ELIXIR Beacons to facilitate sharing of genomics data in Europe

Beacon logo

Scientists across the world can now discover and query data from genomics projects in six different countries in Europe. This has been a success of the ELIXIR collaboration with the Global Alliance for Genomics and Health (GA4GH) on the Beacon project which has been recently expanded and extended into 2017.

The Beacon Project is developing an open sharing platform that helps genomic data centres to make their data discoverable. Beacons allow researchers to query individual datasets to determine whether they contain a specific genetic variant of interest. For example, researchers can ask Beacons simple questions like, ‘Do your data resources have genomes with this allele at that position?’

The first stage of the project (2015-2016) resulted in lighting Beacons in five ELIXIR Nodes - Sweden, Finland, France, Switzerland and Belgium, and in the European Genome-phenome archive (EGA, a joint project of EMBL-EBI and the Center for Genomic Regulation in Barcelona, ELIXIR Spain). Another Beacon will soon be launched in ELIXIR Netherlands. Each ELIXIR Beacon makes one or more genomics datasets discoverable to the international research community.

“The ELIXIR Beacon project is a great example of the added value that ELIXIR brings to its members and the life science community,” said Serena Scollen, ELIXIR Head of Human Genomics and Translational Data. “Working with the Global Alliance for Genomics and Health, we can develop and promote international standards and best practices in data sharing and data discovery and facilitate their adoption in ELIXIR Nodes.”

“Indeed, in the post-genomic era we need to share our data to maximise the knowledge we gain. In the ELIXIR Beacon project we aim to enable researchers to examine their own cohorts in the context of global knowledge by enabling data sharing and discoverability at various levels,” said Macha Nikolski, Head of the Head of the Bordeaux Bioinformatics Center (CBiB), Université Bordeaux and leader the French Beacon initiative.

Ilkka Lappalainen, Biomedical Service Development Manager of ELIXIR Finland, said: “We work closely with the major European biobanks and national cohorts owners to understand their requirements for data sharing. What is important is that  the data ownership does not change when making the data discoverable through a Beacon. We all invite data owners -  if you have a data set that you would like to make discoverable, contact us and we will help you through this process.”

The ELIXIR Beacon project also developed a three-tier data access system which reduces risks to personal data privacy associated with sharing personally identifiable data. Building on the ELIXIR Authentication and Authorization Infrastructure (AAI), researchers can access the data in three tiers (public, registered and controlled), each with increased levels of scrutiny around who can use specific data and for what research purposes. The first ELIXIR Beacon that implemented the three-tier system is in Finland, other Beacons will follow in 2017.

Mikael Linden, the ELIXIR AAI leader said: “As we are dealing with personal data, privacy and security are absolutely essential. However, this often means researchers have to go through lengthy administrative procedures before accessing the data. The ELIXIR AAI reduces this administrative overhead: on the registered tier, the data access requests from registered researches are served automatically, using credentials from their home university or from services like ORCID. That way, researchers receive access to the data immediately and can focus on the research.”

In 2017 ELIXIR and GA4GH expand their partnership to create a network of ELIXIR Beacons and add new security measures to attract stakeholders with more sensitive datasets. The ultimate goal is to make sure human data generated in Europe can be found by any researcher worldwide.

More information:

For data owners who want to get involved in Beacon
Serena Scollen, ELIXIR head of Human Genomics and Translational Data, serena.scollen [at] elixir-europe.org

For journalists:
Premysl Velek, ELIXIR Communications Officer, premysl.velek [at] elixir-europe.org

Contact detail to individual Beacons and ELIXIR Nodes are provided below in Notes to editors.

Notes to editors

The datasets made available to the international genomics community through ELIXIR Beacons include national flagship genomics projects as well as population-based studies


(i) The Three-City Study is a population-based longitudinal study (1999-2012) of the relation between vascular diseases and dementia in people aged 65 years and older from Bordeaux, Dijon and Montpellier. (ii) Genomic disease heterogeneity of HER2-positive breast cancer. Thanks to the French ELIXIR beacon, these datasets (and 1,289,912 variants) are now for the first time accessible to the international research community.

Contact: Macha Nikolski, macha.nikolski [at] u-bordeaux.fr


The ELIXIR Beacon in Sweden gives access to the whole-genome variant frequencies for 1000 Swedish individuals generated within the SweGen project which is part of the Swedish Genomes Program established by SciLifeLab. This cohort reflects a cross-section of the Swedish population, and was selected by using high-density SNP-array data from a larger nation-wide population based cohort.
https://swefreq.nbis.se/#/ (dataset described here)

Contact: Niclas Jareborg, niclas.jareborg [at] nbis.se


The Finnish beacons makes available the Finnish samples sequenced in the 1000genomes project. It is the first beacon connected to the ELIXIR AAI to demonstrate access to the data for registered researchers. The Beacon will release national allele frequencies publicly and provide registered access to the aggregated information from the cohorts used for defining the national allele frequencies during 2017. http://elixir-beacon.csc.fi/#/

Contact: Ilkka Lappalainen, ilkka.lappalainen [at] csc.fi


The Swiss Beacon represents an interface to the arrayMap cancer genome data repository, implementing a forward looking version of the Beacon protocol. arrayMap is a curated reference database targeting structural somatic variations data in human cancer. The arrayMap database currently contains data from 56961 cancer genome profiles. This Swiss Beacon is a collaboration between two groups at SIB Swiss Institute of Bioinformatics, namely the Computational Oncogenomics group led by Michael Baudis, professor at University of Zurich and the SIB technology group, led by Heinz Stockinger.

Contact: Michael Baudis, mbaudis [at] imls.uzh.ch


The ELIXIR Belgium Beacon provides access to exome variant frequencies from patients with rare genetic disorders. The beacon is also supported by the Belgian Medical Genomic Initiative, the network of Belgian accredited genetic counseling centers, and the Exascience Life Lab, a platform for Big Data in the Life Sciences (www.exascience.com).

Contact: Yves Moreau, moreau [at] esat.kuleuven.be

European Genome-phenome Archive (EGA)

The EGA Beacon makes available and discoverable 22 different datasets. The majority of them comes from the UK10K study on rare genetic variants in health and disease, which explores the link between rare genetic changes and diseases caused by changes to the proteins the body produces.

Contact: Jordi Rambla de Argila, jordi.rambla [at] crg.eu

Mon 27 February 2017