Lighting beacons for data access in genomic research

ELIXIR has partnered 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 new collaboration, called "Beacon", will kick off in September 2015. Its goal is to provide consent-based access to genomic data in the European Genome-phenome Archive (EGA, a joint project of EMBL-EBI and the CRG in Barcelona) as well as national resources in Finland, Sweden and the Netherlands by establishing GA4GH Beacons.

GA4GH Beacons allow researchers to discover datasets that are available through many participating institutions, providing a single point of access. 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.

An important objective of this ELIXIR Pilot Action is to provide a reference implementation that will scale to support data discovery across all the ELIXIR Data Nodes.

Niklas Blomberg, Director of ELIXIR, said: "This collaboration between ELIXIR and the GA4GH is a good example of how ELIXIR can help scale up existing standards and good practices in data sharing and data discovery. In addition to the three Beacons, we will provide a technical reference and training to support the establishment of further Beacons in the ELIXIR infrastructure."

Designed for repositories with individual-level data from biomedical research projects, Beacons follow a three-tier data access system: public, registered and controlled.

"Beacons enable data discovery in a way that mitigates the various risks associated with sharing individual data from research participants," says Paul Flicek, Head of Genes, Genomes and Variation resources at EMBL-EBI. "The three-tier system, in which users in each tier have different access rights and can obtain increased level of information, helps balance the desire for data sharing with the need for data protection."

Beacons simplify the way people search for and request access to potentially identifiable data in international and national genomic data resources.

"Beacons will take some of the frustration out of searching controlled-access resources," explains Stephen Keenan of EMBL-EBI, manager of the GA4GH Data Working Group. "Users can ask straightforward questions like, ‘Do any of these data resources have genomes with this allele at that position?’ Beacons aggregate responses from many sources into a single search result, which provides a sensible starting point for making a data access request."

The work of GA4GH is a good example of collaboration between the institutions based on the Wellcome Genome Campus: the Wellcome Trust Sanger Institute, EMBL-EBI and ELIXIR.

"The Sanger institute is one of the three hosts and a funder of the Global Alliance, but it is a true campus-wide effort which brings together the unique skills and expertise of our three entities. This makes the Genome Campus the largest concentration of people directly working on GA4GH activities anywhere in the world," said Julia Wilson, Associate Director at the Sanger Institute.

Related story: Global Alliance for Genomics and Health Marks Two Years of Progress (pdf)

About Global Alliance for Genomics and Health

The Global Alliance for Genomics and Health is an international, non-profit alliance formed to help accelerate the potential of genomic medicine to advance human health. Bringing together over 300 leading organizations working in healthcare, research, disease and patient advocacy, life science, and information technology, GA4GH Members are working together to create a common framework of tools, methods, and harmonized approaches and supporting demonstration projects to enable the responsible, voluntary, and secure sharing of genomic and clinical data.


ELIXIR, the European life-science infrastructure for biological information, brings together Europe’s major life-science data archives and, for the first time, connects these with national bioinformatics infrastructures throughout ELIXIR’s member states. By coordinating local, national and international resources the ELIXIR infrastructure will meet the data-related needs of Europe’s 500,000 life-scientists. ELIXIR supports users addressing the Grand Challenges in diverse domains ranging from marine research via plants and agriculture to health research and medical sciences. 


Fri 12 June 2015