Imaging biobanks, report from the european society of radiology
Biobanks a cornerstone of Research Infrastructure
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Biobanks a cornerstone of Research Infrastructure
Professor Jan-Eric Litton
Director BBMRI.se
EuroBioForum Is Europe ready for Personal Medicine?
18 April 2012, The Dominican Hotel, Brussels
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8 maj 2012 2
Libraries of Flesh: The Sorry State of Human Tissue storage
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8 maj 2012 3
Libraries of Flesh: The Sorry State of Human Tissue storage
Every year, billions of dollars’ worth of research into the genetic
underpinnings of autism, schizophrenia, diabetes, Alzheimer’s disease, and
other devastating disorders hinges on scientists’ ability to tap industrial
quantities of cells and tissue. But Compton found that while our technology
for decoding the inner workings of life is advancing dramatically, the
protocols for collecting and storing specimens of human flesh have barely
evolved in decades. At the same time, innovation in the field of biobanking
has stalled for lack of funding and interest. The science of bio-preservation is
still considered an arcane, musty specialty, more akin to taxidermy than
medicine. “You might have thought that doing the science would be the
biggest challenge of a massive undertaking like the Cancer Genome Atlas,”
Compton told me last fall. “But acquiring the biospecimens turned out to be
the hardest part, bar none. It’s the Wild West out there.”
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8 maj 2012 4
Libraries of Flesh: The Sorry State of Human Tissue storage
One bank at a major university claimed to have more than 12,000 samples of glioblastoma
in its collection.
Only 18 of those were good enough to use.
The rate of unacceptable shipments from other institutions ran as high as 99 percent.
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8 maj 2012 5
Can we do it better in Europe?
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ESFRI European Strategi Forum of Research Infrastructure
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Connecting Biobanks -
leading design principals for BBMRI
8 maj 2012 7
The leading seven design principals during the work for the presented scenarios, use cases and software architecture are:
· Assuring confidentiality of donors
· Following a user centered approach and providing a maximum support for researchers
· Use of up to date Web-Technologies
· Flexibility in terms of biobank content and schema handling
· Extensibility in terms of additional participants and adding new data and information
· Efficiency in terms of query processing
· Low effort for biobanks to participate in federation
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FP7, Grant Agreement Nr. 212111
BBMRI PP 13 countries agreed on a
Minimal Dataset for Biobanks
Andrea Calabria, CNR-ITB (IT) Mario Caccamo, EMBL-EBI (UK) Claus Dabringer, UNI-KLU (AT) Johann Eder, UNI-KLU (AT) Paul Flicek, EMBL-EBI (UK) Ruslan Fomkin, KI (SE) Martin Fransson, KI (SE) Hákon Gudbjartsson, deCODE (IS) Andy Harris, UK Biobank (UK) Hans Hillege, UMCG (NL) Maria Krestyaninova, EMBL-EBI (UK) Klaus Kuhn, TUM (DE)
Erkki Leego, UTARTU (EE) Jan-Eric Litton, KI (SE) Fernando López, VITRO, SA (ES) Ioannis Michalopoulos, BRFAA (GR) Luciano Milanesi, CNR-ITB (IT) Juha Muilu, NPHI (FI) Louis Rechaussat, INSERM (FR) Blandine Rimbault, INSERM (FR) Tore Risch, UU (SE) Pedro Roiz, VITRO, SA (ES) Paolo Romano, IST (IT) Morris Swertz, UMCG (NL)
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Connecting Biobanks –
A simple example
8 maj 2012 9
User scenario 1: Get attributes for biobanks
Peter logs in to the BBMRI portal and goes to the search function.
He then first needs to choose one of the ontologies that are included in UMLS Metathesaurus:
a. Select ontology ICD-10
He makes the following choices of input (by query statements or predefined scrollbars) for the set
"Attributes for biobanks":
b. Type of diagnosis | Using ICD-10 C50. //Note: non-specific code not used for diagnosis
c. Type of sample tissue
d. Method of preservation All
e. Data needed Diagnosis information
Number of samples
Collections with at least 100 samples
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8 maj 2012 10
During this phase eight accounts have been
released:
4 biobanks uploaded data (TU-Munich, MUG-
Biobank, Institute for Molecular Medicine
Finland, CRIP)
~15.000 cases already stored in database
The other account holders only had query-access-
rights (Vitrosoft, CRB-IST, Karolinska Institutet
Biobank, French National Cancer Institute)
Implemented metadata model for the BBMRI-
Demo prototype
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Minimum Information About
Biobank data Sharing – MIABIS 2.0
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8 maj 2012 13
WP1 – Project management
WP2 & WP3
Collection:
Input
Coordinate &
harmonize
sample / data
collection
from
populations
& hospitals
WP4
Analysis:
Output
Optimize
interface to
analysis
resources
WP5
IT
Enforce a
unifying
national IT
platform
WP6
Physical
Facility
Create an
efficient
national,
large scale
sample
handling
platform
WP7
Ethics
Provide
national
expertise and
forum to
address
ethical
issues
WP8
Financing
Ensure long-
term
financing
Distributed sample
handling at local biobanks
and hospitals
Central storage
and withdrawal
Nitrogen tanks (-190° C)
stores ~100 million tubes
= “hard drive”
Automatic repicking unit
at -80° C. Fast
withdrawal of tubes =
“processor and RAM
memory”
BBMRI.se – a unified Swedish
infrastructure for biobanking
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8 maj 2012 14
Nordic BBMRI
Inventory of all Nordic biobanks
Pilot study: Colon cancer
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8 maj 2012 15
How many biobanks to connect ?
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8 maj 2012 16
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Summary of the nature of the 20 million human
biological samples in Europe catalogued
8 maj 2012 17
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Top of the iceberg ?
8 maj 2012 18
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An exampel: Swedish biobanks
600 biobanks
> 60 milj samples
Inventory during 2012
8 maj 2012 19
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SBR-IS
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8 maj 2012 21
Biobank metrics
How to identify biobank publications
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Biobank MeSH profile
8 maj 2012 22
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Biobank MeSH profile
8 maj 2012 23
Database: MEDLINE:
------------------------------------------------------------------------------
1 exp Biological Specimen Banks/
2 exp Tissue Preservation/
3 gene library/
4 specimen handling/ or exp preservation, biological/ or "tissue and organ harvesting"/
5 databases, genetic/ and exp dna/
6 databases, nucleic acid/
7 1 or 2 or 3 or 4 or 5 or 6
8 limit 7 to humans
9 8 not exp diagnostic imaging/
10 9 not exp bacteria/
11 exp transplantation/ or tr.fs.
12 10 not 11
13 (biorepositor* or biobank* or bio-bank*).mp.
14 7 and (lj or es or st or og).fs.
15 12 or 13 or 14
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Biobank publications from selected countries in EU
(Publication year 2009-2010 retrieved via MeSH-profile)
# biobank publications # citations
NETHERLANDS 119 2461
SWEDEN 71 1410
DENMARK 44 1368
AUSTRIA 44 520
NORWAY 37 823
FINLAND 35 1345
HUNGARY 16 173
Certain data included herein are derived from the Web of Science ® prepared by THOMSON REUTERS ®, Inc. (Thomson®),
Philadelphia, Pennsylvania, USA: © Copyright THOMSON REUTERS ® 2011. All rights reserved.
The MeSH Headings used in this analysis were from MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. NLM
represents that its data were formulated with a reasonable standard of care. Except for this representation, NLM makes no
representation or warranties, expressed or implied. This includes, but is not limited to, any implied warranty of merchantability or
fitness for a particular purpose, with respect to the NLM data, and NLM specifically disclaims any such warranties and
representations
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8 maj 2012 25
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8 maj 2012 26
Roadblocks
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8 maj 2012 27
Roadblocks
•Security – privacy/public good ; Its
all about trust
•Ownership of data – Scientific EGO
system
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8 maj 2012 28
conflict
between
Access
Balance
Individual
interest Collective
interests
Privacy
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8 maj 2012 29
“No amount of data will be useful if you can’t
interpret what they mean. We are reaching the
point at which the cost of interpreting genome
information will exceed the cost of generating it, so
the challenge ahead will be to make more sense of
the data we already have. We will also have to
answer the question of whether genome data are
personal, in that they are paid for and controlled by
individuals, or whether such data are medical,
being funded by and accessible to health-care
systems.”
Border P: Sequence sharing. Nature 470:169-170, 2011
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We are ready to connect Biobanks in Europe
8 maj 2012 30