Slides from the Pistoia Alliance Debates webinar on translational data sustainability.

1. 15 July, 2015
Sustaining translational data for
secondary use
a Pistoia Alliance Debates webinar
chaired by Sándor Szalma

2. This webinar is being recorded

3. ©PistoiaAlliance
Panellists
Sustaining translational data for secondary use 315 July, 2015
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

4. Sustaining translational data for
secondary use
Sándor Szalma
Pistoia Alliance Debate Webinar

5. What is Translational Research?
Clinical Research Informatics: Challenges, Opportunities and Definition for an Emerging Domain
Peter J. Embi, MD, MSa , and Philip R.O. Payne, PhDb
J Am Med Inform Assoc. 2009 May-Jun; 16(3): 316–327.

6. 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

7. 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.

8. Sustainability Model Examples
• Private
• Public-Private Partnership
• Charity
• Government
• …

9. Example - Pharma

10. Example – Innovative Medicine
Initiative
> €5 bn
Partnership
2008 - 2024
€2.5 bn€2.5 bn
Infectious diseases
Drug discovery
Brain disorders
Metabolic disorders
Drug safety
Stem cells
Cancer
Data management
Inflamatory disorders
Biologicals
Geriatrics
Lung diseases
Education & training
Sustainable
chemistry
Drug delivery
Drug kinetics
Relative
effectiveness
IMI 1 - 40+ projects, € 2 Bn
Sustainability Pilots through IMI
Strategic Governance Group Data
and Knowledge Management

11. Example – “Disease” Organization

12. Example - Government

13. www.elixir-europe.org
ELIXIR services for biomedical data
archive and discovery services
Ilkka Lappalainen, ELIXIR Human Data Coordinator
Pistoia Alliance – Sustaining translational data for secondary use

14. ELIXIR is an inter-governmental organisation

15. 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
priorities15

16. 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/
ega-helpdesk@ebi.ac.uk

17. 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.

18. 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.

19. 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.

20. EGA works with Data Access Committees (DACs)

21. 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.

22. ELIXIR Beacon pilot project

23. Acknowledgements
23
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

24. ©PistoiaAlliance
Lucila’s slides
2415 July, 2015
• Removed by request

25. Panellist debate

26. Audience Q&A
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27. ©PistoiaAlliance
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Sustaining translational data for secondary use15 July, 2015

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Analytics in Pharma R&D
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