-based access to genomic data in the EGA and national resources by implementing GA4GH Beacons that will scale to support data discovery across all the ELIXIR Data Nodes. Designed to be technically simple so that they can be implemented widely, Beacons represent an important step towards collaborative, responsible sharing of human genomic data in Europe.

How the Use Case is organised

Serena Scollen is Head of Human Genomics and Translational Data and Susheel Varma is the Technical Coordinator of the Use Case at the ELIXIR Hub. The work of the Human Data Use Case is defined in Work Package 9 of the ELIXIR EXCELERATE project. The Work Package is led by Jordi Rambla and Thomas Keane.

Serena Scollen
Serena Scollen
Jordi Rambla
Jordi Rambla
(ELIXIR Spain)
Thomas Keane
Thomas Keane
Susheel Susheel
Susheel Varma

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