Biomolecular Resources Research Infrastructure Research Articles

The Lung Biobank Heidelberg – A 15 Years old Basis for Lung Research

The lung research specimen biobank located at the Thoraxklinik Heidelberg (TK-HD) is an accredited subsidiary (DAP-IS-4153.04 according to DIN EN ISO/IEC 17020) of the National Center for Tumor Diseases Heidelberg (NCT), which is integrated into the BioMaterialBank Heidelberg (BMBH). The NCT Tissue Bank is registered with the German Technology and Method Platform for Medical Research Networks (TMF) and the European Biobanking and Biomolecular Resources Research Infrastructure (BBMRI).

The EuroBioBank Network: 10 years of hands-on experience of collaborative, transnational biobanking for rare diseases.

The EuroBioBank (EBB) network (www.eurobiobank.org) is the first operating network of biobanks in Europe to provide human DNA, cell and tissue samples as a service to the scientific community conducting research on rare diseases (RDs). The EBB was established in 2001 to facilitate access to RD biospecimens and associated data; it obtained funding from the European Commission in 2002 (5th framework programme) and started operation in 2003. The set-up phase, during the EC funding period 2003–2006, established the basis for running the network; the following consolidation phase has seen the growth of the network through the joining of new partners, better network cohesion, improved coordination of activities, and the development of a quality-control system. During this phase the network participated in the EC-funded TREAT-NMD programme and was involved in planning of the European Biobanking and Biomolecular Resources Research Infrastructure. Recently, EBB became a partner of RD-Connect, an FP7 EU programme aimed at linking RD biobanks, registries, and bioinformatics data. Within RD-Connect, EBB contributes expertise, promotes high professional standards, and best practices in RD biobanking, is implementing integration with RD patient registries and ‘omics' data, thus challenging the fragmentation of international cooperation on the field.

The locked genomes: A perspective from Arabia

The locked genomes: A perspective from Arabia

DZL-Platform Biobanking

Broad, coordinated access to biomaterials is essential for the translation of research findings into patient therapies. A centrally-organized DZL Biobanking Platform will guarantee that member of the DZL as well as external partners will have easy and direct access to biomaterials from patients with pulmonary disease. The DZL Biobanking Platform will capitalize on existing biobanking structures within DZL sites and will be connected to the Technology and Methods Platform for Network Research in Medicine (TMF e.V.) and Biobanking and Biomolecular Resources Research Infrastructure (BBMRI) catalogues. The biomaterial banks of DZL sites are not homogeneous. They are varying regarding structure and organizational standards methods of biomaterial collection, sample, data and quality management.

The European Research Infrastructures of the ESFRI Roadmap in Biological and Medical Sciences: status and perspectives.

Since 2002, the European Strategy Forum on Research Infrastructures identified the needs for Research Infrastructures (RIs) in Europe in priority fields of scientific research and drafted a strategic document, the ESFRI Roadmap, defining the specific RIs essential to foster European research and economy. The Biological and Medical Sciences RIs (BMS RIs) were developed thanks to the active participation of many institutions in different European member states associated to address the emerging needs in biomedicine and, among these, the Italian National Institute of Health (ISS), in virtue of its role in public health and research, has been specifically involved in the national development and implementation of three RIs: the Biobanking and Biomolecular Resources Research Infrastructure (BBMRI), the European Advanced Translational Research Infrastructure in Medicine (EATRIS) and the European Clinical Research Infrastructures Network (ECRIN). This article outlines the design and development of these RIs up to the recent achievement of the ERIC status, their importance in the Horizon 2020 programme and their societal and economic potential impact, with special attention to their development and significance in Italy. The ISS plays a unique role in fostering a coordinated participation of excellence Italian institutes/facilities to different European biomedical RIs, thus contributing to health innovation, healthcare optimization, and healthcare cost containment.

Review of the Italian current legislation on research biobanking activities on the eve of the participation of national biobanks’ network in the legal consortium BBMRI-ERIC.

The ethical-legal framework of research biobanking activities is still scarcely defined in Italy, and this constitutes a major obstacle to exploit the potential benefits of existing bioresource patrimony at the national and international levels. Biobanking and Biomolecular Resources Research Infrastructure (BBMRI), which aims to become a major interface between biological samples and data and top-level biological and medical research, is undertaking the crucial transformation to the ERIC (European Research Infrastructure Consortium) legal entity. In this scenario, there is a need to address the national legal and ethical concerns that are strictly correlated with the use of human biosources in research across European countries participating (and not) in BBMRI. In this perspective, this article aims to review the legal framework applying to research biobanking in Italy, including both "soft" nonbinding instruments and binding regulations. Since ethical and societal aspects impact biobanking research activities, the article discusses both the critical ethical and legal open issues that need to be implemented at the national level.

Developing a semantically rich ontology for the biobank-administration domain.

BackgroundBiobanks are a critical resource for translational science. Recently, semantic web technologies such as ontologies have been found useful in retrieving research data from biobanks. However, recent research has also shown that there is a lack of data about the administrative aspects of biobanks. These data would be helpful to answer research-relevant questions such as what is the scope of specimens collected in a biobank, what is the curation status of the specimens, and what is the contact information for curators of biobanks. Our use cases include giving researchers the ability to retrieve key administrative data (e.g. contact information, contact's affiliation, etc.) about the biobanks where specific specimens of interest are stored. Thus, our goal is to provide an ontology that represents the administrative entities in biobanking and their relations. We base our ontology development on a set of 53 data attributes called MIABIS, which were in part the result of semantic integration efforts of the European Biobanking and Biomolecular Resources Research Infrastructure (BBMRI). The previous work on MIABIS provided the domain analysis for our ontology. We report on a test of our ontology against competency questions that we derived from the initial BBMRI use cases. Future work includes additional ontology development to answer additional competency questions from these use cases.ResultsWe created an open-source ontology of biobank administration called Ontologized MIABIS (OMIABIS) coded in OWL 2.0 and developed according to the principles of the OBO Foundry. It re-uses pre-existing ontologies when possible in cooperation with developers of other ontologies in related domains, such as the Ontology of Biomedical Investigation. OMIABIS provides a formalized representation of biobanks and their administration. Using the ontology and a set of Description Logic queries derived from the competency questions that we identified, we were able to retrieve test data with perfect accuracy. In addition, we began development of a mapping from the ontology to pre-existing biobank data structures commonly used in the U.S.ConclusionsIn conclusion, we created OMIABIS, an ontology of biobank administration. We found that basing its development on pre-existing resources to meet the BBMRI use cases resulted in a biobanking ontology that is re-useable in environments other than BBMRI. Our ontology retrieved all true positives and no false positives when queried according to the competency questions we derived from the BBMRI use cases. Mapping OMIABIS to a data structure used for biospecimen collections in a medical center in Little Rock, AR showed adequate coverage of our ontology.

Telethon Network of Genetic Biobanks: a key service for diagnosis and research on rare diseases

Several examples have always illustrated how access to large numbers of biospecimens and associated data plays a pivotal role in the identification of disease genes and the development of pharmaceuticals. Hence, allowing researchers to access to significant numbers of quality samples and data, genetic biobanks are a powerful tool in basic, translational and clinical research into rare diseases. Recently demand for well-annotated and properly-preserved specimens is growing at a high rate, and is expected to grow for years to come. The best effective solution to this issue is to enhance the potentialities of well-managed biobanks by building a network.Here we report a 5-year experience of the Telethon Network of Genetic Biobanks (TNGB), a non-profit association of Italian repositories created in 2008 to form a virtually unique catalogue of biospecimens and associated data, which presently lists more than 750 rare genetic defects. The process of TNGB harmonisation has been mainly achieved through the adoption of a unique, centrally coordinated, IT infrastructure, which has enabled (i) standardisation of all the TNGB procedures and activities; (ii) creation of an updated TNGB online catalogue, based on minimal data set and controlled terminologies; (iii) sample access policy managed via a shared request control panel at web portal. TNGB has been engaged in disseminating information on its services into both scientific/biomedical - national and international - contexts, as well as associations of patients and families. Indeed, during the last 5-years national and international scientists extensively used the TNGB with different purposes resulting in more than 250 scientific publications. In addition, since its inception the TNGB is an associated member of the Biobanking and Biomolecular Resources Research Infrastructure and recently joined the EuroBioBank network. Moreover, the involvement of patients and families, leading to the formalization of various agreements between TNGB and Patients’ Associations, has demonstrated how promoting Biobank services can be instrumental in gaining a critical mass of samples essential for research, as well as, raising awareness, trust and interest of the general public in Biobanks. This article focuses on some fundamental aspects of networking and demonstrates how the translational research benefits from a sustained infrastructure.

A Minimum Data Set for Sharing Biobank Samples, Information, and Data: MIABIS

Numerous successful scientific results have emerged from projects using shared biobanked samples and data. In order to facilitate the discovery of underutilized biobank samples, it would be helpful if a global biobank register containing descriptive information about the samples existed. But first, for shared data to be comparable, it needs to be harmonized. In compliance with the aim of BBMRI (Biobanking and Biomolecular Resources Research Infrastructure), to harmonize biobanking across Europe, and the conclusion that the move towards a universal information infrastructure for biobanking is directly connected to the issues of semantic interoperability through standardized message formats and controlled terminologies, we have developed an updated version of the minimum data set for biobanks and studies using human biospecimens. The data set called MIABIS (Minimum Information About BIobank data Sharing) consists of 52 attributes describing a biobank's content. The aim is to facilitate data discovery through harmonization of data elements describing a biobank at the aggregate level. As many biobanks across Europe possess a tremendous amount of samples that are underutilized, this would help pave the way for biobank networking on a national and international level, resulting in time and cost savings and faster emergence of new scientific results.

Biobanking: from vision to reality

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How to kickstart a national biobanking infrastructure – experiences and prospects of BBMRI-NL

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Biobancos, laboratorios clínicos e investigación biomédica

Biobanks are non-profit public or private institutions for the collection, processing, storage and distribution of human biological specimens, linked to associated data of those samples. The Instituto de Salud Carlos III has set up and funded a hospital biobank network focused on the storage of samples for research. This network is expected to integrate into the Biobanking and Biomolecular Resources Research Infrastructure (BBMR) whose objective is to favour large-scale studies. The main organisational and operational aspects of biobanks are reviewed as well as their relationship with clinical laboratories and biomedical research.

OECI TuBaFrost Tumor Biobanking

OECI TuBaFrost harbors a complete infrastructure for the exchange of frozen tumor samples between European countries. OECI TuBaFrost consists of: * A code of conduct on how to exchange human residual samples in Europe, * A central database application accessible over the Internet (www.tubafrost.org) where data can be uploaded and searched from samples that can be selected and ordered, * Access rules with incentives for collectors, * Standardization needed to enable the analysis of high quality samples derived from different centers, * Virtual Microscopy to support sample selection with difficult pathology. The entire infrastructure was, after completion, which was entirely financed by the European Commission, implemented in the OECI. But so far it has not been used to its capacity. A recent survey held amongst the OECI members shed light on the causes. The main conclusion is that all responders see OECI TuBaFrost as a good platform for exchange of samples, however, the biggest bottleneck found was that potential users are too unfamiliar with the communication between their own biobank tracking system and the TuBaFrost central database application. Therefore, new future plans are drawn. In addition, new infrastructure plans have been developed and the first preparatory steps have been set. For biobanks the BBMRI project has started aiming for Pan-European Biobanking and Biomolecular Resources Research Infrastructure.

Biobanks: transnational, European and global networks

Biobanks contain biological samples and associated information that are essential raw materials for advancement of biotechnology, human health, and research and development in life sciences. Population-based and disease-oriented biobanks are major biobank formats to establish the disease relevance of human genes and provide opportunities to elucidate their interaction with environment and lifestyle. The developments in personalized medicine require molecular definition of new disease subentities and biomarkers for identification of relevant patient subgroups for drug development. These emerging demands can only be met if biobanks cooperate at the transnational or even global scale. Establishment of common standards and strategies to cope with the heterogeneous legal and ethical landscape in different countries are seen as major challenges for biobank networks. The Central Research Infrastructure for Molecular Pathology (CRIP), the concept for a pan-European Biobanking and Biomolecular Resources Research Infrastructure (BBMRI), and the Organization for Economic Co-operation and Development (OECD) global Biological Resources Centres network are examples for transnational, European and global biobank networks that are described in this article.