Biobanks a cornerstone of Research Infrastructure

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

8 maj 2012 2

Libraries of Flesh: The Sorry State of Human Tissue storage

8 maj 2012 3


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 4


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 5

Can we do it better in Europe?

ESFRI European Strategi Forum of Research Infrastructure

Connecting Biobanks -

leading design principals for BBMRI

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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

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)

Connecting Biobanks –

A simple example

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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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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

Minimum Information About

Biobank data Sharing – MIABIS 2.0

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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

8 maj 2012 14

Nordic BBMRI

Inventory of all Nordic biobanks

Pilot study: Colon cancer

8 maj 2012 15

How many biobanks to connect ?

8 maj 2012 16

Summary of the nature of the 20 million human

biological samples in Europe catalogued

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Top of the iceberg ?

8 maj 2012 18

An exampel: Swedish biobanks

600 biobanks

> 60 milj samples

Inventory during 2012

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SBR-IS

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Biobank metrics

How to identify biobank publications

Biobank MeSH profile

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Biobank MeSH profile

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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

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

8 maj 2012 25

8 maj 2012 26

Roadblocks

8 maj 2012 27

Roadblocks

•Security – privacy/public good ; Its

all about trust

•Ownership of data – Scientific EGO

system

8 maj 2012 28

conflict

between

Access

Balance

Individual

interest Collective

interests

Privacy

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

We are ready to connect Biobanks in Europe

8 maj 2012 30

Jan-Eric Litton 31

[email protected]

Biobanks a cornerstone of Research Infrastructure

Technology