Difference between revisions of "Biobanking"

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'''Biobanking''' is one of the task forces of Members of the NBIC [[BioAssist]] consortium and Members of Biomolecular Resources Research Infrastructure – NL branch. Coordinator: Morris Swertz [[User:Mswertz|Mswertz]]
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'''Biobanking''' is one of the [[task force]]s of [[BioAssist]] and has members from Biomolecular Resources Research Infrastructure – NL branch.  
  
 
== Overview ==
 
== Overview ==
  
'Biobanks encompass of collections of basic materials (blood, DNA samples) and/or their descriptions (patients, diseases, phenotypes) and subsequent data (genotypes, microarray gene expressions). These are essential for the study of complex, multifactorial diseases where genetic, environment and lifestyle contribute together to the development of disease like cancer, diabetis, heart and inflammatory diseases. Current estimations state that the Dutch biobanks together contain materials and data on about 400.000 individuals, not counting PSI and LifeLines (ref: list of biobanks). To enable research, these materials and data need to be made findable, accessible and analyzable via suitable infrastructure.  
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Biobanks encompass of collections of basic materials (blood, DNA samples) and/or their descriptions (patients, diseases, phenotypes) and subsequent data (genotypes, microarray gene expressions). These are essential for the study of complex, multifactorial diseases where genetic, environment and lifestyle contribute together to the development of disease like cancer, diabetis, heart and inflammatory diseases. Current estimations state that the Dutch biobanks together contain materials and data on about 400.000 individuals, not counting PSI and LifeLines ([[list of biobanks]]). To enable research, these materials and data need to be made findable, accessible and analyzable via suitable infrastructure.  
  
NBIC has joined hands with the recently funded BBMRI-NL consortium to prioritize, coordinate and implement the bioinformatics resources needed. The remit of BBMRI is to establish European infrastructure for biobabanks. BBMR-NL is the dutch hub of this initiative encompassing the UMCs, String of Pearls, NKI, RIVM, University of Utrecht and the Free University Amsterdam (VU). The NBIC-BBMRI collaboration project is currently in the planning phase. This work is coordinated with strong national partner initiatives like String of Pearls (PSI) and LifeLines as well as infrastructure initiatives like SARA and TARGET and international initiatives such as P3G, Gen2Phen and BBMRI-EU. In this first phase the list of practical objectives is being discussed to produce suitable infrastructure for existing Dutch biobanks, such as:
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== Organization ==
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NBIC has joined hands with the recently funded [http://www.bbmri.nl/ BBMRI-NL consortium] to prioritize, coordinate and implement the bioinformatics resources needed. The remit of BBMRI is to establish European infrastructure for biobabanks. BBMR-NL is the Dutch hub of this initiative encompassing the UMCs, String of Pearls, NKI, RIVM, University of Utrecht and the Free University Amsterdam (VU). The NBIC-BBMRI collaboration project is currently in the planning phase. This work is coordinated with strong national partner initiatives like String of Pearls (PSI) and LifeLines as well as infrastructure initiatives like SARA and TARGET and international initiatives such as P3G, Gen2Phen and BBMRI-EU.  
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=== Projects ===
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We organize our projects on the NBIC Trac server. A list of our running projects can be found in the [http://trac.nbic.nl/biobanking/ biobanking Trac].
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=== Contacts ===
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PI: [[User:Mswertz|Morris Swertz]]
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PL: [[User:David.van.enckevort|David van Enckevort]]
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== Goals ==
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In this first phase the list of practical objectives is being discussed to produce suitable infrastructure for existing Dutch biobanks, such as:
 
* Improve findability of materials and data via a Dutch material and data catalogue listing all available biobanks and meta data on their contents. This is collaboration with the examplar BBMRI-EU and P3G catalogs.
 
* Improve findability of materials and data via a Dutch material and data catalogue listing all available biobanks and meta data on their contents. This is collaboration with the examplar BBMRI-EU and P3G catalogs.
 
* Improve accessibility of data via standardized data access interfaces that local biobanks can adopt to enable data sharing. This work will be strongly connected to, although not depend on, related efforts in European Bioinformatics Institute, GEN2PHEN, Parelsnoer, LifeLines, P3G, NPC, NMC, etc.
 
* Improve accessibility of data via standardized data access interfaces that local biobanks can adopt to enable data sharing. This work will be strongly connected to, although not depend on, related efforts in European Bioinformatics Institute, GEN2PHEN, Parelsnoer, LifeLines, P3G, NPC, NMC, etc.
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* Establish a shared GWAS tool platform with services to QC, impute and analyze SNP array data against phenotypic information and data management capability to manage these kind of data.
 
* Establish a shared GWAS tool platform with services to QC, impute and analyze SNP array data against phenotypic information and data management capability to manage these kind of data.
 
* Establish a Dutch Genotype Archive for GWA Control Cohorts that associated Dutch biobanks can use as source for control sets for GWA studies.
 
* Establish a Dutch Genotype Archive for GWA Control Cohorts that associated Dutch biobanks can use as source for control sets for GWA studies.
For each of these themes ‘software-in-a-box’ implementations will be provided, next to public installations, that interested biobanks can just download and use locally. Also software will be developed as open source to ensure that the global community can join in via partner projects. Pilots of such projects are underway in collaboration with the European Bioinformatics Institute and Gen2Phen such as a phenotype database-in-a-box [1] and a microarray gene expression database-in-a-box [2] each using the novel software development strategy [3] implemented using the MOLGENIS system [4].
 
  
== Resources ==
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== Software in a box solutions ==
# Pheno-OM – phenotype database and exchange format. http://wwwdev.ebi.ac.uk/microarray-srv/pheno/
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# MAGETAB-OM – microarray database using MAGE-TAB format http://wwwdev.ebi.ac.uk/microarray-srv/magetab  
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For each of these themes ‘software-in-a-box’ implementations will be provided, next to public installations, that interested biobanks can just download and use locally. Also software will be developed as open source to ensure that the global community can join in via partner projects. Pilots of such projects are underway in collaboration with the European Bioinformatics Institute and Gen2Phen such as a phenotype database-in-a-box [http://www.phenoflow.org Pheno-OM / PhenoFlow], the extensible genotype and phenotype database [http://www.xgap.org XGAP for GWAS] in collaboration with LifeLines and a microarray gene expression database-in-a-box [http://wwwdev.ebi.ac.uk/microarray-srv/magetab Magetab] together with BBMRI-NL each using the novel software development strategy (Swertz MA, Jansen RC (2007) Beyond standardization: dynamic software infrastructures for systems genetics. Nature Reviews Genetics 8(3)) implemented using the [http://www.molgenis.org MOLGENIS] system.
# Swertz MA, Jansen RC (2007) Beyond standardization: dynamic software infrastructures for systems genetics. Nature Reviews Genetics 8(3).
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# http://www.molgenis.org
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== See Also ==
# [[GwasTools Tools for Genome Wide Association studies]]
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* [[GwasTools Tools for Genome Wide Association studies]]
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* [[Biobanking Tools]]
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* [[Semantic Harmonization]]
  
 
[[Category:Biobanking]]
 
[[Category:Biobanking]]

Latest revision as of 10:47, 29 March 2011

Biobanking is one of the task forces of BioAssist and has members from Biomolecular Resources Research Infrastructure – NL branch.

Overview

Biobanks encompass of collections of basic materials (blood, DNA samples) and/or their descriptions (patients, diseases, phenotypes) and subsequent data (genotypes, microarray gene expressions). These are essential for the study of complex, multifactorial diseases where genetic, environment and lifestyle contribute together to the development of disease like cancer, diabetis, heart and inflammatory diseases. Current estimations state that the Dutch biobanks together contain materials and data on about 400.000 individuals, not counting PSI and LifeLines (list of biobanks). To enable research, these materials and data need to be made findable, accessible and analyzable via suitable infrastructure.

Organization

NBIC has joined hands with the recently funded BBMRI-NL consortium to prioritize, coordinate and implement the bioinformatics resources needed. The remit of BBMRI is to establish European infrastructure for biobabanks. BBMR-NL is the Dutch hub of this initiative encompassing the UMCs, String of Pearls, NKI, RIVM, University of Utrecht and the Free University Amsterdam (VU). The NBIC-BBMRI collaboration project is currently in the planning phase. This work is coordinated with strong national partner initiatives like String of Pearls (PSI) and LifeLines as well as infrastructure initiatives like SARA and TARGET and international initiatives such as P3G, Gen2Phen and BBMRI-EU.

Projects

We organize our projects on the NBIC Trac server. A list of our running projects can be found in the biobanking Trac.

Contacts

PI: Morris Swertz

PL: David van Enckevort

Goals

In this first phase the list of practical objectives is being discussed to produce suitable infrastructure for existing Dutch biobanks, such as:

  • Improve findability of materials and data via a Dutch material and data catalogue listing all available biobanks and meta data on their contents. This is collaboration with the examplar BBMRI-EU and P3G catalogs.
  • Improve accessibility of data via standardized data access interfaces that local biobanks can adopt to enable data sharing. This work will be strongly connected to, although not depend on, related efforts in European Bioinformatics Institute, GEN2PHEN, Parelsnoer, LifeLines, P3G, NPC, NMC, etc.
  • Ease data exchange via harmonization of data formats for genetic and phenotypic data, as well as sample annotations to overcome barriers for scientific collaboration. This is strong collaboration with international efforts such as FuGE, Gen2Phen, XGAP, MAGE-TAB, etc.
  • Ease data integration via harmonization of data annotation mapping systems for phenotypic data and sample annotations. This in strong collaboration with Concept Web Alliance, P3G and various ontology projects.
  • Establish a shared GWAS tool platform with services to QC, impute and analyze SNP array data against phenotypic information and data management capability to manage these kind of data.
  • Establish a Dutch Genotype Archive for GWA Control Cohorts that associated Dutch biobanks can use as source for control sets for GWA studies.

Software in a box solutions

For each of these themes ‘software-in-a-box’ implementations will be provided, next to public installations, that interested biobanks can just download and use locally. Also software will be developed as open source to ensure that the global community can join in via partner projects. Pilots of such projects are underway in collaboration with the European Bioinformatics Institute and Gen2Phen such as a phenotype database-in-a-box Pheno-OM / PhenoFlow, the extensible genotype and phenotype database XGAP for GWAS in collaboration with LifeLines and a microarray gene expression database-in-a-box Magetab together with BBMRI-NL each using the novel software development strategy (Swertz MA, Jansen RC (2007) Beyond standardization: dynamic software infrastructures for systems genetics. Nature Reviews Genetics 8(3)) implemented using the MOLGENIS system.

See Also