1
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Groiss S, Viertler C, Kap M, Bernhardt G, Mischinger HJ, Sieuwerts A, Verhoef C, Riegman P, Kruhøffer M, Svec D, Sjöback SR, Becker KF, Zatloukal K. Inter-patient heterogeneity in the hepatic ischemia-reperfusion injury transcriptome: Implications for research and diagnostics. N Biotechnol 2024; 79:20-29. [PMID: 38072306 DOI: 10.1016/j.nbt.2023.12.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 12/07/2023] [Indexed: 01/16/2024]
Abstract
Cellular responses induced by surgical procedure or ischemia-reperfusion injury (IRI) may severely alter transcriptome profiles and complicate molecular diagnostics. To investigate this effect, we characterized such pre-analytical effects in 143 non-malignant liver samples obtained from 30 patients at different time points of ischemia during surgery from two individual cohorts treated either with the Pringle manoeuvre or total vascular exclusion. Transcriptomics profiles were analyzed by Affymetrix microarrays and expression of selected mRNAs was validated by RT-PCR. We found 179 mutually deregulated genes which point to elevated cytokine signaling with NFκB as a dominant pathway in ischemia responses. In contrast to ischemia, reperfusion induced pro-apoptotic and pro-inflammatory cascades involving TNF, NFκB and MAPK pathways. FOS and JUN were down-regulated in steatosis compared to their up-regulation in normal livers. Surprisingly, molecular signatures of underlying primary and secondary cancers were present in non-tumor tissue. The reported inter-patient variability might reflect differences in individual stress responses and impact of underlying disease conditions. Furthermore, we provide a set of 230 pre-analytically highly robust genes identified from histologically normal livers (<2% covariation across both cohorts) that might serve as reference genes and could be particularly suited for future diagnostic applications.
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Affiliation(s)
- Silvia Groiss
- Diagnostic & Research Institute of Pathology, Medical University of Graz, 8010 Graz, Austria
| | - Christian Viertler
- Diagnostic & Research Institute of Pathology, Medical University of Graz, 8010 Graz, Austria
| | - Marcel Kap
- Pathology Department, Erasmus University Medical Center, 3015CN Rotterdam, the Netherlands
| | - Gerwin Bernhardt
- Division of General Surgery, Department of Surgery, Medical University of Graz, 8010 Graz, Austria; Department of Orthopedics and Trauma Surgery, Medical University of Graz, 8010 Graz, Austria
| | - Hans-Jörg Mischinger
- Division of General Surgery, Department of Surgery, Medical University of Graz, 8010 Graz, Austria
| | - Anieta Sieuwerts
- Department of Medical Oncology, Erasmus MC Cancer Institute and Cancer Genomics Netherlands, Erasmus University Medical Center, 3015CN Rotterdam, the Netherlands
| | - Cees Verhoef
- Department of Surgical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015CN Rotterdam, the Netherlands
| | - Peter Riegman
- Pathology Department, Erasmus University Medical Center, 3015CN Rotterdam, the Netherlands
| | | | - David Svec
- Laboratory of Gene Expression, Institute of Biotechnology CAS, 252 50 Vestec, Czech Republic
| | | | | | - Kurt Zatloukal
- Diagnostic & Research Institute of Pathology, Medical University of Graz, 8010 Graz, Austria.
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2
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Brancato V, Esposito G, Coppola L, Cavaliere C, Mirabelli P, Scapicchio C, Borgheresi R, Neri E, Salvatore M, Aiello M. Standardizing digital biobanks: integrating imaging, genomic, and clinical data for precision medicine. J Transl Med 2024; 22:136. [PMID: 38317237 PMCID: PMC10845786 DOI: 10.1186/s12967-024-04891-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 01/14/2024] [Indexed: 02/07/2024] Open
Abstract
Advancements in data acquisition and computational methods are generating a large amount of heterogeneous biomedical data from diagnostic domains such as clinical imaging, pathology, and next-generation sequencing (NGS), which help characterize individual differences in patients. However, this information needs to be available and suitable to promote and support scientific research and technological development, supporting the effective adoption of the precision medicine approach in clinical practice. Digital biobanks can catalyze this process, facilitating the sharing of curated and standardized imaging data, clinical, pathological and molecular data, crucial to enable the development of a comprehensive and personalized data-driven diagnostic approach in disease management and fostering the development of computational predictive models. This work aims to frame this perspective, first by evaluating the state of standardization of individual diagnostic domains and then by identifying challenges and proposing a possible solution towards an integrative approach that can guarantee the suitability of information that can be shared through a digital biobank. Our analysis of the state of the art shows the presence and use of reference standards in biobanks and, generally, digital repositories for each specific domain. Despite this, standardization to guarantee the integration and reproducibility of the numerical descriptors generated by each domain, e.g. radiomic, pathomic and -omic features, is still an open challenge. Based on specific use cases and scenarios, an integration model, based on the JSON format, is proposed that can help address this problem. Ultimately, this work shows how, with specific standardization and promotion efforts, the digital biobank model can become an enabling technology for the comprehensive study of diseases and the effective development of data-driven technologies at the service of precision medicine.
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Affiliation(s)
| | - Giuseppina Esposito
- Bio Check Up S.R.L, 80121, Naples, Italy
- Department of Advanced Biomedical Sciences, University of Naples Federico II, 80131, Naples, Italy
| | | | | | - Peppino Mirabelli
- UOS Laboratori di Ricerca e Biobanca, AORN Santobono-Pausilipon, Via Teresa Ravaschieri, 8, 80122, Naples, Italy
| | - Camilla Scapicchio
- Academic Radiology, Department of Translational Research, University of Pisa, via Roma, 67, 56126, Pisa, Italy
| | - Rita Borgheresi
- Academic Radiology, Department of Translational Research, University of Pisa, via Roma, 67, 56126, Pisa, Italy
| | - Emanuele Neri
- Academic Radiology, Department of Translational Research, University of Pisa, via Roma, 67, 56126, Pisa, Italy
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3
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Klingler C, von Jagwitz-Biegnitz M, Baber R, Becker KF, Dahl E, Eibner C, Fuchs J, Groenewold MK, Hartung ML, Hummel M, Jahns R, Kirsten R, Kopfnagel V, Maushagen R, Nussbeck SY, Schoneberg A, Winter T, Specht C. Stakeholder engagement to ensure the sustainability of biobanks: a survey of potential users of biobank services. Eur J Hum Genet 2022; 30:1344-1354. [PMID: 34031552 PMCID: PMC9712417 DOI: 10.1038/s41431-021-00905-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 04/06/2021] [Accepted: 04/29/2021] [Indexed: 12/17/2022] Open
Abstract
Biobanks are important infrastructures facilitating biomedical research. After a decade of rolling out such infrastructures, a shift in attention to the sustainability of biobanks could be observed in recent years. In this regard, an increase in the as yet relatively low utilisation rates of biobanks has been formulated as a goal. Higher utilisation rates can only be achieved if the perspectives of potential users of biobanks-particularly researchers not yet collaborating with biobanks-are adequately considered. To better understand their perspectives, a survey was conducted at ten different research institutions in Germany hosting a centralised biobank. The survey targeted potential users of biobank services, i.e. researchers working with biosamples. It addressed the general demand for biosamples, strategies for biosample acquisition/storage and reasons for/against collaborating with biobanks. In total, 354 researchers filled out the survey. Most interestingly, only a minority of researchers (12%) acquired their biosamples via biobanks. Of the respondents not collaborating with biobanks on sample acquisition, around half were not aware of the (services of the) respective local biobank. Those who actively decided against acquiring biosamples via a biobank provided different reasons. Most commonly, respondents stated that the biosamples required were not available, the costs were too high and information about the available biosamples was not readily accessible. Biobanks can draw many lessons from the results of the survey. Particularly, external communication and outreach should be improved. Additionally, biobanks might have to reassess whether their particular collection strategies are adequately aligned with local researchers' needs.
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Affiliation(s)
- Corinna Klingler
- German Biobank Node, Charité Universitätsmedizin Berlin, Berlin, Germany.
| | | | - Ronny Baber
- grid.9647.c0000 0004 7669 9786Leipzig Medical Biobank, University Leipzig, Leipzig, Germany ,grid.9647.c0000 0004 7669 9786Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, University of Leipzig Medical Center, Leipzig, Germany
| | - Karl-Friedrich Becker
- grid.6936.a0000000123222966Gewebebank des Klinikums rechts der Isar und der Technischen Universität München, Am Institut für Pathologie der TU München, Trogerstr. 18, 81675 München, Germany
| | - Edgar Dahl
- grid.1957.a0000 0001 0728 696XRWTH centralized Biomaterial Bank (RWTH cBMB), Institute of Pathology, RWTH Aachen University, Aachen, Germany
| | - Cornelius Eibner
- grid.275559.90000 0000 8517 6224Integrated Biobank Jena (IBBJ), Institute for Clinical Chemistry and Laboratory Diagnostics, University Hospital Jena, Am Klinikum 1, D-07747 Jena, Germany
| | - Jörg Fuchs
- grid.411760.50000 0001 1378 7891Interdisciplinary Bank of Biomaterials and Data Würzburg (ibdw), University Hospital of Würzburg, Straubmühlweg 2a, building A8/A9, 97078 Würzburg, Germany
| | - Maike K. Groenewold
- Research Unit of Molecular Epidemiology/Core Facility Biobank, Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Mara Lena Hartung
- grid.6363.00000 0001 2218 4662German Biobank Node, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Michael Hummel
- grid.6363.00000 0001 2218 4662German Biobank Node, Charité Universitätsmedizin Berlin, Berlin, Germany ,grid.6363.00000 0001 2218 4662Central Biobank Charité (ZeBanC), Institute of Pathology, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Roland Jahns
- grid.411760.50000 0001 1378 7891Interdisciplinary Bank of Biomaterials and Data Würzburg (ibdw), University Hospital of Würzburg, Straubmühlweg 2a, building A8/A9, 97078 Würzburg, Germany
| | - Romy Kirsten
- grid.5253.10000 0001 0328 4908NCT Liquid Biobank, National Center for Tumor Diseases and BioMaterialBank Heidelberg (BMBH), University Hospital Heidelberg, Heidelberg, Germany
| | - Verena Kopfnagel
- grid.10423.340000 0000 9529 9877Hannover Unified Biobank, Hannover Medical School, Hannover, Germany
| | - Regina Maushagen
- grid.4562.50000 0001 0057 2672Interdisciplinary Center for Biobanking-Lübeck (ICB-L), University of Lübeck, Lübeck, Germany
| | - Sara Yasemin Nussbeck
- grid.411984.10000 0001 0482 5331Central Biobank UMG, University Medical Center Göttingen, Göttingen, Germany
| | - Anne Schoneberg
- grid.411984.10000 0001 0482 5331Central Biobank UMG, University Medical Center Göttingen, Göttingen, Germany
| | - Theresa Winter
- grid.5603.0Integrated Research Biobank Greifswald, University Medicine Greifswald, Greifswald, Germany
| | - Cornelia Specht
- grid.6363.00000 0001 2218 4662German Biobank Node, Charité Universitätsmedizin Berlin, Berlin, Germany
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4
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Katsonis P, Wilhelm K, Williams A, Lichtarge O. Genome interpretation using in silico predictors of variant impact. Hum Genet 2022; 141:1549-1577. [PMID: 35488922 PMCID: PMC9055222 DOI: 10.1007/s00439-022-02457-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 04/17/2022] [Indexed: 02/06/2023]
Abstract
Estimating the effects of variants found in disease driver genes opens the door to personalized therapeutic opportunities. Clinical associations and laboratory experiments can only characterize a tiny fraction of all the available variants, leaving the majority as variants of unknown significance (VUS). In silico methods bridge this gap by providing instant estimates on a large scale, most often based on the numerous genetic differences between species. Despite concerns that these methods may lack reliability in individual subjects, their numerous practical applications over cohorts suggest they are already helpful and have a role to play in genome interpretation when used at the proper scale and context. In this review, we aim to gain insights into the training and validation of these variant effect predicting methods and illustrate representative types of experimental and clinical applications. Objective performance assessments using various datasets that are not yet published indicate the strengths and limitations of each method. These show that cautious use of in silico variant impact predictors is essential for addressing genome interpretation challenges.
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Affiliation(s)
- Panagiotis Katsonis
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA.
| | - Kevin Wilhelm
- Graduate School of Biomedical Sciences, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Amanda Williams
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Olivier Lichtarge
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA. .,Department of Biochemistry, Human Genetics and Molecular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA. .,Department of Pharmacology, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA. .,Computational and Integrative Biomedical Research Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA.
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5
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O'Donoghue S, Dee S, Byrne JA, Watson PH. How Many Health Research Biobanks Are There? Biopreserv Biobank 2021; 20:224-228. [PMID: 34582255 DOI: 10.1089/bio.2021.0063] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Introduction: It is important for many research stakeholders to know how many biobanks exist. There are several potential data sources that might be expected to provide biobank numbers, such as institutions, research funders, and literature databases (e.g., PubMed), but in practice this information is rarely available and is hard to find. However, the maturation of several online health research biobank locators (also known as directories and catalogs) that relate to 12 countries and/or states has now provided some initial data to address the question of how many health research biobanks exist in relation to population size. Methods: We have analyzed four biobank locators: the Biobanking and Biomolecular Resources Research Infrastructure-European Research Infrastructure Consortium directory, the Canadian Tissue Repository Network locator, the Australian New South Wales Australia Health Pathology locator, and the UK Clinical Research Collaboration Tissue Directory. Results: We conclude that across these locators, and in those regions with potential for high research capacity as indicated by comparable gross domestic products, there are 11-30 health research biobanks/million population (2 large biobanks with >1000 samples and a further 9-28 are medium-small biobanks). Conclusion: Many locators were established primarily to increase utilization of biobanks. However, locators may be more useful in tracking the numbers of biobanks and in assisting funders and institutions to monitor research strategy and prevent unnecessary duplication of biobank resources.
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Affiliation(s)
- Sheila O'Donoghue
- Biobanking and Biospecimen Research Services, Deeley Research Centre, BC Cancer Victoria Center, Victoria, Canada
| | - Simon Dee
- Biobanking and Biospecimen Research Services, Deeley Research Centre, BC Cancer Victoria Center, Victoria, Canada
| | - Jennifer A Byrne
- New South Wales Health Statewide Biobank, New South Wales Health Pathology, Camperdown, Australia.,School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Camperdown, Australia
| | - Peter Hamilton Watson
- Biobanking and Biospecimen Research Services, Deeley Research Centre, BC Cancer Victoria Center, Victoria, Canada.,Canadian Tissue Repository Network, Vancouver, Canada
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6
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Annaratone L, De Palma G, Bonizzi G, Sapino A, Botti G, Berrino E, Mannelli C, Arcella P, Di Martino S, Steffan A, Daidone MG, Canzonieri V, Parodi B, Paradiso AV, Barberis M, Marchiò C. Basic principles of biobanking: from biological samples to precision medicine for patients. Virchows Arch 2021; 479:233-246. [PMID: 34255145 PMCID: PMC8275637 DOI: 10.1007/s00428-021-03151-0] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2021] [Revised: 06/24/2021] [Accepted: 06/30/2021] [Indexed: 12/15/2022]
Abstract
The term "biobanking" is often misapplied to any collection of human biological materials (biospecimens) regardless of requirements related to ethical and legal issues or the standardization of different processes involved in tissue collection. A proper definition of biobanks is large collections of biospecimens linked to relevant personal and health information (health records, family history, lifestyle, genetic information) that are held predominantly for use in health and medical research. In addition, the International Organization for Standardization, in illustrating the requirements for biobanking (ISO 20387:2018), stresses the concept of biobanks being legal entities driving the process of acquisition and storage together with some or all of the activities related to collection, preparation, preservation, testing, analysing and distributing defined biological material as well as related information and data. In this review article, we aim to discuss the basic principles of biobanking, spanning from definitions to classification systems, standardization processes and documents, sustainability and ethical and legal requirements. We also deal with emerging specimens that are currently being generated and shaping the so-called next-generation biobanking, and we provide pragmatic examples of cancer-associated biobanking by discussing the process behind the construction of a biobank and the infrastructures supporting the implementation of biobanking in scientific research.
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Affiliation(s)
- Laura Annaratone
- Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy.,Department of Medical Sciences, University of Turin, Turin, Italy
| | - Giuseppe De Palma
- Institutional BioBank, Experimental Oncology and Biobank Management Unit, IRCCS Istituto Tumori "Giovanni Paolo II", Bari, Italy
| | - Giuseppina Bonizzi
- Unit of Histopathology and Molecular Diagnostics, Division of Pathology and Laboratory Medicine, IEO, European Institute of Oncology, IRCCS, Milan, Italy
| | - Anna Sapino
- Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy.,Department of Medical Sciences, University of Turin, Turin, Italy
| | - Gerardo Botti
- Istituto Nazionale Tumori, Fondazione G. Pascale, IRCCS, Naples, Italy
| | - Enrico Berrino
- Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy.,Department of Medical Sciences, University of Turin, Turin, Italy
| | | | - Pamela Arcella
- Department of Oncology, University of Turin, Turin, Italy
| | - Simona Di Martino
- Department of Pathology, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | - Agostino Steffan
- Immunopathology and Cancer Biomarkers, IRCCS CRO Aviano-National Cancer Institute, Aviano, Italy
| | | | - Vincenzo Canzonieri
- Department of Medical, Surgical and Health Sciences, University of Trieste, Trieste, Italy.,Pathology Unit, IRCCS CRO Aviano-National Cancer Institute, Aviano, Italy
| | | | - Angelo Virgilio Paradiso
- Institutional BioBank, Experimental Oncology and Biobank Management Unit, IRCCS Istituto Tumori "Giovanni Paolo II", Bari, Italy
| | - Massimo Barberis
- Unit of Histopathology and Molecular Diagnostics, Division of Pathology and Laboratory Medicine, IEO, European Institute of Oncology, IRCCS, Milan, Italy
| | - Caterina Marchiò
- Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy. .,Department of Medical Sciences, University of Turin, Turin, Italy.
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7
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Reihs R, Proynova R, Maqsood S, Ataian M, Lablans M, Quinlan PR, Lawrence E, Bowman E, van Enckevort E, Bučík DF, Müller H, Holub P. BBMRI-ERIC Negotiator: Implementing Efficient Access to Biobanks. Biopreserv Biobank 2021; 19:414-421. [PMID: 34182766 DOI: 10.1089/bio.2020.0144] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Various biological resources, such as biobanks and disease-specific registries, have become indispensable resources to better understand the epidemiology and biological mechanisms of disease and are fundamental for advancing medical research. Nevertheless, biobanks and similar resources still face significant challenges to become more findable and accessible by users on both national and global scales. One of the main challenges for users is to find relevant resources using cataloging and search services such as the BBMRI-ERIC Directory, operated by European Research Infrastructure on Biobanking and Biomolecular Resources (BBMRI-ERIC), as these often do not contain the information needed by the researchers to decide if the resource has relevant material/data; these resources are only weakly characterized. Hence, the researcher is typically left with too many resources to explore and investigate. In addition, resources often have complex procedures for accessing holdings, particularly for depletable biological materials. This article focuses on designing a system for effective negotiation of access to holdings, in which a researcher can approach many resources simultaneously, while giving each resource team the ability to implement their own mechanisms to check if the material/data are available and to decide if access should be provided. The BBMRI-ERIC has developed and implemented an access and negotiation tool called the BBMRI-ERIC Negotiator. The Negotiator enables access negotiation to more than 600 biobanks from the BBMRI-ERIC Directory and other discovery services such as GBA/BBMRI-ERIC Locator or RD-Connect Finder. This article summarizes the principles that guided the design of the tool, the terminology used and underlying data model, request workflows, authentication and authorization mechanism(s), and the mechanisms and monitoring processes to stimulate the desired behavior of the resources: to effectively deliver access to biological material and data.
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Affiliation(s)
- Robert Reihs
- BBMRI-ERIC, Graz, Austria.,BBMRI.at and Medical University Graz, Graz, Austria
| | - Rumyana Proynova
- BBMRI.de/German Biobank Alliance and German Cancer Research Center, Heidelberg, Germany
| | - Saher Maqsood
- BBMRI.de/German Biobank Alliance and German Cancer Research Center, Heidelberg, Germany
| | - Maxmilian Ataian
- BBMRI.de/German Biobank Alliance and German Cancer Research Center, Heidelberg, Germany
| | - Martin Lablans
- BBMRI.de/German Biobank Alliance and German Cancer Research Center, Heidelberg, Germany
| | - Philip R Quinlan
- BBMRI.uk and University of Nottingham, Nottingham, United Kingdom
| | - Emma Lawrence
- BBMRI.uk and University College London, London, United Kingdom
| | - Erinna Bowman
- BBMRI.uk and University College London, London, United Kingdom
| | - Esther van Enckevort
- BBMRI.nl and University of Groningen and University Medical Center Groningen, The Netherlands
| | | | - Heimo Müller
- BBMRI-ERIC, Graz, Austria.,BBMRI.at and Medical University Graz, Graz, Austria
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8
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Gutiérrez-Sacristán A, De Niz C, Kothari C, Kong SW, Mandl KD, Avillach P. GenoPheno: cataloging large-scale phenotypic and next-generation sequencing data within human datasets. Brief Bioinform 2021; 22:55-65. [PMID: 32249310 PMCID: PMC7820848 DOI: 10.1093/bib/bbaa033] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 01/31/2020] [Indexed: 12/17/2022] Open
Abstract
Precision medicine promises to revolutionize treatment, shifting therapeutic approaches from the classical one-size-fits-all to those more tailored to the patient's individual genomic profile, lifestyle and environmental exposures. Yet, to advance precision medicine's main objective-ensuring the optimum diagnosis, treatment and prognosis for each individual-investigators need access to large-scale clinical and genomic data repositories. Despite the vast proliferation of these datasets, locating and obtaining access to many remains a challenge. We sought to provide an overview of available patient-level datasets that contain both genotypic data, obtained by next-generation sequencing, and phenotypic data-and to create a dynamic, online catalog for consultation, contribution and revision by the research community. Datasets included in this review conform to six specific inclusion parameters that are: (i) contain data from more than 500 human subjects; (ii) contain both genotypic and phenotypic data from the same subjects; (iii) include whole genome sequencing or whole exome sequencing data; (iv) include at least 100 recorded phenotypic variables per subject; (v) accessible through a website or collaboration with investigators and (vi) make access information available in English. Using these criteria, we identified 30 datasets, reviewed them and provided results in the release version of a catalog, which is publicly available through a dynamic Web application and on GitHub. Users can review as well as contribute new datasets for inclusion (Web: https://avillachlab.shinyapps.io/genophenocatalog/; GitHub: https://github.com/hms-dbmi/GenoPheno-CatalogShiny).
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Affiliation(s)
| | - Carlos De Niz
- Department of Biomedical Informatics, Harvard Medical School
| | - Cartik Kothari
- Department of Biomedical Informatics, Harvard Medical School
| | - Sek Won Kong
- Department of Biomedical Informatics, Harvard Medical School; Computational Health Informatics Program, Boston Children's Hospital
| | - Kenneth D Mandl
- Department of Biomedical Informatics, Harvard Medical School; Computational Health Informatics Program, Boston Children's Hospital
| | - Paul Avillach
- Department of Biomedical Informatics, Harvard Medical School; Computational Health Informatics Program, Boston Children's Hospital
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9
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Lermen D, Gwinner F, Bartel-Steinbach M, Mueller SC, Habermann JK, Balwir MB, Smits E, Virgolino A, Fiddicke U, Berglund M, Åkesson A, Bergstrom A, Leander K, Horvat M, Snoj Tratnik J, Posada de la Paz M, Castaño Calvo A, Esteban López M, von Briesen H, Zimmermann H, Kolossa-Gehring M. Towards Harmonized Biobanking for Biomonitoring: A Comparison of Human Biomonitoring-Related and Clinical Biorepositories. Biopreserv Biobank 2020; 18:122-135. [PMID: 32281895 PMCID: PMC7185365 DOI: 10.1089/bio.2019.0092] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Human biomonitoring (HBM) depends on high-quality human samples to identify status and trends in exposure and ensure comparability of results. In this context, much effort has been put into the development of standardized processes and quality assurance for sampling and chemical analysis, while effects of sample storage and shipment on sample quality have been less thoroughly addressed. To characterize the currently applied storage and shipment procedures within the consortium of the European Human Biomonitoring Initiative (HBM4EU), which aims at harmonization of HBM in Europe, a requirement analysis based on data from an online survey was conducted. In addition, the online survey was addressed to professionals in clinical biobanking represented by members of the European, Middle Eastern and African Society for Biopreservation and Biobanking (ESBB) to identify the current state-of-the-art in terms of sample storage and shipment. Results of this survey conducted in these two networks were compared to detect processes with potential for optimization and harmonization. In general, many similarities exist in sample storage and shipment procedures applied by ESBB members and HBM4EU partners and many requirements for ensuring sample quality are already met also by HBM4EU partners. Nevertheless, a need for improvement was identified for individual steps in sample storage, shipment, and related data management with potential impact on sample and data quality for HBM purposes. Based on these findings, recommendations for crucial first steps to further strengthen sample quality, and thus foster advancement in HBM on a pan-European level are given.
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Affiliation(s)
- Dominik Lermen
- Fraunhofer Institute for Biomedical Engineering IBMT, Biomonitoring & Biobanks, Sulzbach, Germany
- European, Middle Eastern & African Society for Biopreservation and Biobanking, Brussels, Belgium
- The European Human-Biomonitoring Initiative HBM4EU
| | - Frederik Gwinner
- Fraunhofer Institute for Biomedical Engineering IBMT, Biomonitoring & Biobanks, Sulzbach, Germany
- The European Human-Biomonitoring Initiative HBM4EU
| | - Martina Bartel-Steinbach
- Fraunhofer Institute for Biomedical Engineering IBMT, Biomonitoring & Biobanks, Sulzbach, Germany
- The European Human-Biomonitoring Initiative HBM4EU
| | - Sabine C. Mueller
- Fraunhofer Institute for Biomedical Engineering IBMT, Biomonitoring & Biobanks, Sulzbach, Germany
- The European Human-Biomonitoring Initiative HBM4EU
| | - Jens K. Habermann
- European, Middle Eastern & African Society for Biopreservation and Biobanking, Brussels, Belgium
- University Clinical Center Schleswig-Holstein, University of Luebeck, Translational Surgical Oncology and Biobanking, Luebeck, Germany
| | - Matharoo-Ball Balwir
- European, Middle Eastern & African Society for Biopreservation and Biobanking, Brussels, Belgium
- Nottingham University Hospital, Translational Research and Nottingham Health Science Biobank (NHSB), Nottingham, United Kingdom
| | - Elke Smits
- European, Middle Eastern & African Society for Biopreservation and Biobanking, Brussels, Belgium
- Antwerp University Hospital, University of Antwerp, Division of Medical Director, Edegem, Belgium
| | - Ana Virgolino
- The European Human-Biomonitoring Initiative HBM4EU
- Faculdade de Medicina, Instituto de Saúde Ambiental, Universidade de Lisboa, Lisboa, Portugal
| | - Ulrike Fiddicke
- The European Human-Biomonitoring Initiative HBM4EU
- German Environment Agency (Umweltbundesamt), Berlin, Germany
| | - Marika Berglund
- The European Human-Biomonitoring Initiative HBM4EU
- Institute of Environmental Medicine, Karolinska Institute, Institute of Environmental Medicine (IMM), Stockholm, Sweden
| | - Agneta Åkesson
- The European Human-Biomonitoring Initiative HBM4EU
- Institute of Environmental Medicine, Karolinska Institute, Institute of Environmental Medicine (IMM), Stockholm, Sweden
| | - Anna Bergstrom
- The European Human-Biomonitoring Initiative HBM4EU
- Institute of Environmental Medicine, Karolinska Institute, Institute of Environmental Medicine (IMM), Stockholm, Sweden
| | - Karin Leander
- The European Human-Biomonitoring Initiative HBM4EU
- Institute of Environmental Medicine, Karolinska Institute, Institute of Environmental Medicine (IMM), Stockholm, Sweden
| | - Milena Horvat
- The European Human-Biomonitoring Initiative HBM4EU
- Jožef Stefan Institute, Department of Environmental Sciences, Ljubljana, Slovenia
| | - Janja Snoj Tratnik
- The European Human-Biomonitoring Initiative HBM4EU
- Jožef Stefan Institute, Department of Environmental Sciences, Ljubljana, Slovenia
| | - Manuel Posada de la Paz
- The European Human-Biomonitoring Initiative HBM4EU
- Institute of Rare Diseases Research, CIBERER, EuroBiobanK, Instituto de Salud Carlos III, Madrid, Spain
| | - Argelia Castaño Calvo
- The European Human-Biomonitoring Initiative HBM4EU
- Centro Nacional de Sanidad Ambiental CNSA, Instituto de Salud Carlos III, Majadahonda, Spain
| | - Marta Esteban López
- The European Human-Biomonitoring Initiative HBM4EU
- Centro Nacional de Sanidad Ambiental CNSA, Instituto de Salud Carlos III, Majadahonda, Spain
| | - Hagen von Briesen
- Fraunhofer Institute for Biomedical Engineering IBMT, Biomonitoring & Biobanks, Sulzbach, Germany
- The European Human-Biomonitoring Initiative HBM4EU
| | - Heiko Zimmermann
- Fraunhofer Institute for Biomedical Engineering IBMT, Biomonitoring & Biobanks, Sulzbach, Germany
- The European Human-Biomonitoring Initiative HBM4EU
| | - Marike Kolossa-Gehring
- The European Human-Biomonitoring Initiative HBM4EU
- German Environment Agency (Umweltbundesamt), Berlin, Germany
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10
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Cleynen I, Linsen L, Verstockt S, Verstockt B, Ballet V, Vandeput E, Van Assche G, Ferrante M, Van Landuyt K, Vermeire S, Ectors N. Inflammatory Bowel Disease (IBD)-A Textbook Case for Multi-Centric Banking of Human Biological Materials. Front Med (Lausanne) 2019; 6:230. [PMID: 31681784 PMCID: PMC6813565 DOI: 10.3389/fmed.2019.00230] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Accepted: 10/03/2019] [Indexed: 12/12/2022] Open
Abstract
Inflammatory bowel disease (IBD) is a chronic relapsing inflammatory condition affecting mainly the gastro-intestinal tract with two main entities: Crohn's disease (CD) and ulcerative colitis (UC). Although the exact mechanisms underlying the initial development of IBD are not fully understood, it is believed that an abnormal immune response is elicited against the intestinal microbiota in genetically predisposed individuals. Crucial elements of the etiopathogenesis have been elucidated by research using human biological materials. The estimated prevalence of IBD is 0.5% in the Western world. Although incidence rates are increasing, both conditions are not "common" in general terms mandating a multicentric approach. Biological material from numerous Belgian patients have been collected over time in a number of university hospitals in Belgium (UH Ghent: 800 CD patients, 350 UC patients, 600 normal controls; UH Leuven: 2,600 CD patients, 1,380 UC patients, 98 IC/IBDU patients, 6,260 normal controls). Within the setting of the Flemish Center Medical Innovation (CMI) initiative and later on the Flemish biobank network a prospective study was set-up across three Belgian IBD centers (University Hospitals Brussels, Ghent, and Leuven). Human biological materials and data have been collected prospectively from newly diagnosed CD and UC patients. The analyses hereof have generated new insights which have been published in the most renowned journals. The approach of well-thought off, multi-centric, structured, and systematic biobanking has proven to be a success-story and thus a textbook case for multi-centric banking of human biological materials. This story is being told in this article.
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Affiliation(s)
- Isabelle Cleynen
- Laboratory for Complex Genetics, Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Loes Linsen
- Activity Center Biobanking, University Hospitals Leuven, Leuven, Belgium
| | - Sare Verstockt
- Laboratory for Complex Genetics, Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Bram Verstockt
- Department of Chronic Diseases, Metabolism and Ageing (CHROMETA), Translational Research Center for Gastrointestinal Disorders (TARGID), KU Leuven, Leuven, Belgium
| | - Vera Ballet
- Department of Gastroenterology and Hepatology, University Hospitals Leuven, KU Leuven, Leuven, Belgium
| | - Eline Vandeput
- Department of Gastroenterology and Hepatology, University Hospitals Leuven, KU Leuven, Leuven, Belgium
| | - Gert Van Assche
- Department of Gastroenterology and Hepatology, University Hospitals Leuven, KU Leuven, Leuven, Belgium
| | - Marc Ferrante
- Department of Chronic Diseases, Metabolism and Ageing (CHROMETA), Translational Research Center for Gastrointestinal Disorders (TARGID), KU Leuven, Leuven, Belgium.,Department of Gastroenterology and Hepatology, University Hospitals Leuven, KU Leuven, Leuven, Belgium
| | | | - Séverine Vermeire
- Department of Chronic Diseases, Metabolism and Ageing (CHROMETA), Translational Research Center for Gastrointestinal Disorders (TARGID), KU Leuven, Leuven, Belgium.,Department of Gastroenterology and Hepatology, University Hospitals Leuven, KU Leuven, Leuven, Belgium
| | - Nadine Ectors
- Activity Center Biobanking, University Hospitals Leuven, Leuven, Belgium
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11
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Simell BA, Törnwall OM, Hämäläinen I, Wichmann HE, Anton G, Brennan P, Bouvard L, Slimani N, Moskal A, Gunter M, Zatloukal K, Minion JT, Soini S, Mayrhofer MT, Murtagh MJ, van Ommen GJ, Johansson M, Perola M. Transnational access to large prospective cohorts in Europe: Current trends and unmet needs. N Biotechnol 2019; 49:98-103. [PMID: 30342241 DOI: 10.1016/j.nbt.2018.10.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Revised: 10/15/2018] [Accepted: 10/15/2018] [Indexed: 01/15/2023]
Abstract
Biobank samples and data from studies of large prospective cohorts (LPC) represent an invaluable resource for health research. Efficient sharing and pooling of samples and data is a central pre-requisite for new advances in biomedical science. This requirement, however, is not compatible with the present scattered and traditional access governance structures, where legal and ethical frameworks often form an obstacle for effective sharing. Moreover, the EU General Data Protection Regulation (GDPR) is demanding increasingly rigorous administration from all those organisations processing personal data. The BBMRI-LPC project (Biobanking and Biomolecular Research Infrastructure - Large Prospective Cohorts) assembled 21 LPCs from 10 countries and two EU-wide multinational cohort networks with a key objective to promote collaborative innovative transnational research proposed by external researchers on the broad field of common chronic diseases, and analyze the gaps and needs involved. BBMRI-LPC organized three scientific calls to offer European investigators an opportunity to gain free of charge transnational access to research material available in the participating cohorts. A total of 11 high-quality research proposals involving multiple prospective cohorts were granted, and the access process in the individual projects carefully monitored. Divergent access governance structures, complex legal and ethical frameworks and heterogeneous procedures were identified as currently constituting substantial obstacles for sample and data transfer in Europe. To optimize the scientific value and use of these research resources, practical solutions for more streamlined access governance in collaborative projects are urgently needed. A number of infrastructure developments could be made to improve time-efficiency in access provision.
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Affiliation(s)
- Birgit A Simell
- Institute for Molecular Medicine Finland FIMM, University of Helsinki, Biomedicum 2U, Tukholmankati 8, 00290, Helsinki, Finland.
| | - Outi M Törnwall
- Biobanking and Biomolecular Resources Research Infrastructure, European Research Infrastructure Consortium (BBMRI-ERIC), Neue Stiftingtalstrasse 2/B/6 8010 Graz, Austria
| | - Iiro Hämäläinen
- Institute for Molecular Medicine Finland FIMM, University of Helsinki, Biomedicum 2U, Tukholmankati 8, 00290, Helsinki, Finland; National Institute for Health and Welfare (THL), Biomedicum 1, Haartmaninkatu 8, 00290, Helsinki, Finland
| | - H-Erich Wichmann
- Helmholtz Zentrum Munich, Institute of Epidemiology, Ingolstädter Landstraße 1, D-85764, Neuherberg, Germany; Institute of Medical Informatics, Biometry and Epidemiology, Chair of Epidemiology, Ludwig Maximilians University, Geschwister-Scholl-Platz 1, 80539, Munich, Germany; Institute of Medical Statistics and Epidemiology, Technical University Munich, Arcisstraße 21, 80333, Munich, Germany
| | - Gabriele Anton
- Helmholtz Zentrum Munich, Institute of Epidemiology, Ingolstädter Landstraße 1, D-85764, Neuherberg, Germany; Institute of Medical Statistics and Epidemiology, Technical University Munich, Arcisstraße 21, 80333, Munich, Germany
| | - Paul Brennan
- International Agency for Research on Cancer (IARC), 150 Cours Albert Thomas, 69372, Lyon CEDEX 08, France
| | - Laurene Bouvard
- International Agency for Research on Cancer (IARC), 150 Cours Albert Thomas, 69372, Lyon CEDEX 08, France
| | - Nadia Slimani
- International Agency for Research on Cancer (IARC), 150 Cours Albert Thomas, 69372, Lyon CEDEX 08, France
| | - Aurelie Moskal
- International Agency for Research on Cancer (IARC), 150 Cours Albert Thomas, 69372, Lyon CEDEX 08, France
| | - Marc Gunter
- International Agency for Research on Cancer (IARC), 150 Cours Albert Thomas, 69372, Lyon CEDEX 08, France; Imperial College London, South Kensington Campus, London, SW7 2AZ, United Kingdom
| | - Kurt Zatloukal
- Medical University of Graz, Auenbruggerpl. 2, 8036, Graz, Austria
| | | | - Sirpa Soini
- National Institute for Health and Welfare (THL), Biomedicum 1, Haartmaninkatu 8, 00290, Helsinki, Finland
| | - Michaela T Mayrhofer
- Biobanking and Biomolecular Resources Research Infrastructure, European Research Infrastructure Consortium (BBMRI-ERIC), Neue Stiftingtalstrasse 2/B/6 8010 Graz, Austria
| | | | - Gert-Jan van Ommen
- Leiden University Medical Center, Albinusdreef 2, 2333 ZA, Leiden, the Netherlands
| | - Mattias Johansson
- International Agency for Research on Cancer (IARC), 150 Cours Albert Thomas, 69372, Lyon CEDEX 08, France
| | - Markus Perola
- Institute for Molecular Medicine Finland FIMM, University of Helsinki, Biomedicum 2U, Tukholmankati 8, 00290, Helsinki, Finland; National Institute for Health and Welfare (THL), Biomedicum 1, Haartmaninkatu 8, 00290, Helsinki, Finland; University of Tartu, Estonian Genome Center, Riia 23b, 51010, Tartu, Estonia
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12
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Jarczak J, Lach J, Borówka P, Gałka M, Bućko M, Marciniak B, Strapagiel D. BioSCOOP - Biobank Sample Communication Protocol. New approach for the transfer of information between biobanks. Database (Oxford) 2019; 2019:baz105. [PMID: 31609452 PMCID: PMC6791335 DOI: 10.1093/database/baz105] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 06/06/2019] [Accepted: 08/02/2019] [Indexed: 02/02/2023]
Abstract
Dynamic development of biobanking industry (both business and science) resulted in an increased number of IT systems for samples and data management. The most difficult and complicated case for the biobanking community was cooperation between institutions, equipped with different IT systems, in the field of scientific research, mainly data interchange and information flow. Tools available on the market relate mainly to the biobank or collection level. Efficient and universal protocols including the detailed information about the donor and the sample are still very limited. Here, we have developed BioSCOOP, a communication protocol in the form of a well documented JSON API. The main aim of this study was to harmonize and standardize the rules of communication between biobanks on the level of information about the donor together with information about the sample. The purpose was to create a communication protocol for two applications: to transfer the information between different biobanks and to allow the searching and presentation of the sample and data sets.
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Affiliation(s)
- J Jarczak
- Biobank Lab, Department of Molecular Biophysics, Faculty of Biology and Environmental Protection, University of Łódź, Łódź, Poland
- BBMRI.pl Consortium, Wrocław, Poland
| | - J Lach
- Biobank Lab, Department of Molecular Biophysics, Faculty of Biology and Environmental Protection, University of Łódź, Łódź, Poland
- BBMRI.pl Consortium, Wrocław, Poland
| | - P Borówka
- Biobank Lab, Department of Molecular Biophysics, Faculty of Biology and Environmental Protection, University of Łódź, Łódź, Poland
- Department of Anthropology, Faculty of Biology and Environmental Protection, University of Łódź, Łódź, Poland
| | | | - M Bućko
- Bee2code sp. z o.o., ul. Daszyńskiego 5; 44-100 Gliwice
| | - B Marciniak
- Biobank Lab, Department of Molecular Biophysics, Faculty of Biology and Environmental Protection, University of Łódź, Łódź, Poland
- BBMRI.pl Consortium, Wrocław, Poland
| | - D Strapagiel
- Biobank Lab, Department of Molecular Biophysics, Faculty of Biology and Environmental Protection, University of Łódź, Łódź, Poland
- BBMRI.pl Consortium, Wrocław, Poland
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13
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Doiron D, Marcon Y, Fortier I, Burton P, Ferretti V. Software Application Profile: Opal and Mica: open-source software solutions for epidemiological data management, harmonization and dissemination. Int J Epidemiol 2018; 46:1372-1378. [PMID: 29025122 PMCID: PMC5837212 DOI: 10.1093/ije/dyx180] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/08/2017] [Indexed: 01/11/2023] Open
Abstract
Motivation Improving the dissemination of information on existing epidemiological studies and facilitating the interoperability of study databases are essential to maximizing the use of resources and accelerating improvements in health. To address this, Maelstrom Research proposes Opal and Mica, two inter-operable open-source software packages providing out-of-the-box solutions for epidemiological data management, harmonization and dissemination. Implementation Opal and Mica are two standalone but inter-operable web applications written in Java, JavaScript and PHP. They provide web services and modern user interfaces to access them. General features Opal allows users to import, manage, annotate and harmonize study data. Mica is used to build searchable web portals disseminating study and variable metadata. When used conjointly, Mica users can securely query and retrieve summary statistics on geographically dispersed Opal servers in real-time. Integration with the DataSHIELD approach allows conducting more complex federated analyses involving statistical models. Availability Opal and Mica are open-source and freely available at [www.obiba.org] under a General Public License (GPL) version 3, and the metadata models and taxonomies that accompany them are available under a Creative Commons licence.
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Affiliation(s)
- Dany Doiron
- Research Institute of the McGill University Health Centre, Montreal, QC, Canada.,Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Yannick Marcon
- Research Institute of the McGill University Health Centre, Montreal, QC, Canada
| | - Isabel Fortier
- Research Institute of the McGill University Health Centre, Montreal, QC, Canada
| | - Paul Burton
- University of Bristol, School of Social and Community Medicine, Bristol, UK
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14
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Zatloukal K, Stumptner C, Kungl P, Mueller H. Biobanks in personalized medicine. EXPERT REVIEW OF PRECISION MEDICINE AND DRUG DEVELOPMENT 2018. [DOI: 10.1080/23808993.2018.1493921] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Kurt Zatloukal
- Diagnostic and Research Center for Molecular BioMedicine, Medical University of Graz, Graz, Austria
| | - Cornelia Stumptner
- Diagnostic and Research Center for Molecular BioMedicine, Medical University of Graz, Graz, Austria
| | - Penelope Kungl
- Diagnostic and Research Center for Molecular BioMedicine, Medical University of Graz, Graz, Austria
| | - Heimo Mueller
- Diagnostic and Research Center for Molecular BioMedicine, Medical University of Graz, Graz, Austria
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15
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Abstract
Biobanking and BioMolecular resources Research Infrastructure (BBMRI)- European Research Infrastructure Consortium (ERIC) is the largest infrastructure launched in Europe in health research. By nature it is a distributed infrastructure, in which biological samples and data are hosted by the European Member States biobanks. As of today, BBMRI-ERIC consists of 19 European Member States and 1 international organization, the International Agency for Research on Cancer. This means that BBMRI-ERIC has a population of >500 million individuals in Europe. BBMRI-ERIC is a truly Pan-European Research Infrastructure for health research. Given that BBMRI-ERIC is set up to become a key source for users in both academic and scientific institutions as well as in the pharmaceutical and life science industries, it contributes directly to the Innovation Union concept. It is pan-European because BBMRI-ERIC already shows an excellent geographic and regional coverage all over Europe involving countries from South, East, West, North, and Central Europe. BBMRI-ERIC is a service-driven infrastructure for the European Member States, driven by science. The BBMRI-ERIC Directory consists of 100 million samples and a roadmap for better-defined quality in European biobanks for improving reproducibility and reliability of the biological sample and data.
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Affiliation(s)
- Jan-Eric Litton
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
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16
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Liu X, Hoene M, Yin P, Fritsche L, Plomgaard P, Hansen JS, Nakas CT, Niess AM, Hudemann J, Haap M, Mendy M, Weigert C, Wang X, Fritsche A, Peter A, Häring HU, Xu G, Lehmann R. Quality Control of Serum and Plasma by Quantification of (4E,14Z)-Sphingadienine-C18-1-Phosphate Uncovers Common Preanalytical Errors During Handling of Whole Blood. Clin Chem 2018; 64:810-819. [PMID: 29567661 DOI: 10.1373/clinchem.2017.277905] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 02/05/2018] [Indexed: 01/08/2023]
Abstract
BACKGROUND Nonadherence to standard operating procedures (SOPs) during handling and processing of whole blood is one of the most frequent causes affecting the quality of serum and plasma. Yet, the quality of blood samples is of the utmost importance for reliable, conclusive research findings, valid diagnostics, and appropriate therapeutic decisions. METHODS UHPLC-MS-driven nontargeted metabolomics was applied to identify biomarkers that reflected time to processing of blood samples, and a targeted UHPLC-MS analysis was used to quantify and validate these biomarkers. RESULTS We found that (4E,14Z)-sphingadienine-C18-1-phosphate (S1P-d18:2) was suitable for the reliable assessment of the pronounced changes in the quality of serum and plasma caused by errors in the phase between collection and centrifugation of whole blood samples. We rigorously validated S1P-d18:2, which included the use of practicality tests on >1400 randomly selected serum and plasma samples that were originally collected during single- and multicenter trials and then stored in 11 biobanks in 3 countries. Neither life-threatening disease states nor strenuous metabolic challenges (i.e., high-intensity exercise) affected the concentration of S1P-d18:2. Cutoff values for sample assessment were defined (plasma, ≤0.085 μg/mL; serum, ≤0.154 μg/mL). CONCLUSIONS Unbiased valid monitoring to check for adherence to SOP-dictated time for processing to plasma or serum and/or time to storage of whole blood at 4 °C is now feasible. This novel quality assessment step could enable scientists to uncover common preanalytical errors, allowing for identification of serum and plasma samples that should be excluded from certain investigations. It should also allow control of samples before long-term storage in biobanks.
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Affiliation(s)
- Xinyu Liu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Miriam Hoene
- Division of Clinical Chemistry and Pathobiochemistry (Central Laboratory), University Hospital Tübingen, Tübingen, Germany
| | - Peiyuan Yin
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - Louise Fritsche
- Core Facility German Center for Diabetes Research (DZD) Clinical Chemistry Laboratory, Institute for Diabetes Research and Metabolic Diseases, Helmholtz Center Munich, University of Tübingen, Tübingen, Germany.,German Center for Diabetes Research (DZD), Tübingen, Germany
| | - Peter Plomgaard
- Department of Clinical Biochemistry, Rigshospitalet, Copenhagen, Denmark.,Center of Inflammation and Metabolism and Center for Physical Activity Research, Department of Infectious Diseases and Copenhagen Muscle Research Center (CMRC), Rigshospitalet, Copenhagen, Denmark
| | - Jakob S Hansen
- Center of Inflammation and Metabolism and Center for Physical Activity Research, Department of Infectious Diseases and Copenhagen Muscle Research Center (CMRC), Rigshospitalet, Copenhagen, Denmark
| | - Christos T Nakas
- University Institute of Clinical Chemistry, Center of Laboratory Medicine, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland.,Laboratory of Biometry, University of Thessaly, Volos, Greece
| | - Andreas M Niess
- Department of Sports Medicine, University Hospital Tübingen, Tübingen, Germany
| | - Jens Hudemann
- Department of Sports Medicine, University Hospital Tübingen, Tübingen, Germany
| | - Michael Haap
- Department of Internal Medicine, Medical Intensive Care Unit, University of Tübingen, Tübingen, Germany
| | - Maimuna Mendy
- Laboratory Services and Biobank Group, International Agency for Research on Cancer (IARC) of the World Health Organization (WHO), Lyon, France
| | - Cora Weigert
- Division of Clinical Chemistry and Pathobiochemistry (Central Laboratory), University Hospital Tübingen, Tübingen, Germany.,German Center for Diabetes Research (DZD), Tübingen, Germany
| | - Xiaolin Wang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - Andreas Fritsche
- Division of Clinical Chemistry and Pathobiochemistry (Central Laboratory), University Hospital Tübingen, Tübingen, Germany.,Core Facility German Center for Diabetes Research (DZD) Clinical Chemistry Laboratory, Institute for Diabetes Research and Metabolic Diseases, Helmholtz Center Munich, University of Tübingen, Tübingen, Germany.,German Center for Diabetes Research (DZD), Tübingen, Germany
| | - Andreas Peter
- Division of Clinical Chemistry and Pathobiochemistry (Central Laboratory), University Hospital Tübingen, Tübingen, Germany.,Core Facility German Center for Diabetes Research (DZD) Clinical Chemistry Laboratory, Institute for Diabetes Research and Metabolic Diseases, Helmholtz Center Munich, University of Tübingen, Tübingen, Germany.,German Center for Diabetes Research (DZD), Tübingen, Germany
| | - Hans-Ulrich Häring
- Division of Clinical Chemistry and Pathobiochemistry (Central Laboratory), University Hospital Tübingen, Tübingen, Germany.,Core Facility German Center for Diabetes Research (DZD) Clinical Chemistry Laboratory, Institute for Diabetes Research and Metabolic Diseases, Helmholtz Center Munich, University of Tübingen, Tübingen, Germany.,German Center for Diabetes Research (DZD), Tübingen, Germany
| | - Guowang Xu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China;
| | - Rainer Lehmann
- Division of Clinical Chemistry and Pathobiochemistry (Central Laboratory), University Hospital Tübingen, Tübingen, Germany; .,Core Facility German Center for Diabetes Research (DZD) Clinical Chemistry Laboratory, Institute for Diabetes Research and Metabolic Diseases, Helmholtz Center Munich, University of Tübingen, Tübingen, Germany.,German Center for Diabetes Research (DZD), Tübingen, Germany
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17
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Lablans M, Kadioglu D, Muscholl M, Ückert F. Exploiting Distributed, Heterogeneous and Sensitive Data Stocks while Maintaining the Owner’s Data Sovereignty. Methods Inf Med 2018. [PMID: 26196653 DOI: 10.3414/me14-01-0137] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
SummaryBackground: To achieve statistical significance in medical research, biological or data samples from several bio- or databanks often need to be complemented by those of other institutions. For that purpose, IT-based search services have been established to locate datasets matching a given set of criteria in databases distributed across several institutions. However, previous approaches require data owners to disclose information about their samples, raising a barrier for their participation in the network.Objective: To devise a method to search distributed databases for datasets matching a given set of criteria while fully maintaining their owner’s data sovereignty.Methods: As a modification to traditional federated search services, we propose the decentral search, which allows the data owner a high degree of control. Relevant data are loaded into local bridgeheads, each under their owner’s sovereignty. Researchers can formulate criteria sets along with a project proposal using a central search broker, which then notifies the bridgeheads. The criteria are, however, treated as an inquiry rather than a query: Instead of responding with results, bridgeheads notify their owner and wait for his/her decision regarding whether and what to answer based on the criteria set, the matching datasets and the specific project proposal. Without the owner’s explicit consent, no data leaves his/ her institution.Results: The decentral search has been deployed in one of the six German Centers for Health Research, comprised of eleven university hospitals. In the process, compliance with German data protection regulations has been confirmed. The decentral search also marks the centerpiece of an open source registry software toolbox aiming to build a national registry of rare diseases in Germany.Conclusions: While the sacrifice of real-time answers impairs some use-cases, it leads to several beneficial side effects: improved data protection due to data parsimony, tolerance for incomplete data schema mappings and flexibility with regard to patient consent. Most importantly, as no datasets ever leave their institution, owners can reject projects without facing potential peer pressure. By its lower barrier for participation, a decentral search service is likely to attract a larger number of partners and to bring a researcher into contact with the right potential partners.
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Affiliation(s)
- M Lablans
- Martin Lablans, University Medical Center Mainz, Obere Zahlbacher Straße 69, 55131 Mainz, Germany, E-mail:
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18
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Schwenk JM, Omenn GS, Sun Z, Campbell DS, Baker MS, Overall CM, Aebersold R, Moritz RL, Deutsch EW. The Human Plasma Proteome Draft of 2017: Building on the Human Plasma PeptideAtlas from Mass Spectrometry and Complementary Assays. J Proteome Res 2017; 16:4299-4310. [PMID: 28938075 PMCID: PMC5864247 DOI: 10.1021/acs.jproteome.7b00467] [Citation(s) in RCA: 141] [Impact Index Per Article: 20.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Human blood plasma provides a highly accessible window to the proteome of any individual in health and disease. Since its inception in 2002, the Human Proteome Organization's Human Plasma Proteome Project (HPPP) has been promoting advances in the study and understanding of the full protein complement of human plasma and on determining the abundance and modifications of its components. In 2017, we review the history of the HPPP and the advances of human plasma proteomics in general, including several recent achievements. We then present the latest 2017-04 build of Human Plasma PeptideAtlas, which yields ∼43 million peptide-spectrum matches and 122,730 distinct peptide sequences from 178 individual experiments at a 1% protein-level FDR globally across all experiments. Applying the latest Human Proteome Project Data Interpretation Guidelines, we catalog 3509 proteins that have at least two non-nested uniquely mapping peptides of nine amino acids or more and >1300 additional proteins with ambiguous evidence. We apply the same two-peptide guideline to historical PeptideAtlas builds going back to 2006 and examine the progress made in the past ten years in plasma proteome coverage. We also compare the distribution of proteins in historical PeptideAtlas builds in various RNA abundance and cellular localization categories. We then discuss advances in plasma proteomics based on targeted mass spectrometry as well as affinity assays, which during early 2017 target ∼2000 proteins. Finally, we describe considerations about sample handling and study design, concluding with an outlook for future advances in deciphering the human plasma proteome.
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Affiliation(s)
- Jochen M. Schwenk
- Affinity Proteomics, SciLifeLab, School of Biotechnology, KTH Royal Institute of Technology, Tomtebodavägen 23, SE-171 65 Solna, Sweden
| | - Gilbert S. Omenn
- Departments of Computational Medicine & Bioinformatics, Internal Medicine, and Human Genetics and School of Public Health, University of Michigan, Ann Arbor, MI, 48109-2218, USA
- Institute for Systems Biology, Seattle, WA, USA
| | - Zhi Sun
- Institute for Systems Biology, Seattle, WA, USA
| | | | - Mark S. Baker
- Department of Biomedical Sciences, Faculty of Medicine and Health Science, Macquarie University, NSW, 2109. Australia
| | - Christopher M. Overall
- Centre for Blood Research, Departments of Oral Biological & Medical Sciences, and Biochemistry & Molecular Biology, Faculty of Dentistry, University of British Columbia, Vancouver, Canada
| | - Ruedi Aebersold
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
- Faculty of Science, University of Zurich, 8006 Zurich, Switzerland
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19
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Wichmann HE. Epidemiology in Germany-general development and personal experience. Eur J Epidemiol 2017; 32:635-656. [PMID: 28815360 DOI: 10.1007/s10654-017-0290-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2017] [Accepted: 07/27/2017] [Indexed: 12/19/2022]
Abstract
Did you ever hear about epidemiology in Germany? Starting from an epidemiological desert the discipline has grown remarkably, especially during the last 10-15 years: research institutes have been established, research funding has improved, multiple curriculae in Epidemiology and Public Health are offered. This increase has been quite steep, and now the epidemiological infrastructure is much better. Several medium-sized and even big population cohorts are ongoing, and the number and quality of publications from German epidemiologists has reached a respectable level. My own career in epidemiology started in the field of environmental health. After German reunification I concentrated for many years on environmental problems in East Germany and observed the health benefits after improvement of the situation. Later, I concentrated on population-based cohorts in newborns (GINI/LISA) and adults (KORA, German National Cohort), and on biobanking. This Essay describes the development in Germany after worldwar 2, illustrated by examples of research results and build-up of epidemiological infractructures worth mentioning.
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Affiliation(s)
- Heinz-Erich Wichmann
- Institute of Epidemiology, 2, Helmholtz Center Munich, Munich, Germany. .,Chair of Epidemiology, University of Munich, Munich, Germany.
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20
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Quansah E, McGregor NW. Towards diversity in genomics: The emergence of neurogenomics in Africa? Genomics 2017; 110:1-9. [PMID: 28774809 DOI: 10.1016/j.ygeno.2017.07.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Revised: 07/24/2017] [Accepted: 07/30/2017] [Indexed: 12/11/2022]
Abstract
There is a high burden of mental and neurological disorders in Africa. Nevertheless, there appears to be an under-representation of African ancestry populations in large-scale genomic studies. Here, we evaluated the extent of under-representation of Africans in neurogenomic studies in the GWAS Catalog. We found 569 neurogenomic studies, of which 88.9% were exclusively focused on people with European ancestry and the remaining 11.1% having African ancestry cases included. In terms of population, only 1.2% of the total populations involved in these 569 GWAS studies were of African descent. Further, most of the individuals in the African ancestry category were identified to be African-Americans/Afro-Caribbeans, highlighting the huge under-representation of homogenous African populations in large-scale neurogenomic studies. Efforts geared at establishing strong collaborative ties with European/American researchers, maintaining freely accessible biobanks and establishing comprehensive African genome data repositories to track African genome variations are critical for propelling neurogenomics/precision medicine in Africa.
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Affiliation(s)
- Emmanuel Quansah
- Pharmacology, Faculty of Health and Life Sciences, De Montfort University, Leicester LE1 9BH, UK.
| | - Nathaniel W McGregor
- Department of Genetics, Stellenbosch University, Stellenbosch, South Africa; Department of Psychiatry, Stellenbosch University, Tygerberg Medical Campus, Tygerberg, South Africa.
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21
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Ioannidis JPA, Bossuyt PMM. Waste, Leaks, and Failures in the Biomarker Pipeline. Clin Chem 2017; 63:963-972. [DOI: 10.1373/clinchem.2016.254649] [Citation(s) in RCA: 90] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Accepted: 11/30/2016] [Indexed: 01/05/2023]
Abstract
Abstract
BACKGROUND
The large, expanding literature on biomarkers is characterized by almost ubiquitous significant results, with claims about the potential importance, but few of these discovered biomarkers are used in routine clinical care.
CONTENT
The pipeline of biomarker development includes several specific stages: discovery, validation, clinical translation, evaluation, implementation (and, in the case of nonutility, deimplementation). Each of these stages can be plagued by problems that cause failures of the overall pipeline. Some problems are nonspecific challenges for all biomedical investigation, while others are specific to the peculiarities of biomarker research. Discovery suffers from poor methods and incomplete and selective reporting. External independent validation is limited. Selection for clinical translation is often shaped by nonrational choices. Evaluation is sparse and the clinical utility of many biomarkers remains unknown. The regulatory environment for biomarkers remains weak and guidelines can reach biased or divergent recommendations. Removing inefficient or even harmful biomarkers that have been entrenched in clinical care can meet with major resistance.
SUMMARY
The current biomarker pipeline is too prone to failures. Consideration of clinical needs should become a starting point for the development of biomarkers. Improvements can include the use of more stringent methodology, better reporting, larger collaborative studies, careful external independent validation, preregistration, rigorous systematic reviews and umbrella reviews, pivotal randomized trials, and implementation and deimplementation studies. Incentives should be aligned toward delivering useful biomarkers.
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Affiliation(s)
- John P A Ioannidis
- Departments of Medicine, Health Research and Policy, and Statistics, and the Meta-Research Innovation Center at Stanford (METRICS), Stanford University, Stanford, CA
| | - Patrick M M Bossuyt
- Department of Clinical Epidemiology, Biostatistics & Bioinformatics, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
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22
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Langhof H, Kahrass H, Sievers S, Strech D. Access policies in biobank research: what criteria do they include and how publicly available are they? A cross-sectional study. Eur J Hum Genet 2017; 25:293-300. [PMID: 28000694 PMCID: PMC5315509 DOI: 10.1038/ejhg.2016.172] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Revised: 08/31/2016] [Accepted: 11/01/2016] [Indexed: 12/22/2022] Open
Abstract
Access policies of biobanks specify the governance of sample and data sharing. Basic guidance on relevant access criteria exists, but so far little is known about their public availability and what criteria for access and prioritization they actually include. Access policies were gathered by hand searching the websites of biobanks identified via registries (eg, BBMRI and P3G), and by additional search strategies. Criteria for access and prioritization were synthesized by thematic analysis. Of 523 biobank websites screened, 9% included a publicly available access policy. With all applied search strategies, we finally retrieved 74 access policies. Thematic analysis resulted in 62 different access criteria in three main categories: (a) scientific quality, (b) value and (c) ethical soundness. 'Scientific quality' criteria were mentioned in 70% of all policies, 'value' criteria in 33% and 'ethical soundness' criteria in 73%. Criteria for prioritization were specified in 27% of all policies. Access policies differed broadly in number, specification and operationalization of the included access criteria. In order to make biobank research more effective, efficient and trustworthy, access policies should be more available to the public. Furthermore, access policies should aim for precise and more harmonized wording of access criteria. From a public and governance perspective, the issue of how to prioritize access to scarce samples should form part of access policies.
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Affiliation(s)
- Holger Langhof
- Institute for History, Ethics and Philosophy of Medicine, CELLS – Centre for Ethics and Law in the Life Sciences, Hannover Medical School (MHH), Hannover, Germany
| | - Hannes Kahrass
- Institute for History, Ethics and Philosophy of Medicine, CELLS – Centre for Ethics and Law in the Life Sciences, Hannover Medical School (MHH), Hannover, Germany
| | - Sören Sievers
- Institute for History, Ethics and Philosophy of Medicine, CELLS – Centre for Ethics and Law in the Life Sciences, Hannover Medical School (MHH), Hannover, Germany
| | - Daniel Strech
- Institute for History, Ethics and Philosophy of Medicine, CELLS – Centre for Ethics and Law in the Life Sciences, Hannover Medical School (MHH), Hannover, Germany
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23
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Witoń M, Strapagiel D, Gleńska-Olender J, Chróścicka A, Ferdyn K, Skokowski J, Kalinowski L, Pawlikowski J, Marciniak B, Pasterk M, Matera-Witkiewicz A, Kozera Ł. Organization of BBMRI.pl: The Polish Biobanking Network. Biopreserv Biobank 2017; 15:264-269. [PMID: 28103080 DOI: 10.1089/bio.2016.0091] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
In Poland storage of human biological samples takes place at most universities and scientific institutions conducting research projects in the field of biomedicine. The First International Biobanking Conference organized by the Ministry of Science and Higher Education in 2014 shed a light on the situation of Polish biobanking infrastructures. The country has around 40 large biorepositories, which store unique biological material such as whole brains, muscle fibers from patients with rare diseases, as well as thousands of samples from patients with lifestyle diseases. There are only two population-based biobanks working locally and several disease-oriented biobanks specializing mainly in oncological diseases. Consortium BBMRI.pl created plans for establishing a Polish Network of Biobanks, with national node which meets standards for biobanks and cooperation to guarantee development of biomedical sciences and international collaboration between Poland and other countries. The Polish network will enhance research activities, due to better visibility of samples and data that are stored in the national biobanking catalogue. However, it requires more than a comprehensive understanding of all benefits. The list of examples of benefits can be presented as follows: (i) a reduction of the duration and cost of clinical trials and subsequent time to market for anticancer drugs; (ii) more precise patient diagnosis and the associated impact on treatment and lower healthcare costs for providers, individuals, and the nation; (iii) improvements in research experiment time frames and data efficiencies; (iv) convergence to an industry standards for biospecimen quality; (v) optimization of capital infrastructure and IT technology.
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Affiliation(s)
- Małgorzata Witoń
- 1 Regional Science and Technology Center , Swietokrzyski Biobank, Checiny, Poland
| | - Dominik Strapagiel
- 2 Biobank Lab, Department of Molecular Biophysics, University of Lodz , Lodz, Poland
| | | | - Anna Chróścicka
- 3 Department of Histology and Embryology, Center for Biostructure Research, Center for Preclinical Research and Technology, Medical University of Warsaw , Warsaw, Poland
| | | | - Jarosław Skokowski
- 5 Department of Medical Laboratory Diagnostics and Bank of Frozen Tissues & Genetic Specimens, Medical University of Gdansk , Gdansk, Poland .,6 Department of Surgical Oncology, Medical University of Gdansk , Gdansk, Poland
| | - Leszek Kalinowski
- 5 Department of Medical Laboratory Diagnostics and Bank of Frozen Tissues & Genetic Specimens, Medical University of Gdansk , Gdansk, Poland
| | - Jakub Pawlikowski
- 7 Department of Ethics and Human Philosophy, Medical University of Lublin , Lublin, Poland
| | - Błażej Marciniak
- 2 Biobank Lab, Department of Molecular Biophysics, University of Lodz , Lodz, Poland
| | | | - Agnieszka Matera-Witkiewicz
- 9 Screening Laboratory of Biological Activity Test and Collection of Biological Material, Wroclaw Medical University , Wrocław, Poland
| | - Łukasz Kozera
- 10 Wroclaw Research Centre EIT+, Biobank, Wrocław, Poland
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24
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Holub P, Swertz M, Reihs R, van Enckevort D, Müller H, Litton JE. BBMRI-ERIC Directory: 515 Biobanks with Over 60 Million Biological Samples. Biopreserv Biobank 2017; 14:559-562. [PMID: 27936342 PMCID: PMC5180080 DOI: 10.1089/bio.2016.0088] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Affiliation(s)
| | - Morris Swertz
- 1 BBMRI-ERIC , Graz, Austria .,2 BBMRI.nl and University Medical Center Groningen , Groningen, the Netherlands
| | - Robert Reihs
- 1 BBMRI-ERIC , Graz, Austria .,3 BBMRI.at and Medical University Graz , Graz, Austria
| | - David van Enckevort
- 1 BBMRI-ERIC , Graz, Austria .,2 BBMRI.nl and University Medical Center Groningen , Groningen, the Netherlands
| | - Heimo Müller
- 1 BBMRI-ERIC , Graz, Austria .,3 BBMRI.at and Medical University Graz , Graz, Austria
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25
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From the evaluation of existing solutions to an all-inclusive package for biobanks. HEALTH AND TECHNOLOGY 2017; 7:89-95. [PMID: 28344915 PMCID: PMC5346419 DOI: 10.1007/s12553-016-0175-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Accepted: 12/19/2016] [Indexed: 11/26/2022]
Abstract
The domain of biobanking has gone through many stages and as a result there are a wide range of commercial and open source software solutions available. The utilization of these software tools requires different levels of domain and technical skills for installation, configuration and ultimate us of these biobank software tools. To compound this complexity the biobanking community are required to work together in order to share knowledge and jointly build solutions to underpin the research infrastructure. We have evaluated the available tools, described them in a catalogue (BiobankApps) and made a selection of tools available to biobanks in a reference toolbox (BIBBOX) that are use-case driven. In the BiobankApps tool catalogue, both commercial and open source software solutions related to the biobanking domain are included, classified and evaluated. The evaluation covers: 1) “user review” by an authenticated user 2) domain expert: quick analysis by BBMRI members and 3) domain expert: detailed analysis and test installation with real world data. The evaluation is paired with a survey across the more “advanced” (from a technology perspective) biobanks to investigate what tools are currently used and summarises known benefits/drawbacks of the respective packages. In the second step we recommend tools for specific use cases, and install, configure and connect these in the BIBBOX framework. This service also builds on the existing work in the United Kingdom in seeking to establish the motivations for different stakeholders to become involved and therefore assisting in prioritising the use-cases based on the level of need and support within the research community. All tools associated to a use-case are available as BIBBOX applications (technically this is achieved by docker containers), which are integrated in the BIBBOX framework with central identification and user management. In future work we plan to share the acquired knowledge with other networks, develop an Application Programmable Interface (API) for the exchange of metadata with other tool catalogues and work on an ontology for the evaluation of biobank software.
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26
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Ciaburri M, Napolitano M, Bravo E. Business Planning in Biobanking: How to Implement a Tool for Sustainability. Biopreserv Biobank 2016; 15:46-56. [PMID: 27898226 PMCID: PMC5327055 DOI: 10.1089/bio.2016.0045] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Worldwide, the sustainability of public health systems is challenged by the increasing number and cost of personalized therapies. Quality biological samples stored in biobanks are essential for the provision of appropriate health services and also act as a reservoir for the development of precision medicine and biotechnological innovation. Economic sustainability is a crucial factor in the maintenance of biobanking activities. Traditionally, management of biobanking is performed by health researchers and/or clinicians whose knowledge of economic issues is inadequate. On the other hand, familiarity with financial instruments used by economists is not often accompanied by a consolidated understanding of biobanking features. This article aims to be a guide for the implementation of business plans in biobanking and proposes models for the facilitation of their preparation, thus contributing to recognition of the importance of efficient management of resources of public health services.
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Affiliation(s)
- Mirella Ciaburri
- 1 Department of Management, University LUISS Guido Carli , Rome, Italy .,2 Departments of Haematology, Oncology and Molecular Medicine, Istituto Superiore di Sanità , Rome, Italy
| | - Mariarosaria Napolitano
- 2 Departments of Haematology, Oncology and Molecular Medicine, Istituto Superiore di Sanità , Rome, Italy
| | - Elena Bravo
- 2 Departments of Haematology, Oncology and Molecular Medicine, Istituto Superiore di Sanità , Rome, Italy
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27
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Dirks RAM, Stunnenberg HG, Marks H. Genome-wide epigenomic profiling for biomarker discovery. Clin Epigenetics 2016; 8:122. [PMID: 27895806 PMCID: PMC5117701 DOI: 10.1186/s13148-016-0284-4] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2016] [Accepted: 11/02/2016] [Indexed: 12/24/2022] Open
Abstract
A myriad of diseases is caused or characterized by alteration of epigenetic patterns, including changes in DNA methylation, post-translational histone modifications, or chromatin structure. These changes of the epigenome represent a highly interesting layer of information for disease stratification and for personalized medicine. Traditionally, epigenomic profiling required large amounts of cells, which are rarely available with clinical samples. Also, the cellular heterogeneity complicates analysis when profiling clinical samples for unbiased genome-wide biomarker discovery. Recent years saw great progress in miniaturization of genome-wide epigenomic profiling, enabling large-scale epigenetic biomarker screens for disease diagnosis, prognosis, and stratification on patient-derived samples. All main genome-wide profiling technologies have now been scaled down and/or are compatible with single-cell readout, including: (i) Bisulfite sequencing to determine DNA methylation at base-pair resolution, (ii) ChIP-Seq to identify protein binding sites on the genome, (iii) DNaseI-Seq/ATAC-Seq to profile open chromatin, and (iv) 4C-Seq and HiC-Seq to determine the spatial organization of chromosomes. In this review we provide an overview of current genome-wide epigenomic profiling technologies and main technological advances that allowed miniaturization of these assays down to single-cell level. For each of these technologies we evaluate their application for future biomarker discovery. We will focus on (i) compatibility of these technologies with methods used for clinical sample preservation, including methods used by biobanks that store large numbers of patient samples, and (ii) automation of these technologies for robust sample preparation and increased throughput.
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Affiliation(s)
- René A M Dirks
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University, 6500HB Nijmegen, The Netherlands
| | - Hendrik G Stunnenberg
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University, 6500HB Nijmegen, The Netherlands
| | - Hendrik Marks
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University, 6500HB Nijmegen, The Netherlands
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28
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Gee S, Oliver R, Corfield J, Georghiou L, Yuille M. Biobank Finances: A Socio-Economic Analysis and Review. Biopreserv Biobank 2016; 13:435-51. [PMID: 26697914 DOI: 10.1089/bio.2015.0030] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
This socio-economic study is based on the widely held view that there is an inadequate supply of human biological samples that is hampering biomedical research development and innovation (RDI). The potential value of samples and the associated data are thus not being realized. We aimed to examine whether the financing of biobanks contributes to this problem and then to propose a national solution. We combined three methods: a qualitative case study; literature analysis; and informal consultations with experts. The case study enabled an examination of the complex institutional arrangements for biobanks, with a particular focus on cost models. For the purposes of comparison, a typology for biobanks was developed using the three methods. We found that it is not possible to apply a standard cost model across the diversity of biobanks, and there is a deficit in coordination and sustainability and an excess of complexity. We propose that coordination across this diversity requires dedicated resources for a national biobanking distributed research infrastructure. A coordination center would establish and improve standards and support a national portal for access. This should be financed centrally by public funds, possibly supplemented by industrial funding. We propose that: a) sample acquisition continues to be costed into projects and project proposals to ensure biobanking is driven by research needs; b) core biobanking activities and facilities be supported by central public funds distributed directly to host public institutions; and c) marginal costs for access be paid for by the user.
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Affiliation(s)
- Sally Gee
- 1 Manchester Institute of Innovation Research, Manchester Business School, The University of Manchester , Manchester, United Kingdom
| | - Rob Oliver
- 2 Research and Development Directorate, Salford Royal Hospitals NHS Trust , Salford, United Kingdom
| | | | - Luke Georghiou
- 1 Manchester Institute of Innovation Research, Manchester Business School, The University of Manchester , Manchester, United Kingdom
| | - Martin Yuille
- 4 Center for Integrated Genomic Medical Research, Institute of Population Health, The University of Manchester , Manchester, United Kingdom
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29
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Ahmad-Nejad P, Duda A, Sucker A, Werner M, Bronsert P, Stickeler E, Reifenberger G, Malzkorn B, Oberländer M, Habermann JK, Bruch HP, Linnebacher M, Schadendorf D, Neumaier M. Assessing quality and functionality of DNA isolated from FFPE tissues through external quality assessment in tissue banks. Clin Chem Lab Med 2016; 53:1927-34. [PMID: 26053008 DOI: 10.1515/cclm-2014-1202] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Accepted: 04/30/2015] [Indexed: 11/15/2022]
Abstract
BACKGROUND Biobanks are becoming increasingly important for assessment of disease risk as well as identification and validation of new diagnostic biomarkers and druggable targets. The validity of data obtained from biobanks is critically limited by the biomaterial quality of the biological samples. External quality assessment (EQA) programs suitable to comprehensively measure the biomaterial quality in archived materials are currently lacking. We report on quantitative assay designs for the analysis of both structural and functional integrity of DNAs that were applied in a first pilot EQA within the priority program on tumor tissue biobanking funded by the German Cancer Aid. METHODS Participating biobanks isolated DNAs from a standardized set of 10 samples comprising sections of four different formalin-fixed paraffin-embedded tissues using their standard operating procedures. Isolated DNAs and analytical results were returned and analyzed centrally for nucleic acids yield, purity, fragmentation and amplificability at a quantitative level using dedicated assay designs. RESULTS The amount of extracted DNA varied in isolates ranging between 1.5 μg and 25.8 μg. Quantification of DNA fragmentation and amplificability allowed to highlight considerable discrepancies in DNA quality. Amplicons yielded from the isolates of these identical EQA samples ranged from 105 to 411 bp suggesting differences between residual inhibitors of downstream enzymatic reactions. CONCLUSIONS The quality of extraction of bioanalytes from biomaterial archives is heterogeneous even for stable biomolecules like DNA isolated with highly standardized methods. EQAs are appropriate tools to uncover strengths and weaknesses in biobanks in a systematic fashion. Biomaterial integrity is insufficiently reflected by standard methods, but needs to be assessed to improve biobank interoperability. Finally, our results also point towards the problem of measuring the quality of more delicate biomolecules like proteins or metabolites.
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30
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Groeneveld LF, Gregusson S, Guldbrandtsen B, Hiemstra SJ, Hveem K, Kantanen J, Lohi H, Stroemstedt L, Berg P. Domesticated Animal Biobanking: Land of Opportunity. PLoS Biol 2016; 14:e1002523. [PMID: 27467395 PMCID: PMC4965055 DOI: 10.1371/journal.pbio.1002523] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
In the past decade, biobanking has fuelled great scientific advances in the human medical sector. Well-established domesticated animal biobanks and integrated networks likewise harbour immense potential for great scientific advances with broad societal impacts, which are currently not being fully realised. Political and scientific leaders as well as journals and ethics committees should help to ensure that we are well equipped to meet future demands in livestock production, animal models, and veterinary care of companion animals.
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Affiliation(s)
| | | | | | - Sipke J. Hiemstra
- Centre for Genetic Resources, the Netherlands (CGN), Wageningen University and Research Centre, Wageningen, the Netherlands
| | - Kristian Hveem
- Department of Public Health, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Juha Kantanen
- Natural Resources Institute Finland (Luke), Helsinki, Finland
- Department of Environmental and Biological Sciences, University of Eastern Finland, Kuopio, Finland
| | - Hannes Lohi
- Research Programs Unit, Molecular Neurology, and Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
| | - Lina Stroemstedt
- SLU Biobank, Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden
| | - Peer Berg
- NordGen—the Nordic Genetic Resource Center, Ås, Norway
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31
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van Zon SKR, Scholtens S, Reijneveld SA, Smidt N, Bültmann U. Active recruitment and limited participant-load related to high participation in large population-based biobank studies. J Clin Epidemiol 2016; 78:52-62. [PMID: 27032874 DOI: 10.1016/j.jclinepi.2016.03.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Revised: 02/15/2016] [Accepted: 03/21/2016] [Indexed: 12/31/2022]
Abstract
OBJECTIVES Insight into baseline participation rates and their determinants is crucial for designing future population-based biobank studies. We therefore conducted a systematic review and meta-analysis of baseline participation rates and their determinants in large longitudinal population-based biobank studies. STUDY DESIGN AND SETTING We screened studies registered within the Public Population Project in Genomics and Society and in the Biobanking and Biomolecular Resources Research Infrastructure catalogues to find potentially eligible studies. We retrieved data with regard to participation rate, biobank design, performed measurements, and specific strategies for improving participation. We calculated weighted pooled proportions for each determinant using random-effects models. RESULTS We included 25 studies (participation rates 5-96%). Participation rates were highest for studies involving face-to-face recruitment [82.6%; 95% confidence interval (CI): 72.2%, 90.9%], for studies in which participants were visited for an examination (77.5%; 95% CI: 64.0%, 88.6%) and for studies in which at maximum four measurements were performed (78.2%; 95% CI: 69.7%, 85.7%). Specific strategies to improve participation were not found to be associated with higher participation rates. CONCLUSION Specific choices of recruitment methods and design have consequences for participation rates. These insights may help to increase participation in future studies, thereby enhancing the validity of their findings.
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Affiliation(s)
- Sander K R van Zon
- Department of Health Sciences, Community & Occupational Medicine, University Medical Center Groningen, University of Groningen, P.O Box 196, FA 10, Antonius Deusinglaan 1, 9700 AD Groningen, The Netherlands.
| | - Salome Scholtens
- LifeLines Cohort Study and Biobank, Bloemsingel 1, 9713 BZ Groningen, Groningen, The Netherlands
| | - Sijmen A Reijneveld
- Department of Health Sciences, Community & Occupational Medicine, University Medical Center Groningen, University of Groningen, P.O Box 196, FA 10, Antonius Deusinglaan 1, 9700 AD Groningen, The Netherlands
| | - Nynke Smidt
- Department of Epidemiology, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713 GZ Groningen, Groningen, The Netherlands
| | - Ute Bültmann
- Department of Health Sciences, Community & Occupational Medicine, University Medical Center Groningen, University of Groningen, P.O Box 196, FA 10, Antonius Deusinglaan 1, 9700 AD Groningen, The Netherlands
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Merino-Martinez R, Norlin L, van Enckevort D, Anton G, Schuffenhauer S, Silander K, Mook L, Holub P, Bild R, Swertz M, Litton JE. Toward Global Biobank Integration by Implementation of the Minimum Information About BIobank Data Sharing (MIABIS 2.0 Core). Biopreserv Biobank 2016; 14:298-306. [PMID: 26977825 DOI: 10.1089/bio.2015.0070] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Biobanks are the biological back end of data-driven medicine, but lack standards and generic solutions for interoperability and information harmonization. The move toward a global information infrastructure for biobanking demands semantic interoperability through harmonized services and common ontologies. To tackle this issue, the Minimum Information About BIobank data Sharing (MIABIS) was developed in 2012 by the Biobanking and BioMolecular Resources Research Infrastructure of Sweden (BBMRI.se). The wide acceptance of the first version of MIABIS encouraged evolving it to a more structured and descriptive standard. In 2013 a working group was formed under the largest infrastructure for health in Europe, Biobanking and BioMolecular Resources Research Infrastructure (BBMRI-ERIC), with the remit to continue the development of MIABIS (version 2.0) through a multicountry governance process. MIABIS 2.0 Core has been developed with 22 attributes describing Biobanks, Sample Collections, and Studies according to a modular structure that makes it easier to adhere to and to extend the standard. This integration standard will make a great contribution to the discovery and exploitation of biobank resources and lead to a wider and more efficient use of valuable bioresources, thereby speeding up the research on human diseases. Many within the European Union have accepted MIABIS 2.0 Core as the "de facto" biobank information standard.
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Affiliation(s)
- Roxana Merino-Martinez
- 1 BBMRI.se, Department of Medical Epidemiology and Biostatistics, Karolinska Institutet , Stockholm, Sweden
| | - Loreana Norlin
- 1 BBMRI.se, Department of Medical Epidemiology and Biostatistics, Karolinska Institutet , Stockholm, Sweden
| | - David van Enckevort
- 2 BBMRI-NL, Department of Genetics, Genomics Coordination Center, University Medical Center Groningen, University of Groningen , Groningen, the Netherlands
| | - Gabriele Anton
- 3 Institute of Epidemiology II, Helmholtz Center Munich , Munich, Germany
| | | | - Kaisa Silander
- 5 BBMRI.fi, National Institute for Health and Welfare , Genomics and Biomarkers Unit, Helsinki, Finland
| | - Linda Mook
- 2 BBMRI-NL, Department of Genetics, Genomics Coordination Center, University Medical Center Groningen, University of Groningen , Groningen, the Netherlands
| | | | | | - Morris Swertz
- 2 BBMRI-NL, Department of Genetics, Genomics Coordination Center, University Medical Center Groningen, University of Groningen , Groningen, the Netherlands
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[Connecting biobanks of large European cohorts (EU Project BBMRI-LPC)]. Bundesgesundheitsblatt Gesundheitsforschung Gesundheitsschutz 2016; 59:385-9. [PMID: 26809823 DOI: 10.1007/s00103-015-2300-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
BACKGROUND In addition to the Biobanking and BioMolecular resources Research Initiative (BBMRI), which is establishing a European research infrastructure for biobanks, a network for large European prospective cohorts (LPC) is being built to facilitate transnational research into important groups of diseases and health care. One instrument for this is the database "LPC Catalogue," which supports access to the biomaterials of the participating cohorts. OBJECTIVES To present the LPC Catalogue as a relevant tool for connecting European biobanks. In addition, the LPC Catalogue has been extended to establish compatibility with existing Minimum Information About Biobank data Sharing (MIABIS) and to allow for more detailed search requests. This article describes the LPC Catalogue, its organizational and technical structure, and the aforementioned extensions. MATERIALS AND METHODS The LPC Catalogue provides a structured overview of the participating LPCs. It offers various retrieval possibilities and a search function. To support more detailed search requests, a new module has been developed, called a "data cube". The provision of data by the cohorts is being supported by a "connector" component. RESULTS The LPC Catalogue contains data on 22 cohorts and more than 3.8 million biosamples. At present, data on the biosamples of three cohorts have been acquired for the "cube," which is continuously being expanded. In the BBMRI-LPC, tendering for scientific projects using the data and samples of the participating cohorts is currently being carried out. In this context, several proposals have already been approved. CONCLUSIONS The LPC Catalogue is supporting transnational access to biosamples. A comparison with existing solutions illustrates the relevance of its functionality.
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Die Biobank der Nationalen Kohorte als Ressource der epidemiologischen Forschung. Bundesgesundheitsblatt Gesundheitsforschung Gesundheitsschutz 2016; 59:351-60. [DOI: 10.1007/s00103-015-2305-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Lablans M, Kadioglu D, Mate S, Leb I, Prokosch HU, Ückert F. Strategien zur Vernetzung von Biobanken. Bundesgesundheitsblatt Gesundheitsforschung Gesundheitsschutz 2016; 59:373-8. [DOI: 10.1007/s00103-015-2299-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Zusammenfassung
Hintergrund
Nicht selten benötigt ein medizinisches Forschungsvorhaben mehr biologisches Material, als in einer einzigen Biobank verfügbar ist. Daher unterstützt eine Vielzahl von Strategien das Auffinden potentieller Forschungspartner mit passenden Proben, auch ohne dass diese zuvor in einer zentralisierten Sammlung zusammengeführt werden müssen.
Ziel
Der vorliegende Beitrag beschreibt die Klassifizierung verschiedener Strategien zur Vernetzung von Biomaterialbanken, speziell zur Probensuche, sowie eine IT-Infrastruktur, die diese Ansätze kombiniert.
Material und Methoden
Bestehende Strategien lassen sich nach drei Kriterien klassifizieren: a) Granularität der Probendaten: grobe Daten auf Bankebene (Katalog) vs. feingranulare Daten auf Probenebene, b) Speicherort der Probendaten: zentrale (zentraler Suchdienst) vs. dezentrale Datenhaltung (föderierte Suchdienste) und c) Automatisierungsgrad: automatisch (abfragebasiert, föderierter Suchdienst) vs. halbautomatisch (anfragebasiert, dezentrale Suche). Alle genannten Suchdienste setzen eine Datenintegration voraus; dabei helfen Metadaten bei der Überwindung semantischer Heterogenität.
Ergebnisse
Der „Common Service IT“ in BBMRI-ERIC („Biobanking and Biomolecular Resources Research Infrastructure-European Research Infrastructure Consortium“) vereint einen Katalog, die dezentrale Suche und Metadaten in einer integrierten Plattform, um Forschern vielseitige Werkzeuge zur Suche nach passendem Probenmaterial zu geben und bei den Biobankern gleichzeitig ein hohes Maß an Datenhoheit zu bewahren.
Diskussion
Trotz ihrer Unterschiede schließen sich die vorgestellten Strategien zur Vernetzung von Biomaterialbanken gegenseitig nicht aus. Vielmehr lassen sie sich in gemeinsamen Forschungsinfrastrukturen sinnvoll ergänzen und sie können sogar voneinander profitieren.
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Affiliation(s)
- Martin Lablans
- Medizinische Informatik in der Translationalen Onkologie, Deutsches Krebsforschungszentrum, Im Neuenheimer Feld 280, 69120, Heidelberg, Deutschland.
| | - Dennis Kadioglu
- Institut für medizinische Biometrie, Epidemiologie und Informatik (IMBEI), Universitätsmedizin Mainz, 55101, Mainz, Deutschland
| | - Sebastian Mate
- Lehrstuhl für Medizinische Informatik, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Deutschland
| | - Ines Leb
- Lehrstuhl für Medizinische Informatik, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Deutschland
| | - Hans-Ulrich Prokosch
- Lehrstuhl für Medizinische Informatik, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Deutschland
| | - Frank Ückert
- Medizinische Informatik in der Translationalen Onkologie, Deutsches Krebsforschungszentrum, Im Neuenheimer Feld 280, 69120, Heidelberg, Deutschland
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Lautenschläger R, Kohlmayer F, Prasser F, Kuhn KA. A generic solution for web-based management of pseudonymized data. BMC Med Inform Decis Mak 2015; 15:100. [PMID: 26621059 PMCID: PMC4665916 DOI: 10.1186/s12911-015-0222-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Accepted: 11/25/2015] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND Collaborative collection and sharing of data have become a core element of biomedical research. Typical applications are multi-site registries which collect sensitive person-related data prospectively, often together with biospecimens. To secure these sensitive data, national and international data protection laws and regulations demand the separation of identifying data from biomedical data and to introduce pseudonyms. Neither the formulation in laws and regulations nor existing pseudonymization concepts, however, are precise enough to directly provide an implementation guideline. We therefore describe core requirements as well as implementation options for registries and study databases with sensitive biomedical data. METHODS We first analyze existing concepts and compile a set of fundamental requirements for pseudonymized data management. Then we derive a system architecture that fulfills these requirements. Next, we provide a comprehensive overview and a comparison of different technical options for an implementation. Finally, we develop a generic software solution for managing pseudonymized data and show its feasibility by describing how we have used it to realize two research networks. RESULTS We have found that pseudonymization models are highly heterogeneous, already on a conceptual level. We have compiled a set of requirements from different pseudonymization schemes. We propose an architecture and present an overview of technical options. Based on a selection of technical elements, we suggest a generic solution. It supports the multi-site collection and management of biomedical data. Security measures are multi-tier pseudonymity and physical separation of data over independent backend servers. Integrated views are provided by a web-based user interface. Our approach has been successfully used to implement a national and an international rare disease network. CONCLUSIONS We were able to identify a set of core requirements out of several pseudonymization models. Considering various implementation options, we realized a generic solution which was implemented and deployed in research networks. Still, further conceptual work on pseudonymity is needed. Specifically, it remains unclear how exactly data is to be separated into distributed subsets. Moreover, a thorough risk and threat analysis is needed.
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Affiliation(s)
- Ronald Lautenschläger
- Chair for Biomedical Informatics, Department of Medicine, Technical University of Munich (TUM), Grillparzerstraße 18, 81675 Munich, Germany
| | - Florian Kohlmayer
- Chair for Biomedical Informatics, Department of Medicine, Technical University of Munich (TUM), Grillparzerstraße 18, 81675 Munich, Germany
| | - Fabian Prasser
- Chair for Biomedical Informatics, Department of Medicine, Technical University of Munich (TUM), Grillparzerstraße 18, 81675 Munich, Germany
| | - Klaus A. Kuhn
- Chair for Biomedical Informatics, Department of Medicine, Technical University of Munich (TUM), Grillparzerstraße 18, 81675 Munich, Germany
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A critical analysis of cancer biobank practices in relation to biospecimen quality. Biophys Rev 2015; 7:369-378. [PMID: 28510101 DOI: 10.1007/s12551-015-0178-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Accepted: 09/17/2015] [Indexed: 12/26/2022] Open
Abstract
There are concerns that a substantial proportion of published research data is not reproducible, which may partially explain the frequent failure to translate pre-clinical results to clinical care. High-quality cancer biospecimens are needed for robust, reproducible research findings, with most researchers obtaining these specimens from cancer biobanks or tumour banks. This review provides an overview of the types of quality control (QC) activities conducted within cancer biobanks that pertain to biospecimen quality and of biospecimen quality reporting tools, including SPREC and BRISQ. We examine how QC assay results and other biospecimen data are communicated from biobanks to researchers, and whether these activities lead to improved biospecimen quality reporting within the literature and/or to improved research outcomes. We also discuss operational factors that limit QC activities within biobanks and evidence gaps requiring further research. In summary, whereas the provision of quality biospecimens is a common aim of cancer biobanks, QC activities remain underreported and are rarely discussed in the literature, compared with other aspects of biobank operations. Further research is required to determine how biobanks can most efficiently optimise biospecimen quality, and how communication between biobanks and researchers can be improved.
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Challenges and Opportunities for Exploring Patient-Level Data. BIOMED RESEARCH INTERNATIONAL 2015; 2015:150435. [PMID: 26504779 PMCID: PMC4609340 DOI: 10.1155/2015/150435] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/05/2015] [Accepted: 08/27/2015] [Indexed: 11/28/2022]
Abstract
The proper exploration of patient-level data will pave the way towards personalised medicine. To better assess the state of the art in this field we identify the challenges and uncover the opportunities for the exploration of patient-level data through the review of well-known initiatives and projects focusing on the exploration of patient-level data. These cover a broad array of topics, from genomics to patient registries up to rare diseases research, among others. For each, we identified basic goals, involved partners, defined strategies and key technological and scientific outcomes, establishing the foundation for our analysis framework with four pillars: control, sustainability, technology, and science.
Substantial research outcomes have been produced towards the exploration of patient-level data. The potential behind these data will be essential to realise the personalised medicine premise in upcoming years. Hence, relevant stakeholders continually push forward new developments in this domain, bringing novel opportunities that are ripe for exploration.
Despite last decade's translational research advances, personalised medicine is still far from being a reality. Patients' data underlying potential goes beyond daily clinical practice. There are miscellaneous challenges and opportunities open for the exploration of these data by academia and business stakeholders.
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Verlinden M, Nys H, Ectors N, Huys I. Access to biobanks: harmonization across biobank initiatives. Biopreserv Biobank 2015; 12:415-22. [PMID: 25496154 DOI: 10.1089/bio.2014.0034] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
PURPOSE The current study investigates whether access arrangements relevant for biobanking contain clear information on key access conditions. It furthermore assesses the extent to which these access conditions are harmonized across biobank initiatives. METHODS A comparative analysis was conducted of access arrangements developed by 26 organizations, 36 biobank networks, and 20 biobanks worldwide. RESULTS The study demonstrates a lack of clear information on 21 key access conditions relevant for biobanking. Furthermore, it confirms that the harmonization across biobank initiatives is limited. CONCLUSION Many biobank initiatives need to be more transparent on how they apply the studied access conditions.
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Tigchelaar EF, Zhernakova A, Dekens JAM, Hermes G, Baranska A, Mujagic Z, Swertz MA, Muñoz AM, Deelen P, Cénit MC, Franke L, Scholtens S, Stolk RP, Wijmenga C, Feskens EJM. Cohort profile: LifeLines DEEP, a prospective, general population cohort study in the northern Netherlands: study design and baseline characteristics. BMJ Open 2015; 5:e006772. [PMID: 26319774 PMCID: PMC4554905 DOI: 10.1136/bmjopen-2014-006772] [Citation(s) in RCA: 155] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
PURPOSE There is a critical need for population-based prospective cohort studies because they follow individuals before the onset of disease, allowing for studies that can identify biomarkers and disease-modifying effects, and thereby contributing to systems epidemiology. PARTICIPANTS This paper describes the design and baseline characteristics of an intensively examined subpopulation of the LifeLines cohort in the Netherlands. In this unique subcohort, LifeLines DEEP, we included 1539 participants aged 18 years and older. FINDINGS TO DATE We collected additional blood (n = 1387), exhaled air (n = 1425) and faecal samples (n = 1248), and elicited responses to gastrointestinal health questionnaires (n = 1176) for analysis of the genome, epigenome, transcriptome, microbiome, metabolome and other biological levels. Here, we provide an overview of the different data layers in LifeLines DEEP and present baseline characteristics of the study population including food intake and quality of life. We also describe how the LifeLines DEEP cohort allows for the detailed investigation of genetic, genomic and metabolic variation for a wide range of phenotypic outcomes. Finally, we examine the determinants of gastrointestinal health, an area of particular interest to us that can be addressed by LifeLines DEEP. FUTURE PLANS We have established a cohort of which multiple data levels allow for the integrative analysis of populations for translation of this information into biomarkers for disease, and which will offer new insights into disease mechanisms and prevention.
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Affiliation(s)
- Ettje F Tigchelaar
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- Top Institute Food and Nutrition, Wageningen, The Netherlands
| | - Alexandra Zhernakova
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- Top Institute Food and Nutrition, Wageningen, The Netherlands
| | - Jackie A M Dekens
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- Top Institute Food and Nutrition, Wageningen, The Netherlands
| | - Gerben Hermes
- Top Institute Food and Nutrition, Wageningen, The Netherlands
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
| | - Agnieszka Baranska
- Top Institute Food and Nutrition, Wageningen, The Netherlands
- Department of Toxicology, Nutrition and Toxicology Research (NUTRIM), Maastricht University Medical Center+, Maastricht, The Netherlands
| | - Zlatan Mujagic
- Top Institute Food and Nutrition, Wageningen, The Netherlands
- Division of Gastroenterology-Hepatology, Maastricht University Medical Center+, Maastricht, The Netherlands
| | - Morris A Swertz
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- Top Institute Food and Nutrition, Wageningen, The Netherlands
- University of Groningen, University Medical Center Groningen, Genomics Coordination Center, Groningen, The Netherlands
| | - Angélica M Muñoz
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- Research Group in Food and Human Nutrition, University of Antioquia, Medellín, Colombia
| | - Patrick Deelen
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- University of Groningen, University Medical Center Groningen, Genomics Coordination Center, Groningen, The Netherlands
| | - Maria C Cénit
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Lude Franke
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Salome Scholtens
- LifeLines Cohort Study, Groningen, The Netherlands
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Ronald P Stolk
- LifeLines Cohort Study, Groningen, The Netherlands
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Cisca Wijmenga
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- Top Institute Food and Nutrition, Wageningen, The Netherlands
| | - Edith J M Feskens
- Top Institute Food and Nutrition, Wageningen, The Netherlands
- Division of Human Nutrition, Section Nutrition and Epidemiology, Wageningen University, Wageningen, The Netherlands
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Anton G, Wilson R, Yu ZH, Prehn C, Zukunft S, Adamski J, Heier M, Meisinger C, Römisch-Margl W, Wang-Sattler R, Hveem K, Wolfenbuttel B, Peters A, Kastenmüller G, Waldenberger M. Pre-analytical sample quality: metabolite ratios as an intrinsic marker for prolonged room temperature exposure of serum samples. PLoS One 2015; 10:e0121495. [PMID: 25823017 PMCID: PMC4379062 DOI: 10.1371/journal.pone.0121495] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Accepted: 02/01/2015] [Indexed: 11/19/2022] Open
Abstract
Advances in the "omics" field bring about the need for a high number of good quality samples. Many omics studies take advantage of biobanked samples to meet this need. Most of the laboratory errors occur in the pre-analytical phase. Therefore evidence-based standard operating procedures for the pre-analytical phase as well as markers to distinguish between 'good' and 'bad' quality samples taking into account the desired downstream analysis are urgently needed. We studied concentration changes of metabolites in serum samples due to pre-storage handling conditions as well as due to repeated freeze-thaw cycles. We collected fasting serum samples and subjected aliquots to up to four freeze-thaw cycles and to pre-storage handling delays of 12, 24 and 36 hours at room temperature (RT) and on wet and dry ice. For each treated aliquot, we quantified 127 metabolites through a targeted metabolomics approach. We found a clear signature of degradation in samples kept at RT. Storage on wet ice led to less pronounced concentration changes. 24 metabolites showed significant concentration changes at RT. In 22 of these, changes were already visible after only 12 hours of storage delay. Especially pronounced were increases in lysophosphatidylcholines and decreases in phosphatidylcholines. We showed that the ratio between the concentrations of these molecule classes could serve as a measure to distinguish between 'good' and 'bad' quality samples in our study. In contrast, we found quite stable metabolite concentrations during up to four freeze-thaw cycles. We concluded that pre-analytical RT handling of serum samples should be strictly avoided and serum samples should always be handled on wet ice or in cooling devices after centrifugation. Moreover, serum samples should be frozen at or below -80°C as soon as possible after centrifugation.
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Affiliation(s)
- Gabriele Anton
- Institute of Epidemiology II, Helmholtz Center Munich, Munich, Germany
- * E-mail:
| | - Rory Wilson
- Institute of Epidemiology II, Helmholtz Center Munich, Munich, Germany
| | - Zhong-hao Yu
- Institute of Epidemiology II, Helmholtz Center Munich, Munich, Germany
| | - Cornelia Prehn
- Institute of Experimental Genetics, Helmholtz Center Munich, Munich, Germany
| | - Sven Zukunft
- Institute of Experimental Genetics, Helmholtz Center Munich, Munich, Germany
| | - Jerzy Adamski
- Institute of Experimental Genetics, Helmholtz Center Munich, Munich, Germany
| | - Margit Heier
- Institute of Epidemiology II, Helmholtz Center Munich, Munich, Germany
- Central Hospital of Augsburg, KORA Myocardial Infarction Registry, Augsburg, Germany
| | - Christa Meisinger
- Institute of Epidemiology II, Helmholtz Center Munich, Munich, Germany
- Central Hospital of Augsburg, KORA Myocardial Infarction Registry, Augsburg, Germany
| | - Werner Römisch-Margl
- Institute for Bioinformatics and Systems Biology, Helmholtz Center Munich, Munich, Germany
| | - Rui Wang-Sattler
- Institute of Epidemiology II, Helmholtz Center Munich, Munich, Germany
| | - Kristian Hveem
- Department of Public Health and General Practice, Norwegian University of Science and Technology, Levanger, Norway
| | - Bruce Wolfenbuttel
- Department of Endocrinology, University Medical Center Groningen, Groningen, The Netherlands
| | - Annette Peters
- Institute of Epidemiology II, Helmholtz Center Munich, Munich, Germany
| | - Gabi Kastenmüller
- Institute for Bioinformatics and Systems Biology, Helmholtz Center Munich, Munich, Germany
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Bovenberg JA, Knoppers BM, Hansell A, de Hoogh K. Exposing participants? Population biobanks go geo. Eur J Hum Genet 2015; 24:155-6. [PMID: 25804402 DOI: 10.1038/ejhg.2015.43] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
| | - Bartha Maria Knoppers
- Department of Human Genetics, Faculty of Medicine, McGill University, Montreal, QC, Canada
| | - Anna Hansell
- Small Area Health Statistics Unit (SAHSU), MRC-PHE Centre for Environment and Health, Public Health and Primary Care, Imperial College Healthcare NHS Trust, London, UK
| | - Kees de Hoogh
- Environmental Exposure and Health Unit, Department of Epidemiology and Public Health, Swiss Tropical and Public Health Institute, Basel, Switzerland
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Monaco L, Crimi M, Wang CM. The challenge for a European network of biobanks for rare diseases taken up by RD-Connect. Pathobiology 2015; 81:231-236. [PMID: 25792211 PMCID: PMC5079099 DOI: 10.1159/000358492] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Access to biological materials is a key prerequisite for scientific research in any medical field and in particular for research into rare diseases (RDs), for which obtaining high-quality samples and the related clinical data remains a major hurdle. RD biobanks play a pivotal role in making such materials and data available to the scientific community. In order to increase the effectiveness of RD biobanks, three major challenges need to be met: maximise access to rare biological samples stored in RD biobanks spread globally by the international scientific community, promote networking among such biobanks to share quality standards and procedures and allow collaboration with RD registries and databases, and finally adopt an efficient management model compliant with legal and ethical issues and ensuring biobank sustainability. The European program RD-Connect, funded under the FP7 program, addresses all of these issues through an articulated action plan aimed at building a network of European RD biobanks. Ultimately, RD-Connect will offer access to precious, quality-controlled biological samples from RD patients through an online, searchable, dynamic catalogue in the context of an integrated platform that links RD patient registries to biobanks and to clinical bioinformatics data for RD research.
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Affiliation(s)
- Lucia Monaco
- *Lucia Monaco, Fondazione Telethon, Piazza Cavour 1, IT-20121 Milan (Italy), E-Mail
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Starkbaum J, Gottweis H, Gottweis U, Kleiser C, Linseisen J, Meisinger C, Kamtsiuris P, Moebus S, Jöckel KH, Börm S, Wichmann HE. Public perceptions of cohort studies and biobanks in Germany. Biopreserv Biobank 2014; 12:121-30. [PMID: 24749879 DOI: 10.1089/bio.2013.0071] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Cohort studies and biobank projects have led to public discussions in several European countries in the past. In Germany, many medium-sized studies are currently running successfully in terms of respondent rates. However, EU-wide research on general public perceptions of biobanks and cohort studies have shown that Germany is among those countries where people express the highest reluctance for providing body material and other data for research purposes. Because of early efforts of the just-initiated German National Cohort Study, we are able to begin to investigate in greater detail how various groups of people across Germany reflect and discuss the ongoing implementation of cohort studies and biobanking in Germany. Our research is based on 15 focus group discussions in four German regions, as well as on Eurobarometer poll data on biobanking.
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Affiliation(s)
- Johannes Starkbaum
- 1 Friedrich Alexander University Erlangen-Nuremberg , Section for Systematic Theology II (Ethics), Nuremberg, Germany
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Clement B, Yuille M, Zaltoukal K, Wichmann HE, Anton G, Parodi B, Kozera L, Brechot C, Hofman P, Dagher G. Public Biobanks: Calculation and Recovery of Costs. Sci Transl Med 2014; 6:261fs45. [DOI: 10.1126/scitranslmed.3010444] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Galli J, Oelrich J, Taussig MJ, Andreasson U, Ortega-Paino E, Landegren U. The Biobanking Analysis Resource Catalogue (BARCdb): a new research tool for the analysis of biobank samples. Nucleic Acids Res 2014; 43:D1158-62. [PMID: 25336620 PMCID: PMC4383877 DOI: 10.1093/nar/gku1008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
We report the development of a new database of technology services and products
for analysis of biobank samples in biomedical research. BARCdb, the Biobanking
Analysis Resource Catalogue, is a
freely available web resource, listing expertise and molecular resource
capabilities of research centres and biotechnology companies. The database is
designed for researchers who require information on how to make best use of
valuable biospecimens from biobanks and other sample collections, focusing on
the choice of analytical techniques and the demands they make on the type of
samples, pre-analytical sample preparation and amounts needed. BARCdb has been
developed as part of the Swedish biobanking infrastructure (BBMRI.se), but now
welcomes submissions from service providers throughout Europe. BARCdb can help
match resource providers with potential users, stimulating transnational
collaborations and ensuring compatibility of results from different labs. It can
promote a more optimal use of European resources in general, both with respect
to standard and more experimental technologies, as well as for valuable biobank
samples. This article describes how information on service and reagent providers
of relevant technologies is made available on BARCdb, and how this resource may
contribute to strengthening biomedical research in academia and in the
biotechnology and pharmaceutical industries.
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Affiliation(s)
- Joakim Galli
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, SE-751 08 Uppsala, Sweden
| | - Johan Oelrich
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, SE-751 08 Uppsala, Sweden
| | - Michael J Taussig
- Protein Technology Group, The Babraham Institute, Cambridge CB22 3AT, UK
| | - Ulrika Andreasson
- Department of Immunotechnology, Lund University, Medicon Village, SE-223 81 Lund, Sweden CREATE Health, Lund University Medicon Village, SE-223 81 Lund, Sweden
| | - Eva Ortega-Paino
- Department of Immunotechnology, Lund University, Medicon Village, SE-223 81 Lund, Sweden CREATE Health, Lund University Medicon Village, SE-223 81 Lund, Sweden
| | - Ulf Landegren
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, SE-751 08 Uppsala, Sweden
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Köpke J, Eder J, Schicho M. Efficient Projection of Ontologies. JOURNAL ON DATA SEMANTICS 2014. [DOI: 10.1007/s13740-014-0043-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Thompson R, Johnston L, Taruscio D, Monaco L, Béroud C, Gut IG, Hansson MG, ’t Hoen PBA, Patrinos GP, Dawkins H, Ensini M, Zatloukal K, Koubi D, Heslop E, Paschall JE, Posada M, Robinson PN, Bushby K, Lochmüller H. RD-Connect: an integrated platform connecting databases, registries, biobanks and clinical bioinformatics for rare disease research. J Gen Intern Med 2014; 29 Suppl 3:S780-7. [PMID: 25029978 PMCID: PMC4124112 DOI: 10.1007/s11606-014-2908-8] [Citation(s) in RCA: 104] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Research into rare diseases is typically fragmented by data type and disease. Individual efforts often have poor interoperability and do not systematically connect data across clinical phenotype, genomic data, biomaterial availability, and research/trial data sets. Such data must be linked at both an individual-patient and whole-cohort level to enable researchers to gain a complete view of their disease and patient population of interest. Data access and authorization procedures are required to allow researchers in multiple institutions to securely compare results and gain new insights. Funded by the European Union's Seventh Framework Programme under the International Rare Diseases Research Consortium (IRDiRC), RD-Connect is a global infrastructure project initiated in November 2012 that links genomic data with registries, biobanks, and clinical bioinformatics tools to produce a central research resource for rare diseases.
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Affiliation(s)
- Rachel Thompson
- />Institute of Genetic Medicine, MRC Centre for Neuromuscular Diseases, Newcastle University, London, UK
| | - Louise Johnston
- />Institute of Genetic Medicine, MRC Centre for Neuromuscular Diseases, Newcastle University, London, UK
| | | | | | - Christophe Béroud
- />Aix Marseille Université, INSERM, GMGF UMR_S 910, 13385 Marseille, France
| | - Ivo G. Gut
- />Centre Nacional d’Anàlisi Genòmica, Barcelona, Spain
| | | | | | | | - Hugh Dawkins
- />Office of Population Health Genomics, Department of Health Western Australia, Perth, Australia
| | - Monica Ensini
- />Institute of Genetic Medicine, MRC Centre for Neuromuscular Diseases, Newcastle University, London, UK
| | | | | | - Emma Heslop
- />Institute of Genetic Medicine, MRC Centre for Neuromuscular Diseases, Newcastle University, London, UK
| | - Justin E. Paschall
- />European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | - Manuel Posada
- />Instituto de Salud Carlos III, Instituto de Investigación de Enfermedades Raras, CIBERER, Madrid, Spain
| | - Peter N. Robinson
- />Institute for Medical Genetics and Human Genetics, Charité-Universitätsmedizin, Berlin, Germany
| | - Kate Bushby
- />Institute of Genetic Medicine, MRC Centre for Neuromuscular Diseases, Newcastle University, London, UK
| | - Hanns Lochmüller
- />Institute of Genetic Medicine, MRC Centre for Neuromuscular Diseases, Newcastle University, London, UK
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Branković I, Malogajski J, Morré SA. Biobanking and translation of human genetics and genomics for infectious diseases. Appl Transl Genom 2014; 3:30-5. [PMID: 27275411 PMCID: PMC4881987 DOI: 10.1016/j.atg.2014.04.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2014] [Revised: 02/22/2014] [Accepted: 04/02/2014] [Indexed: 11/21/2022]
Abstract
Biobanks are invaluable resources in genomic research of both the infectious diseases and their hosts. This article examines the role of biobanks in basic research of infectious disease genomics, as well as the relevance and applicability of biobanks in the translation of impending knowledge and the clinical uptake of knowledge of infectious diseases. Our research identifies potential fields of interaction between infectious disease genomics and biobanks, in line with global trends in the integration of genome-based knowledge into clinical practice. It also examines various networks and biobanks that specialize in infectious diseases (including HIV, HPV and Chlamydia trachomatis), and provides examples of successful research and clinical uptake stemming from these biobanks. Finally, it outlines key issues with respect to data privacy in infectious disease genomics, as well as the utility of adequately designed and maintained electronic health records. We maintain that the public should be able to easily access a clear and detailed outline of regulations and procedures for sample and data utilization by academic or commercial investigators, and also should be able to understand the precise roles of relevant governing bodies. This would ultimately facilitate uptake by researchers and clinics. As a result of the efforts and resources invested by several networks and consortia, there is an increasing awareness of the prospective uses of biobanks in advancing infectious disease genomic research, diagnostics and their clinical management. The role of biobanks in research of host genomic factors and infectious diseases. Examples of translation of HIV, HPV and Chlamydia research results into clinics. Lack of published overviews of infectious disease biobanks, result is low visibility. Regulations and sample utilization procedures should be more easily accessible.
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Affiliation(s)
- Ivan Branković
- Institute for Public Health Genomics, Department of Genetics and Cell Biology, Research School GROW, Maastricht University, Maastricht, The Netherlands
| | - Jelena Malogajski
- Institute for Public Health Genomics, Department of Genetics and Cell Biology, Research School GROW, Maastricht University, Maastricht, The Netherlands
| | - Servaas A Morré
- Institute for Public Health Genomics, Department of Genetics and Cell Biology, Research School GROW, Maastricht University, Maastricht, The Netherlands; Laboratory of Immunogenetics, Department of Medical Microbiology and Infection Control, VU University Medical Center, Amsterdam, The Netherlands
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Toward a common language for biobanking. Eur J Hum Genet 2014; 23:22-8. [PMID: 24713663 DOI: 10.1038/ejhg.2014.45] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2013] [Revised: 01/29/2014] [Accepted: 02/19/2014] [Indexed: 11/09/2022] Open
Abstract
To encourage the process of harmonization, the biobank community should support and use a common terminology. Relevant terms may be found in general thesauri for medicine, legal instruments or specific glossaries for biobanking. A comparison of the use of these sources has so far not been conducted and would be a useful instrument to further promote harmonization and data sharing. Thus, the purpose of the present study was to investigate the preference of definitions important for sharing biological samples and data. Definitions for 10 terms -[human] biobank, sample/specimen, sample collection, study, aliquot, coded, identifying information, anonymised, personal data and informed consent-were collected from several sources. A web-based questionnaire was sent to 560 European individuals working with biobanks asking to select their preferred definition for the terms. A total of 123 people participated in the survey, giving a response rate of 23%. The result was evaluated from four aspects: scope of definitions, potential regional differences, differences in semantics and definitions in the context of ontologies, guided by comments from responders. Indicative from the survey is the risk of focusing only on the research aspect of biobanking in definitions. Hence, it is recommended that important terms should be formulated in such a way that all areas of biobanking are covered to improve the bridges between research and clinical application. Since several of the terms investigated here within can also be found in a legal context, which may differ between countries, establishing what is a proper definition on how it adheres to law is also crucial.
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