Mass spectrometry

Microarray technology

Nanoscopy and imaging

Next generation sequencing

NMR Spectroscopy

Medical imaging

Generic infrastructure

Biobanking

Biobank

Biobanks are collections of biological material, such as DNA, tissue, cells and blood, and the data that go with each sample (in the form of medical records, environmental information, lifestyle information and follow-up data, for example). Biobanking thus deals with a secure repository for long-term storage and protection of confidential medical, health, and lifestyle data of patients of volunteers. The challenge is to provide access and data sharing within the Biobank community, sample handling, and integration of phenotype and genotype data.

The main project involves building a model infrastructure for the Dutch Biobank community, BBMRI-NL, that manages resources for the future of biomedical research. It forms a hub in the European Biobanking and Biomolecular Resources Research Infrastructure.

e-BioGrid is open to take Biobanking dedicated projects on board. Contact us if you are involved in Biobanking and you need support in software or hardware infrastructure.


Projects in this technology area

Using large scale computing facilities for Biobanks, knowledge discovery across biobanks and Enrichment of Biobanks with whole genome information. *
description:The Netherlands have 150 biobanks with over 400,000 samples in total. To exploit these billions worth of material they are now embarking on large scale genetic profiling. An example is the highly visible Genome of the Netherlands project that will sequence the DNA of 750 Dutch individuals completely to elucidate the genetic diversity in the Dutch population, and to impute this new information onto existing more sparse genetic information of 100.000 Dutch individuals. However, the data handling and computational needs are enormous and Dutch Institutes are struggling to effectively use the hardware infrastructures available.

This e-BioGrid subproject will overcome this barrier by interfacing the data processing tools used in biobanking to the existing BiGGrid infrastructure and by supporting the Dutch biobanking community to deploy these tools for their large data and processing challenges. Applications include (1) high-throughput genetics studies from next generation sequencing of biobank samples (>750), (2) genome wide imputation and association studies (>100,000) and (3) follow-up BBMRI-NL projects that are currently being drafted by the BBMRI-NL steering commitee. We also aim to pilot knowledge discovery across biobanks by connecting this new information with existing information from over 150 existing Dutch biobanks.

Envisioned short-term results are high-impact scientific publications of these biobank studies. Long-term results are availability of flexible and scalable e-Science tools for large scale biobanking and optimized GRID infrastructure for biobanks within BigGrid, SARA, NBIC and the Life Sciences community to bring the Netherlands at the forefront of the next generation of genetics and populations research.
applicant:Morris Swertz, University Medical Center Groningen
results:Whereas some of the analysis pipelines are already available on Grid resources (e.g. imputation), others are ongoing and planned (SNP calling, analysis of structural variations). The read alignment pipeline is further being developed such that other genome sequencing projects can make use of the analysis infrastructure as well. See also the wiki for progress updates.
status:ongoing
team:Jan Bot, Pieter Neerincx, Abhishek Narain, George Byelas, Tom Visser
type:This is a main project.


* This is the main project in this technology area

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