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  • Roadmap
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Leveraging European infrastructures to access 1 million human genomes by 2022

An Author Correction to this article was published on 13 September 2019

This article has been updated


Human genomics is undergoing a step change from being a predominantly research-driven activity to one driven through health care as many countries in Europe now have nascent precision medicine programmes. To maximize the value of the genomic data generated, these data will need to be shared between institutions and across countries. In recognition of this challenge, 21 European countries recently signed a declaration to transnationally share data on at least 1 million human genomes by 2022. In this Roadmap, we identify the challenges of data sharing across borders and demonstrate that European research infrastructures are well-positioned to support the rapid implementation of widespread genomic data access.

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Fig. 1: Examples of current health care-focused and genomics-based national initiative projects across ELIXIR members.
Fig. 2: The concept of EGA federation — from data discoverability to raw sensitive human data access.

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  • 13 September 2019

    An amendment to this paper has been published and can be accessed via a link at the top of the paper.


  1. Lochmüller, H. et al. RD-Connect, NeurOmics and EURenOmics: collaborative European initiative for rare diseases. Eur. J. Hum. Genet. 26, 778–785 (2018).

    Article  Google Scholar 

  2. Horgan, D. From here to 2025: personalised medicine and healthcare for an immediate future. J. Cancer Policy 16, 6–21 (2018).

    Article  Google Scholar 

  3. Auffray, C. et al. Making sense of big data in health research: towards an EU action plan. Genome Med. 8, 71 (2016).

    Article  Google Scholar 

  4. Birney, E., Vamathevan, J. & Goodhand, P. Genomics in healthcare: GA4GH looks to 2022. Preprint at bioRxiv (2017).

  5. The European Commission. Declaration of cooperation: towards access to at least 1 million sequenced genomes in the European Union by 2022. European Commission (2018). This declaration from the European Commission posits the provision of transnational access to at least 1 million human genomes by 2022.

  6. Philippakis, A. A. et al. The Matchmaker Exchange: a platform for rare disease gene discovery. Hum. Mut. 36, 915–921 (2015).

    Article  Google Scholar 

  7. Lappalainen, I. et al. The European Genome-phenome Archive of human data consented for biomedical research. Nat. Genet. 47, 692–695 (2015).

    Article  CAS  Google Scholar 

  8. Durinx, C. et al. Identifying ELIXIR core data resources. Version 2. F1000Res. 5, 2422 (2016).

    Article  Google Scholar 

  9. Fiume, M. et al. Federated discovery and sharing of genomic data using Beacons. Nat. Biotechnol. 37, 220–224 (2019). The Beacon API protocol is an approved GA4GH to federated genomics data discoverability and has many implementations across ELIXIR.

    Article  CAS  Google Scholar 

  10. Holub, P. et al. BBMRI-ERIC directory: 515 biobanks with over 60 million biological samples. Biopreserv. Biobank. 14, 559–562 (2016).

    Article  Google Scholar 

  11. Litton, J. E. Launch of an infrastructure for health research: BBMRI-ERIC. Biopreserv. Biobank. 16, 233–241 (2018).

    Article  Google Scholar 

  12. Merino-Martinez, R. et al. Toward global biobank integration by implementation of the minimum information about biobank data sharing (MIABIS 2.0 Core). Biopreserv. Biobank. 14, 298–306 (2016).

    Article  Google Scholar 

  13. European Union. Regulation (EU) 2016/679 of the European Parliament and of the Council of 27 April 2016 on the protection of natural persons with regard to the processing of personal data and on the free movement of such data, and repealing Directive 95/46/EC (General Data Protection Regulation). EUR-Lex (2016).

  14. Linden, M. et al. Common ELIXIR service for researcher authentication and authorisation. F1000Res. 7, 1199 (2018).

    Article  Google Scholar 

  15. Kaye, J. et al. Are requirements to deposit data in research repositories compatible with the European Union’s General Data Protection Regulation? Ann. Intern. Med. 170, 332–334 (2019).

    Article  Google Scholar 

  16. Dove, E. S. The EU General Data Protection Regulation: implications for international scientific research in the digital era. J. Law Med. Ethics 46, 1013–1030 (2018).

    Article  Google Scholar 

  17. Shabani, M. & Borry, P. Rules for processing genetic data for research purposes in view of the new EU General Data Protection Regulation. Eur. J. Hum. Genet. 26, 149–156 (2018).

    Article  Google Scholar 

  18. Harris, S. Data protection act 2018 (section 36(2)) (health research) regulations 2018. eISB (2018).

  19. Government of the Netherlands. Regels ter uitvoering van Verordening (EU) 2016/679 van het Europees Parlement en de Raad van 27 april 2016 [Dutch]. Rijksoverheid (2017).

  20. Government Offices of Sweden. Lag (2003:460) om etikprövning av forskning som avser människor [Swedish]. Regeringskansliet (2018).

  21. Mayrhofer, M. & Schlünder, I. Mind the gap: from tool to knowledge base. Biopreserv. Biobank. 16, 458–462 (2018).

    Article  Google Scholar 

  22. Genomics England. The UK has sequenced 100,000 whole genomes in the NHS. Genomics England (2018).

  23. Rozenblatt-Rosen, O. et al. The Human Cell Atlas: from vision to reality. Nature 550, 451–453 (2017).

    Article  CAS  Google Scholar 

  24. Paten, B. et al. The NIH BD2K center for big data in translational genomics. J. Am. Med. Inform. Assoc. 22, 1143–1147 (2015).

    PubMed  PubMed Central  Google Scholar 

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The authors thank D. Lloyd (ELIXIR-Hub), U. Gerst-Talas (ELIXIR-EE), A. Jene and J. Dopazo (ELIXIR-ES) for reviewing and commenting on this manuscript whilst in preparation. Additionally, the authors would like to acknowledge all members of the ELIXIR Federated Human Data, Rare Diseases, and Human Copy Number Variation Communities whose input and work has contributed to this manuscript and whose combined work in future under the banner of the ELIXIR Human Data Communities, along with the five ELIXIR Platforms (Compute, Data, Interoperability, Tools and Training), shall provide workable solutions to meet the aims of the EU Declaration to share at least 1 million genomes transnationally by 2022. Within this group the authors would like to specifically acknowledge V. Satagopam (ELIXIR-LU), N. Jareborg (ELIXIR-SE), M. Chiara (ELIXIR-IT), H. Peterson (ELIXIR-EE), A. Dimopoulos (ELIXIR-GR) and A. Ardeshirdavani (ELIXIR-BE). The authors would like to thank all the contributors of BBMRI-ERIC Common Service IT.

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Authors and Affiliations



G.S., E.B., S.Br., P.F., N.B. and S.S. researched the literature. G.S., E.B., S.Br., P.F., I.G., N.B. and S.S. provided substantial contributions to discussions of the content. G.S., R.B., S.Be., C.Bé., C.Br., M.V.d.B., S.C.-G., F.F., J.He., P.H., J.Ho., N.J., T.M.K., J.O.K., G.M., M.T.M., A.M., T.N., A.Pag., B.P., H.P., J.R., D.S., M.A.S., S.V., N.B. and S.S. wrote the article. G.S., M.B., R.B., S.Be., C.Bé., C.Br., M.V.d.B., R.D., S.C.-G., F.F., P.G., I.G., J.He., P.H., J.Ho., N.J., T.M.K., J.O.K., I.L., B.L., G.M., M.T.M., A.M., A.N., A.V., S.N., T.N., A.Pag., B.P., A.Pal., H.P., J.R., D.S., E.S., M.A.S., S.V., N.B. and S.S. reviewed and/or edited the manuscript before submission.

Corresponding author

Correspondence to Serena Scollen.

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Competing interests

E.B. is a paid consultant to Oxford Nanopore, GlaxoSmithKline and Dovetail Inc. S.Br. acknowledges funding from the Danish Agency for Science, Technology and Innovation (09–067306), Novo Nordisk Foundation (NNF14CC0001). P.F. is a member of the scientific advisory boards of Fabric Genomics, Inc., and Eagle Genomics, Ltd. The other authors declare no competing interests.

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Nature Reviews Genetics thanks H. Rehm, B. Knoppers, E. Dove and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.

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BBMRI-ERIC Directory:



Data Use Ontology:

ELIXIR core data resources:

ELIXIR Europe:

ELIXIR Rare Diseases Community:

ELIXIR Scientific Programme (2019–2023):

Ethical, Legal, and Social Issues in Biobanking:



European Genome–phenome Archive (EGA):

European Open Science Cloud (EOSC):

European Strategy Forum on Research Infrastructures (ESFRIs):

Executive Master’s in Management of Research Infrastructure:

GA4GH data repository service schemas:

GA4GH ‘data use and researcher identities’ work stream:

GA4GH driver projects:

GA4GH task execution schemas:

GA4GH work streams:

GA4GH workflow execution service schemas:

GDPR article 9(4):

GDPR Code of Conduct for Health Research initiative:

Global Alliance for Genomics and Health (GA4GH):

High Performance Computing Research Infrastructure Eastern Region:

Innovative Medicines Initiative:

Matchmaker Exchange:

Minimum Information About BIobank data Sharing (MIABIS) 2.0:

Personal Health Train (PHT):

Proyecto Genoma 1000 Navarra:


Training eSupport System:

Tryggve project:


Precision medicine

An approach for disease treatment and prevention that takes into account individual variability in genes, environment and lifestyle for each person.

Biobanking and Biomolecular Resources Research Infrastructure

(BBMRI-ERIC). A research infrastructure that brings together key stakeholders from the biobanking field to support biomedical research and facilitate the development of new therapies by offering management services, support with ethical, legal and societal issues, and a number of online tools and software solutions.


An intergovernmental organization that coordinates life science resources from across Europe, including databases, software tools, training materials, cloud storage and supercomputers, to form a single infrastructure that facilitates data sharing, exchange of expertise and best practice development. Ultimately, ELIXIR’s goal is to help researchers gain new insights into how living organisms work.


A term used to describe an architecture that allows information sharing between information technology systems and applications.


One or more research institutes within a member country that run the resources and services that are part of ELIXIR; there are currently 23 ELIXIR Nodes.

Application programming interface

(API). An access point that enables applications to communicate with one another, for example, allowing an application to access a particular database.

General Data Protection Regulation (GDPR) 2016/679

A regulation in European Union (EU) law on data protection and privacy for all individuals within the EU and the European Economic Area. It also addresses the export of personal data outside the EU and European Economic Area.


A system for building highly portable packages of bioinformatics software, containerization and virtualization technologies for isolating reusable execution environments for these packages and an integrated workflow system that automatically orchestrates the composition of these packages for entire pipelines.


Biorepositories that store biological samples (usually human) for use in research.

Broad consent

Consent for an unspecified range of future research subject to a few content and/or process restrictions.

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Saunders, G., Baudis, M., Becker, R. et al. Leveraging European infrastructures to access 1 million human genomes by 2022. Nat Rev Genet 20, 693–701 (2019).

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