Leveraging European infrastructures to access 1 million human genomes by 2022

Abstract

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.

Change history

  • 13 September 2019

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

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Acknowledgements

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.

Author information

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.

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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Related links

BBMRI-ERIC: http://www.bbmri-eric.eu/

BBMRI-ERIC AAI: https://web.bbmri-eric.eu/Policies/

BBMRI-ERIC Directory: https://directory.bbmri-eric.eu/

CINECA: https://edukad.etag.ee/project/4011?lang=en

CORBEL: http://www.corbel-project.eu/about-corbel.html

Data Use Ontology: https://github.com/EBISPOT/DUO

ELIXIR core data resources: https://elixir-europe.org/platforms/data/core-data-resources

ELIXIR Europe: https://elixir-europe.org/

ELIXIR Rare Diseases Community: https://www.elixir-europe.org/communities/rare-diseases

ELIXIR Scientific Programme (2019–2023): https://elixir-europe.org/about-us/what-we-do/elixir-programme

Ethical, Legal, and Social Issues in Biobanking: http://www.bbmri-eric.eu/services/common-service-elsi/

EUCANCan: https://eucancan.com/

euCanSHare: http://www.eucanshare.eu/

European Genome–phenome Archive (EGA): https://ega-archive.org/

European Open Science Cloud (EOSC): https://www.eosc-portal.eu/

European Strategy Forum on Research Infrastructures (ESFRIs): https://www.esfri.eu/roadmap-2018

Executive Master’s in Management of Research Infrastructure: http://www.emmri.unimib.it/en/

GA4GH data repository service schemas: https://github.com/ga4gh/data-repository-service-schemas

GA4GH ‘data use and researcher identities’ work stream: https://ga4gh-duri.github.io

GA4GH driver projects: https://www.ga4gh.org/how-we-work/driver-projects/

GA4GH task execution schemas: https://github.com/ga4gh/task-execution-schemas

GA4GH work streams: https://www.ga4gh.org/how-we-work/workstreams/

GA4GH workflow execution service schemas: https://ga4gh.github.io/workflow-execution-service-schemas/

GDPR article 9(4): https://gdpr-info.eu/art-9-gdpr/

GDPR Code of Conduct for Health Research initiative: http://www.code-of-conduct-for-health-research.eu/

Global Alliance for Genomics and Health (GA4GH): https://www.ga4gh.org

High Performance Computing Research Infrastructure Eastern Region: https://www.hpc-rivr.si/home_en/

Innovative Medicines Initiative: https://www.imi.europa.eu/

Matchmaker Exchange: https://www.matchmakerexchange.org/

Minimum Information About BIobank data Sharing (MIABIS) 2.0: http://www.bbmri-eric.eu/services/miabis/

Personal Health Train (PHT): http://www.dtls.nl/fair-data/personal-health-train/

Proyecto Genoma 1000 Navarra: https://www.nagen1000navarra.es/en/home

RItrain: http://ritrain.eu/

Training eSupport System: https://tess.elixir-europe.org/

Tryggve project: https://neic.no/tryggve/

Glossary

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.

ELIXIR

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.

Federated

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

ELIXIR Nodes

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.

Containers

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.

Biobanks

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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