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Review
. 2019 Nov;20(11):693-701.
doi: 10.1038/s41576-019-0156-9. Epub 2019 Aug 27.

Leveraging European infrastructures to access 1 million human genomes by 2022

Gary Saunders  1 , Michael Baudis  2 , Regina Becker  3 , Sergi Beltran  4   5 , Christophe Béroud  6   7 , Ewan Birney  8 , Cath Brooksbank  8 , Søren Brunak  9   10 , Marc Van den Bulcke  11 , Rachel Drysdale  1 , Salvador Capella-Gutierrez  12 , Paul Flicek  8 , Francesco Florindi  13 , Peter Goodhand  14   15 , Ivo Gut  4   5 , Jaap Heringa  16 , Petr Holub  13 , Jef Hooyberghs  17 , Nick Juty  18 , Thomas M Keane  8 , Jan O Korbel  19 , Ilkka Lappalainen  20 , Brane Leskosek  21 , Gert Matthijs  22 , Michaela Th Mayrhofer  13 , Andres Metspalu  23 , Arcadi Navarro  24   25   26 , Steven Newhouse  8 , Tommi Nyrönen  20 , Angela Page  15   27 , Bengt Persson  28 , Aarno Palotie  29 , Helen Parkinson  8 , Jordi Rambla  26 , David Salgado  6 , Erik Steinfelder  13 , Morris A Swertz  30 , Alfonso Valencia  12   31 , Susheel Varma  8 , Niklas Blomberg  1 , Serena Scollen  32
Affiliations
Review

Leveraging European infrastructures to access 1 million human genomes by 2022

Gary Saunders et al. Nat Rev Genet. 2019 Nov.

Erratum in

  • Author Correction: Leveraging European infrastructures to access 1 million human genomes by 2022.
    Saunders G, Baudis M, Becker R, Beltran S, Béroud C, Birney E, Brooksbank C, Brunak S, Van den Bulcke M, Drysdale R, Capella-Gutierrez S, Flicek P, Florindi F, Goodhand P, Gut I, Heringa J, Holub P, Hooyberghs J, Juty N, Keane TM, Korbel JO, Lappalainen I, Leskosek B, Matthijs G, Mayrhofer MT, Metspalu A, Navarro A, Newhouse S, Nyrönen T, Page A, Persson B, Palotie A, Parkinson H, Rambla J, Salgado D, Steinfelder E, Swertz MA, Valencia A, Varma S, Blomberg N, Scollen S. Saunders G, et al. Nat Rev Genet. 2019 Nov;20(11):702. doi: 10.1038/s41576-019-0178-3. Nat Rev Genet. 2019. PMID: 31520075

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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Figures

Figure 1
Figure 1. Current healthcare-focussed and genomics-based national initiative projects across ELIXIR members.
Figure 2
Figure 2. The concept of EGA federation, including a potential user workflow from data discoverability to raw sensitive human data access.
1 = Discoverability: metadata is shared from each of the sensitive data archives to a centralised database upon which queryable interfaces can be built; these can be project specific portals, or interfaces to query the metadata associated with all datasets across a federated network. The GA4GH Driver Projects ELIXIR Beacon and MatchMaker Exchange, for example, provide standards and interfaces to query such metadata in order to aid discoverability. 2 = Controlled-access archival: as a GA4GH Driver Project EGA/ENA/EVA provides interoperable programmatic interfaces that are required to enable metadata transfer and user authentication and authorisation (provided by ELIXIR AAI, for example) across the federated network of controlled-access archives. 3 = Cloud computing environment(s) = community-curated workflows (e.g. those found in BioContainers) are able to be executed remotely and run locally at one or more sensitive data archives utilising the standards from the GA4GH Cloud and Large Scale Genomics Work Streams.
See this image and copyright information in PMC

References

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