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Biobank of the Center for Integrated Oncology Köln Bon

Access to both benign and malignant tissue samples comprehensively annotated with histopathological and clinical data is a prerequisite for basic and translational cancer research in the era of genomic medicine. The centralized Biobank of the Center for Integrated Oncology (CIO) Köln Bonn has been established at the Institutes of Pathology in Bonn and Cologne. Its aim is to collect and store high quality tissue and blood specimens from a variety of sources in combination with patient consent, clinical and histopathological data and to make these available for basic and translational research projects.

Aims of the CIO Biobank

1. To set up a comprehensive Biobank for all biological needed for research in the CIO including cryo tissue and blood samples, formalin fixed and paraffin embedded (FFPE) tissue from the archives of the Institutes of Pathology.
2. To make frozen and FFPE tissue from orthotopic mouse tumor models available in the CIO available to research groups.
3. To make frozen and FFPE tissue from xenografts in nude mice and the cell lines that are used to generate them available.
4. To assemble molecularly defined patient cohorts with clinical follow-up for NSCLC (EGFR and KRAS status), melanoma (BRAF mutations in an ongoing collaboration with Roche), and breast cancer (basal type in an ongoing collaboration with Agendia).
5. To generate TMAs for the molecularly defined cohorts.
6. To set-up a central TMA facility with digital image based evaluation and supporting clinical database Using the Zeiss Mirax Scanner system for virtual microscopy

Organisation & Infrastructure

Organisation

On an organisational level the Biobank of CIO Köln Bonn has a virtually identical set-up at both sites in Bonn and Cologne, with a central storage facility for tissue and blood samples at both Institutes of Pathology, respectively. Responsible for the daily running of the Biobank, sample management and sample allocation is the gatekeeper, who is an appointed member of staff of the Institute of Pathology. They are supported by technical staff funded by the CIO and reports to Biobank committee that comprises members of the participating clinical specialties. The tumor bank committee is accountable to the CIO and the Medical Faculty.

The gate keeper makes samples and data exclusively available in a pseudo-anonymized form.

Organisation Chart of the CIO Biobank

   Click image to enlarge!

Infrastructure

The frozen blood and tissue samples are stored at temperatures below the glass transition temperature of water (-130°C). The sample storage has an in build fail-safe mechanism that ensures sufficient cooling for 36 hours after power supply loss and is additionally equipped with an alarm system liked to the central technical emergency service of the hospital. In emergency the Biobank staff is contacted by mobile at any time.
Since the beginning of the funding period the total capacity of the Biobank has been extended to a total of 48,000 sample spaces of which approx. 85% are already in use. The space is expected to run out in mid 2010.
In addition to the fast-section laboratory at the Institute of Pathology an additional Biobank location with barcode labeling station, linked to the central BiobankPRO database has been set-up at the Institute of Clinical Biochemistry. This allows blood products to be processed and frozen directly. This has reduced the ischemic time for these samples significantly.

BiobankPRO Database

The BiobankPRO database developed in house to print barcoded sample label, annotate and trace samples has been significantly updated. This includes:

• A complete sample history
  Tracking of every single sample history is now documented. This includes freezing time, freeze thaw cycles, reference documents (RIN value, reference slide), aliquots, and remaining tissue, protein and nucleic acid extracts.
• Consent management
  Consent forms are available in the central patient management system (ORBIS/KAS) in the clinical departments for download. Once consent has been obtained by a physician the forms are electronically transmitted to the Biobank and stored as pdf-files directly in the patient record. When samples are selected for research projects the consent forms are directly accessible and can be checked.
• Project management
  All project applications are electronically stored and linked to the sample base.
• The Clinical database for patient follow-up (Mega-manager) has been linked to BiobankPro.
• Electronic management of the FFPE tissue blocks archive has been added.
• Anonymized clinical and histopathological data is fully indexed and fully searchable via a simple user interface to identify relevant samples for research use.
• Interfaces to cooperating Biobanks such as Patients Tumorbank of Hope have been established.

Contact

External Cooperations

We have strived to harmonize the infrastructure between the different CCCs funded by German Cancer Aid and have made our SOPs as well as the BiobankPro Database available to other centers on a shareware basis.  Currently the system is used in Bonn, Cologne and Dresden. Heidelberg and Münster have voiced their intent to use the database.

Stiftung PATH

Close collaboration with the patient run multicenter Biobank Stiftung PATH Patients Tumorbank of Hope and the biobanks of the breast cancer care centers in Dortmund, Herne/Bochum, Kassel, Marburg and Offenbach.

Selected publications

» Publications CIO Biobank (PDF)