EuroBioForum 2012 | 18 April 2012 Presentation by Jan-Eric Litton, Professor at Department for Medical Epidemiology and Biostatistics, Karolinska Institutet

1. EuroBioForum
Is Europe ready for Personal Medicine?
18 April 2012, The Dominican Hotel, Brussels
Biobanks a cornerstone of Research
Infrastructure
Professor Jan-Eric Litton
Director BBMRI.se

2. Libraries of Flesh: The Sorry State of Human Tissue storage
8 maj 2012 2

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.”
8 maj 2012 3

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.
8 maj 2012 4

5. Can we do it better in Europe?
8 maj 2012 5

6. ESFRI
European Strategi Forum of Research Infrastructure

7. Connecting Biobanks -
leading design principals for BBMRI
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
8 maj 2012 7

8. BBMRI PP 13 countries agreed on a
Minimal Dataset for Biobanks
Andrea Calabria, CNR-ITB (IT) Erkki Leego, UTARTU (EE)
Mario Caccamo, EMBL-EBI (UK) Jan-Eric Litton, KI (SE)
Claus Dabringer, UNI-KLU (AT) Fernando López, VITRO, SA (ES)
Johann Eder, UNI-KLU (AT) Ioannis Michalopoulos, BRFAA (GR)
Paul Flicek, EMBL-EBI (UK) Luciano Milanesi, CNR-ITB (IT)
Ruslan Fomkin, KI (SE) Juha Muilu, NPHI (FI)
Martin Fransson, KI (SE) Louis Rechaussat, INSERM (FR)
Hákon Gudbjartsson, deCODE (IS) Blandine Rimbault, INSERM (FR)
Andy Harris, UK Biobank (UK) Tore Risch, UU (SE)
Hans Hillege, UMCG (NL) Pedro Roiz, VITRO, SA (ES)
Maria Krestyaninova, EMBL-EBI (UK) Paolo Romano, IST (IT)
Klaus Kuhn, TUM (DE) Morris Swertz, UMCG (NL)
FP7, Grant Agreement Nr. 212111

9. Connecting Biobanks –
A simple example
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
8 maj 2012 9

10. Implemented metadata model for the BBMRI-
Demo prototype
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)
8 maj 2012 10

11. Minimum Information About
Biobank data Sharing – MIABIS 2.0

13. BBMRI.se – a unified Swedish
infrastructure for biobanking
WP1 – Project management
WP2 & WP3 WP4 WP5 WP6 WP7 WP8
Collection: Analysis: IT Physical Ethics Financing
Input Output Facility
Coordinate & Optimize Enforce a Create an Provide Ensure long-
harmonize interface to unifying efficient national term
sample / data analysis national IT national, expertise and financing
collection resources platform large scale forum to
from sample address
populations handling ethical
& hospitals platform issues
Nitrogen tanks (-190° C)
Central storage stores ~100 million tubes
and withdrawal = “hard drive”
Distributed sample
handling at local biobanks Automatic repicking unit
and hospitals at -80° C. Fast
withdrawal of tubes =
“processor and RAM
memory”
8 maj 2012 13

14. Nordic BBMRI
Inventory of all Nordic biobanks
Pilot study: Colon cancer
8 maj 2012 14

15. How many biobanks to connect ?
8 maj 2012 15

16. 8 maj 2012 16

17. Summary of the nature of the 20 million human
biological samples in Europe catalogued
8 maj 2012 17

18. Top of the iceberg ?
8 maj 2012 18

19. An exampel: Swedish biobanks
 600 biobanks
 > 60 milj samples
 Inventory during 2012
8 maj 2012 19

20. SBR-IS

21. Biobank metrics
How to identify biobank publications
8 maj 2012 21

22. Biobank MeSH profile
8 maj 2012 22

23. Biobank MeSH profile
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 harvestin
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
8 maj 2012 23

24. 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

25. 8 maj 2012 25

26. Roadblocks
8 maj 2012 26

27. Roadblocks
•Security – privacy/public good ; Its
all about trust
•Ownership of data – Scientific EGO
system
8 maj 2012 27

28. Individual Collective
interest interests
conflict
between
Privacy Access
Balance
8 maj 2012 28

29. Border P: Sequence sharing. Nature 470:169-170, 2011
 “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.”
8 maj 2012 29

30. We are ready to connect Biobanks in Europe
8 maj 2012 30

31. jan-eric.litton@ki.se
Jan-Eric Litton 31