Biomedical and Life Sciences

1
Biomedical and Life Sciences

• Chair Ruth Barrington, Ireland
• Scandinavian members
• Håkan Billig, Sweden
• Liselotte Hoejgaard, Denmark
• Chair of Clinical and translational research
  expert group
• Hans Krokan, Norway
• Taina Pihlajaniemi, Finland
• Chair of Bioinformatics, genomics, animal models,
  and chemical and structural biology expert group

2
OBSERVATIONS DURING ESFRI WORKESTABLISHED MODES
VS. NEW CONCEPTS

• Single sited vs. distributed
• Massive up-front investment vs. successive
  up-grades
• Equipment vs. mice, fish etc.
• Commercially mature vs. nascent in terms of
  applications
• Existing intress groups vs. less-organised fields

3
MORE OBSERVATIONS

• BMS Expert groups broad coverage of areas
• EG on Clinical and translational research
• EG on Biodiversity and the environment
• EG on Genomics, bioinformatics, animal models,
  and structural and chemical biology
• Broadness had effects on mode of working
• Effects on percieved maturity
• Compare with single-topic EGs
• 3 fields of research became 7 in Roadmap report
• PSE, BMS, SSH
• PSE split to
• energy
• material sciences
• astronomy, astrophysics, nuclear and particle
  physics

4
POINTS RAISED BY EG ON GENOMICS, BIOINFORMATICS
ET AL.

• The Roadmap should reflect the Century of
  Biology
• Historical emphasis of infrastructure funding on
  PSE, particularly in Europe
• in US and Australia life sciences strongly
  emphasised
• BMS infrastructure funding should increase
  towards parity with the physical sciences
• BMS infrastructres construction AND continuous
  up-grading
• Short-term support a problem not decomissioning
  but recomissioning
• Infrastructures are beneficial for big research
  centres mechanisms should be created to support
  smaller institutions and individual scientists

5
CONTINUUM FROM PAN-EUROPEAN TO NATIONAL AND LOCAL
INFRASTRUCTURES

• Viable policies for national and local
  infrastructures are essential
• The ESFRI process should influence national level
  infrastructure developments
• High importance for small countries lacking
  large-scale European infrastructures
• How do we motivate policy makers and funding
  agencies towords susteinable infrastructure
  policies?

6
The Biomedical and Life Sciences
Landscape
7
European biobanking and biomolecular resources
infrastructure
Background A pan-European, broadly accessible,
networked database and biological resource system
of collections of well-documented, up-to-date
clinical, biological, epidemiological and
life-style data. It will include samples from
patients and healthy persons, molecular genomic
resources and bioinformatics tools to optimally
exploit this resource for global biomedical
research.
Picture
Novelty / Impact The availability of sufficient
well-characterised biospecimens from legitimate
sources will allow European pre-clinical
/clinical research to take a frontline position
commensurate with the advanced quality of our
health care systems. This will prevent
discoveries and valuable downstream IP inventions
from draining to non-European countries at the
cost of European jobs and ethical standards.
Timeline for Construction / estimated
life-time 1-7yrs /3-10yrs
Estimated Costs (construction, operational,
decommissioning) 170m / 100m /NA
Supporting consortium Blood, sample and DNA
banks located around Europe (eg UK Biobank,
Estonian Biobank, Netherlands Biobanking
Consortium) Molecular resource centers and
technology networks (eg Finnish Genome Center),
and Bioinformatic centers
8
Biobanks and Biomolecular Resources
Biobanks (blood, DNA, tissue, cells, body fluids,
and data)

• Population-based biobanks
• Clinical case-control biobanks
• Population isolates biobanks
• Twin registries
• Antibody collections
• Affinity binder collections
• Full-length ORF clone collections
• siRNA libraries

Biomolecular resources
Courtesy of Kurt Zatloukal
9
Why a Research Infrastructure for Biobanking and
Biomolecluar Resources?

• Existing biobanks are a specific strength of
  Europe and an essential resource for
• Discovery of gene function
• Identification of disease relevance of genes
• Exploration of gene-environment interactions
• Identification of new targets for drug discovery
• Identification of biomarkers for individualized
  therapy

10
Why a Research Infrastructure for Biobanking and
Biomolecluar Resources?

• The research infrastructure should further
  develop the potential of these resources and
  facilitate the access for academia and industry
  of all EU member states by
• providing a pan-European inventory
• facilitating transnational combination and
  exchange of biological materials and data
• reducing the fragmentation of the scientific
  community
• developing a sustained financial basis

11
The Structure
a distributed hub structure,
Hubs for domains
Biobanks Biomolecular resources Technology centers

Associated partners Hospitals Universities
not members of the research infrastructure
12
Contact Persons

• Biobanks (epidemiological, population genetics)
  Leena Peltonen-Palotie, Andres Metspalu, Erich
  Wichman
• Clinical sample collections Kurt Zatloukal
  (chair), Thomas Meitinger
• Molecular methods and resources Mike Taussig,
  Ulf Landegren
• Databases, analysis, harmonisation Jan-Eric
  Litton, Paul Burton
• Technologies, biocomputing GertJan van Ommen
  (Lon Cardon)
• ELSI Anne Cambon-Thomsen, Jasper Bovenberg
• Secretary Martin Yuille

13
Bioinformatics infrastructure for Europe
Background The worlds body of bioinformatics
data is a critical input for all biomedical
sciences and related industries. The proposed
infrastructure will ensure free provision of this
essential input to the entire scientific
community.
Picture
Novelty / Impact By boldly developing, upgrading
or linking the proposed data resources, Europe is
capable of establishing infrastructure facilities
second to none which, together with ancillary
research and training, will enable Europe-wide,
world-leading biomedical research and industrial
development.
Timeline for Construction / estimated
life-time 1-7 Years /NA
Estimated Costs (construction, operational,
recommissioning) 550m /50m /100m
Supporting consortium European Bioinformatics
Institute, Swiss Institute of Bioinformatics,
Wellcome Trust Sanger Institute
www.ebi.ac.uk
14
Global Context
Data are freely exchanged daily
Data are freely deposited
Data are made freely available to all
15
Data Integration is vital
Genes
Proteins
Expression Data
Genomes
Pathways
fructose-6-phosphate
ATP
pfkA pfkB
H ADP
Courtesy of J. Thornton
fructose-1,6-bisphosphate
16
A European Bioinformatics Research Infrastructure
- Elixir

• Infrastructure should provide
• Interlinked collection of core and specialised
  biological data resources and literature
• Standards and ontologies for newly emerging data
• Development of new resources as appropriate
• Integration and interoperability of diverse
  heterogeneous data
• Rapid search and access through friendly
  portal(s)
• Links to developing resources for medicine (e.g.
  biobanks), agriculture and the environment (e.g.
  biodiversity)

17
Integrated Structural Biology Infrastructure for
Europe
Background The Integrated Structural Biology
Infrastructure Project will provide a central
framework for 21st century biology and
pharmaceuticalsgrand challenge will be addressed
by building a pan-European infrastructure of
distributed Integrated Structural Biology
Centres, linked into a network. The Centres will
combine excellence in structural biology with
specific technologic and developmental tasks.
Picture
Novelty / Impact A major aim of this
infrastructure is to move structural biology from
the study of single protein molecules to the
study of the more complex systems used by cells
with the long-term aim of using structural
biology, together with cell and systems biology
to be able to describe in detail how a cell
functions.
Timeline for Construction / estimated
life-time 2007-2013
Estimated Costs (construction, operational,
decommissioning) 300m /125m / NA
Supporting consortium The potential centres are
well established strong sites already supported
by their national/international organisations
www.strubi.ox.ac.uk/
18
INFRAFRONTIER
Background Infrafrontier will organise two
complementary and linked European infrastructure
networks for large scale and comprehensive
phenotyping (Phenomefrontier) and archiving
(Archivefrontier) of mouse models.
Picture
Novelty / Impact Infrafrontier is expected to
give Europe a leading position in a worldwide
competition on resources and knowledge for
medically relevant mouse models. The launch of
Infrafrontier is required to speed up the
discovery of molecular mechanisms of diseases and
health - this is an important step for the future
of molecular medicine and the advancement of
diagnosis and therapy.
Timeline for Construction / estimated
life-time 2006-2012
Estimated Costs (construction, operational,
decommissioning) 320m /36m p.a./NA
Supporting consortium Eumorphia/Eumodic- and
EMMA-consortium
www.eumorphia.org/ www.emma.rm.cnr.it/
19
Infrafrontier - Phenomefrontier

• Why do we need Phenomefrontier?
• Thousands of models will be engineered
• Systemic view is required for next level in
  biology and medicine

Courtesy of M. Hrabé de Angelis
20
Infrafrontier - Archivefrontier

• Why do we need Archivefrontier?
• 30.000 new mouse mutants will be made
  until 2010
• We have no infrastructure in place to benefit
  from this rich source

21
Infrafrontier partners 9 countries 14 partners
- plus funding agencies

• Germany GSF HZI
• UK MRC/MGU, Welcome Trust Sanger EBI
• France ICS, CDTA/CDTA
• Italy CNR Government
• Sweden Karolinska
• Spain Univ. Barcelona Madrid
• Portugal Gulbenkian Institute
• Greece Fleming Institute
• Finland Biocenter Finland

Coordinator GSF/HGF - M. Hrabé de Angelis
22
EATRIS - The European Advanced Translational
Research Infrastructure in Medicine
Background There is a striking gap between basic
science and clinical medicine that is much more
pronounced in Europe than in the USA and that has
tended to widen in most European countries due to
increasing clinical demands and reduction in
hospital budgets. Thus the implementation of a
large infrastructure for translational research
that links and engages both clinical and basic
scientists as well as strong industrial partners
is of key importance.
Picture
Novelty / Impact EATRIS constitutes a strategic
investment built on a strong cooperation between
research centers, clinical centers and industry
towards the goal to systematically exploit the
dramatic progress made in European biomedical
research and molecular medicine.
Timeline for Construction / estimated
life-time 2007-2010 /2010 on
Estimated Costs (construction, operational,
decommissioning) 250m / 300m/NA
Supporting consortium In collaboration with
EMBL, NTRAC, Clinical Trial Center Network,
European Bio-banking and biomolecular resources
infrastructure, the European pharmaceutical
industry and others
23
EATRIS European Advanced Translational Research
Infrastructure in Medicine
24
EATRIS-Partners
HZI/MHH Braunschweig/Hannover
Free University Amsterdam
Imperial College London
DKFZ Heidelberg
Karolinska Stockholm
Neurospin Paris
25
Steering committee

• France D. Bihan, C. Olivier
• Germany R. Balling, Ottmar Wiestler
• Netherlands B. Pinedo, H. Hofstraat
• Sweden A. Aperia, Bo Angelin
• United Kingdom M. Yacoub

26
Network of distributed infrastructures for
clinical trials in Europe
Background The capacity of the EU to perform
highly competitive clinical research, and to
promote innovative pharmaceutical and
biotechnology development requires an integrated,
EU-wide clinical research infrastructure,
bridging the fragmentation of Europe and allowing
high-quality, multinational clinical trials.
Picture
Novelty / Impact This programme will impact on
the competitiveness of both academic and industry
biomedical research in the EU, hence the capacity
of Europe to develop new treatments and to
improve citizens health.
Timeline for Construction / estimated
life-time 1-2yrs/2007 on
Estimated Costs (construction, operational,
decommissioning) 6m /29m/ NA
Supporting consortium ECRIN member states with
plans to extend to other EU member states
www.ecrin.org
27
EATRIS
ECRIN
28

• Biocenter Finland
• Joint organisation of bioinstitutes in 5 cities
• Added value
• Co-ordination of activities, division of tasks
• National biotechnology infrastructure platform
• Critical mass for partcipating in EU
  infrastructure (ESFRI)
• Co-operation in research training
• Linking to developmental and entrepreneurial
  networks
• EFFICIENCY, CRITICAL MASS AND INNOVATIONS

J Heino, K Hiltunen, M Saarma, J Koistinaho I
Thesleff, O Silvennoinen, T Pihlajaniemi
Founding meeting, June 2006
29
Pan-European infrastructures (ESFRI)

• BBMRI European research infrastructure for
  biobanks and biomolecular resources
• Finnish participation co-ordinated by L. Palotie
• Structural biology
• Biocenter Finland as affilited partner ?
• Infrafrontier (mouse archiving and phenotyping)
• Biocenter Finland as partner
• EBRI European bioinformatics research
  infrastructure
• Finnish participation co-ordinated by CSC
• ECRIN European clinical research infrastructure
  network
• EATRIS European advanced translational research
  infrastructure in medicine
• Life watch (biodiversity)
• Finnish participation via science community