Work package 10: Access to Biobanks

Brief description and aims of work

It is not the intention of p-medicine to build a biobank. This WP addresses solely the question on how to get access to existing clinically annotated biobanks and biomaterial repositories in the cancer domain. To contribute knowledge for new VPH simulation tools, it is essential to find biomaterial where clinical and other data are already available and that can be used to run new experiments in postgenomic trials. It is therefore one goal of p-medicine to enable through its ICT infrastructure the sharing and searching of high quality biological material for clinical research and personalized medicine in addition to the sharing and searching of corresponding clinical data in p-medicine's data warehouse.

Driven by the growing needs of clinical researchers and the pharmaceutical industry very large numbers of patient samples and related data from assays on these and from the clinical case are being collected and stored in biobanks and other biomaterial repositories. Collection sizes are approaching millions of samples from a variety of cohorts and cases, with thousands of phenotypes or other types of sample data collected in a variety of experimental conditions or in clinical routine. To acquire sample cohorts for VPH models and retrospective clinical studies, technical solutions are needed to index, annotate, browse, integrate and access such complex heterogeneous content from diverse human biomaterial repositories. In particular for rare diseases such as childhood cancer it is extremely important that distributed biomaterial stocks are merged and presented to the research community through one homogenous search and ordering interface with a clear legal and ethical policy for getting access to samples and implementing patients' consent. In consequence, we aim at developing an integrated service framework within the p-medicine platform to enhance and simplify access to existing biobanks but also to make own biomaterial collections available to larger research communities.
In order to avoid redundant work this will be done in close coordination with the European Biobanking and Biomolecular Research Infrastructure Project BBMRI that has prepared a respective pan-European infrastructure for large-scale biobanking planed to implement in the following years based on existing infrastructures and technologies. p-medicine will therefore harmonize its service framework development for biobank access with BBMRI. We will make use of public BBMRI results such as tools, core data sets or ethical and legal frameworks and we plan to connect the p-medicine platform to the BBMRI infrastructure when available in order to get access to large-scale biobanks. As the p-medicine partner Fraunhofer IBMT is also a participant of BBMRI’ preparatory phase, Fraunhofer IBMT will provide the optimal link to BBMRI. This work package deals with the access to already existing biobanks and biomaterial repositories in the cancer domain with a particular focus on
biomaterial repositories from clinical trials where structured clinical data about the patient case can also be made available in the data warehouse for new retrospective studies on biomaterials. The following main objectives will be addressed in this work package:

  • To analyze existing open biobank frameworks which enable the sharing of biomaterial in respect to usability, GCP criteria and legal aspects. This will be done in close cooperation with WP2 (User needs and requirements) and WP5 (Legal and ethical framework). One aspect is the evaluation of potential re-usability of existing tools for p-medicine.
  • To develop an integrated biobanking infrastructure in close cooperation with BBMRI. This service framework includes a biobank annotation service, a generic wrapper tool, a meta search engine for biomaterial with the possibility to integrate biomaterial stocks into larger bio-databanks.
  • To provide a semantic biobank query interface that allows users to search for cases and materials in various bio-repositories according to their selection criteria and to match this with corresponding case related data in the data ware house. This tool shall serve as a meta search engine for biomaterial.
  • To integrate a mechanism for monitoring and safeguarding the patients’ / donors’ decisions on research that might or shall be performed on their samples. This mechanism will be provided by WP14 ‘Collaborative
    Environment for Patient Empowerment’.
  • To evaluate the biobanking framework by integrating distributed biomaterial resources of the SIOP Wilms Tumour Trial into the p-medicine infrastructure in addition to the publicly available German-Austrian metabiobank in the cancer domain namely the biobank Central Research Infrastructure for molecular Pathology CRIP.

As this work package deals with the integration of heterogenous data sources related to human biomaterial it will build on WP4’s tools for semantic interoperability.

Work package leader

Stephan Kiefer Email

Fraunhofer-Gesellschaft zur Förderung der Angewandten Forschung e. V.
Institut für Biomedizinische Technik IBMT
Ensheimer Strasse 48
66386 St. Ingbert/Germany