EuroBioForumIs Europe ready for Personal Medicine?18 April 2012, The Dominican Hotel, BrusselsBiobanks a cornerstone of Re...
Libraries of Flesh: The Sorry State of Human Tissue storage                                                      8 maj 201...
Libraries of Flesh: The Sorry State of Human Tissue storage Every year, billions of dollars’ worth of research into the ge...
Libraries of Flesh: The Sorry State of Human Tissue storage One bank at a major university claimed to have more than 12,00...
Can we do it better in Europe?                                 8 maj 2012   5
ESFRIEuropean Strategi Forum of Research Infrastructure
Connecting Biobanks -leading design principals for BBMRI      The leading seven design principals during the work for the ...
BBMRI PP 13 countries agreed on a       Minimal Dataset for BiobanksAndrea Calabria, CNR-ITB (IT)         Erkki Leego, UTA...
Connecting Biobanks –A simple example   User scenario 1: Get attributes for biobanks     Peter logs in to the BBMRI portal...
Implemented metadata model for the BBMRI-Demo prototype  During this phase eight accounts have been  released:  4 biobanks...
Minimum Information AboutBiobank data Sharing – MIABIS 2.0
BBMRI.se – a unified Swedish infrastructure for biobanking                               WP1 – Project managementWP2 & WP3...
Nordic BBMRI      Inventory of all Nordic biobanks      Pilot study: Colon cancer                                         ...
How many biobanks to connect ?                                 8 maj 2012   15
8 maj 2012   16
Summary of the nature of the 20 million humanbiological samples in Europe catalogued                                      ...
Top of the iceberg ?                       8 maj 2012   18
An exampel: Swedish biobanks 600 biobanks > 60 milj samples Inventory during 2012                               8 maj 2...
SBR-IS
Biobank metricsHow to identify biobank publications                                       8 maj 2012   21
Biobank MeSH profile                       8 maj 2012   22
Biobank MeSH profileDatabase: MEDLINE:------------------------------------------------------------------------------1 exp ...
Biobank publications from selected countries in EU     (Publication year 2009-2010 retrieved via MeSH-profile)            ...
8 maj 2012   25
Roadblocks             8 maj 2012   26
Roadblocks•Security – privacy/public good ; Itsall about trust•Ownership of data – Scientific EGOsystem                   ...
Individual              Collective interest               interests             conflict             betweenPrivacy       ...
Border P: Sequence sharing. Nature 470:169-170, 2011   “No amount of data will be useful if you can’t    interpret what t...
We are ready to connect Biobanks in Europe                                        8 maj 2012   30
jan-eric.litton@ki.se                        Jan-Eric Litton   31
Biobanks a cornerstone of Research Infrastructure
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Biobanks a cornerstone of Research Infrastructure

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

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Biobanks a cornerstone of Research Infrastructure

  1. 1. EuroBioForumIs Europe ready for Personal Medicine?18 April 2012, The Dominican Hotel, BrusselsBiobanks a cornerstone of ResearchInfrastructure Professor Jan-Eric Litton Director BBMRI.se
  2. 2. Libraries of Flesh: The Sorry State of Human Tissue storage 8 maj 2012 2
  3. 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. 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. 5. Can we do it better in Europe? 8 maj 2012 5
  6. 6. ESFRIEuropean Strategi Forum of Research Infrastructure
  7. 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. 8. BBMRI PP 13 countries agreed on a Minimal Dataset for BiobanksAndrea 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. 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. 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. 11. Minimum Information AboutBiobank data Sharing – MIABIS 2.0
  12. 12. BBMRI.se – a unified Swedish infrastructure for biobanking WP1 – Project managementWP2 & WP3 WP4 WP5 WP6 WP7 WP8 Collection: Analysis: IT Physical Ethics Financing Input Output FacilityCoordinate & Optimize Enforce a Create an Provide Ensure long-harmonize interface to unifying efficient national termsample / data analysis national IT national, expertise and financingcollection resources platform large scale forum tofrom sample addresspopulations 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
  13. 13. Nordic BBMRI Inventory of all Nordic biobanks Pilot study: Colon cancer 8 maj 2012 14
  14. 14. How many biobanks to connect ? 8 maj 2012 15
  15. 15. 8 maj 2012 16
  16. 16. Summary of the nature of the 20 million humanbiological samples in Europe catalogued 8 maj 2012 17
  17. 17. Top of the iceberg ? 8 maj 2012 18
  18. 18. An exampel: Swedish biobanks 600 biobanks > 60 milj samples Inventory during 2012 8 maj 2012 19
  19. 19. SBR-IS
  20. 20. Biobank metricsHow to identify biobank publications 8 maj 2012 21
  21. 21. Biobank MeSH profile 8 maj 2012 22
  22. 22. Biobank MeSH profileDatabase: MEDLINE:------------------------------------------------------------------------------1 exp Biological Specimen Banks/2 exp Tissue Preservation/3 gene library/4 specimen handling/ or exp preservation, biological/ or "tissue and organ harvestin5 databases, genetic/ and exp dna/6 databases, nucleic acid/7 1 or 2 or 3 or 4 or 5 or 68 limit 7 to humans9 8 not exp diagnostic imaging/10 9 not exp bacteria/11 exp transplantation/ or tr.fs.12 10 not 1113 (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
  23. 23. 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 173Certain 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. NLMrepresents that its data were formulated with a reasonable standard of care. Except for this representation, NLM makes norepresentation or warranties, expressed or implied. This includes, but is not limited to, any implied warranty of merchantability orfitness for a particular purpose, with respect to the NLM data, and NLM specifically disclaims any such warranties andrepresentations
  24. 24. 8 maj 2012 25
  25. 25. Roadblocks 8 maj 2012 26
  26. 26. Roadblocks•Security – privacy/public good ; Itsall about trust•Ownership of data – Scientific EGOsystem 8 maj 2012 27
  27. 27. Individual Collective interest interests conflict betweenPrivacy Access Balance 8 maj 2012 28
  28. 28. 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
  29. 29. We are ready to connect Biobanks in Europe 8 maj 2012 30
  30. 30. jan-eric.litton@ki.se Jan-Eric Litton 31

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