Leveraging European infrastructures to access 1 million human genomes by 2022

Saunders, Gary; Baudis, Michael; Becker, Regina; Beltrán, Sergi; Béroud, Christophe; Birney, Ewan; Brooksbank, Cath; Brunak, Søren; Bulcke, Marc Van den; Drysdale, Rachel; Capella-Gutiérrez, Salvador; Flicek, Paul; Florindi, Francesco; Goodhand, Peter; Gut, Ivo; Heringa, Jaap; Holub, Petr; Hooyberghs, Jef; Juty, Nick; Keane, Thomas; Korbel, Jan O.; Lappalainen, Ilkka; Leskošek, Brane; Matthijs, Gert; Mayrhofer, Michaela Th.; Metspalu, Andres; Navarro, Arcadi; Newhouse, Steven; Nyrönen, Tommi; Page, Angela; Persson, Bengt L.; Palotie, Aarno; Parkinson, Helen; Rambla, Jordi; Salgado, David; Steinfelder, Erik; Swertz, Morris A.; Valencia, Alfonso; Varma, Susheel; Blomberg, Niklas; Scollen, Serena

doi:10.1038/s41576-019-0156-9

Cited by 76 publications

(69 citation statements)

References 20 publications

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“…Planned large scale whole-genome sequencing projects and increasing GWAS samples sizes (Saunders et al, 2019) are expected to increasingly reveal infrequent 10 and rare variants associated with complex traits. These variants will increasingly not be contained in eQTL catalogs thus other tools are needed to filter credible variants and make testable hypotheses about the mechanisms by which these variants drive disease, or other phenotypes of interest.…”

Section: Discussionmentioning

confidence: 99%

Predicting cell-type-specific non-coding RNA transcription from genome sequence

Koido

Hon

Koyama

et al. 2020

Preprint

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Transcription is regulated through complex mechanisms involving non-coding RNAs (ncRNAs).However, because transcription of ncRNAs, especially enhancer RNAs, is often low and cell type-specific, its dependency on genotype remains largely unexplored. Here, we developed mutation effect prediction on ncRNA transcription (MENTR), a quantitative machine learning 5 framework reliably connecting genetic associations with expression of ncRNAs, resolved to the level of cell type. MENTR-predicted mutation effects on ncRNA transcription were concordant with estimates from previous genetic studies in a cell type-dependent manner. We inferred reliable causal variants from 41,223 GWAS variants, and proposed 7,775 enhancers and 3,548 long-ncRNAs as complex trait-associated ncRNAs in 348 major human primary cells and tissues, 10 including plausible enhancer-mediated functional alterations in single-variant resolution in Crohn's disease. In summary, we present new resources for discovering causal variants, the biological mechanisms driving complex traits, and the sequence-dependency of ncRNA regulation in relevant cell types. (145/150 words)

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Section: Discussionmentioning

confidence: 99%

Predicting cell-type-specific non-coding RNA transcription from genome sequence

Koido

Hon

Koyama

et al. 2020

Preprint

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“…GDPR). In addition, the rapid response to the COVID-19 pandemic provides a blueprint for European data access in projects such as 1 Million European Genomes [12].…”

Section: Create Federated European Genome-phenome Archives For Transnmentioning

confidence: 99%

Connecting data, tools and people across Europe: ELIXIR’s response to the COVID-19 pandemic

Blomberg¹,

Lauer²

2020

Eur J Hum Genet

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ELIXIR, the European research infrastructure for life science data, provides open access to data, tools and workflows in the response to the COVID-19 pandemic. ELIXIR's 23 nodes have reacted swiftly to support researchers in their combined efforts against the pandemic setting out three joint priorities: 1. Connecting national COVID-19 data platforms to create federated European COVID-19 Data Spaces; 2. Fostering good data management to make COVID-19 data open, FAIR and reusable over the long term; 3. Providing open tools, workflows and computational resources to drive reproducible and collaborative science. ELIXIR's strategy is based on the support given by our national nodes -collectively spanning over 200 institutes -to research projects and on partnering with community initiatives to drive development and adoption of good data practice and community driven standards. ELIXIR Nodes provide support activities locally and internationally, from provisioning compute capabilities to helping collect viral sequence data from hospitals. Some Nodes have prioritised access to their national cloud and compute facilities for all COVID-19 research projects, while others have developed tools to search, access and share all data related to the pandemic in a national healthcare setting. 1234567890();,:1234567890();,:

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“…This federation of national initiatives [28] will provide secure access to such data resources in the member states to enable the discovery of personalized therapies and diagnostics for the benefit of patients. The initiative involves aligning strategies of ongoing national genomic sequencing campaigns with complementary de novo genome sequencing to obtain a total cohort of one million Europeans, accessible in a transnational framework, by 2022 [29]. The HRIC would form a basis for such large-scale, permanent collaborations.…”

Section: Standards In Interoperability and Data Securitymentioning

confidence: 99%

“…28 geneXplain GmbH, Wolfenbüttel, Germany. 29 Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland. 30 European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany.…”

Section: Acknowledgementsmentioning

confidence: 99%

Towards a European health research and innovation cloud (HRIC)

Aarestrup

Albeyatti

Armitage³

et al. 2020

Genome Med

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The European Union (EU) initiative on the Digital Transformation of Health and Care (Digicare) aims to provide the conditions necessary for building a secure, flexible, and decentralized digital health infrastructure. Creating a European Health Research and Innovation Cloud (HRIC) within this environment should enable data sharing and analysis for health research across the EU, in compliance with data protection legislation while preserving the full trust of the participants. Such a HRIC should learn from and build on existing data infrastructures, integrate best practices, and focus on the concrete needs of the community in terms of technologies, governance, management, regulation, and ethics requirements. Here, we describe the vision and expected benefits of digital data sharing in health research activities and present a roadmap that fosters the opportunities while answering the challenges of implementing a HRIC. For this, we put forward five specific recommendations and action points to ensure that a European HRIC: i) is built on established standards and guidelines, providing cloud technologies through an open and decentralized infrastructure; ii) is developed and certified to the highest standards of interoperability and data security that can be trusted by all stakeholders; iii) is supported by a robust ethical and legal framework that is compliant with the EU General Data Protection Regulation (GDPR); iv) establishes a proper environment for the training of new generations of data and medical scientists; and v) stimulates research and innovation in transnational collaborations through public and private initiatives and partnerships funded by the EU through Horizon 2020 and Horizon Europe.

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Leveraging European infrastructures to access 1 million human genomes by 2022

Cited by 76 publications

References 20 publications

Predicting cell-type-specific non-coding RNA transcription from genome sequence

Predicting cell-type-specific non-coding RNA transcription from genome sequence

Connecting data, tools and people across Europe: ELIXIR’s response to the COVID-19 pandemic

Towards a European health research and innovation cloud (HRIC)

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