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15 April 2023
Sustaining translational data for secondary use
a Pistoia Alliance Debates webinar
chaired by Sándor Szalma
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Sustaining translational data for secondary use 315 April 2023
Panellists
Sándor Szalma is head of Translational Informatics and External Innovation, R&D IT in Janssen Research & Development, LLC. He is responsible for implementing the translational informatics capability and establishing and fostering large scale open innovation collaborations to support discovery, translational, clinical and safety science including public-private partnerships and various pre-competitive collaborations such as Innovative Medicines Initiative (IMI) consortia.
llkka Lappalainen is ELIXIR Human Data Coordinator. Prior to this position he worked at the EMBL-EBI and played an important role establishing the European Genome phenome Archive (EGA) as a global service. The EGA service provides long term secure archival solutions for data consented for research but not for fully public dissemination.
Lucila Ohno-Machado, Professor of Medicine, University of California San Diego; Chair, Department of Biomedical Informatics; Associate Dean for Informatics and Technology
Sustaining translational data for secondary use
Sándor SzalmaPistoia Alliance Debate Webinar
What is Translational Research?
Clinical Research Informatics: Challenges, Opportunities and Definition for an Emerging DomainPeter J. Embi, MD, MS a , and Philip R.O. Payne, PhD b
J Am Med Inform Assoc. 2009 May-Jun; 16(3): 316–327.
Prototypical Translational Research Study
Patient
Cancer tissue
sample
Healthy tissue
sample
Group of mice grafted with same XG model
and treated
Group of mice grafted with same XG model
and untreated
Omics profiling
Omics profiling
Blood sample
(CTC, etc.)
Omics profiling
Profiling
Cell line estabilishment and treatment
Omics profiling
Data Generators
• Private – E.g.: pharma, etc.
• Publicly-funded– E.g.: by NIH, etc.
• Public-private – E.g.: IMI, etc.
• Charities/disease groups/patients/etc.– E.g.: Accelerated Cure Project, etc.
Sustainability Model Examples
• Private• Public-Private Partnership• Charity• Government• …
Example - Pharma
Example – Innovative Medicine Initiative
> €5 bn
Partnership2008 - 2024
€2.5 bn€2.5 bn
Infectious diseases
Drug discovery
Brain disorders
Metabolic disordersDrug safety
Stem cellsCancer
Data management
Inflamatory disordersBiologicals
Geriatrics
Lung diseases
Education & training
Sustainable chemistry
Drug delivery
Drug kineticsRelative effectiveness
IMI 1 - 40+ projects, € 2 Bn
Sustainability Pilots through IMI Strategic Governance Group Data and Knowledge Management
Example – “Disease” Organization
Example - Government
www.elixir-europe.org
ELIXIR services for biomedical dataarchive and discovery services
Ilkka Lappalainen, ELIXIR Human Data Coordinator
Pistoia Alliance – Sustaining translational data for secondary use
ELIXIR is an inter-governmental organisation
What is ELIXIR?
• ELIXIR infrastructure for Europe’s life science research sector
• ELIXIR Nodes build local bioinformatics capacity throughout Europe
• ELIXIR Nodes build on national strengths and priorities
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European Genome-phenome Archive (EGA)
The EGA was created by the EBI in 2008.
In 2013, EBI and Centre for Genome Regulation (CRG), Spain started working together to establish EGA as a joint venture.
https://www.ebi.ac.uk/ega/https://ega.crg.eu/
European Genome-phenome Archive (EGA)
• Primary archive for any data consented for sharing in the context of research but not for fully public distribution.
• Data must have a release policy and it must be governed by a dedicated Data Access Committee (DAC).
• Submissions must be de-identified and in accordance with the informed consent.
European Genome-phenome Archive (EGA)
• Most data submitted include sequencing or array-based experiments from biomedical research projects.
• Over 700 public studies with more than 1300 datasets of mainly cancer and common diseases (e.g. Wellcome Trust Case Control Consortium and International Cancer Genome Consortium).
• Submission includes data files and meta information describing the project, samples and experimentation.
• In some cases submission is split between other archives at the EBI.
European Genome-phenome Archive (EGA)
• Data are packed into datasets that are governed by a Data Access Committee (DAC).
• Authentication - DAC approved individual will have a personal EGA account.
• Authorization – DACs attach access permission(s) to the EGA account(s).
• Over 6500 authorized users world wide download 100 TB of data from the archive each month.
• ELIXIR provides tools for DACs to manage their data access approval process electronically.
EGA works with Data Access Committees (DACs)
ELIXIR - Beacon project
3
• GA4GH Beacons are a discovery service
• e.g. which datasets include genomes with allele of interest
• Complies to the GA4GH Beacon project standard and security working group policies.
• Align with ELIXIR Nodes & service architecture.
• For example ELIXIR Beacon will use ELIXIR authentication and authorization infrastructure (AAI).
• Technical solution requires integration to existing national resources.
• Collaborates with the European Genome-phenome Archive (EGA).
• Provide ELIXIR standards for data types that can be made available through these authorization levels.
ELIXIR Beacon pilot project
Acknowledgements
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For more information about EGA in the recent Nature Genetics publication that also lists the funding sources:
http://www.nature.com/ng/journal/v47/n7/full/ng.3312.html
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2415 April 2023
Lucila’s slides
• Removed by request
Panellist debate
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Sustaining translational data for secondary use15 April 2023
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